A high-quality Brassica napus genome reveals expansion of transposable elements, subgenome evolution and disease resistance.
A high-quality Brassica napus genome reveals expansion of transposable elements, subgenome evolution and disease resistance.
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高质量甘蓝型油菜基因组揭示了转座元件的扩展、亚基因组进化和抗病性
DOI：
10.1111/pbi.13493
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发表时间：
2021-03
影响因子：
13.8
通讯作者：
Zhang L
中科院分区：
文献类型：
--
作者：
Chen X;Tong C;Zhang X;Song A;Hu M;Dong W;Chen F;Wang Y;Tu J;Liu S;Tang H;Zhang L
油菜（Brassica napus L.）是一种新的异源四倍体作物，以其高产油而闻名。在这里，我们报告了一个高质量的基因组组装的一个典型的半冬油菜品种，'中双11'（以下简称'双11'），使用单分子测序和染色体构象捕获（Hi-C）技术的组合。大多数高置信度序列（93.1%）锚定在单个染色体上，共识别出19个着丝粒，与B的精确染色体计数匹配。油菜。B中A和C亚基因组中的重复序列。从50万年前开始，特别是在过去的10万年里，纳普斯的规模显著扩大。这些年轻的和最近扩增的LTR-RT显示分散的染色体分布，但显着优先聚集到着丝粒区域。我们详尽地注释了核苷酸结合富含亮氨酸重复序列（NLR）基因库，在B中总共产生了597个NLR基因。napus基因组，其中17.4%是配对的（头对头排列）。根据991 B.通过对18 759 245个单核苷酸多态性（SNPs）位点的分析，我们在B的3个主要生态型（冬性、半冬性和春性）中检测到了18 759 245个单核苷酸多态性位点。油菜。我们发现49个NLR基因和5个NLR基因对共定位在不同生态型的选择性扫描区域，表明在驯化过程中B的NLR基因的快速多样化。油菜。我们B的高品质。甘蓝型油菜“双11”基因组拼接体可作为油菜基因组学研究的重要资源，揭示与重要农艺性状相关的遗传变异。
Rapeseed (Brassica napus L.) is a recent allotetraploid crop, which is well known for its high oil production. Here, we report a high‐quality genome assembly of a typical semi‐winter rapeseed cultivar, 'Zhongshuang11' (hereafter 'ZS11'), using a combination of single‐molecule sequencing and chromosome conformation capture (Hi‐C) techniques. Most of the high‐confidence sequences (93.1%) were anchored to the individual chromosomes with a total of 19 centromeres identified, matching the exact chromosome count of B. napus. The repeat sequences in the A and C subgenomes in B. napus expanded significantly from 500 000 years ago, especially over the last 100 000 years. These young and recently amplified LTR‐RTs showed dispersed chromosomal distribution but significantly preferentially clustered into centromeric regions. We exhaustively annotated the nucleotide‐binding leucine‐rich repeat (NLR) gene repertoire, yielding a total of 597 NLR genes in B. napus genome and 17.4% of which are paired (head‐to‐head arrangement). Based on the resequencing data of 991 B. napus accessions, we have identified 18 759 245 single nucleotide polymorphisms (SNPs) and detected a large number of genomic regions under selective sweep among the three major ecotype groups (winter, semi‐winter and spring) in B. napus. We found 49 NLR genes and five NLR gene pairs colocated in selective sweep regions with different ecotypes, suggesting a rapid diversification of NLR genes during the domestication of B. napus. The high quality of our B. napus 'ZS11' genome assembly could serve as an important resource for the study of rapeseed genomics and reveal the genetic variations associated with important agronomic traits.
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影响因子：
12.3
作者：
Akdemir KC;Chin L
通讯作者：
Chin L
影响因子：
13.8
作者：
Dolatabadian, Aria;Bayer, Philipp E.;Batley, Jacqueline
通讯作者：
Batley, Jacqueline
影响因子：
1.2
作者：
Cingolani, Pablo;Platts, Adrian;Ruden, Douglas M.
通讯作者：
Ruden, Douglas M.
影响因子：
12.3
作者：
Haas, Brian J.;Salzberg, Steven L.;Zhu, Wei;Pertea, Mihaela;Allen, Jonathan E.;Orvis, Joshua;White, Owen;Buell, C. Robin;Wortman, Jennifer R.
通讯作者：
Wortman, Jennifer R.
影响因子：
5.6
作者：
Fu, Ying;Zhang, Yaofeng;Fu, Donghui
通讯作者：
Fu, Donghui