Chloroplast genome structure in Ilex (Aquifoliaceae).
Chloroplast genome structure in Ilex (Aquifoliaceae).
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DOI：
10.1038/srep28559
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发表时间：
2016-07-05
影响因子：
4.6
通讯作者：
Corlett RT
中科院分区：
文献类型：
--
作者：
Yao X;Tan YH;Liu YY;Song Y;Yang JB;Corlett RT
水青科是钟形目水青科中最大的科。它由冬青属(Ilex)组成，冬青是被子植物中最大的木本雌雄异株属。大多数物种分布在东亚或南美洲。由于缺乏强有力的物种水平的系统发育，分类和进化史仍然不清楚。我们通过对长程PCR产物的Illumina测序和随后的参考引导从头组装，获得了该家族中第一个完整的叶绿体基因组，包括7个Ilex物种。这些基因组具有典型的双环结构，基因组排列保守，分歧适中。全长157,741 ，有一个87,109 的大单复制区，一个18,436 的小单复制区，以及52,196 的一对反向重复序列。共鉴定出144个基因，包括96个蛋白质编码基因、40个tRNA基因和8个rRNA基因。在毛冬青中发现了34个重复序列，长度为14 ，同源性为90%，11个发散热点区域可作为系统发育标记的靶标。这项研究将有助于提高冬青属系统发育的深层分支的分辨率，并有助于冬青属物种的鉴定。
Aquifoliaceae is the largest family in the campanulid order Aquifoliales. It consists of a single genus, Ilex, the hollies, which is the largest woody dioecious genus in the angiosperms. Most species are in East Asia or South America. The taxonomy and evolutionary history remain unclear due to the lack of a robust species-level phylogeny. We produced the first complete chloroplast genomes in this family, including seven Ilex species, by Illumina sequencing of long-range PCR products and subsequent reference-guided de novo assembly. These genomes have a typical bicyclic structure with a conserved genome arrangement and moderate divergence. The total length is 157,741 bp and there is one large single-copy region (LSC) with 87,109 bp, one small single-copy with 18,436 bp, and a pair of inverted repeat regions (IR) with 52,196 bp. A total of 144 genes were identified, including 96 protein-coding genes, 40 tRNA and 8 rRNA. Thirty-four repetitive sequences were identified in Ilex pubescens, with lengths >14 bp and identity >90%, and 11 divergence hotspot regions that could be targeted for phylogenetic markers. This study will contribute to improved resolution of deep branches of the Ilex phylogeny and facilitate identification of Ilex species.