The DOI matches its Crossref record; 54 of the 54 references it cites were found in a registry or an index.
Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps
Open accessAbstract
Large-scale (segmental or whole) genome duplication has been recurring in angiosperm evolution. Subsequent gene loss and rearrangements further affect gene copy numbers and fractionate ancestral gene linkages across multiple chromosomes. The fragmented “multiple-to-multiple” correspondences resulting from this distinguishing feature of angiosperm evolution complicates comparative genomic studies. Using a robust computational framework that combines information from multiple orthologous and duplicated regions to construct local syntenic networks, we show that a shared ancient hexaploidy event (or perhaps two roughly concurrent genome fusions) can be inferred based on the sequences from several divergent plant genomes. This “paleo-hexaploidy” clearly preceded the rosid–asterid split, but it remains equivocal whether it also affected monocots. The model resulting from our multi-alignments lays the foundation for approximating the number and arrangement of genes in the last universal common ancestor of angiosperms. Comparative analysis of inferred homologous genes derived from this model shows patterns of preferential gene retention or loss after polyploidy and reveals large variability of nucleotide substitution rates among plant nuclear genomes.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669
Thompson, J. D., Higgins, D. G., & Gibson, T. J. (1994) · Nucleic Acids Research · doi:10.1093/nar/22.22.4673 · Cited by 64,617
MrBayes 3: Bayesian phylogenetic inference under mixed models
Ronquist, F., & Huelsenbeck, J. P. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg180 · Cited by 29,077
MODELTEST: testing the model of DNA substitution.
Posada, D., & Crandall, K. A. (1998) · Bioinformatics · doi:10.1093/bioinformatics/14.9.817 · Cited by 19,820
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
Initiative, T. A. G. (2000) · Nature · doi:10.1038/35048692 · Cited by 9,301
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
Li, L., Stoeckert, C. J., & Roos, D. S. (2003) · Genome Research · doi:10.1101/gr.1224503 · Cited by 5,707
PAML: a program package for phylogenetic analysis by maximum likelihood
Yang, Z. (1997) · Bioinformatics · doi:10.1093/bioinformatics/13.5.555 · Cited by 5,373
Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions.
(1986) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040410 · Cited by 4,894
The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray)
Tuskan, G. A., DiFazio, S., Jansson, S., Bohlmann, J., Grigoriev, I., Hellsten, U., Putnam, N., Ralph, S., Rombauts, S., Salamov, A., et al. (2006) · Science · doi:10.1126/science.1128691 · Cited by 4,326
The map-based sequence of the rice genome
International Rice Genome Sequencing Project, & Sasaki, T. (2005) · Nature · doi:10.1038/nature03895 · Cited by 3,797
Cited by
MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity
Wang, Y., Tang, H., DeBarry, J. D., Tan, X., Li, J., Wang, X., Lee, T.-H., Jin, H., Marler, B., Guo, H., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr1293 · Cited by 7,093
Self-citationThe genome of the mesopolyploid crop species Brassica rapa
The Brassica rapa Genome Sequencing Project Consortium, Wang, X., Wang, H., Wang, J., Sun, R., Wu, J., Liu, S., Bai, Y., Mun, J.-H., Bancroft, I., et al. (2011) · Nature Genetics · doi:10.1038/ng.919 · Cited by 2,074
Self-citationGenome sequence and analysis of the tuber crop potato
The Potato Genome Sequencing Consortium (2011) · Nature · doi:10.1038/nature10158 · Cited by 2,065
The evolutionary significance of ancient genome duplications
Van de Peer, Y., Maere, S., & Meyer, A. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2600 · Cited by 1,129
Genome sequence of the cultivated cotton Gossypium arboreum
Li, F., Fan, G., Wang, K., Sun, F., Yuan, Y., Song, G., Li, Q., Ma, Z., Lu, C., Zou, C., et al. (2014) · Nature Genetics · doi:10.1038/ng.2987 · Cited by 870
Metadata
- Authors
- Tang, H., Wang, X., Bowers, J. E., Ming, R., Alam, M., & Paterson, A. H.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2008-10-02
- Volume
- 18
- Issue
- 12
- Pages
- 1944-1954
- ISSN
- 1088-9051 (ISSN-L)
- OpenAlex
- W2056871145
- Cited by
- 656
- References
- 54
- Type
- posted content
- Language
- en
- Open access
- bronze
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.
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.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps. https://app.cochat.ai/papers/10.1101/gr.080978.108
- The paper
- Tang, H., Wang, X., Bowers, J. E., Ming, R., Alam, M., & Paterson, A. H. (2008). Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps. Genome Research. https://doi.org/10.1101/gr.080978.108
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
