Extremely low levels of chloroplast genome sequence variability in Astelia pumila (Asteliaceae, Asparagales)
Extremely low levels of chloroplast genome sequence variability in Astelia pumila (Asteliaceae, Asparagales)
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DOI：
10.7717/peerj.6244
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发表时间：
2019-01-17
期刊：
影响因子：
2.7
通讯作者：
von Hagen, K. Bernhard
中科院分区：
文献类型：
--
作者：
Pfanzelt, Simon;Albach, Dirk C.;von Hagen, K. Bernhard
矮紫菀Astelia pumila（G. Forst.）高迪（紫菀科，天门冬目）是西巴塔哥尼亚垫泥炭沼泽植被的主要成分。为了筛选适合于植物地理学研究的叶绿体标记，对5个A.收集来自该物种几乎整个地理范围的矮柚种质，并筛选可变位置。叶绿体基因组序列是通过作图方法获得的，使用宽叶真丝酵母（芦笋科）作为参考。A. pumila的长度在158，215 bp到158，221 bp之间，包含85，981 - 85，983 bp的大的单拷贝区，18，182 - 18，186 bp的小的单拷贝区和27，026 bp的两个反向重复序列。基因组注释共预测了113个基因，包括30个tRNA和4个rRNA基因。序列比较显示，种内遗传变异程度非常低，因为只有37个可变位点（18个插入缺失，18个单核苷酸多态性，一个3-bp突变）-其中大部分是autapomorphies-被发现在5个组装的叶绿体基因组。最大似然分析，基于代表目前公认的14个科中的6个的几个芦笋目加入物的全叶绿体基因组序列（意义上的APG IV），证实了A. pumila。A. pumila是首次报道的astelioid分支的成员（14属与c. 215种），一个基部分支的组内天门冬目。
Astelia pumila (G.Forst.) Gaudich. (Asteliaceae, Asparagales) is a major element of West Patagonian cushion peat bog vegetation. With the aim to identify appropriate chloroplast markers for the use in a phylogeographic study, the complete chloroplast genomes of five A. pumila accessions from almost the entire geographical range of the species were assembled and screened for variable positions. The chloroplast genome sequence was obtained via a mapping approach, using Eustrephus latifolius (Asparagaceae) as a reference. The chloroplast genome of A. pumila varies in length from 158,215 bp to 158,221 bp, containing a large single copy region of 85,981-85,983 bp, a small single copy region of 18,182-18,186 bp and two inverted repeats of 27,026 bp. Genome annotation predicted a total of 113 genes, including 30 tRNA and four rRNA genes. Sequence comparisons revealed a very low degree of intraspecific genetic variability, as only 37 variable sites (18 indels, 18 single nucleotide polymorphisms, one 3-bp mutation)-most of them autapomorphies-were found among the five assembled chloroplast genomes. A Maximum Likelihood analysis, based on whole chloroplast genome sequences of several Asparagales accessions representing six of the currently recognized 14 families (sensu APG IV), confirmed the phylogenetic position of A. pumila. The chloroplast genome of A. pumila is the first to be reported for a member of the astelioid clade (14 genera with c. 215 species), a basally branching group within Asparagales.