The Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China; Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, Changchun, 130012, China.
J Integr Plant Biol. 2014 Jan;56(1):24-37. doi: 10.1111/jipb.12121.
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.
存在/缺失变异体 (PAVs) 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深远的影响。然而，人们对植物基因组中的 PAVs 知之甚少。我们之前对三个高粱 (Sorghum bicolour L.) 基因组进行了 12×重测序，每个基因组都发现了 5364 个 PAVs。在这里，我们报告了对 51 个大型 (>30kb) PAVs 的详细特征描述。这些 PAVs 跨越了高粱基因组的 2.92 Mb 大小，包含 202 个已知和预测的基因，其中 38 个基因被注释为编码细胞死亡和应激反应基因。这些 PAVs 在重复序列和移动元件方面差异很大，其中 DNA 转座子是主要成分。这些 PAVs 在 96 个高粱自交系中分布差异很大，低频和高频 PAVs 在基因类别上也存在差异。本报告揭示了高粱基因组中 PAVs 的发生和多样性。我们的研究为植物育种中探索基因组结构变异以进行遗传改良提供了新的视角。
