Genome-wide patterns of large-size presence/absence variants in sorghum.
Genome-wide patterns of large-size presence/absence variants in sorghum.
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DOI：
10.1111/jipb.12121
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发表时间：
2014
影响因子：
11.4
通讯作者：
Li-Min Zhang;Hong Luo;Zhi-Quan Liu;Yi Zhao;Jingchu Luo;D. Hao;Hai-Chun Jing
中科院分区：
文献类型：
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作者：
Li-Min Zhang;Hong Luo;Zhi-Quan Liu;Yi Zhao;Jingchu Luo;D. Hao;Hai-Chun Jing
存在/缺失变异（pav）是基因组结构变异的主要来源，对动物和人类的表型和基因组变异有着深远的影响。然而，人们对植物基因组中的pav知之甚少。我们之前对三种高粱（sorghum bicolour L.）基因组进行了重测序，每个基因组的覆盖率为12倍，共发现了5 364个pav。在这里，我们报告了51个大尺寸（bbb30 kb） pav的详细特性。这些pav的总大小为2.92 Mb，包含202个已知和预测的基因，其中包括38个被注释为编码细胞死亡和应激反应基因的基因。以DNA转座子为主要成分的重复序列和可移动元件的pav变化很大。这些pav的频率和分布在96个高粱自交系中存在显著差异，且低频pav和高频pav在基因类别上存在差异。该报告对高粱pav的发生和多样性有了新的认识。本研究为探索基因组结构变异在植物育种中的遗传改良提供了新的视角。
The presence/absence variants (PAVs) are a major source of genome structural variation and have profound effects on phenotypic and genomic variation in animals and humans. However, little is understood about PAVs in plant genomes. Our previous resequencing effort on three sorghum (Sorghum bicolour L.) genomes, each 12× coverage, uncovered 5 364 PAVs. Here, we report a detailed characterization of 51 large-size (>30 kb) PAVs. These PAVs spanned a total size of 2.92 Mb of the sorghum genome containing 202 known and predicted genes, including 38 genes annotated to encode cell death and stress response genes. The PAVs varied considerably for repeat sequences and mobile elements with DNA transposons as the major components. The frequency and distribution of these PAVs differed substantially across 96 sorghum inbred lines, and the low- and high frequency PAVs differed in their gene categories. This report shed new light on the occurrence and diversity of PAVs in sorghum genomes. Our research exemplifies a new perspective to explore genome structural variation for genetic improvement in plant breeding.