Re-exploration of U's Triangle Brassica Species Based on Chloroplast Genomes and 45S nrDNA Sequences.
Re-exploration of U's Triangle Brassica Species Based on Chloroplast Genomes and 45S nrDNA Sequences.
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DOI：
10.1038/s41598-018-25585-4
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发表时间：
2018-05-09
影响因子：
4.6
通讯作者：
Yang TJ
中科院分区：
文献类型：
--
作者：
Kim CK;Seol YJ;Perumal S;Lee J;Waminal NE;Jayakodi M;Lee SC;Jin S;Choi BS;Yu Y;Ko HC;Choi JW;Ryu KY;Sohn SH;Parkin I;Yang TJ
U's三角形的概念揭示了多倍体化在植物基因组进化中的重要性，描述了芸苔属中使用三个二倍体的天然异源多倍体化事件[B. rapa（A基因组）、B. nigra（B）和B. oleracea（C）]和衍生的异源四倍体[B. juncea（AB基因组），B. napus（AC）和B. carinata（BC）]。然而，对芸苔属植物基因组进化的全面了解尚未完全实现。本研究对28份芸苔属植物和萝卜属植物进行了低覆盖度（2-6×）全基因组测序，以探讨6种芸苔属植物叶绿体基因组和核糖体DNA变异的进化。我们的基因组分析得出了两个主要结论。(1)三种异源四倍体植物叶绿体基因组的种内变异较少（2~7个SNPs），而二倍体植物叶绿体基因组的种内变异丰富（7~193个SNPs）。(2)三个异源四倍体保持两个45 SnrDNA类型来自两个祖先物种与母系优势。此外，这项研究揭示了AC叶绿体基因组的母系起源。总之，本研究从基因组学的角度阐明了U's三角形物种的亲缘关系，为相关和进化研究提供了重要的基因组资源。
The concept of U’s triangle, which revealed the importance of polyploidization in plant genome evolution, described natural allopolyploidization events in Brassica using three diploids [B. rapa (A genome), B. nigra (B), and B. oleracea (C)] and derived allotetraploids [B. juncea (AB genome), B. napus (AC), and B. carinata (BC)]. However, comprehensive understanding of Brassica genome evolution has not been fully achieved. Here, we performed low-coverage (2–6×) whole-genome sequencing of 28 accessions of Brassica as well as of Raphanus sativus [R genome] to explore the evolution of six Brassica species based on chloroplast genome and ribosomal DNA variations. Our phylogenomic analyses led to two main conclusions. (1) Intra-species-level chloroplast genome variations are low in the three allotetraploids (2~7 SNPs), but rich and variable in each diploid species (7~193 SNPs). (2) Three allotetraploids maintain two 45SnrDNA types derived from both ancestral species with maternal dominance. Furthermore, this study sheds light on the maternal origin of the AC chloroplast genome. Overall, this study clarifies the genetic relationships of U’s triangle species based on a comprehensive genomics approach and provides important genomic resources for correlative and evolutionary studies.
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影响因子：
10
作者：
Li, Xiwen;Yang, Yang;Chen, Shilin
通讯作者：
Chen, Shilin
影响因子：
4.1
作者：
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3.1
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通讯作者：
Hasterok, Robert
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Li P;Zhang S;Li F;Zhang S;Zhang H;Wang X;Sun R;Bonnema G;Borm TJ
通讯作者：
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影响因子：
14.9
作者：
Frazer, KA;Pachter, L;Dubchak, I
通讯作者：
Dubchak, I