野生六棱大麦叶绿体基因组特征及系统发育分析  

Characterization and Phylogenetic Comparative Analysis of the Complete Chlo⁃roplast Genome of Hordeum agriocrithon

作　　者：余鑫莲 李新 YU Xinlian;LI Xin(State Key Laboratory of Plateau Ecology and Agriculture,Qinghai University,Xining,810016;Academy of Agriculture and Fore-stry Sciences,Qinghai University,Xining,810016;Qinghai Key Laboratory of Hulless Barley Genetics and Breeding,Xining,810016;Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources,Xining,810016)

机构地区：[1]青海大学省部共建三江源生态与高原农牧业国家重点实验室,西宁810016 [2]青海大学农林科学院,西宁810016 [3]青海省青稞遗传育种重点实验室,西宁810016 [4]青藏高原种质资源研究与利用实验室,西宁810016

出　　处：《基因组学与应用生物学》2024年第5期788-802,共15页Genomics and Applied Biology

基　　金：青海大学省部共建三江源生态与高原农牧业国家重点实验室自主课题项目(2022⁃ZZ⁃07);青海省自然科学基金计划——创新团队项目(2022⁃ZJ⁃902);青海省科技创新平台建设专项(2023⁃1⁃5)共同资助。

摘　　要：野生六棱大麦(Hordeum agriocrithon)广泛分布在青藏高原上,被认为是六棱栽培大麦的野生祖先。为揭示野生六棱大麦叶绿体基因组(chloroplast DNA,cpDNA)结构特征和系统发育关系,利用Illumina Hiseq 6000测序平台对其进行高通量测序,并以钝稃野大麦(H.spontaneum)叶绿体基因组为参考进行序列组装及质控;利用生物信息学手段,对野生六棱大麦的叶绿体基因组进行注释及特征分析;同时,以玉米(Zea mays)和禾本科(Gramineae)针茅属(Stipa)物种Stipa lipskyi为外类群,通过MEGA X软件构建最大似然法(maximum likelihood method,ML)系统发育树,分析野生六棱大麦系统发育关系。研究表明,野生六棱大麦叶绿体基因组总G+C含量为38.32%,全长136462 bp,包含1对长度为21582 bp的反向重复区(in⁃verted repeats region,IRs),1个长度为80597 bp的大单拷贝区(large single copy region,LSC)和1个长度为12701 bp的小单拷贝区(small single copy region,SSC),为典型的四分体结构。在野生六棱大麦叶绿体基因组中共检测到129个基因,分别是83个编码基因、38个tRNA基因和8个rRNA基因;另外,共检测到46个散在重复序列(dispersedrepeated sequences)和178个简单重复序列(simple sequence repeats,SSR)位点,大部分SSR是由A/T组成的单碱基重复序列。密码子偏好性分析结果表明,野生六棱大麦有偏好性,且偏好使用以A/U结尾的密码子。结合IR边界分析和序列比较分析,结果表明,除碱大麦(Hordeum marinum)外,野生六棱大麦、栽培二棱大麦(Hordeum distichon)、钝稃野大麦和大麦(Hordeum vulgare)的叶绿体基因组结构具有较高保守性,且序列变异主要发生在LSC的非编码序列上。系统发育分析结果表明野生六棱大麦与大麦属(Hordeum)物种聚类在一起,且与大麦亲缘关系最近。本研究获得了野生六棱大麦的叶绿体基因组序列,明确了与小麦族(Triticeae)物种间的亲缘关系,为研究大麦属物种的系统进化及Hordeum agriocrithon is considered as the wild progenitor of six⁃rowed cultivated barley and is widely distributed in the Qinghai⁃Tibet Plateau.In order to reveal the structural characteristics and phylogenetic relationship of chloroplast DNA(cpDNA)of H.agriocrithon,the H.agriocrithon cpDNA was sequenced by using the Illumina Hiseq 6000 sequencing platform,and the cpDNA of H.spontaneum was used as a reference to sequence assembly and quality control.The cpDNA of H.agriocrithon was annotated and char⁃acterized by bioinformatics.Meanwhile,the maximum likelihood method(ML)phylogenetic tree was constructed by MEGA X soft⁃ware,with Zea mays and Gramineae Stipa species Stipa lipskyi as outgroups,to analyze the phylogenetic relationships of Hordeum agri⁃ocrithon.The results showed that the cpDNA of H.agriocrithon was 136462 bp in length,with a G+C content of 38.32%,which was a typical tetrad structure,including a pair of inverted repeats region(IRs)of 21582 bp,a large single copy region(LSC)of 80597 bp,and a small single copy region(SSC)of 12701 bp.A total of 129 genes were identified in the cpDNA of H.agriocrithon,inclu⁃ding 83 protein⁃coding genes,38 tRNA genes,and 8 rRNA genes.A total of 46 dispersed repeated sequences and 178 simple se⁃quence repeats(SSR)loci were detected,most of SSR were single base repeats composed of A/T.Codon usage bias analysis showed that H.agriocrithon had a preference and preferred to use the codons ending with A/U.IR boundary analysis combined with compara⁃tive sequence analysis showed that the chloroplast genome structures of H.agriocrithon,H.distichon,H.spontaneum,and H.vulgare were highly conserved,in which the sequence variation mainly occurred in the non⁃coding sequence of the LSC,except for H.mari⁃num.The phylogenetic analysis showed that the H.agriocrithon clustered with Hordeum species and had the closest genetic relationship with H.vulgare.In this study,the complete chloroplast genome sequence of H.agriocrithon was obtained,which clarified the affinities betw

关 键 词：野生六棱大麦 叶绿体基因组 重复序列 密码子偏好性 系统发育关系 

分 类 号：S512.3[农业科学—作物学]