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Cited by 191Genetic and Environmental Crop StudiesGenomics and Phylogenetic StudiesChromosomal and Genetic Variations

Improved pea reference genome and pan-genome highlight genomic features and evolutionary characteristics

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Yang, Tao, Liu, Rong, Luo, Yingfeng, Hu, Songnian, Wang, Dong, Wang, Chenyu, Pandey, Manish K., Ge, Song +16 more·2022·Nature Genetics
DOI 10.1038/s41588-022-01172-2PMC PMC9534762
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Abstract

Complete and accurate reference genomes and annotations provide fundamental resources for functional genomics and crop breeding. Here we report a de novo assembly and annotation of a pea cultivar ZW6 with contig N50 of 8.98 Mb, which features a 243-fold increase in contig length and evident improvements in the continuity and quality of sequence in complex repeat regions compared with the existing one. Genome diversity of 118 cultivated and wild pea demonstrated that Pisum abyssinicum is a separate species different from P. fulvum and P. sativum within Pisum . Quantitative trait locus analyses uncovered two known Mendel’s genes related to stem length ( Le/le ) and seed shape ( R/r ) as well as some candidate genes for pod form studied by Mendel. A pan-genome of 116 pea accessions was constructed, and pan-genes preferred in P. abyssinicum and P. fulvum showed distinct functional enrichment, indicating the potential value of them as pea breeding resources in the future.

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  • MUMmer 4.0 introduces improved speed and memory usage through parallel processing of input query sequences.

    “In addition, MUMmer 4.0 introduces improved speed and memory usage through parallel processing of input query sequences [20].”

    From Whole-Genome Alignment: Methods, Challenges, and Future Directions (2024) · cites this paper as [20]

    The Methods section (Pisum pan-genome assembly, annotation and PAV analysis; page unavailable) says the authors used MUMmer v4.0 to align contigs. The References list calls MUMmer4 a fast genome-alignment system, but our copy does not address improved memory usage or parallel processing of input query sequences; searches for those features found no supporting passage. (LLM, conf=0.78)

    Experimental — accuracy not yet measured

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Cited by

Sorted by citations

Authors
Yang, T., Liu, R., Luo, Y., Hu, S., Wang, D., Wang, C., Pandey, M. K., Ge, S., Xu, Q., Li, N., Li, G., Huang, Y., Saxena, R. K., Ji, Y., Li, M., Yan, X., He, Y., Liu, Y., Wang, X., Xiang, C., Varshney, R. K., Ding, H., Gao, S., & Zong, X.
Affiliations
  • Chinese Academy of Agricultural Sciences (CN)
  • Chinese Academy of Sciences (CN)
  • Shandong Academy of Agricultural Sciences (CN)
  • International Crops Research Institute for the Semi-Arid Tropics (IN)
  • Northwest A&F University (CN)
  • Shandong Normal University (CN)
  • Yunnan Academy of Agricultural Sciences (CN)
  • Qinghai University (CN)
  • Sichuan Academy of Agricultural Sciences (CN)
  • Murdoch University (AU)
Corresponding author
  • Varshney, Rajeev K.
  • Ding, Hanfeng
  • Gao, Shenghan
  • Zong, Xuxiao
ORCID
Venue
Nature Genetics
Publisher
Springer Science and Business Media LLC
Published
2022-09-22
Volume
54
Issue
10
Pages
1553-1563
ISSN
  • 1061-4036 (ISSN-L)
  • 1546-1718
DOI
10.1038/s41588-022-01172-2
PMC
PMC9534762
OpenAlex
W4296683311
Cited by
191
References
4
Citations by year
2026: 46 · 2025: 56 · 2024: 53 · 2023: 33 · 2022: 3
FWCI
21.13
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Genetics (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Open Access Repository of ICRISAT (International Crops Research Institute for the Semi-Arid Tropics) (acceptedVersion)
  • Murdoch University Research Portal (submittedVersion, cc-by)
  • Murdoch University Research Portal (submittedVersion)
  • Institute of Botany, CAS Institutional Repository (submittedVersion)
Funders
  • Murdoch University
  • National Natural Science Foundation of China (2018YFD1000701, CARS-08, 2130135, 31801428, 2018YFD1000700)
  • Chinese Academy of Agricultural Sciences
  • Shandong Academy of Agricultural Sciences
  • Agricultural Variety Improvement Project of Shandong Province (2019LZGC017, SDAIT-15-01, CARS-08)
  • Agricultural Science and Technology Innovation Program
  • Youth Innovation Promotion Association
  • Modern Agricultural Technology Industry System of Shandong province
Topics
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Genetic and Environmental Crop Studies
  • 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
Keywords
pea, Pisum, de novo genome assembly, genome annotation, pan-genome, Pisum abyssinicum, Pisum fulvum, Pisum sativum, genomic diversity, quantitative trait loci, Mendelian inheritance, stem length, seed shape, crop breeding
MeSH terms
Plant Breeding, Biological Evolution, Pisum sativum, Genomics, Quantitative Trait Loci

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