摘要
【目的】根据基因组浅层测序结果,解析无毛青藤叶绿体基因组的结构、大小、基因组成、密码子偏好性、简单重复序列(SSR)位点及系统发育关系。【方法】以无毛青藤为材料,对其叶绿体基因组进行测序,组装后获得其叶绿体DNA全长序列并进行基因组特征、密码子偏好性、SSR位点及系统发育分析。【结果】无毛青藤叶绿体基因组全长为156 513 bp。其中,GC含量为39.1%。其结构包括大单拷贝区(LSC,85 225 bp)、小单拷贝区(SSC,18 779 bp)以及反向重复序列(IRs,26 254 bp)。4个区段中,IR区的GC含量最高(43.3%),LSC区的GC含量为37.7%,SSC区最低。共注释得到131个基因,其中,84个位于LSC区,SSC区13个,两个IR区各17个。鉴定出61个SSR位点,碱基组成以A/T碱基类型为主;33个无毛青藤叶绿体基因组密码子的使用具有偏好性,并以A/U碱基结尾。系统发育进化树表明,青藤属6个种分为两支,其中大花青藤与无毛青藤具有较近的亲缘关系,IR/SC边界分析结果显示除红花青藤外,其余5种青藤属植物的JLB(LSC/IRb)边界较为保守。6种青藤叶绿体基因组的基因构成和顺序较为保守,大多数变异存在于相邻基因间隔区内。【结论】无毛青藤的叶绿体基因组相对较大,且较为保守,并与大花青藤具有较近的亲缘关系。研究结果可为无毛青藤及其近缘种叶绿体基因组系统进化分析提供重要的理论参考。
【Objective】According to the results of shallow genome sequencing,the structure,size,gene composition,codon preference,SSR sites and phylogenetic relationship of Illigera glabra were analyzed.【Method】The chloroplast genome was sequenced by using Illigera glabra as the material.After assembly,the full-length DNA sequence was obtained and the genome characteristics,codon preference,SSR loci and phylogenetics were analyzed.【Result】The results showed that the I.glabra chloroplast genome had a size of 156513 bp and a GC content of 39.1%.The structure contained the LSC region(85225 bp),the SSC region(18779 bp)and IR regions(26254 bp).Among the 4 regions,the GC content was the highest in IR regions(43.3%),followed by the LSC region(37.7%),which was the lowest in the SSC region.A total of 131 genes were annotated.Among them,84 genes were located in the LSC region,13 genes were in the SSC region,and 17 genes were in the IR regions.61 SSR sites were found,and the base composition was mainly the A/T base type.33 genome codons of I.glabra chloroplast had code usage preferences,which were terminated with the A/U base.The phylogenetic tree showed that the 6 species of Illigera were divided into two branches,among which I.celebiea and I.parviflora belonged to the first branch,and the others compromised the second branch.Among them,I.grandiflora had a close genetic relationship with I.glabra.The results of IR/SC boundary analysis showed that the JLB(LSC/IRb)boundary of 5 Illigera species was relatively conservative,except for I.rhodantha.The gene composition and sequences of the chloroplast genomes of 6 Illigera species were relatively conservative.Most of the variation existed in the adjacent gene interval region.【Conclusion】The chloroplast genome of I.glabra is relatively large and conservative,and has a close genetic relationship with I.grandiflora.The results can provide important theoretical references for the phylogenetic analysis of the chloroplast genome of I.glabra and its related species.
作者
赵文植
杨琳懿
曹正英
辛静
马路遥
王飞
李卫英
辛培尧
ZHAO Wenzhi;YANG Linyi;CAO Zhengying;XIN Jing;MA Luyao;WANG Fei;LI Weiying;XIN Peiyao(Southwest Research Center for Landscape Architecture Engineering,State Forestry and Grassland Administration,Southwest Forestry University,Kunming 650224,Yunnan,China;Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Southwest China,Southwest Forestry University,Kunming 650224,Yunnan,China)
出处
《中南林业科技大学学报》
CAS
CSCD
北大核心
2023年第5期149-157,共9页
Journal of Central South University of Forestry & Technology
基金
云南省科技人才与平台计划项目(202205AF150022)
西南林业大学科研预研基金资助项目。
作者简介
第一作者:赵文植(1635037122@qq.com),硕士研究生;通信作者:辛培尧(xpytgyx@163.com),教授,博士,博士研究生导师。
