冯楚航,何彩云,王莹,曾艳飞,张建国.叶绿体全基因组序列确定钻天柳在杨柳科中的系统发育位置[J].林业科学研究,2019,32(2):73-77
叶绿体全基因组序列确定钻天柳在杨柳科中的系统发育位置
Phylogenetic Position of Chosenia arbutifolia in the Salicaceae Inferred from Whole Chloroplast Genome
投稿时间:2018-03-21  修订日期:2019-01-15
DOI:10.13275/j.cnki.lykxyj.2019.02.011
中文关键词:  二代测序  柳属  杨柳科  叶绿体基因组  钻天柳
英文关键词:Chosenia arbutifolia  chloroplast genome  next-generation sequencing  Salicaceae  Salix
基金项目:国家自然科学基金(31670666)
作者单位E-mail
冯楚航 国家林业和草原局林木培育重点实验室, 中国林业科学研究院林业研究所, 北京 100091  
何彩云 国家林业和草原局林木培育重点实验室, 中国林业科学研究院林业研究所, 北京 100091  
王莹 深圳华大基因科技有限公司, 广东 深圳 518083  
曾艳飞 国家林业和草原局林木培育重点实验室, 中国林业科学研究院林业研究所, 北京 100091 zengyf@caf.acf.ac.cn 
张建国 国家林业和草原局林木培育重点实验室, 中国林业科学研究院林业研究所, 北京 100091  
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中文摘要:
      [目的]为解决濒危物种钻天柳在杨柳科中分类学位置的争议。[方法]本研究通过二代测序技术,从头测序、拼接得到钻天柳叶绿体基因组全序列,并与已发表的9种杨属植物和4种柳属植物的叶绿体基因组全序列进行比较,采用最大似然法、最大简约法和贝叶斯推断法分析了这些物种的系统发育关系。[结果]研究发现:钻天柳总基因组为155 661 bp,由长度为84 536 bp的长单拷贝(LSC)区域和16 215 bp的短单拷贝(SSC)区域,以及一对分隔开它们的27 455 bp的反向重复序列(IRS)组成。钻天柳叶绿体基因组总GC含量为36.68%,共有113个不同的基因,包括79个蛋白质编码基因,30个tRNA基因和4个rRNA基因,其中,有20个基因分布于反向重复区;在所有基因中,有14个基因包含1个内含子,3个基因(rps12、clpPycf3)内含有2个内含子;系统发育分析以100%的支持率将钻天柳与柳属黄花柳亚属的2个物种聚为一支,杨属的所有物种聚为另一支。[结论]本研究首次组装并注释了钻天柳叶绿体基因组全序列,并明确支持钻天柳并入柳属,而非单独成属,这将为钻天柳甚至杨柳科的系统进化研究提供重要参考。
英文摘要:
      [Objective] To resolve the controversy over the phylogenetic position of Chosenia arbutifolia in Salicaceae.[Method] The whole chloroplast genome sequences of C. arbutifolia was determined by next-generation sequencing, and the phylogenetic position of C. arbutifolia was investigated by comparing its sequences with all available complete chloroplast genome sequences from the genera Populus and Salix.[Result] The total genome was 155, 661 bp, consisting of two single-copy regions separated by a pair of inverted repeats (IRs) of 27, 455 bp. The large single-copy (LSC) and small single-copy (SSC) regions spanned 84, 536 bp and 16, 215 bp, respectively. The total GC content of the chloroplast genome was 36.68% and 113 unique genes were annotated, including 79 protein coding genes, 30 tRNA genes, and four rRNA genes. Twenty genes were duplicated in the inverted repeat regions, 14 genes contained one intron, and three genes (rps12, clpP, and ycf3) contained two introns.[Conclusion] A phylogenetic tree constructed from all available complete chloroplast genome sequences from the genera Populus and Salix based on maximum likelihood, maximum parsimony and Bayesian inference strongly supports the merging of C. arbutifolia into the genus Salix. This study would supply an important basis for the genetic study as well as conservation of C. arbutifolia.
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