豇豆(Vigna unguiculata [L.] Walp.)

IF 3.9 2区 生物学 Q1 GENETICS & HEREDITY
Plant Genome Pub Date : 2024-03-01 Epub Date: 2023-03-22 DOI:10.1002/tpg2.20319
Qihua Liang, María Muñoz-Amatriaín, Shengqiang Shu, Sassoum Lo, Xinyi Wu, Joseph W Carlson, Patrick Davidson, David M Goodstein, Jeremy Phillips, Nadia M Janis, Elaine J Lee, Chenxi Liang, Peter L Morrell, Andrew D Farmer, Pei Xu, Timothy J Close, Stefano Lonardi
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引用次数: 0

摘要

豇豆(Vigna unguiculata L. Walp.)是一种二倍体暖季豆科植物,在撒哈拉以南非洲既是食物又是饲料,具有极其重要的意义。非洲北部、欧洲、拉丁美洲、北美洲、东亚和东南亚也有种植。为了捕捉这种重要豆科植物驯化品的基因组多样性,我们为之前通过对几百个不同品种的基因分型确定的栽培豇豆的六个亚群的代表制作了全新的基因组组装。在最完整的基因组组装(IT97K-499-35)中,共鉴定出 26,026 个核心基因和 4963 个非核心基因,如果考虑到所有七个登录基因,则共有 35,436 个泛基因。在非核心基因中,与应激反应和防御反应相关的 GO 术语高度富集,而核心基因则富集在与转录因子活性、运输和代谢过程相关的术语中。通过比较基因组,发现了相对于每个装配的 500 多万个单核苷酸多态性(SNPs)和 40 多个大小大于 1 Mb 的结构变异。Vu10 是 SNP 频率最高的染色体,而 Vu04 的结构变异最多。与核心基因相比,非核心基因蕴藏着更大比例的潜在破坏性变异,包括错义突变、停止增益突变和换框突变;这表明非核心基因对豇豆驯化过程中的多样性做出了重大贡献。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
A view of the pan-genome of domesticated Cowpea (Vigna unguiculata [L.] Walp.).

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.

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来源期刊
Plant Genome
Plant Genome PLANT SCIENCES-GENETICS & HEREDITY
CiteScore
6.00
自引率
4.80%
发文量
93
审稿时长
>12 weeks
期刊介绍: The Plant Genome publishes original research investigating all aspects of plant genomics. Technical breakthroughs reporting improvements in the efficiency and speed of acquiring and interpreting plant genomics data are welcome. The editorial board gives preference to novel reports that use innovative genomic applications that advance our understanding of plant biology that may have applications to crop improvement. The journal also publishes invited review articles and perspectives that offer insight and commentary on recent advances in genomics and their potential for agronomic improvement.
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