Phylogenomic Analysis and Dynamic Evolution of Chloroplast Genomes in Salicaceae.
Phylogenomic Analysis and Dynamic Evolution of Chloroplast Genomes in Salicaceae.
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杨柳科叶绿体基因组的系统发育分析及动态进化
DOI：
10.3389/fpls.2017.01050
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发表时间：
2017
影响因子：
5.6
通讯作者：
Chen J
中科院分区：
文献类型：
--
作者：
Huang Y;Wang J;Yang Y;Fan C;Chen J
植物叶绿体基因组在基因顺序和基因内容上都是高度保守的。已知对整个叶绿体基因组的分析可提供更多信息的DNA位点，从而产生用于植物叶绿体基因组的高分辨率。本文报道了杨柳科三种柳属植物的叶绿体全基因组。从完整的叶绿体基因组推断杨柳科的系统发育与以前的研究基本一致，但解决了更高的统计支持。然而，在杨属中观察到异源生殖的不一致性，这很可能是同源性的结果。通过对柳属植物叶绿体基因组与其它杨柳科植物叶绿体基因组的比较，我们发现杨柳科植物叶绿体基因组的同线性和长度是高度保守的，但在物种间经历了动态进化。我们在杨柳科植物中鉴定了7个正选择的叶绿体基因，这些基因可能与杨柳科植物的适应性进化有关。对叶绿体基因组的比较分析也表明，部分叶绿体基因丢失或成为假基因，推测叶绿体基因水平转移到核基因组中。基于两种杨柳科植物的全核基因组序列，我们显著地鉴定出，在参比基因组的个体中，整个叶绿体基因组确实至少一次转移并整合到核基因组中。这一观察结果，沿着存在的大核质体DNA（NUPT）和NUPT含有多个叶绿体基因在其原来的顺序在叶绿体基因组中，有利于DNA介导的细胞器到核DNA转移的假说。总之，利用叶绿体全基因组进行的染色体组学分析清楚地阐明了杨柳科的染色体发生。杨柳科植物叶绿体正选择基因的鉴定和叶绿体到核的动态基因转移为更好地理解杨柳科植物的成功适应提供了资源。
Chloroplast genomes of plants are highly conserved in both gene order and gene content. Analysis of the whole chloroplast genome is known to provide much more informative DNA sites and thus generates high resolution for plant phylogenies. Here, we report the complete chloroplast genomes of three Salix species in family Salicaceae. Phylogeny of Salicaceae inferred from complete chloroplast genomes is generally consistent with previous studies but resolved with higher statistical support. Incongruences of phylogeny, however, are observed in genus Populus, which most likely results from homoplasy. By comparing three Salix chloroplast genomes with the published chloroplast genomes of other Salicaceae species, we demonstrate that the synteny and length of chloroplast genomes in Salicaceae are highly conserved but experienced dynamic evolution among species. We identify seven positively selected chloroplast genes in Salicaceae, which might be related to the adaptive evolution of Salicaceae species. Comparative chloroplast genome analysis within the family also indicates that some chloroplast genes are lost or became pseudogenes, infer that the chloroplast genes horizontally transferred to the nucleus genome. Based on the complete nucleus genome sequences from two Salicaceae species, we remarkably identify that the entire chloroplast genome is indeed transferred and integrated to the nucleus genome in the individual of the reference genome of P. trichocarpa at least once. This observation, along with presence of the large nuclear plastid DNA (NUPTs) and NUPTs-containing multiple chloroplast genes in their original order in the chloroplast genome, favors the DNA-mediated hypothesis of organelle to nucleus DNA transfer. Overall, the phylogenomic analysis using chloroplast complete genomes clearly elucidates the phylogeny of Salicaceae. The identification of positively selected chloroplast genes and dynamic chloroplast-to-nucleus gene transfers in Salicaceae provide resources to better understand the successful adaptation of Salicaceae species.