新型水果空心泡叶绿体基因组特征及其系统发育分析

Characteristics and phylogenetic analysis of chloroplast genome of a new type of fruit Rubus rosaefolius

摘要:

为探究空心泡（Rubus rosaefolius）叶绿体基因组特征，本研究以空心泡为试验材料，采用Illumina NovaSeq平台进行高通量测序，获得空心泡完整的叶绿体基因组序列，并进行空心泡叶绿体基因序列特征和系统发育分析。结果表明：空心泡的完整叶绿体基因组总长度为155 650 bp，具有典型的四分体结构，包括2个反向重复序列（各25 748 bp）、1个大拷贝区（85 443 bp）、1个小拷贝区（18 711 bp）。空心泡叶绿体全基因组共鉴定出131个基因，包括86个蛋白质编码基因、37个tRNA基因和8个rRNA基因，全基因组的GC含量为36.9%。空心泡叶绿体基因组包含47个散在重复序列、72个简单重复序列（simple sequence repeating，SSR）位点，密码子偏好性为亮氨酸密码子，偏好使用A/U结尾的密码子。系统发育分析表明，空心泡与小叶悬钩子（Rubus taiwanicola）亲缘关系最近，其次是能高悬钩子（Rubus rubroangustifolius）和腺萼悬钩子（Rubus glandulosopunctatus）。空心泡的叶绿体基因组特征及其系统发育分析，为空心泡的遗传多样性研究和叶绿体开发利用提供理论依据。

Abstract:

The genomic DNA of Rubus rosaefolius was extracted and sequenced by Illumina NovaSeq platform to obtain the complete chloroplast genome sequence, and the sequence characteristics and phylogenetic analysis of chloroplast genes were carried out. The results showed that the complete chloroplast genome of the R. rosaefolius was 155 650 bp in length and had a typical tetrad structure, including two reverse repeats (25 748 bp each), a large copy region (85 443 bp) and a small copy region (18 711 bp). A total of 131 genes were identified in the whole genome of R. rosaefolius chloroplast, including 86 protein coding genes, 37 tRNA genes and 8 rRNA genes. The GC content of the whole genome was 36.9%. The genome of R. rosaefolius chloroplast contains 47 scattered repeats and 72 simple sequence repeating (SSR) loci. The codon preference is leucine codon, and the codon at the end of A/U is preferred. Phylogenetic analysis showed that R. rosaefolius had the closest relationship with R. taiwanicola, followed by R. rubraangustifolius and R. glandulosopunctatus. The chloroplast genome characteristics and phylogenetic analysis of R. rosaefolius provide a theoretical basis for its genetic diversity research and chloroplast development and utilization.