黑喉石斛叶绿体基因组特征及比较分析

本研究结合Illumina高通量测序和Nanopore测序技术,对黑喉石斛（Dendrobium ochreatum）的叶绿体基因组（cpDNA）进行测序,组装得到其cpDNA全长序列并绘制结构图谱。黑喉石斛cpDNA全长154 935 bp,注释共得到125个基因,其中有unigenes 103种,包含73种蛋白编码基因,26种tRNA基因和4种rRNA基因。特征分析结果表明：黑喉石斛cpDNA中共存在58个SSR （simple sequence repeat）位点,大部分为单核苷酸重复和二核苷酸重复类型,碱基组成以A/T碱基类型为主;其偏好的密码子共32个,其中有30个以A/U碱基结尾。以黑喉石斛与其他13种石斛的cpDNA构建系统发育进化树,结果显示,鼓槌石斛（D. chrysotoxum）和梳唇石斛（D. strongylanthum）与黑喉石斛具有较近的亲缘关系,IR/SC边界分析结果也映证了此结论。以黑喉石斛为参照,与3种近缘石斛的cpDNA进行全序列长对比,结果显示,4种石斛的序列变异主要发生在单拷贝区,基因间隔区的变异明显高于基因编码区。

Characteristics of the Complete Chloroplast Genome of Dendrobium ochreatum and Its Comparative Analysis

In this research, the complete chloroplast genome (cpDNA) of D. ochreatum was sequenced through the combination of high-throughput and nanopore sequencing, and the full-length sequence (154 935 bp) of chloroplast genome (cpDNA) was assembled and annotated. A total of 125 genes (103 unigenes) were annotated in the cpDNA, including 73 protein-coding genes, 26 tRNA genes and 4 rRNA genes. Characteristic analysis showed that the number of SSR sites in the cpDNA of D. ochreatum was 58, most of which were mononucleotide or dinucleotide repeats with A/T base preference. Codon bias analysis showed that there were 32 biased codons and the majority of the biased codons were ended with A/U base. The phylogenetic tree of D. ochreatum and 13 Dendrobium species was constructed using cpDNA sequences. Result indicated that D. chrysotoxum and D. strongylanthum were closely related to D. ochreatum, and the IR/SC junctions analysis of Dendrobium species was consistent with the former. Global alignment of cpDNA of 4 Dendrobium species showed that the sequence variations were mainly concentrated in single copy regions, and variations in the intergenic region were significantly higher than that in the gene coding region.