金铁锁叶绿体基因组序列及其系统发育分析

Analysis on structure and phylogeny of complete chloroplast genomes in Psammosilene tunicoides

目的解析金铁锁叶绿体基因组结构和确定其在石竹科的系统位置。方法基于二代测序技术IlluminaHiseq平台,对金铁锁叶绿体基因组进行测序,使用生物信息学分析软件进行组装和注释,并以苋科植物千穗谷为外类群,通过RAx ML 8.2.11软件构建ML系统发育树,分析石竹科属间的亲缘关系。结果金铁锁叶绿体基因组总长为153977bp。LSC和SSC区被2个反向重复区域IRs隔开,其大小分别为84385、17526、26033 bp。除去重复后,共编码109个基因,包含75个PCGs,30个t RNA和4个r RNA基因。总的CG含量为36.5%,IR区(42.4%)GC含量明显高于LSC(34.2%)和SSC(30.1%)区。在系统进化树中,金铁锁与长萼瞿麦互为姊妹类群,且各节点的支持率较高,能够清晰反映属间的亲缘关系。结论本研究对金铁锁叶绿体基因组结构进行了解析,并探讨了石竹科属间系统发育关系,为金铁锁种质资源综合评价、系统进化等研究提供有效的科学数据。

Objective To obtain the structural characteristics of chloroplast genome in Psammosilene tunicoides and analyze its phylogenetic position within the family of Caryophyllaceae.Methods High-through-put sequencing technology and bioinformatic analysis softwares were used to analyze the structures of complete chloroplast genome of P.tunicoides.RAxML 8.2.11 software was utilized to reconstruct the Caryophyllaceae phylogentic tree with Amaranthus hypochondriacus as outgroup.Results The complete chloroplast genome was 153977 base pairs(bp)in size,including two inverted repeat(IR,26033 bp)regions separated by one large singe copy region(LSC,84385 bp)and one small singe copy region(SSC,17526 bp).The genome encoded 125 genes,of which 109 were unique,including 75 protein-coding genes(PCGs),30 tRNA genes and 4 rRNA genes.The overall GC content of P.tunicoides was 36.5%,while those ofIR regions(42.4%)were higher than LSC(34.2%)and SSC(30.1%)regions.The phylogenetic tree showed that P.tunicoides and Dian thus longicalyx were sister groups with 100%bootstrap value.All nodes of the phylogenetic tree of Caryophyllaceae were of high supports,and the ML tree had good resolution to reflect the phylogeny relationship among the Caryophyllaceae.Conclusion The complete chloroplast genome of P.tunicoides and the phylogenetic relationship within Caryophyllaceae were analyzed in this study.The results will provide effective molecular information for further studies on evaluation of germplasm and molecular phylogeny of Caryophyllaceae.