The complete plastid genome sequence of Welwitschia mirabilis: an unusually compact plastome with accelerated divergence rates.
The complete plastid genome sequence of Welwitschia mirabilis: an unusually compact plastome with accelerated divergence rates.
复制标题
Welwitschia mirabilis的完整质体基因组序列：一种异常紧凑的质体，具有加速的发散速率。
DOI：
10.1186/1471-2148-8-130
复制
发表时间：
2008-05-01
影响因子：
3.4
通讯作者：
Raubeson LA
中科院分区：
文献类型：
--
作者：
McCoy SR;Kuehl JV;Boore JL;Raubeson LA
奇异千岁兰是千岁兰科中唯一现存的成员，千岁兰科是买麻植物的三个谱系之一，是一组神秘的裸子植物，与开花植物或针叶树有不同的亲缘关系。有限的序列数据和快速的分化率使得人们无法就基于分子特征的轮叶植物的进化定位达成共识。在这里，我们报告了来自奇异千岁兰的第一个完整的轮叶植物叶绿体基因组序列，以及对蛋白质编码基因的分歧率的分析、基因内容和顺序的比较以及系统发育的影响。奇异千岁兰的叶绿体基因组 [GenBank: EU342371] 由 119,726 个碱基对组成，具有大小单拷贝区域和两个大反向重复序列 (IR) 拷贝。仅编码了 101 个独特的基因种类。千岁兰质体是迄今为止测序的最紧凑的光合陆地植物质体； 66%的产品序列代码。该基因组还表现出稍微扩展的 IR、至少 9 个改变基因顺序的倒位以及 19 个丢失或作为假基因存在的基因。系统发育分析，包括每个现存种子植物谱系的一个代表，并基于 57 个串联的蛋白质编码序列，将千岁兰置于所有种子植物的基部（距离，最大简约性）或作为单系裸子植物分支中的松属（唯一的针叶树代表）的姐妹（最大似然，贝叶斯）。对这些基因序列的相对速率测试表明，千岁兰序列的进化速度比其他种子植物更快。对于这些单独的基因，平均成对距离的比较表明，千岁兰的相对差异范围从大约等于其他种子植物的数量到几乎比非买葡萄植物种子植物的平均值大三倍。尽管千岁兰质体的基本组织是典型的，但其致密性、基因含量和高核苷酸分歧率是非典型的。目前缺乏额外的针叶树质体序列，排除了种子植物关系的买麻树和买麻松假说之间的任何区别。然而，这里确定的系统发育分析和共享基因组特征都与将针叶植物与针叶树联系起来的假设一致，但与花生植物假设不一致。
Welwitschia mirabilis is the only extant member of the family Welwitschiaceae, one of three lineages of gnetophytes, an enigmatic group of gymnosperms variously allied with flowering plants or conifers. Limited sequence data and rapid divergence rates have precluded consensus on the evolutionary placement of gnetophytes based on molecular characters. Here we report on the first complete gnetophyte chloroplast genome sequence, from Welwitschia mirabilis, as well as analyses on divergence rates of protein-coding genes, comparisons of gene content and order, and phylogenetic implications. The chloroplast genome of Welwitschia mirabilis [GenBank: EU342371] is comprised of 119,726 base pairs and exhibits large and small single copy regions and two copies of the large inverted repeat (IR). Only 101 unique gene species are encoded. The Welwitschia plastome is the most compact photosynthetic land plant plastome sequenced to date; 66% of the sequence codes for product. The genome also exhibits a slightly expanded IR, a minimum of 9 inversions that modify gene order, and 19 genes that are lost or present as pseudogenes. Phylogenetic analyses, including one representative of each extant seed plant lineage and based on 57 concatenated protein-coding sequences, place Welwitschia at the base of all seed plants (distance, maximum parsimony) or as the sister to Pinus (the only conifer representative) in a monophyletic gymnosperm clade (maximum likelihood, bayesian). Relative rate tests on these gene sequences show the Welwitschia sequences to be evolving at faster rates than other seed plants. For these genes individually, a comparison of average pairwise distances indicates that relative divergence in Welwitschia ranges from amounts about equal to other seed plants to amounts almost three times greater than the average for non-gnetophyte seed plants. Although the basic organization of the Welwitschia plastome is typical, its compactness, gene content and high nucleotide divergence rates are atypical. The current lack of additional conifer plastome sequences precludes any discrimination between the gnetifer and gnepine hypotheses of seed plant relationships. However, both phylogenetic analyses and shared genome features identified here are consistent with either of the hypotheses that link gnetophytes with conifers, but are inconsistent with the anthophyte hypothesis.
登录
查看更多内容
影响因子：
3.4
作者：
Cai Z;Penaflor C;Kuehl JV;Leebens-Mack J;Carlson JE;dePamphilis CW;Boore JL;Jansen RK
通讯作者：
Jansen RK
影响因子：
10.7
作者：
Chaw, SM;Zharkikh, A;Li, WH
通讯作者：
Li, WH
影响因子：
3
作者：
Graham, SW;Olmstead, RG
通讯作者：
Olmstead, RG
影响因子：
1
作者：
DOYLE, JJ;DOYLE, JL;PALMER, JD
通讯作者：
PALMER, JD
影响因子：
2.5
作者：
Cosner, ME;Jansen, RK;Downie, SR
通讯作者：
Downie, SR