Comparative Chloroplast Genomics of Gossypium Species: Insights Into Repeat Sequence Variations and Phylogeny.
Comparative Chloroplast Genomics of Gossypium Species: Insights Into Repeat Sequence Variations and Phylogeny.
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DOI：
10.3389/fpls.2018.00376
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发表时间：
2018
影响因子：
5.6
通讯作者：
Li ZH
中科院分区：
文献类型：
--
作者：
Wu Y;Liu F;Yang DG;Li W;Zhou XJ;Pei XY;Liu YG;He KL;Zhang WS;Ren ZY;Zhou KH;Ma XF;Li ZH
棉花是世界上最重要的经济纤维作物之一。棉属（Gossypium）包括一个异源四倍体群（AD）和八个二倍体基因组群（A-G和K）。然而，叶绿体基因组中重复序列的进化和棉属物种的系统发育关系尚不清楚。因此，我们确定了40个棉花叶绿体基因组的重复序列变异和进化关系，这些基因组代表了该属中最多样化的基因组，其中包括5个新测序的二倍体物种，即，G. nandawarense（C1-n）、南瓦链格孢G. armourianum（D2-1）、盾壳霉G. lobatum（D 7）、裂叶棉G. trilobum（D8）和G. schwendimanii（D11）和高地棉重要的半野生小种G.多毛类宽叶变种（AD 1）。棉花的基因组结构、基因顺序和GC含量与其他高等植物质体基因组相似。总共鉴定了2860个长重复序列（长度>10 bp），其中F基因组物种具有最多的重复序列（G. longicalyx F1：108），E基因组种的遗传多样性最低（G. stocksii E1：53）。大规模重复序列可能丰富棉花物种的遗传信息并维持基因组的稳定性。我们还确定了10个分歧热点区域，即，rp 133-rps 18、psbZ-trnG（GCC）、rps 4-trnT（UGU）、trnL（UAG）-rp 132、trnE（UUC）-trnT（GGU）、atpE、ndhI、rps 2、ycf 1和ndhF等7个分子标记，可作为今后群体遗传学和系统发育研究的分子标记。位点特异性选择分析表明，10个叶绿体基因（atpB、atpE、rps 2、rps 3、petB、petD、ccsA、cemA、ycf 1和rbcL）的部分编码位点处于蛋白质序列进化中。基于全质体的系统发育分析表明，棉属植物可分为6个遗传分支。有趣的是，所有13个D-基因组物种聚集成一个强大的单系分支。出乎意料的是，具有C、G和K基因组的棉花物种混合并嵌套在一个大的进化枝中，这可能是由于它们最近的辐射、不完全的谱系排序以及不同棉花谱系之间的渐渗杂交。总之，本研究的结果提供了新的见解叶绿体基因组重复序列的进化和种间关系的棉属。
Cotton is one of the most economically important fiber crop plants worldwide. The genus Gossypium contains a single allotetraploid group (AD) and eight diploid genome groups (A–G and K). However, the evolution of repeat sequences in the chloroplast genomes and the phylogenetic relationships of Gossypium species are unclear. Thus, we determined the variations in the repeat sequences and the evolutionary relationships of 40 cotton chloroplast genomes, which represented the most diverse in the genus, including five newly sequenced diploid species, i.e., G. nandewarense (C1-n), G. armourianum (D2-1), G. lobatum (D7), G. trilobum (D8), and G. schwendimanii (D11), and an important semi-wild race of upland cotton, G. hirsutum race latifolium (AD1). The genome structure, gene order, and GC content of cotton species were similar to those of other higher plant plastid genomes. In total, 2860 long sequence repeats (>10 bp in length) were identified, where the F-genome species had the largest number of repeats (G. longicalyx F1: 108) and E-genome species had the lowest (G. stocksii E1: 53). Large-scale repeat sequences possibly enrich the genetic information and maintain genome stability in cotton species. We also identified 10 divergence hotspot regions, i.e., rpl33-rps18, psbZ-trnG (GCC), rps4-trnT (UGU), trnL (UAG)-rpl32, trnE (UUC)-trnT (GGU), atpE, ndhI, rps2, ycf1, and ndhF, which could be useful molecular genetic markers for future population genetics and phylogenetic studies. Site-specific selection analysis showed that some of the coding sites of 10 chloroplast genes (atpB, atpE, rps2, rps3, petB, petD, ccsA, cemA, ycf1, and rbcL) were under protein sequence evolution. Phylogenetic analysis based on the whole plastomes suggested that the Gossypium species grouped into six previously identified genetic clades. Interestingly, all 13 D-genome species clustered into a strong monophyletic clade. Unexpectedly, the cotton species with C, G, and K-genomes were admixed and nested in a large clade, which could have been due to their recent radiation, incomplete lineage sorting, and introgression hybridization among different cotton lineages. In conclusion, the results of this study provide new insights into the evolution of repeat sequences in chloroplast genomes and interspecific relationships in the genus Gossypium.
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5.3
作者：
Bausher MG;Singh ND;Lee SB;Jansen RK;Daniell H
通讯作者：
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