Analysis of complete nucleotide sequences of 12 Gossypium chloroplast genomes: origin and evolution of allotetraploids.
Analysis of complete nucleotide sequences of 12 Gossypium chloroplast genomes: origin and evolution of allotetraploids.
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12个棉叶绿体基因组的完整核苷酸序列分析：异源四倍体的起源和进化
DOI：
10.1371/journal.pone.0037128
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Hua J
中科院分区：
文献类型：
--
作者：
Xu Q;Xiong G;Li P;He F;Huang Y;Wang K;Li Z;Hua J
背景棉花（Gossypium spp.）是分析多倍化的模型系统。虽然确定异源四倍体棉花的供体物种已被深入研究，但棉花叶绿体基因组的序列比较仍然是理解棉花异源四倍体进化机制的兴趣所在，而一般认为亲本是含有A和D基因组的物种。本文对13个棉属植物叶绿体基因组进行了比较分析，其中12个是首次报道。研究中的12个叶绿体基因组的大小从159，959 bp到160，433 bp不等。染色体高度相似，具有>98%的序列同一性。它们编码相同的112个独特基因，这些基因以统一的顺序出现，只有边界连接略有不同。由于插入缺失以及取代的分歧分别检查基因组，编码和非编码序列。异源四倍体物种与A基因组之间的基因组分化率为0.374%~ 0.583%，异源四倍体物种内部的基因组分化率为0.159%~ 0.454%。40个蛋白质编码基因在蛋白质水平上完全相同，20个基因间序列完全保守。这9个异源四倍体在全基因组中有5个插入和9个缺失，蛋白质编码基因有7个碱基的替换。系统发育树表明异源四倍体与A基因组的祖先有较近的亲缘关系，并将异源四倍体分为4个类群。异源四倍体棉花起源于43 - 68万年前（MYA）。结论尽管棉属植物叶绿体基因组具有高度的保守性，但仍存在种间序列变异。棉花叶绿体基因组中5-bp和1-3-bp indel的优势主要归因于SSR多态性。本研究支持棉花属二倍体A染色体组物种的共同祖先是现存异源四倍体物种的母系来源，异源四倍体具有单系起源的观点。G.与其他异源四倍体相比，hirsutum AD 1谱系在基因间区域经历了更多的序列变异。12个棉属叶绿体基因组的完整核苷酸序列为揭示棉属异源四倍体分室协同进化和物种形成的分子机制提供了基础。
Background Cotton (Gossypium spp.) is a model system for the analysis of polyploidization. Although ascertaining the donor species of allotetraploid cotton has been intensively studied, sequence comparison of Gossypium chloroplast genomes is still of interest to understand the mechanisms underlining the evolution of Gossypium allotetraploids, while it is generally accepted that the parents were A- and D-genome containing species. Here we performed a comparative analysis of 13 Gossypium chloroplast genomes, twelve of which are presented here for the first time. Methodology/Principal Findings The size of 12 chloroplast genomes under study varied from 159,959 bp to 160,433 bp. The chromosomes were highly similar having >98% sequence identity. They encoded the same set of 112 unique genes which occurred in a uniform order with only slightly different boundary junctions. Divergence due to indels as well as substitutions was examined separately for genome, coding and noncoding sequences. The genome divergence was estimated as 0.374% to 0.583% between allotetraploid species and A-genome, and 0.159% to 0.454% within allotetraploids. Forty protein-coding genes were completely identical at the protein level, and 20 intergenic sequences were completely conserved. The 9 allotetraploids shared 5 insertions and 9 deletions in whole genome, and 7-bp substitutions in protein-coding genes. The phylogenetic tree confirmed a close relationship between allotetraploids and the ancestor of A-genome, and the allotetraploids were divided into four separate groups. Progenitor allotetraploid cotton originated 0.43–0.68 million years ago (MYA). Conclusion Despite high degree of conservation between the Gossypium chloroplast genomes, sequence variations among species could still be detected. Gossypium chloroplast genomes preferred for 5-bp indels and 1–3-bp indels are mainly attributed to the SSR polymorphisms. This study supports that the common ancestor of diploid A-genome species in Gossypium is the maternal source of extant allotetraploid species and allotetraploids have a monophyletic origin. G. hirsutum AD1 lineages have experienced more sequence variations than other allotetraploids in intergenic regions. The available complete nucleotide sequences of 12 Gossypium chloroplast genomes should facilitate studies to uncover the molecular mechanisms of compartmental co-evolution and speciation of Gossypium allotetraploids.
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影响因子：
9.4
作者：
Flagel, Lex E.;Wendel, Jonathan F.
通讯作者：
Wendel, Jonathan F.
影响因子：
10.7
作者：
Goremykin, VV;Holland, B;Hellwig, FH
通讯作者：
Hellwig, FH
影响因子：
3.9
作者：
GU, X;LI, WH
通讯作者：
LI, WH
DOI：
10.1073/pnas.96.25.14406
发表时间：
1999-12-07
影响因子：
11.1
作者：
Cronn, RC;Small, RL;Wendel, JF
通讯作者：
Wendel, JF
影响因子：
--
作者：
Endrizzi, J. E.;Turcotte, E. L.;Kohel, R. J.
通讯作者：
Kohel, R. J.