摘要
【目的】分析悬钩子属植物叶绿体基因组结构特征和系统演化机制,为悬钩子属物种的分类及演化提供分类依据,并为DNA条形码的编制和悬钩子属植物的保护提供理论支持。【方法】利用生物信息学及比较基因组学的方法对16种悬钩子属植物叶绿体基因组的大小、结构、组成、重复序列、边界扩张、基因组共线性、正向选择作用及系统发育进行了分析。【结果】16种植物的叶绿体基因组都具有典型的四联体结构,长度为155286~156668 bp,平均GC含量为37.15%,基因组大小变异整体较小,其中SSC区域和IR区域的长度更为稳定。在编码基因的功能分类中发现仅8种悬钩子属植物具有2个完整拷贝的ycf1基因且一些基因在部分植物中只有单个拷贝。边界扩张分析结果显示,反向重复区边界不存在明显的收缩或扩张现象。共线性与系统发育分析结果显示,太平莓与其余15种植物具较高的相似度,有良好的共线性关系;太平莓与柔毛梨叶悬钩子、竹叶鸡爪茶的亲缘关系较近,但太平莓与竹叶鸡爪茶的相似度最低。对悬钩子属植物进行Taijima’test分析发现悬钩子属植物有群体扩张的趋势,且蛋白质编码基因具有一定程度的纯化选择或中性选择作用。【结论】悬钩子属植物叶绿体基因组高度保守,物种间亲缘关系越近,叶绿体基因组相似性越高,反之并不成立。根据叶绿体基因组的序列,可以定位它们在系统发育树中的位置,并分析它们之间的亲缘关系。
【Objective】The study provides a basis for the classification and evolution of Rubus,which provides theoretical support for DNA barcoding and protection of Rubus species.【Method】Using bioinformatics and comparative genomics methods to analyze the chloroplast genome size,structure,composition,repeats,boundary extension,genomic collinearity,forward selection and phylogeny of 16 Rubus.【Result】The chloroplast genome of 16 plants had a typical tetrad structure,length of 155286 bp to 156668 bp,37.15%of average GC content.The variation of genome size was small and the length of SSC region and IR region was more stable.In the functional classification of coding genes,it was found that only eight Rubus species had two full copies of ycf1 gene and some genes had only a single copy in some plats.The results of boundary expansion analysis showed that there was no obvious contraction or expansion in the boundary of the reverse repetition region.The results of collinearity and phylogenetic analysis showed that there was a high similarity between R.pacificus and the other 15 plants.R.pacificus and R.pyrifolius var.Permollis,R.bambusarum were close relatives,but had the lowest similarity with R.bambusarum.The Taijima’test analysis showed that there was a tendency of population expansion in Rubus,and protein-coding genes had a certain degree of purification selection or neutral selection.【Conclusion】The chloroplast genome of Rubus is highly conserved,the closer the relationship between species,the higher the chloroplast genome similarity,but the reverse is not true.Based on the sequence of chloroplast genomes,we can locate them in the phylogenetic tree and analyze their relationship.
作者
江转转
陈淑娜
鲍红艳
叶龙雨
JIANG Zhuanzhuan;CHEN Shuna;BAO Hongyan;YE Longyu(College of Life Science,Anqing Normal University,Anqing 246133,Anhui,China;The Province Key laboratory of the Biodiversity Study and Ecology Conservation in Southwest College,Anqing Normal University,Anqing 246133,Anhui,China)
出处
《中南林业科技大学学报》
CAS
CSCD
北大核心
2024年第4期148-158,共11页
Journal of Central South University of Forestry & Technology
基金
国家自然科学基金项目(32301126)
安徽省高等学校科学研究项目(2022AH051034)
安徽省大学生创新创业训练项目(S202310372079)。
