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GENESPACE tracks regions of interest and gene copy number variation across multiple genomes
Open accessPublished version of a preprint
Abstract
The development of multiple chromosome-scale reference genome sequences in many taxonomic groups has yielded a high-resolution view of the patterns and processes of molecular evolution. Nonetheless, leveraging information across multiple genomes remains a significant challenge in nearly all eukaryotic systems. These challenges range from studying the evolution of chromosome structure, to finding candidate genes for quantitative trait loci, to testing hypotheses about speciation and adaptation. Here, we present GENESPACE, which addresses these challenges by integrating conserved gene order and orthology to define the expected physical position of all genes across multiple genomes. We demonstrate this utility by dissecting presence–absence, copy-number, and structural variation at three levels of biological organization: spanning 300 million years of vertebrate sex chromosome evolution, across the diversity of the Poaceae (grass) plant family, and among 26 maize cultivars. The methods to build and visualize syntenic orthology in the GENESPACE R package offer a significant addition to existing gene family and synteny programs, especially in polyploid, outbred, and other complex genomes.
Overview
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Written from the paper’s full text.
TL;DR
GENESPACE is an R package/pipeline that integrates conserved gene order (synteny) and orthology to build pan-genome annotations and track presence–absence, copy-number, and structural variation across multiple genomes. It outperformed OrthoFinder and MCScanX in single-copy orthogroup and syntenic block recovery across diverse plant and vertebrate comparisons, including polyploid and recently diverged genomes.
Key findings
- Across seven genome pairs, GENESPACE increased the percentage of genes in single-copy orthogroups and single-copy syntenic blocks versus OrthoFinder/MCScanX; for cotton, single-copy orthogroups rose from 35.6% (OrthoFinder) to 85.7% (GENESPACE) and single-copy syntenic blocks from 14.1% (orthogroup-constrained MCScanX) to 96.2% (GENESPACE).
- In vertebrate sex chromosome comparisons, a 91.7 M bp region is shared between human X and sand lizard Z, representing 59.0% of human X genic sequence; 107.2 M bp (68.8%) of human X is syntenic with 77.8 M bp (93.9%) of Tasmanian devil X; chicken Z is retained across five avian genomes except for a budgie partial fusion with a 19.5 M bp segment of chicken chromosome 11.
- For 86 C3/C4 photosynthesis genes, absence was lower than background (9.7% vs. 38.2%, odds ratio = 5.7, p < 1 × 10−16), but C3 species had more absences than C4 species (15.3% vs. 5.5%, odds ratio = 3.1, p = 6.25 × 10−8); among 190 maize NAM QTLs, three had single-parent outlier effects, and the two Mo18W QTL regions fell within an 11.7 M bp Mo18W-specific inversion.
- Rho WGD paralogs were less conserved than primary syntenic orthologs (median peptide identity 90.6% vs. 71.4%, 26.9% more similar; Wilcoxon p < 1 × 10−16), except one over-retained S. viridis chromosome 8 region where paralogs were not significantly less conserved (91.6% vs. 91.9%, p = 0.13).
Methods
- GENESPACE takes gff3 annotations and peptide FASTAs, computes DIAMOND2 BLAST-like hits, runs OrthoFinder for orthogroups, extracts syntenic regions with MCScanX-based and graph/cluster approaches, condenses tandem arrays to representative genes, and collapses syntenic orthogroups into a reference-anchored pan-genome annotation.
- Analyses used seven haploid genome pairs spanning <0.01 Mya maize to 310 Mya human–chicken, 15 avian/mammalian genomes plus two reptile outgroups, eight grass genomes, and 26 maize NAM founders; public annotations were downloaded on or before October 8, 2021.
- Comparisons calculated percent genes in single-copy orthogroups and single-copy syntenic blocks; statistics included Wilcoxon signed rank tests, ungapped percent peptide identity from Needleman–Wunsch alignments, and Grubbs tests for outliers, using R 4.1.2 and GENESPACE v0.9.3.
Limitations
- Stated: only a single C3/C4 phylogenetic split prevents testing evolutionary hypotheses about causes of PAV; the phylogenetic scale precludes inference about the origin of shared sex chromosome sequences; and it is not clear that within-block OrthoFinder improves much over global orthogroups for purely haploid genomes.
- Stated/evident: GENESPACE relies on syntenic regions, so errors in syntenic block coordinates can have major downstream effects; true orthologs can exist outside syntenic regions, with 1096 non-syntenic human–chimpanzee orthologs (6.3% of all orthologs) and 9002 non-syntenic Sorghum–Brachypodium orthologs.
- Evident: results depend on parameterization, outgroup choice, and ploidy treatment; polyploids had only a primary haplotype assembled into chromosomes, maize was treated as diploid in the multispecies run but haploid in the NAM run, and some maize alternative haplotype scaffolds were dropped.
Model-written summary. Check it against the paper before relying on it.
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Claims the paper makes
9 of 34 cited sources checked · 2 supported · 0 flagged · accuracy not yet measured
- Premisecitation
The physical position of homologs offers a second line of evidence that can help overcome challenges posed by WGDs, tandem arrays, heterozygous-duplicated regions, and other genomic complexities.
“The physical position of homologs offers a second line of evidence that can help overcome challenges posed by WGDs, tandem arrays, heterozygous-duplicated regions, and other genomic complexities (Drillon et al., 2020; Haug-Baltzell et al., 2017; Wang et al., 2012).”
Quote in the paperSubstantial claim3 of 3 sources checked- cites Drillon et al., 2020 source
Materials and Methods (Synteny Blocks; Testing the Conservation of Block Adjacencies) uses the positions and adjacency of homologous genes as phylogenetic evidence. The PhyChro Algorithm section says the method is designed to handle duplicated blocks, and Results (Robustness of PhyChro) includes simulated whole-genome duplications. The copy does not establish that this evidence overcomes challenges from tandem arrays or heterozygous-duplicated regions specifically. (LLM, conf=0.87)
Experimental — accuracy not yet measured - cites Haug-Baltzell et al., 2017 source
The Introduction says synteny can be inferred from colinear sets of homologous genes, supporting the use of their genomic positions as evidence. The Description and §2.1 say the tools help visualize polyploidy, but our copy does not address overcoming challenges from tandem arrays or heterozygous-duplicated regions. (LLM, conf=0.86)
Experimental — accuracy not yet measured - cites Wang et al., 2012 source
The Methods section, “Classification of duplicate gene origins,” uses chromosome order and collinear position to distinguish tandem from WGD/segmental duplicates, supporting the value of homolog position for those complexities. The passages do not address heterozygous-duplicated regions or show that positional evidence overcomes that challenge; page numbers were unavailable in our copy. (LLM, conf=0.86)
Experimental — accuracy not yet measured
- Premisecitation
GENESPACE was originally designed to solve the problem between the two P. hallii reference genomes and their F2 progeny using synteny to project the positions of genes across multiple genomes onto the physical positions of a reference.
“GENESPACE is ideally suited for this type of exploration, and indeed was originally designed to solve this problem between the two P. hallii reference genomes and their F2 progeny (Lovell et al., 2018) using synteny to project the positions of genes across multiple genomes onto the physical positions of a reference.”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites Lovell et al., 2018 source
The Results section, “Development and comparison of two complete de novo genomes” (page unavailable), identifies GENESPACE as the authors’ pipeline for comparing the HAL2 and FIL2 genomes using synteny-constrained gene networks. The Methods section, “Comparative genomics” (page unavailable), describes orthology inference within syntenic blocks, but does not say the pipeline was designed to project gene positions onto a reference or to solve a problem involving the F2 progeny. The paper describes F2 genetic-map construction separately. (LLM, conf=0.85)
Experimental — accuracy not yet measured
- Findingown data
GENESPACE utility is demonstrated by dissecting presence-absence, copy-number, and structural variation at three levels of biological organization: spanning 300 million years of vertebrate sex chromosome evolution, across the diversity of the Poaceae plant family, and among 26 maize cultivars.
“We demonstrate this utility by dissecting presence–absence, copy-number, and structural variation at three levels of biological organization: spanning 300 million years of vertebrate sex chromosome evolution, across the diversity of the Poaceae (grass) plant family, and among 26 maize cultivars.”
Quote in the paperSubstantial claim - Findingreasoning
PAV among C3/C4 genes was lower than the background (9.7% vs. 38.2%, odds ratio = 5.7, p < 1 × 10−16).
“Given that many of these genes were discovered in part because of sequence similarity to genes in Arabidopsis and other diverged plant species, it is not surprising that PAV among C3/C4 genes was lower than the background (9.7% vs. 38.2%, odds ratio = 5.7, p < 1 × 10−16; Figure 3B).”
Quote in the paperSubstantial claim - Findingown data
Default parameters produced a largely contiguous map of synteny even across notoriously difficult comparisons like the paleo-homeologs between the maize subgenomes.
“Default parameters produced a largely contiguous map of synteny even across notoriously difficult comparisons like the paleo-homeologs between the maize subgenomes (Figure 3A).”
Quote in the paperSubstantial claim
- Findingcitation
Cultivar 'Ki11' contributed an allele that reduced plant height under drought at a QTL on chromosome 6.
“cultivar ‘Ki11’ contributed an allele that reduced plant height under drought at a QTL on chromosome 6 (‘Chr6’) (Li et al., 2016).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Li et al., 2016
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Findingown data
S. viridis chromosome 8 contained a single over-retained paralogous region.
“However, S. viridis chromosome 8 contained a single over-retained paralogous region.”
Quote in the paperNot a substantial claim - Findingown data
Two genes in the smaller Chr3 and one gene in the larger Chr3 interval were private to Mo18W.
“Two genes in the smaller Chr3 and one gene in the larger Chr3 interval were private to Mo18W,”
Quote in the paperNot a substantial claim - Findingown data
The mirrored 'fast' method significantly speeds up OrthoFinder runs by calling DIAMOND2 on each nonredundant pairwise combination of genomes.
“The mirrored ‘fast’ method significantly speeds up OrthoFinder runs by calling DIAMOND2 on each nonredundant pairwise combination of genomes.”
Quote in the paperNot a substantial claim - Findingown data
When controlling for the elevated level of absent genes globally in C3 species, the odds of C3 species having more of these C3/C4 genes at syntenic pan-genome positions than the background was always lower than the C4 species.
“However, when controlling for the elevated level of absent genes globally in C3 species, the effect was still very strong: the odds of C3 species having more of these C3/C4 genes at syntenic pan-genome positions than the background was always lower than the C4 species (Figure 3C).”
Quote in the paperSubstantial claim - Findingown data
The improved performance of GENESPACE synteny-constrained orthogroups was most subtle between highly diverged haploid animal assemblies.
“The improved performance of GENESPACE synteny-constrained orthogroups was most subtle between highly diverged haploid animal assemblies.”
Quote in the paperNot a substantial claim - Findingown data
The budgie Z chromosome features a partial fusion between the Z and an otherwise autosomal 19.5 M bp segment of chicken chromosome 11.
“The only notable exception being the budgie Z chromosome, which features a partial fusion between the Z and an otherwise autosomal 19.5 M bp segment of chicken chromosome 11 (Figure 2), potentially representing a neo-sex chromosome fusion that has not yet been described.”
Quote in the paperSubstantial claim - Findingown data
All syntenic over-retained regions were at the extreme termini of the chromosomes outside of maize, B. distachyon and wheat.
“It is interesting to note that all syntenic over-retained regions were at the extreme termini of the chromosomes outside of maize, B. distachyon and wheat;”
Quote in the paperSubstantial claim - Findingcitation
Among the 190 QTLs, three displayed outlier effects of one parent.
“Among the 190 QTLs, three displayed outlier effects of one parent:”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Li et al., 2016
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Findingown data
The shared 91.7 M bp region between the human X and sand lizard Z represents 59.0% of the human X chromosome genic sequence.
“The shared 91.7 M bp region between the human X and sand lizard Z represents 59.0% of the human X chromosome genic sequence.”
Quote in the paperSubstantial claim - Findingown data
Single-copy orthogroups between two meso-tetraploid cotton species that share a WGD that predated speciation by ~1 M ya were uncommon in the default OrthoFinder run (35.6%) but far more prevalent in GENESPACE syntenic orthogroups (85.7%).
“Single-copy orthogroups between two meso-tetraploid cotton species that share a WGD that predated speciation by ~1 M ya, were uncommon in the default OrthoFinder run (35.6%) but far more prevalent in GENESPACE syntenic orthogroups (85.7%).”
Quote in the paperSubstantial claim - Findingreasoning
The X chromosome is syntenic across all five eutherian mammals studied here.
“Consistent with this evolutionary history, the X chromosome is syntenic across all five eutherian mammals studied here.”
Quote in the paperNot a substantial claim - Findingown data
Homeologs derived from the cotton WGD impacted estimates of syntenic blocks: only 14% of the genomes were single-copy syntenic in orthogroup-constrained MCScanX but 96.2% were single copy in GENESPACE syntenic blocks.
“Similarly, homeologs derived from the cotton WGD impacted estimates of syntenic blocks: only 14% of the genomes were single-copy syntenic in orthogroup-constrained MCScanX but 96.2% were single copy in GENESPACE syntenic blocks.”
Quote in the paperSubstantial claim - Findingown data
The GENESPACE run treating the eight genomes as haploid representations could not distinguish between the Rho-derived paralogs in the over-retained region across all grasses, except for all chromosome pairs between B. distachyon, wheat, and blocks connecting Maize chromosome 10 to sorghum chromosome 5.
“In line with this observation, the GENESPACE run treating the eight genomes as haploid representations could not distinguish between the Rho-derived paralogs in the over-retained region across all grasses (Figures 3A and 4C), except for of all chromosome pairs between B. distachyon, wheat, and blocks connecting Maize chromosome 10 to sorghum chromosome 5.”
Quote in the paperNot a substantial claim - Findingown data
The benefits of GENESPACE were most pronounced in recently diverged genomes with a history of WGDs.
“In contrast, the benefits of GENESPACE were most pronounced in recently diverged genomes with a history of WGDs.”
Quote in the paperSubstantial claim - Findingnone given
Closely related genomes without a history of WGDs tend to have few non-syntenic orthologs.
“Closely related genomes without a history of WGDs tend to have few non-syntenic orthologs.”
Quote in the paperNot a substantial claim - Findingown data
The remaining 64.0 M bp of human X linked sequences are syntenic with autosomes in the sand lizard and garter snake genomes.
“The remaining 64.0 M bp of human X linked sequences are syntenic with autosomes in the sand lizard and garter snake genomes (Figure 2).”
Quote in the paperSubstantial claim - Findingcitation
The complex monotreme XnYn sex chromosomes are only partially syntenic between the two sampled genomes.
“In contrast to conserved eutherian and avian sex chromosomes, the complex monotreme XnYn sex chromosomes are only partially syntenic between the two sampled genomes.”
Quote in the paperNot a substantial claim - Findingown data
For every pair of genomes, GENESPACE produced a greater percentage of single-copy syntenic blocks and genes in single chromosome orthogroups than either OrthoFinder or MCScanX in isolation.
“For every pair of genomes, GENESPACE produced a greater percentage of single-copy syntenic blocks and genes in single chromosome orthogroups than either OrthoFinder or MCScanX in isolation.”
Quote in the paperSubstantial claim - Findingown data
The chicken Z chromosome is retained in its entirety across all five avian genomes.
“Similarly, the chicken Z chromosome is retained in its entirety across all five avian genomes.”
Quote in the paperNot a substantial claim - Findingown data
Four genes in three pan-genome entries (one two-member array) were private to Ki11 in the Chr6 interval.
“and four genes in three pan-genome entries (one two-member array) were private to Ki11 in the Chr6 interval (Figure 3F, Figure 3—figure supplement 1).”
Quote in the paperNot a substantial claim - Findingown data
Outside of this region, the peptide identity of paralogs returned to the genome-wide average.
“Outside of this region, the peptide identity of paralogs returned to the genome-wide average (Figure 4B).”
Quote in the paperNot a substantial claim - Findingown data
The peptide sequences of single-copy gene hits in primary syntenic regions (median identity = 90.6%) between chromosome 8 of P. hallii and S. viridis were 26.9% more similar than the secondary Rho-derived regions (median identity = 71.4%, Wilcoxon W = 87,842, p < 1 × 10−16).
“As an example, the peptide sequences of single-copy gene hits in primary syntenic regions (median identity = 90.6%) between chromosome 8 of P. hallii and S. viridis, were 26.9% more similar than the secondary Rho-derived regions (Figure 4B; median identity = 71.4%, Wilcoxon W = 87,842, p < 1 × 10−16).”
Quote in the paperNot a substantial claim - Findingown data
GENESPACE outperformed simple integration between OrthoFinder and MCScanX through MCScanX on orthogroup-constrained hits.
“GENESPACE also outperformed simple integration between the two methods through MCScanX on orthogroup-constrained hits.”
Quote in the paperSubstantial claim - Findingown data
The peptide identity between Rho-derived paralogous regions was much lower than orthologs between species.
“Overall, the peptide identity between Rho-derived paralogous regions was much lower than orthologs between species (e.g., S. viridis vs. P. hallii: Wilcoxon W = 88,094,632, p < 1 × 10−16),”
Quote in the paperSubstantial claim - Findingcitation
Cultivar 'Mo18W' contributed an allele for delayed anthesis-silking interval at two adjacent chromosome 3 QTLs.
“cultivar ‘Mo18W’ contributed an allele for delayed anthesis-silking interval at two adjacent chromosome 3 (‘Chr3’) QTLs”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Li et al., 2016
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Findingcitation
The homomorphic X and Z chromosomes have remained surprisingly intact over the >100 M years of independent mammalian and avian evolution.
“As such, we chose to focus on the homomorphic X and Z chromosomes, which have remained surprisingly intact over the >100 M years of independent mammalian (Murphy et al., 1999) and avian evolution (Zhou et al., 2014; Figure 2, Figure 2—figure supplement 1).”
Quote in the paperSubstantial claim0 of 2 sources checked - Findingreasoning
The within-maize NAM parent run (Figure 3D) excludes homeologs.
“Hence, the within-maize NAM parent run (Figure 3D) excludes homeologs.”
Quote in the paperSubstantial claim- Rests on an assumption: The coalescence of any two maize genotypes occurred more recently than the ~12M ya whole-genome duplication.
- Interpretationnone given
GENESPACE integrates conserved gene order and orthology to define the expected physical position of all genes across multiple genomes.
“Here, we present GENESPACE, which addresses these challenges by integrating conserved gene order and orthology to define the expected physical position of all genes across multiple genomes.”
Quote in the paperSubstantial claim - Interpretationown data
This method provides additional candidates that would not have been discovered by B73-only candidate gene exploration.
“this method provides additional candidates that would not have been discovered by B73-only candidate gene exploration.”
Quote in the paperSubstantial claim - Interpretationreasoning
The effect of C3 species having more absences is due in part to the increased evolutionary distance between maize and the C3 species compared to the other C4 species.
“This effect is undoubtedly due in part to the increased evolutionary distance between maize and the C3 species compared to the other C4 species.”
Quote in the paperNot a substantial claim - Interpretationreasoning
GENESPACE is ideally suited to conduct comparisons across species with diverse polyploidy events owing to its use of within-block orthology and synteny constraints.
“Owing to its use of within-block orthology and synteny constraints (Figure 1), GENESPACE is ideally suited to conduct comparisons across species with diverse polyploidy events.”
Quote in the paperSubstantial claim - Premisecitation
Originally, candidates for the 26-parent NAM QTL were defined by the proximate gene models only in the B73 reference genome.
“Originally, candidates for these QTL were defined by the proximate gene models only in the B73 reference genome (Li et al., 2016);”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Li et al., 2016
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Premisenone given
Integrating synteny and collinearity into comparative genomics pipelines physically anchors the positions of related gene sequences onto the assemblies of each genome.
“Integrating synteny and collinearity into comparative genomics pipelines also physically anchors the positions of related gene sequences onto the assemblies of each genome.”
Quote in the paperSubstantial claim - Interpretationreasoning
GENESPACE operates on OrthoFinder-derived orthogroups with one-to-one relationships for any accurately defined syntenic region, regardless of ploidy or level of sequence conservation.
“Thus, GENESPACE operates on OrthoFinder-derived orthogroups with one-to-one relationships for any accurately defined syntenic region, regardless of ploidy or level of sequence conservation.”
Quote in the paperSubstantial claim - Interpretationreasoning
The scale of the run matters, often significantly, for OrthoFinder orthogroup inference.
“As such, the scale of the run matters, often significantly.”
Quote in the paperSubstantial claim - Interpretationnone given
The process of rerunning OrthoFinder within syntenic blocks can improve the sensitivity of orthogroup discovery in paralogous or homeologous regions.
“While using significant computational resources, this process can improve the sensitivity of orthogroup discovery in paralogous or homeologous regions;”
Quote in the paperSubstantial claim - Interpretationcitation
These results are consistent with the proposed evolutionary mechanism where concerted evolution and 'illegitimate' homeologous recombination may have homogenized these paralogous regions.
“These results are consistent with the proposed evolutionary mechanism (Wang et al., 2011) where concerted evolution and ‘illegitimate’ homeologous recombination may have homogenized these paralogous regions.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Wang et al., 2011 source
- Interpretationown data
The budgie Z chromosome fusion potentially represents a neo-sex chromosome fusion that has not yet been described.
“The only notable exception being the budgie Z chromosome, which features a partial fusion between the Z and an otherwise autosomal 19.5 M bp segment of chicken chromosome 11 (Figure 2), potentially representing a neo-sex chromosome fusion that has not yet been described.”
Quote in the paperNot a substantial claim - Interpretationcitation
This process would be less effective in pericentromeric regions than the chromosome tails, where a single crossover event would be sufficient to homogenize two paralogous regions.
“This process would be less effective in pericentromeric regions than the chromosome tails, where a single crossover event would be sufficient to homogenize two paralogous regions.”
Quote in the paperSubstantial claim - Premisecitation
By exploring only syntenic orthologs it is possible to examine all putatively functional variants within a genomic region of interest, even those in genes that are absent in the focal reference genome.
“For example, by exploring only syntenic orthologs it is possible to examine all putatively functional variants within a genomic region of interest, even those in genes that are absent in the focal reference genome (Lovell et al., 2018).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Lovell et al., 2018 source
Checked before — its earlier verdict is held back until a new check runs.
- Premisecitation
There is significant variation in the relative similarity of Rho-duplicated sequences.
“However, as has been previously observed (Wang et al., 2011), there is significant variation in the relative similarity of Rho-duplicated sequences.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Wang et al., 2011 source
- Interpretationreasoning
An orthogroup would not be likely to contain homeologs across the two ancient subgenomes for a run that included only two maize genomes.
“For example, an orthogroup would not be likely to contain homeologs across the two ancient subgenomes for a run that included only two maize genomes.”
Quote in the paperSubstantial claim- Rests on an assumption: The coalescence of any two maize genotypes occurred more recently than the ~12M ya whole-genome duplication.
- Interpretationreasoning
GENESPACE includes and flags non-syntenic orthologs within the pan-genome annotation.
“Since the non-syntenic orthologs can be important in some situations, GENESPACE embraces this complexity by including and flagging non-syntenic orthologs within the pan-genome annotation (Figure 1).”
Quote in the paperSubstantial claim - Interpretationown data
These results demonstrate significant flexibility and utility of GENESPACE across a range of evolutionary histories and divergence.
“Combined, these results demonstrate significant flexibility and utility of GENESPACE across a range of evolutionary histories and divergence.”
Quote in the paperSubstantial claim - Premisecitation
The grasses radiated following a whole-genome duplication, the ~70 M ya Rho WGD.
“Like most plant families (Barker et al., 2016; Stebbins, 1950; One Thousand Plant Transcriptomes Initiative, 2019), but unlike nearly all animal lineages (Muller, 1925), the grasses radiated following a whole-genome duplication: the ~70 M ya Rho WGD.”
Quote in the paperSubstantial claim0 of 3 sources checked - Interpretationreasoning
If an outgroup to maize was included in the run, both maize homeologs would be likely to show common ancestry to a single gene in the outgroup, thus connecting the maize homeologs into a single orthogroup.
“However, if an outgroup to maize was included in the run, both maize homeologs would be likely to show common ancestry to a single gene in the outgroup, thus connecting the maize homeologs into a single orthogroup.”
Quote in the paperSubstantial claim- Rests on an assumption: The coalescence of any two maize genotypes occurred more recently than the ~12M ya whole-genome duplication.
- Interpretationnone given
GENESPACE facilitates the exploration and analysis of sequence evolution across multiple genomes within regions of interest.
“GENESPACE facilitates the exploration and analysis of sequence evolution across multiple genomes within regions of interest (e.g., quantitative trait loci [QTL] intervals, see the next section).”
Quote in the paperSubstantial claim - Interpretationreasoning
Few homeologs would both be descended from the same common ancestor when considering only maize genotypes.
“few homeologs would both be descended from the same common ancestor when considering only maize genotypes”
Quote in the paperSubstantial claim- Rests on an assumption: The coalescence of any two maize genotypes occurred more recently than the ~12M ya whole-genome duplication.
- Interpretationreasoning
The sensitive synteny construction pipeline implemented by GENESPACE effectively masks additional paralogous regions like those from the Rho duplication that gave rise to all extant grasses.
“Furthermore, the sensitive synteny construction pipeline implemented by GENESPACE effectively masks additional paralogous regions like those from the Rho duplication that gave rise to all extant grasses.”
Quote in the paperNot a substantial claim - Interpretationreasoning
Combined evidence of gene collinearity and sequence similarity should improve the ability to classify paralogous and orthologous relationships beyond either approach in isolation.
“Combined, evidence of gene collinearity and sequence similarity should improve the ability to classify paralogous and orthologous relationships beyond either approach in isolation.”
Quote in the paperSubstantial claim - Interpretationcitation
With GENESPACE and the recently released NAM parent genomes, it is now possible to evaluate candidate genes present in the genomes of other NAM founder lines but either absent or unannotated in the B73 reference genome.
“however, with GENESPACE and the recently released NAM parent genomes (Hufford et al., 2021), it is now possible to evaluate candidate genes present in the genomes of other NAM founder lines but either absent or unannotated in the B73 reference genome.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Hufford et al., 2021 source
Checked before — its earlier verdict is held back until a new check runs.
- Premisenone given
Some evolutionary processes, including small-scale translocations, can cause true orthologs to exist outside of syntenic regions.
“It is important to note that some evolutionary processes, including small-scale translocations, can cause true orthologs to exist outside of syntenic regions.”
Quote in the paperNot a substantial claim
- Probably not a substantial claim. 35
- It may state two separate claims as one. 30
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
PremisecitationOrthoFinder leverages graphs and gene trees to test for orthology, permitting more robust analyses in systems with gene copy number or presence-absence variation.
“Other sequence similarity approaches such as OrthoFinder (Emms and Kelly, 2019; Emms and Kelly, 2015) leverage graphs and gene trees to test for orthology, permitting more robust analyses in systems with gene copy number (CNV) or presence–absence variation (PAV).”
Quote in the paperNot a substantial claim2 of 2 sources checked- cites Emms and Kelly, 2019 source
The Methods (OrthoFinder workflow; page not provided) describe inferring orthogroups and gene trees, then using the trees to identify orthologs and gene duplications. The Methods (Species tree inference and rooting; page not provided) also describe handling multi-copy orthogroups and cases where no one-to-one orthologs are present in all species. Our copy does not establish the claimed use of graphs or specifically demonstrate more robust analyses in systems with CNV or PAV. (LLM, conf=0.84)
Experimental — accuracy not yet measured - cites Emms and Kelly, 2015 source
The Methodological overview describes a graph-based algorithm for inferring orthogroups, and the Discussion reports robustness to missing genes. But the Algorithm implementation section says OrthoFinder does not classify pairwise gene relationships; gene trees are used to validate inferred orthogroups, not as part of the inference algorithm. The paper also does not establish the claimed robustness specifically for CNV or PAV systems. (LLM, conf=0.88)
Experimental — accuracy not yet measured
It may state two separate claims as one.
PremisecitationSynteny is preserved across hundreds of millions of years of evolution and is retained over multiple WGDs in some taxa.
“In some taxa, synteny is preserved across hundreds of millions of years of evolution and is retained over multiple WGDs (Jiao et al., 2014; Simakov et al., 2020; Zhao and Schranz, 2019).”
Quote in the paperSubstantial claim2 of 3 sources checked- cites Jiao et al., 2014 source
- cites Simakov et al., 2020 source
- cites Zhao and Schranz, 2019 source
The Results and Discussion (no page available) describe conserved syntenic clusters and say some clusters could have been maintained through several rounds of whole-genome duplication. The paper states that the mammalian and angiosperm lineages studied evolved over approximately 170 million years (introductory text; no page available), but does not establish preservation across hundreds of millions of years. (LLM, conf=0.86)
Experimental — accuracy not yet measured
Probably not a substantial claim.
PremisecitationPrivate allelic contributions in multi-parent populations offer a powerful opportunity to define high-confidence candidates as genes with parent-specific sequences that match parent-specific allelic contributions to phenotypic trait variation.
“Such ‘private’ allelic contributions in multi-parent populations offer a powerful opportunity to define high-confidence candidates as genes with parent-specific sequences that match parent-specific allelic contributions to phenotypic trait variation (Abdulkina et al., 2019).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites Abdulkina et al., 2019 source
It may state two separate claims as one.
Findingnone givenThe 50 M ya diverged Sorghum and Brachypodium genomes have 9002 non-syntenic orthologs, many of which are the result of over-retained Rho WGD-derived paralogs.
“In contrast, the 50 M ya diverged Sorghum and Brachypodium genomes have 9002 non-syntenic orthologs, many of which are the result of over-retained Rho WGD-derived paralogs (see below).”
Quote in the paperNot a substantial claimIt may state two separate claims as one.
Findingown dataThe 'fast' approach is less sensitive than the default performance and is suggested for only closely related haploid genomes, as the recall of 2:2:2 OGs is less sensitive than the default specification.
“However, this approach is less sensitive than the default performance and is suggested for only closely related haploid genomes, as the recall of 2:2:2 OGs is less sensitive than the default specification.”
Quote in the paperNot a substantial claimIt may state two separate claims as one.
Findingown dataA 107.2 M bp (68.8%) segment of the human X, which corresponds with the X-conserved region, is syntenic with 77.8 M bp (93.9%) of the Tasmanian devil X chromosome and represents the entire syntenic region between the human and all three marsupial X chromosomes.
“Further, a 107.2 M bp (68.8%) segment of the human X, which corresponds with the X-conserved region, is syntenic with 77.8 M bp (93.9%) of the Tasmanian devil X chromosome and represents the entire syntenic region between the human and all three marsupial X chromosomes (Figure 2).”
Quote in the paperSubstantial claimProbably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds. It may state two separate claims as one.
Findingnone givenThis method results in significant speed improvements with little loss of fidelity among closely related haploid genomes.
“This method results in significant speed improvements with little loss of fidelity among closely related haploid genomes.”
Quote in the paperNot a substantial claimProbably not a substantial claim. The paper’s conclusions may not depend on it.
FindingreasoningNon-homeologous paralogs are typically excluded in the default GENESPACE parameterization.
“Non-homeologous paralogs are typically excluded in the default GENESPACE parameterization.”
Quote in the paperNot a substantial claimIt may state two separate claims as one.
Findingown dataThe two Mo18W QTL regions exist within an 11.7 M bp derived inversion that is only found in the Mo18W genome.
“we were surprised to find that the two Mo18W QTL regions exist within a 11.7 M bp derived inversion that is only found in the Mo18W genome (Figure 3D, E).”
Quote in the paperSubstantial claimIt may state two separate claims as one.
FindingreasoningBoth maize homeologous regions are present in the across grasses synteny graph (Figure 3A) despite using identical synteny parameters to the maize NAM parent run.
“Hence, both maize homeologous regions are present in the across grasses synteny graph (Figure 3A) despite using identical synteny parameters to the maize NAM parent run.”
Quote in the paperNot a substantial claim- Rests on an assumption: The coalescence of any two maize genotypes occurred more recently than the ~12M ya whole-genome duplication.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
Findingnone givenThere are 1096 non-syntenic orthologs (6.3% of all orthologs) between human and chimpanzee.
“For example, there are 1096 non-syntenic orthologs (6.3% of all orthologs) between human and chimpanzee.”
Quote in the paperNot a substantial claimProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
Findingnone givenSetting orthofinderInBlk to TRUE causes pairs of genomes to be considered and genes without a solid hit in the outgroup are not excluded.
“it will be far better to set orthofinderInBlk to TRUE, so that pairs of genomes are considered and genes without a solid hit in the outgroup are not excluded.”
Quote in the paperNot a substantial claimProbably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.
Findingnone givenIt is not clear that rerunning OrthoFinder within syntenic blocks offers much improvement over global orthogroups between purely haploid genomes.
“however, it is not clear that this offers much improvement over global orthogroups between purely haploid genomes.”
Quote in the paperNot a substantial claimProbably not a substantial claim. The paper’s conclusions may not depend on it.
Findingnone givenThese genes do not have functional annotations relating to drought.
“While these genes do not have functional annotations relating to drought,”
Quote in the paperNot a substantial claimProbably not a substantial claim. The paper’s conclusions may not depend on it.
Findingnone givenGENESPACE was originally designed for work with plants.
“GENESPACE was originally designed for work with plants”
Quote in the paperNot a substantial claimIt may state two separate claims as one.
Findingown dataIn the comparison between human and chicken, GENESPACE resolved 2% and 1.8% more single-copy orthogroups and syntenic blocks than default OrthoFinder and orthogroup-constrained MCScanX, respectively.
“For example, in the comparison between human and chicken, GENESPACE resolved 2% and 1.8% more single-copy orthogroups and syntenic blocks than default OrthoFinder and orthogroup-constrained MCScanX, respectively.”
Quote in the paperNot a substantial claimIt may state two separate claims as one.
Findingown dataThese ratios were highly variable among genomes, particularly among the C3 species (wheat, rice, B. distachyon), which had far more absences than the C4 species (15.3% vs. 5.5%, odds ratio = 3.1, p = 6.25 × 10−8).
“However, these ratios were highly variable among genomes, particularly among the C3 species (wheat, rice, B. distachyon), which had far more absences than the C4 species (15.3% vs. 5.5%, odds ratio = 3.1, p = 6.25 × 10−8, Figure 3B).”
Quote in the paperNot a substantial claimIt may state two separate claims as one.
Findingown dataThe entirety of the echidna X4 and 47.6 M bp (67.9%) of the genic region of the platypus X5 chromosomes are syntenic with the avian Z chromosome.
“Interestingly, the entirety of the echidna X4 and 47.6 M bp (67.9%) of the genic region of the platypus X5 chromosomes are syntenic with the avian Z chromosome (Figure 2).”
Quote in the paperNot a substantial claimProbably not a substantial claim.
FindingreasoningGENESPACE offers an 'outgroup' parameter, which specifies the genomes that should be included in the orthofinder run but excluded from all downstream analyses.
“GENESPACE offers an ‘outgroup’ parameter, which specifies the genomes that should be included in the orthofinder run but excluded from all downstream analyses.”
Quote in the paperSubstantial claimIt may state two separate claims as one.
Findingown dataBuilding pan-genome annotations across the seven grasses anchored to C4 maize resulted in 159 pan-genome entries: nearly always two placements for each gene in the paleo-tetraploid maize genome.
“This resulted in 159 pan-genome entries: nearly always two placements for each gene in the paleo-tetraploid maize genome.”
Quote in the paperNot a substantial claimProbably not a substantial claim. The paper’s conclusions may not depend on it.
Findingnone givenIf OrthoFinder was run using the 'fast' orthofinderMethod, orthologs will not be produced nor added into the pan-genome annotation.
“Note that if OrthoFinder was run using the ‘fast’ orthofinderMethod, orthologs will not be produced nor added into the pan-genome annotation.”
Quote in the paperNot a substantial claimIt may state two separate claims as one.
Findingown dataThe only genome with complete segregation of the two paralogs, wheat, also retains these regions in the center of all six chromosomes.
“further, the only genome with complete segregation of the two paralogs, wheat, also retains these regions in the center of all six chromosomes (Figure 4C).”
Quote in the paperSubstantial claimProbably not a substantial claim. The paper may give no reason why it holds.
Premisenone givenWhole-genome duplications, chromosomal deletions, and variable rates of sequence evolution, such as subgenome dominance in polyploids, can confound the evidence of orthology from sequence similarity alone.
“However, whole-genome duplications (WGDs), chromosomal deletions, and variable rates of sequence evolution, such as subgenome dominance in polyploids, can confound the evidence of orthology from sequence similarity alone.”
Quote in the paperNot a substantial claimProbably not a substantial claim. The paper’s conclusions may not depend on it.
PremisecitationThe Rho duplication predated the split among most extant grasses.
“consistent with the previous discovery that the Rho duplication predated the split among most extant grasses (Ma et al., 2021).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Ma et al., 2021
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
Probably not a substantial claim. The paper may give no reason why it holds.
Premisenone givenParalogs derived from WGDs notoriously obscure contrasts between orthologs in these systems.
“Paralogs derived from these WGDs notoriously obscure contrasts between orthologs in these systems.”
Quote in the paperNot a substantial claimIt may state two separate claims as one.
PremisecitationThe eutherian mammalian X chromosome is largely composed of two regions, an X-conserved ancestral sex chromosome region that arose in the common ancestor of therian mammals, and an X-added region that arose in the common ancestor of eutherians.
“The eutherian mammalian X chromosome is largely composed of two regions, an X-conserved ancestral sex chromosome region that arose in the common ancestor of therian mammals, and an X-added region that arose in the common ancestor of eutherians (Ross et al., 2005).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Ross et al., 2005 source
Probably not a substantial claim.
Premisenone givenThere are two major violations of the single-copy assumption that cause copy number variation within a syntenic block: tandem arrays and gene PAV.
“There are two major violations of this assumption that cause copy number variation within a syntenic block: (1) tandem arrays and (2) gene PAV.”
Quote in the paperSubstantial claim- The authors state this as an assumption: Homologs should be exactly single copy within any syntenic region between a pair of genomes.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
Interpretationown dataThe defaults of GENESPACE synteny are sufficient for most high-quality genomes and evolutionary scenarios.
“however, the defaults are sufficient for most high-quality genomes and evolutionary scenarios.”
Quote in the paperNot a substantial claimProbably not a substantial claim.
PremisereasoningErrors in syntenic block coordinates can have major effects on downstream estimates.
“Given GENESPACE’s reliance on syntenic regions between genomes, errors in syntenic block coordinates can have major effects on downstream estimates.”
Quote in the paperSubstantial claimProbably not a substantial claim.
InterpretationreasoningAll syntenic orthogroups, even those that do not include a reference genome gene model, need to have reference positional information to extract PAV by physical coordinates.
“Since we want to extract PAV by physical coordinates, all syntenic orthogroups, even those that do not include a reference genome gene model, need to have reference positional information.”
Quote in the paperSubstantial claimIt may state two separate claims as one.
Interpretationown dataThe mammalian X and sand lizard Z chromosomes partially share syntenic orthology, an outcome consistent with common descent from a shared ancestral sex chromosome or autosome containing sex-related genes.
“Nonetheless, the mammalian X and sand lizard Z chromosomes partially share syntenic orthology, an outcome that would be consistent with common descent from a shared ancestral sex chromosome or autosome containing sex-related genes.”
Quote in the paperSubstantial claimProbably not a substantial claim. The paper may give no reason why it holds. It may state two separate claims as one.
PremisereasoningA priori knowledge of gene copy number is needed to effectively infer orthology and synteny, yet measures of synteny and orthology are needed to infer copy number between a pair of sequences.
“These issues boil down to a simple circular problem: a priori knowledge of gene copy number is needed to effectively infer orthology and synteny, yet measures of synteny and orthology are needed to infer copy number between a pair of sequences.”
Quote in the paperNot a substantial claimIt may state two separate claims as one.
InterpretationreasoningGENESPACE condenses physically proximate multigene families (tandem arrays) to the physically most central gene of the array, and recalculates gene rank order on these array representative genes, effectively masking copy number variation due to tandem arrays.
“First, physically proximate multigene families (hereon, ‘tandem arrays’, Box 1) are condensed to the physically most central gene of the array. Gene rank order along the genome is recalculated on these ‘array representative’ genes, effectively masking copy number variation due to tandem arrays.”
Quote in the paperSubstantial claimIt may state two separate claims as one.
Study design and conductreasoningTreating all genomes as haploid and not including an outgroup means orthogroups should not include homeologs since the genomes share a common ancestor that arose after the WGD.
“As such, we treated all genomes as haploid and did not include an outgroup; therefore, orthogroups should not include homeologs since the genomes share a common ancestor that arose after the WGD (see ‘additional considerations’ methods section: Outgroups and the phylogenetic context of orthology inference).”
Quote in the paperSubstantial claim- Rests on an assumption: The genomes in each comparison share a common ancestor that arose after the WGD.
Probably not a substantial claim. It may be too vague to check against evidence.
InterpretationreasoningGENESPACE R package is a framework to help bridge the current gaps between comparative and quantitative genomics, especially in complex evolutionary systems.
“Here, we presented the GENESPACE R package as a framework to help bridge the current gaps between comparative and quantitative genomics, especially in complex evolutionary systems.”
Quote in the paperNot a substantial claimProbably not a substantial claim. The paper’s conclusions may not depend on it.
Study design and conductnone givenThe orthologs and syntenic mapping between v2 and the two v5 versions used here are included as text files in the data repository.
“The orthologs and syntenic mapping between these versions are included as text files in the data repository.”
Quote in the paperNot a substantial claimProbably not a substantial claim.
PremisecitationA pan-genome annotation framework permits access to multi-genome networks of high-confidence orthologs and paralogs, regardless of ploidy or other complicating aspects of genome biology.
“Such a ‘pan-genome annotation’ framework (Lovell et al., 2021a) permits access to multi-genome networks of high-confidence orthologs and paralogs, regardless of ploidy or other complicating aspects of genome biology.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Lovell et al., 2021a
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
Probably not a substantial claim.
Study design and conductnone givenThe reference pan-genome built in step 3 only acts on direct syntenic blast hits (edges), which allows for strict construction of interpolated positions without the potential polluting positional effects of orthogroups in minor or miss-assembled syntenic blocks.
“The reference pan-genome built in step 3 only acts on direct syntenic blast hits (edges), which allows for strict construction of interpolated positions without the potential polluting positional effects of orthogroups in minor or miss-assembled syntenic blocks.”
Quote in the paperSubstantial claimProbably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.
InterpretationreasoningSince the final coding of blocks is conducted within broad syntenic regions, the parameters passed should be robust to variation in ploidy and sequence divergence between genomes.
“Since the final coding of blocks is conducted within broad syntenic regions, the parameters passed should be robust to variation in ploidy and sequence divergence between genomes.”
Quote in the paperNot a substantial claimProbably not a substantial claim. The paper’s conclusions may not depend on it.
PremisecitationEvidence about the nonrandomness of sex chromosome evolution is still contentious.
“While the same or similar genomic regions often recurrently evolve into sex chromosomes, perhaps due to ancestral gene functions involved in gonadogenesis, evidence about the nonrandomness of sex chromosome evolution is still contentious (Kratochvíl et al., 2021).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Kratochvíl et al., 2021 source
Probably not a substantial claim. The paper’s conclusions may not depend on it.
InterpretationreasoningIt is possible that multiple Mo18W causal variants have been fixed in linkage disequilibrium in this NAM population.
“Since inversions reduce recombination, it is possible that multiple Mo18W causal variants have been fixed in linkage disequilibrium in this NAM population.”
Quote in the paperNot a substantial claim- Rests on an assumption: Inversions reduce recombination.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
Premisecitation86 genes are involved in the transition between C3 and C4 photosynthesis.
“As an example of the exploration of lists of a priori-defined candidate genes, we analyzed PAV of 86 genes shown to be involved in the transition between C3 and C4 photosynthesis (Ding et al., 2015), the latter permitting ecological dominance in arid climates and agricultural productivity under forecasted increased heat load of the next century.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Ding et al., 2015 source
Checked before — its earlier verdict is held back until a new check runs.
Probably not a substantial claim. The paper may give no reason why it holds.
Interpretationnone givenGENESPACE resolves the circular problem of inferring orthology and synteny by operating on the assumption that homologs should be exactly single copy within any syntenic region between a pair of genomes.
“GENESPACE resolves this circular problem by operating on a foundational assumption: homologs should be exactly single copy within any syntenic region between a pair of genomes.”
Quote in the paperNot a substantial claim- The authors state this as an assumption: Homologs should be exactly single copy within any syntenic region between a pair of genomes.
It may state two separate claims as one.
InterpretationreasoningGENESPACE allows multiple placements not only for each nonreference gene, but also for genes in the reference genome itself, because we do not want to rely on single-copy references.
“However, we do not want to rely on single-copy references, so GENESPACE allows multiple placements not only for each nonreference gene, but also for genes in the reference genome itself.”
Quote in the paperSubstantial claimProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
PremisecitationMaize is an 11.4 M ya paleo-polyploid, allo-tetraploid switchgrass formed 4-6 M ya, and allo-hexaploid bread wheat arose about 8 k ya.
“For example, maize is an 11.4 M ya paleo-polyploid (Gaut and Doebley, 1997), allo-tetraploid switchgrass formed 4–6 M ya (Lovell et al., 2021b), and allo-hexaploid bread wheat arose about 8 k ya (Haas et al., 2019).”
Quote in the paperNot a substantial claim0 of 3 sources checkedProbably not a substantial claim. It may be too vague to check against evidence. The paper may give no reason why it holds.
Interpretationnone givenThe incorporation of synteny and orthology into comparative genomics and quantitative genetics pipelines offers a mechanism to bridge these disparate disciplines.
“The incorporation of synteny and orthology into comparative genomics and quantitative genetics pipelines offers a mechanism to bridge these disparate disciplines.”
Quote in the paperNot a substantial claimProbably not a substantial claim. It may state two separate claims as one.
PremisecitationOrthoFinder can also use gene trees to split orthogroups into pairwise orthologs, which represent a stricter definition of orthology.
“OrthoFinder can also use gene trees to split orthogroups into pairwise orthologs (Emms and Kelly, 2019), which represent a stricter definition of orthology.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Emms and Kelly, 2019 source
Probably not a substantial claim. It may be too vague to check against evidence. The paper may give no reason why it holds.
Interpretationnone givenThe historical abundance of genetic mapping studies and ongoing proliferation of genome resources provides a strong foundation for the integration of comparative and quantitative genomics to accelerate discoveries in evolutionary biology, medicine, and agriculture.
“Combined, the historical abundance of genetic mapping studies and ongoing proliferation of genome resources provides a strong foundation for the integration of comparative and quantitative genomics to accelerate discoveries in evolutionary biology, medicine, and agriculture.”
Quote in the paperNot a substantial claimIt may state two separate claims as one.
Interpretationnone givenGENESPACE is an analytical pipeline that explicitly links synteny and sequence similarity to provide high-confidence inference about networks of genes that share a common ancestor and represents these networks as a pan-genome annotation.
“Here, we present GENESPACE, an analytical pipeline that explicitly links synteny and sequence similarity to provide high-confidence inference about networks of genes that share a common ancestor and represents these networks as a ‘pan-genome annotation’.”
Quote in the paperSubstantial claimProbably not a substantial claim. The paper’s conclusions may not depend on it.
InterpretationreasoningThis result suggests a possible role of gene loss or gain as an evolutionary mechanism for drought- and heat-adapted photosynthesis.
“Nonetheless, this result suggests a possible role of gene loss or gain as an evolutionary mechanism for drought- and heat-adapted photosynthesis.”
Quote in the paperNot a substantial claimIt may state two separate claims as one.
Premisenone givenGenomic comparisons among grasses are difficult, in part because of an ancient polyploid origin and because subsequent WGDs are a feature of most clades of grasses.
“Despite the tremendous genetic resources of these and other grasses, genomic comparisons among grasses are difficult, in part because of an ancient polyploid origin (see the next section), and because subsequent WGDs are a feature of most clades of grasses.”
Quote in the paperSubstantial claimIt may state two separate claims as one.
InterpretationreasoningGENESPACE infers synteny in a pairwise manner only using potential anchor protein BLAST hits where both the query and target genes are in the same orthogroup, and recalculates rank-order positions of these potential anchor genes prior to synteny inference, effectively masking orthogroups missing a gene in one genome (PAV).
“Second, synteny is inferred in a pairwise manner only using ‘potential anchor’ protein BLAST hits (hereon ‘hits’) where both the query and target genes are in the same orthogroup. The rank-order positions of these potential anchor genes are also recalculated prior to synteny inference, which effectively masks orthogroups missing a gene in one genome (i.e., PAV).”
Quote in the paperSubstantial claimIt may state two separate claims as one.
PremisecitationOnly the first X chromosomes are ancestral to both echidna and platypus, and all are unrelated to the mammalian X chromosomes, consistent with their independent evolution.
“Only the first X chromosomes are ancestral to both echidna and platypus (Rens et al., 2007), and all are unrelated to the mammalian X chromosomes (Figure 2—figure supplement 1), consistent with their independent evolution (Rens et al., 2007).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Rens et al., 2007 source
Checked before — its earlier verdict is held back until a new check runs.
It may state two separate claims as one.
Interpretationown dataThe avian Z chromosome clearly did not evolve from either of the two reptile Z chromosomes sampled here, but instead likely arose from autosomal regions or unsampled ancestral sex chromosomes.
“Given our analysis, the avian Z chromosome clearly did not evolve from either of the two reptile Z chromosomes sampled here, but instead likely arose from autosomal regions or unsampled ancestral sex chromosomes.”
Quote in the paperSubstantial claimProbably not a substantial claim. The paper may give no reason why it holds. It may state two separate claims as one.
Premisenone givenIn some cases, homeologous gene duplications from polyploidy have generated genetic diversity that can be targeted for crop improvement; in other cases the genetic basis of trait variation may be restricted to sequences that arose in a single subgenome.
“In some cases, homeologous gene duplications from polyploidy have generated genetic diversity that can be targeted for crop improvement; however, in other cases the genetic basis of trait variation may be restricted to sequences that arose in a single subgenome.”
Quote in the paperNot a substantial claimProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
Study design and conductnone givenAll results were generated programmatically; the accompanying scripts and key output are available on github: jtlovell/GENESPACE_data.
“All results were generated programmatically; the accompanying scripts and key output are available on github: jtlovell/GENESPACE_data.”
Quote in the paperNot a substantial claimIt may state two separate claims as one.
PremisecitationConserved gene order collinearity along local regions of chromosomes can provide evidence of homology and in some cases enable determination of whether two regions diverged as a result of speciation or a large-scale duplication event.
“Like chromosome-scale synteny, conserved gene order collinearity along local regions of chromosomes can provide evidence of homology, and in some cases enable determination of whether two regions diverged as a result of speciation or a large-scale duplication event (Drillon et al., 2020).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Drillon et al., 2020 source
Checked before — its earlier verdict is held back until a new check runs.
The authors state this as an assumption.
Homologs should be exactly single copy within any syntenic region between a pair of genomes.
“GENESPACE resolves this circular problem by operating on a foundational assumption: homologs should be exactly single copy within any syntenic region between a pair of genomes.”
The paper relies on this without support.
The three vertebrate genome comparisons have no recent history of WGDs, while WGDs predated evolutionary divergence of the four plant contrasts.
“The three comparisons between vertebrate genomes have no recent history of WGDs, while WGDs predated evolutionary divergence of the four plant contrasts: maize is a 12 M ya paleo-tetraploid, cotton is a 1.6 M ya meso-tetraploid, and the ~70 M ya Rho WGD predated grass diversification.”
The paper relies on this without support.
The genomes in each comparison share a common ancestor that arose after the WGD.
“As such, we treated all genomes as haploid and did not include an outgroup; therefore, orthogroups should not include homeologs since the genomes share a common ancestor that arose after the WGD (see ‘additional considerations’ methods section: Outgroups and the phylogenetic context of orthology inference).”
The paper relies on this without support.
The heteromorphic chromosomes (Y and W) are often unassembled, or, where assemblies exist, lack sufficient synteny to provide a useful metric for comparative genomics.
“The heteromorphic chromosomes (Y and W) are often unassembled, or, where assemblies exist, lack sufficient synteny to provide a useful metric for comparative genomics.”
The paper relies on this without support.
Many genetic mapping populations now have reference genome sequences for all parents.
“However, many genetic mapping populations now have reference genome sequences for all parents; this offers an opportunity to explore variation among functional alleles and PAV, which would be impossible with a single reference genome.”
The paper relies on this without support.
Inversions reduce recombination.
“Since inversions reduce recombination, it is possible that multiple Mo18W causal variants have been fixed in linkage disequilibrium in this NAM population.”
The paper relies on this without support.
In most pairwise comparisons between genomes, some syntenic orthogroups will be missing in the reference.
“In most pairwise comparisons between genomes, some syntenic orthogroups will be missing in the reference.”
The paper relies on this without support.
Most plant lineages have undergone one or more whole-genome duplications.
“most plant lineages have undergone one or more WGDs”
The paper relies on this without support.
The coalescence of any two maize genotypes occurred more recently than the ~12M ya whole-genome duplication.
“the coalescence of any two maize genotypes occurred more recently than the ~12M ya WGD”
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
Each contradiction between two passages listed here was confirmed by an independent check.
Cotton parameter changes omitted from the stated exceptions
MinorThe methods say all runs used default parameters except for the Rho grass and maize runs. The Table 1 note says the cotton comparison also changed two parameters from their defaults.
“All GENESPACE runs used default parameterization, with the following exceptions: (1) the Rho grass run allowed a single secondary hit (default is 0, this is how the paralogs are explicitly searched for) and maximum number of gaps in secondary regions of 10 (default is 5, relaxed to reduce ancient paralogous block splitting), and (2) the maize run used the ‘fast’ OrthoFinder method”
“to avoid confusion between subgenomes, blkSize, and nGaps parameters were increased from 5 (default) to 10 genes.”
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Self-citationNew whole-genome alignment tools are needed for tapping into plant diversity
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Adaptation repeatedly uses complex structural genomic variation
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Self-citationCephalopod sex determination and its ancient evolutionary origin
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Self-citation
Metadata
- Authors
- Lovell, J. T., Sreedasyam, A., Schranz, M. E., Wilson, M., Carlson, J. W., Harkess, A., Emms, D., Goodstein, D. M., & Schmutz, J.
- Affiliations
- Lawrence Berkeley National Laboratory (US)
- HudsonAlpha Institute for Biotechnology (US)
- Wageningen University & Research (NL)
- Arizona State University (US)
- University of Oxford (GB)
- Corresponding author
- Lovell, John T
- ORCID
- Venue
- eLife
- Publisher
- eLife Sciences Publications, Ltd
- Published
- 2022-09-09
- Volume
- 11
- ISSN
- 2050-084X (ISSN-L)
- PMC
- PMC9462846
- OpenAlex
- W4295078843
- Cited by
- 391
- References
- 54
- Citations by year
- 2026: 144 · 2025: 130 · 2024: 78 · 2023: 37 · 2022: 2
- FWCI
- 18.24
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- eLife (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (submittedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Socio-Environmental Systems Modeling (acceptedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- eScholarship (California Digital Library) (submittedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion, cc-by)
- Funders
- U.S. Department of Energy (DE-AC02-05CH1123)
- National Institute of General Medical Sciences (R35GM124827)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Keywords
- gene order, orthology, synteny, copy number variation, presence/absence variation, structural variants, sex chromosome evolution, Poaceae, maize varieties, polyploidy, comparative genomics, R package
- MeSH terms
- Gene Dosage, Genome, Plant, Evolution, Molecular, Synteny, Quantitative Trait Loci, DNA Copy Number Variations
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
A language model drew the claims from the paper on 2026-11-10, under version 3 of the claim definition (model deepseek-v4.1-flash, prompt extract-v3).
A second model labelled each claim on 2026-11-10 (model jev-1.13-20260917, definition revision gold-guideline-v0.2).
Cited sources are checked with a language model’s help (gpt-6-sol).
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
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