Comparative Genomics and Phylogenomics of East Asian Tulips (Amana, Liliaceae).
Comparative Genomics and Phylogenomics of East Asian Tulips (Amana, Liliaceae).
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东亚郁金香（Amana，百合科）的比较基因组学和系统发育组学
DOI：
10.3389/fpls.2017.00451
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发表时间：
2017
影响因子：
5.6
通讯作者：
Fu CX
中科院分区：
文献类型：
--
作者：
Li P;Lu RS;Xu WQ;Ohi-Toma T;Cai MQ;Qiu YX;Cameron KM;Fu CX
百合科（Liliaceae）的Amana本田属（AmanaHonda），当其被视为与郁金香属（Tulipa）分开时，包括六种多年生草本植物，仅限于中国、日本和朝鲜半岛。虽然所有六种Amana都有重要的药用和园艺用途，但专注于物种鉴定和分子遗传学的研究很少。在这里，我们报告了六个完整的Amana叶绿体（cp）基因组的核苷酸序列。Amana的cp基因组长度范围为150，613 bp至151，136 bp，均包括一对反向重复序列（25，629 - 25，859 bp），由大单拷贝（81，482 - 82，218 bp）和小单拷贝（17，366 - 17，465 bp）区域分隔。每个cp基因组含有112个独特的基因，包括30个转运RNA基因、4个核糖体RNA基因和78个蛋白质编码基因。所有Amana cp基因组的基因含量、基因顺序、AT含量和IR/SC边界结构几乎相同。然而，相对收缩和扩张的IR/SC边界之间的6 Amana cp基因组的结果在它们之间的长度变化。对这些Amana cp基因组的简单重复序列（SSR）分析表明，最丰富的SSR是A/T单核苷酸。6种Amana的重复序列数从54个（A. anhuiensis）到69（阔苍山鹅膏菌Amana kuocangshanica），以回文重复（28-35）和正向重复（23-30）为最常见的类型。基于这些完整的CP基因组和74个共同的蛋白质编码基因的系统基因组学分析强烈支持属的单系性，和姐妹关系Amana和Erythronium，而不是共享的共同祖先郁金香。结果表明：rps 15-ycf 1、accD-psaI、petA-psbJ、rp 132-trnL、atpH-atpI、petD-rpoA、trnS-trnG、psbM-trnD和ycf 4-cemA等9个DNA标记的变异位点数均大于0.9%。
The genus Amana Honda (Liliaceae), when it is treated as separate from Tulipa, comprises six perennial herbaceous species that are restricted to China, Japan and the Korean Peninsula. Although all six Amana species have important medicinal and horticultural uses, studies focused on species identification and molecular phylogenetics are few. Here we report the nucleotide sequences of six complete Amana chloroplast (cp) genomes. The cp genomes of Amana range from 150,613 bp to 151,136 bp in length, all including a pair of inverted repeats (25,629–25,859 bp) separated by the large single-copy (81,482–82,218 bp) and small single-copy (17,366–17,465 bp) regions. Each cp genome equivalently contains 112 unique genes consisting of 30 transfer RNA genes, four ribosomal RNA genes, and 78 protein coding genes. Gene content, gene order, AT content, and IR/SC boundary structure are nearly identical among all Amana cp genomes. However, the relative contraction and expansion of the IR/SC borders among the six Amana cp genomes results in length variation among them. Simple sequence repeat (SSR) analyses of these Amana cp genomes indicate that the richest SSRs are A/T mononucleotides. The number of repeats among the six Amana species varies from 54 (A. anhuiensis) to 69 (Amana kuocangshanica) with palindromic (28–35) and forward repeats (23–30) as the most common types. Phylogenomic analyses based on these complete cp genomes and 74 common protein-coding genes strongly support the monophyly of the genus, and a sister relationship between Amana and Erythronium, rather than a shared common ancestor with Tulipa. Nine DNA markers (rps15–ycf1, accD–psaI, petA–psbJ, rpl32–trnL, atpH–atpI, petD–rpoA, trnS–trnG, psbM–trnD, and ycf4–cemA) with number of variable sites greater than 0.9% were identified, and these may be useful for future population genetic and phylogeographic studies of Amana species.