Molecular Evolution of Chloroplast Genomes of Orchid Species: Insights into Phylogenetic Relationship and Adaptive Evolution.
Molecular Evolution of Chloroplast Genomes of Orchid Species: Insights into Phylogenetic Relationship and Adaptive Evolution.
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兰花物种叶绿体基因组的分子进化：深入了解系统发育关系和适应性进化
DOI：
10.3390/ijms19030716
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发表时间：
2018-03-02
影响因子：
5.6
通讯作者：
Li ZH
中科院分区：
文献类型：
--
作者：
Dong WL;Wang RN;Zhang NY;Fan WB;Fang MF;Li ZH
兰科是被子植物中的第三大科，是单子叶植物的一个进化的幼分支。该科包含许多经济上重要的园艺和开花植物。然而，基因组信息的有限性极大地阻碍了兰科植物分子进化和系统发育的研究。在这项研究中，我们确定了整个叶绿体（cp）基因组的进化特征以及兰科植物的系统发育关系。本研究首次对四种兰科植物的cp基因组进行了分析，它们是：山慈姑、虾脊兰、美丽草和舌唇兰。叶绿体基因组大小为153，629 bp（C. davidi）到160，427 bp（E. mairei）。其基因序列、GC含量和基因组成与其它被子植物相似。结果表明，ndhC、ndhI和ndhK基因在C. ndh I基因在日本对虾和E. mairei。此外，四种类型的重复序列（正向，回文，反向和互补重复序列）在兰花物种进行了检查。E. mairei的重复序列数最高（81个），而C. davidii的数量最少（57个）。在C中，简单重复序列的总数至少为50。davidii，而日本对虾最多为78个。有趣的是，我们鉴定了16个具有正选择位点的基因（psbH、petD、petL、rpl 22、rpl 32、rpoC 1、rpoC 2、rps 12、rps 15、rps 16、accD、ccsA、rbcL、ycf 1、ycf 2和ycf 4基因），这些基因可能在兰花物种适应不同环境中发挥重要作用。此外，确定了11个突变热点区域，包括5个非编码区（ndhB内含子、ccsA-ndhD、rpl 33-rps 18、ndhE-ndhG和ndhF-rpl 32）和6个编码区（rps 16、ndhC、rpl 32、ndhI、ndhK和ndhF）。基于全cp基因组的系统发育分析表明，C. apapriculata与C.条纹小环vreelandii，而C. davidii和C.一式三份形成了一个小的单系进化分支，具有高的自举支持。此外，兰科的五个亚科Apostasioideae、Cypripedioideae、Epidendroideae、Orchidoideae和Vanilloideae在系统发育树中形成了嵌套的进化关系。这些结果为兰科植物的适应性进化和生殖发育提供了重要的信息。
Orchidaceae is the 3rd largest family of angiosperms, an evolved young branch of monocotyledons. This family contains a number of economically-important horticulture and flowering plants. However, the limited availability of genomic information largely hindered the study of molecular evolution and phylogeny of Orchidaceae. In this study, we determined the evolutionary characteristics of whole chloroplast (cp) genomes and the phylogenetic relationships of the family Orchidaceae. We firstly characterized the cp genomes of four orchid species: Cremastra appendiculata, Calanthe davidii, Epipactis mairei, and Platanthera japonica. The size of the chloroplast genome ranged from 153,629 bp (C. davidi) to 160,427 bp (E. mairei). The gene order, GC content, and gene compositions are similar to those of other previously-reported angiosperms. We identified that the genes of ndhC, ndhI, and ndhK were lost in C. appendiculata, in that the ndh I gene was lost in P. japonica and E. mairei. In addition, the four types of repeats (forward, palindromic, reverse, and complement repeats) were examined in orchid species. E. mairei had the highest number of repeats (81), while C. davidii had the lowest number (57). The total number of Simple Sequence Repeats is at least 50 in C. davidii, and, at most, 78 in P. japonica. Interestingly, we identified 16 genes with positive selection sites (the psbH, petD, petL, rpl22, rpl32, rpoC1, rpoC2, rps12, rps15, rps16, accD, ccsA, rbcL, ycf1, ycf2, and ycf4 genes), which might play an important role in the orchid species’ adaptation to diverse environments. Additionally, 11 mutational hotspot regions were determined, including five non-coding regions (ndhB intron, ccsA-ndhD, rpl33-rps18, ndhE-ndhG, and ndhF-rpl32) and six coding regions (rps16, ndhC, rpl32, ndhI, ndhK, and ndhF). The phylogenetic analysis based on whole cp genomes showed that C. appendiculata was closely related to C. striata var. vreelandii, while C. davidii and C. triplicate formed a small monophyletic evolutionary clade with a high bootstrap support. In addition, five subfamilies of Orchidaceae, Apostasioideae, Cypripedioideae, Epidendroideae, Orchidoideae, and Vanilloideae, formed a nested evolutionary relationship in the phylogenetic tree. These results provide important insights into the adaptive evolution and phylogeny of Orchidaceae.
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影响因子：
3.3
作者：
Guo W;Grewe F;Cobo-Clark A;Fan W;Duan Z;Adams RP;Schwarzbach AE;Mower JP
通讯作者：
Mower JP
DOI：
10.1111/j.1355-4905.2005.00466.x
发表时间：
2005-02-01
期刊：
Curtis's Botanical Magazine
影响因子：
--
作者：
Chase, Mark W.
通讯作者：
Chase, Mark W.
影响因子：
4.4
作者：
Hu S;Sablok G;Wang B;Qu D;Barbaro E;Viola R;Li M;Varotto C
通讯作者：
Varotto C
影响因子：
11.6
作者：
Bendich, AJ
通讯作者：
Bendich, AJ
影响因子：
3
作者：
Barrett, Craig F.;Davis, Jerrold I.
通讯作者：
Davis, Jerrold I.