The Complete Chloroplast Genomes of Three Cardiocrinum (Liliaceae) Species: Comparative Genomic and Phylogenetic Analyses.
The Complete Chloroplast Genomes of Three Cardiocrinum (Liliaceae) Species: Comparative Genomic and Phylogenetic Analyses.
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三种心百合科物种的完整叶绿体基因组：比较基因组和系统发育分析
DOI：
10.3389/fpls.2016.02054
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发表时间：
2016
影响因子：
5.6
通讯作者：
Qiu YX
中科院分区：
文献类型：
--
作者：
Lu RS;Li P;Qiu YX
大百合属（Cardiocrinum（Endlicher）Lindley）（百合科）包括三种多年生草本植物，分布于东亚温带落叶林。虽然这三种大百合属植物都有园艺和医学用途，但有关该属植物的物种鉴定和分子系统发育分析的研究还没有报道。在这里，我们报告了完整的叶绿体（CP）序列的每个心百合属物种使用Illumina配对末端测序技术。对C.阿图姆角cathayanum和C. cordatum的长度分别为152，653、152，415和152，410 bp，包括一对反向重复（IR）区域（26，364 - 26，500 bp），其由大的单拷贝（LSC）区域（82，186 - 82，368 bp）和小的单拷贝（SSC）区域（17，309 - 17，344 bp）分隔。每个cp基因组包含相同的112个独特的基因，包括30个转移RNA基因，4个核糖体RNA基因和78个蛋白质编码基因。基因含量，基因顺序，AT含量，IR/SC边界结构几乎是相同的三个大百合cp基因组，但它们的长度变化，由于收缩/扩张的IR/SC边界。简单重复序列（SSR）分析进一步表明这些cp基因组中最丰富的SSR是A/T单核苷酸。在C.阿图姆角cathayanum和C. cordatum，分别。结果表明，rps 19、rpoC 2-rpoC 1、trnS-psbZ、trnM-atpE、psaC-ndhE、ycf 15-ycf 1等6个cpDNA标记的变异位点百分率均大于0.95%。系统基因组学分析表明，大百合属的单系性和大百合属与大百合属的姐妹关系是一致的。cathayanum和C.心脏这些cp基因组的获得为大百合属植物的种群遗传学和地理学研究提供了有价值的遗传信息。
The genus Cardiocrinum (Endlicher) Lindley (Liliaceae) comprises three herbaceous perennial species that are distributed in East Asian temperate-deciduous forests. Although all three Cardiocrinum species have horticultural and medical uses, studies related to species identification and molecular phylogenetic analysis of this genus have not been reported. Here, we report the complete chloroplast (cp) sequences of each Cardiocrinum species using Illumina paired-end sequencing technology. The cp genomes of C. giganteum, C. cathayanum, and C. cordatum were found to be 152,653, 152,415, and 152,410 bp in length, respectively, including a pair of inverted repeat (IR) regions (26,364–26,500 bp) separated by a large single-copy (LSC) region (82,186–82,368 bp) and a small single-copy (SSC) region (17,309–17,344 bp). Each cp genome contained the same 112 unique genes consisting of 30 transfer RNA genes, 4 ribosomal RNA genes, and 78 protein-coding genes. Gene content, gene order, AT content, and IR/SC boundary structures were almost the same among the three Cardiocrinum cp genomes, yet their lengths varied due to contraction/expansion of the IR/SC borders. Simple sequence repeat (SSR) analysis further indicated the richest SSRs in these cp genomes to be A/T mononucleotides. A total of 45, 57, and 45 repeats were identified in C. giganteum, C. cathayanum, and C. cordatum, respectively. Six cpDNA markers (rps19, rpoC2-rpoC1, trnS-psbZ, trnM-atpE, psaC-ndhE, ycf15-ycf1) with the percentage of variable sites higher than 0.95% were identified. Phylogenomic analyses of the complete cp genomes and 74 protein-coding genes strongly supported the monophyly of Cardiocrinum and a sister relationship between C. cathayanum and C. cordatum. The availability of these cp genomes provides valuable genetic information for further population genetics and phylogeography studies on Cardiocrinum.