粗叶悬钩子叶绿体基因组特征及系统发育分析

Characteristics and Phylogenetic of the Chloroplast Genome of Rubus alceifolius

为探讨粗叶悬钩子(Rubus alceifolius)叶绿体基因组特征及其与同科属植物叶绿体基因组的系统发育关系,本研究采用Illumina HiSeq 4000平台对粗叶悬钩子叶绿体基因组进行了测序、组装和注释,并对其序列特征、密码子偏好性、重复序列、简单重复序列(simple sequence repeats,SSR)和系统发育进行分析。结果表明,粗叶悬钩子叶绿体基因组总长度为156266 bp,呈典型的四分体结构,包括大单拷贝区85874 bp、小单拷贝区18850 bp和反向互补重复区25771 bp;共含有基因128个,其中蛋白质编码基因86个,tRNA基因34个,rRNA基因8个。密码子偏好性分析表明,亮氨酸(Leu)的密码子数量最多(5189个),而半胱氨酸(Cys)的密码子数量最少(590个)。从粗叶悬钩子叶绿体基因组中共检测出39个长重复序列及52个SSR位点。系统发育分析表明,粗叶悬钩子与七裂叶悬钩子(Rubus reflexus var.lanceolobus)、越南悬钩子(Rubus cochinchinensis)、棕红悬钩子(Rubus rufus)聚为一支,亲缘关系最密切。本研究为蔷薇科(Rosaceae)悬钩子属(Rubus)植物的分子标记、物种鉴定、亲属关系解析和遗传多样性分析等研究提供科学依据。

In order to explore the characteristics of chloroplast genome of Rubus alceifolius and its phylogenetic relationship with chloroplast genome of the same family,the Illumina HiSeq 4000 platform was used to sequence,assemble and annotate Rubus alceifolius,and its sequence characteristics,codon preference,sequence repeats,simple sequence repeats(SSR)and phylogeny were analyzed.The results showed that the chloroplast genome of Rubus alceifolius showed a typical tetrad structure,with a total length of 156266 bp,including a large single copy region of 85874 bp,a small single copy region of 18850 bp and a reverse complementary repeat region of 25771 bp.A total of 128 genes were detected,including 86 protein coding genes,34 tRNA genes and 8 rRNA genes.Codon preference analysis showed that leucine(Leu)had the largest number of codons(5189),while cysteine(Cys)had the least number of codons(590).A total of 39 long repeats and 52 SSR loci were detected from the chloroplast genome of Rubus alceifolius.Phylogeny analysis showed that Rubus reflexus var.lanceolobus,Rubus cochinchinensis,Rubus rufus and Rubus alceifolius were clustered into one branch,and the relationship was the closest.This study provides scientific basis for molecular markers,species identification,kinship analysis and genetic diversity analysis of Rosaceae and Rubus.