A view of the pan‐genome of domesticated Cowpea ( Vigna unguiculata [L.] Walp.)
- Department of Computer Science and Engineering University of California Riverside Riverside CA USA
- Department of Botany and Plant Sciences University of California Riverside Riverside CA USA, Departamento de Biología Molecular Universidad de León León Spain
- US Department of Energy Joint Genome Institute Lawrence Berkeley National Laboratory Berkeley CA USA
- Department of Botany and Plant Sciences University of California Riverside Riverside CA USA, Department of Plant Sciences University of California Davis Davis CA USA
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products Institute of Vegetables Zhejiang Academy of Agricultural Sciences Hangzhou China
- Department of Agronomy and Plant Genetics University of Minnesota Twin Cities Saint Paul MN USA
- National Center for Genome Resources Santa Fe NM USA
- Key Lab of Specialty Agri‐Product Quality and Hazard Controlling Technology of Zhejiang Province China Jiliang University Hangzhou China
- Department of Botany and Plant Sciences University of California Riverside Riverside CA USA
Cowpea, Vigna unguiculata L . Walp., is a diploid warm‐season legume of critical importance as both food and fodder in sub‐Saharan Africa. This species is also grown in Northern Africa, Europe, Latin America, North America, and East to Southeast Asia. To capture the genomic diversity of domesticates of this important legume, de novo genome assemblies were produced for representatives of six subpopulations of cultivated cowpea identified previously from genotyping of several hundred diverse accessions. In the most complete assembly (IT97K‐499‐35), 26,026 core and 4963 noncore genes were identified, with 35,436 pan genes when considering all seven accessions. GO terms associated with response to stress and defense response were highly enriched among the noncore genes, while core genes were enriched in terms related to transcription factor activity, and transport and metabolic processes. Over 5 million single nucleotide polymorphisms (SNPs) relative to each assembly and over 40 structural variants >1 Mb in size were identified by comparing genomes. Vu10 was the chromosome with the highest frequency of SNPs, and Vu04 had the most structural variants. Noncore genes harbor a larger proportion of potentially disruptive variants than core genes, including missense, stop gain, and frameshift mutations; this suggests that noncore genes substantially contribute to diversity within domesticated cowpea.
- Research Organization:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Organization:
- Agricultural Research Service; National Natural Science Foundation of China; National Science Foundation (NSF); National Ten-Thousand Talents Program of China; US Department of Agriculture; USDOE; USDOE Office of Science (SC), Biological and Environmental Research (BER)
- Grant/Contract Number:
- AC02-05CH11231
- OSTI ID:
- 1962959
- Alternate ID(s):
- OSTI ID: 1962961
OSTI ID: 2228882
- Journal Information:
- The Plant Genome, Journal Name: The Plant Genome Journal Issue: 1 Vol. 17; ISSN 1940-3372
- Publisher:
- Wiley Blackwell (John Wiley & Sons)Copyright Statement
- Country of Publication:
- United States
- Language:
- English