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Cited by 10Genomics and Phylogenetic StudiesChromosomal and Genetic VariationsGenome Rearrangement Algorithms

A multiple alignment workflow shows the effect of repeat masking and parameter tuning on alignment in plants

Open access
Wu, Yaoyao, Johnson, Lynn, Song, Baoxing, Romay, Cinta, Stitzer, Michelle, Siepel, Adam, Buckler, Edward, Scheben, Armin·2022·The Plant Genome
DOI 10.1002/tpg2.20204PMC PMC12807243
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Abstract

Alignments of multiple genomes are a cornerstone of comparative genomics, but generating these alignments remains technically challenging and often impractical. We developed the msa_pipeline workflow (https://bitbucket.org/bucklerlab/msa_pipeline) to allow practical and sensitive multiple alignment of diverged plant genomes and calculation of conservation scores with minimal user inputs. As high repeat content and genomic divergence are substantial challenges in plant genome alignment, we also explored the effect of different masking approaches and parameters of the LAST aligner using genome assemblies of 33 grass species. Compared with conventional masking with RepeatMasker, a masking approach based on k ‐mers (nucleotide sequences of k length) increased the alignment rate of coding sequence and noncoding functional regions by 25 and 14%, respectively. We further found that default alignment parameters generally perform well, but parameter tuning can increase the alignment rate for noncoding functional regions by over 52% compared with default LAST settings. Finally, by increasing alignment sensitivity from the default baseline, parameter tuning can increase the number of noncoding sites that can be scored for conservation by over 76%. Overall, tuning of masking and alignment parameters can generate optimized multiple alignments to drive biological discovery in plants.

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  • Tools like LASTZ and MULTIZ have been designed to tackle the challenges of aligning divergent genomes, enabling the alignment of divergent genomes.

    “However, tools like LASTZ and MULTIZ have been designed to tackle these challenges, enabling the alignment of divergent genomes [25,69].”

    From Whole-Genome Alignment: Methods, Challenges, and Future Directions (2024) · cites this paper as [69]

    The Introduction identifies LASTZ as a pairwise genome-alignment tool, and Methods (Evaluation of alignments; page unavailable) says the interspecies-alignment pipeline Cactus relies on LASTZ. Features and implementation of msa_pipeline links to a multiz repository for its multiple-alignment program, ROAST, but the paper does not establish that MULTIZ itself was designed to align divergent genomes. Its explicit claim of suitability for diverged interspecies genomes concerns LAST, not LASTZ. (LLM, conf=0.82)

    Experimental — accuracy not yet measured

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Cited by

Sorted by citations

Authors
Wu, Y., Johnson, L., Song, B., Romay, C., Stitzer, M., Siepel, A., Buckler, E., & Scheben, A.
Affiliations
  • Cornell University (US)
  • Institute for Genomic Diversity Cornell Univ. Ithaca NY 14853 USA
  • Cold Spring Harbor Laboratory (US)
  • Agricultural Research Service (US)
Corresponding author
Scheben, Armin
ORCID
Venue
The Plant Genome
Publisher
Wiley
Published
2022-04-13
Volume
15
Issue
2
Pages
e20204-e20204
ISSN
1940-3372 (ISSN-L)
DOI
10.1002/tpg2.20204
PMC
PMC12807243
OpenAlex
W4223521963
Cited by
10
References
3
Citations by year
2025: 1 · 2024: 5 · 2023: 3 · 2022: 1
FWCI
0.82
Type
journal article
Language
en
Open access
Licence
Locations
  • The Plant Genome (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • PubMed Central (publishedVersion, cc-by)
  • Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory) (acceptedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
Funders
  • National Natural Science Foundation of China (32102376)
  • National Science Foundation (IOS‐1822330, PRFB 1907343)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
Keywords
multiple sequence alignment, plant genome, repeat masking, conservation scores, grass genome, genome assembly, non-coding regions, comparative genomics
MeSH terms
Base Sequence, Genome, Plant, Genomics, Workflow

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