五爪金龙叶绿体基因组特征分析

Characteristics of the Chloroplast Genome of Ipomoea cairica

关键词:  五爪金龙  叶绿体基因组  密码子偏好性  简单重复序列  系统进化关系

Key words:  Ipomoea cairica  chloroplast genome  codon bias  simple sequence repeat  phylogenetic relationship

摘要:

为了阐明药用植物五爪金龙Ipomoea cairica的叶绿体基因组特征，选用五爪金龙叶片为样品，采用试剂盒法提取DNA并建立测序文库，随后使用新一代细胞器基因组测序技术进行高通量测序，并利用生物信息学手段进行序列组装和特征分析。结果显示，五爪金龙叶绿体基因组为环状双链四分体分子，全长161 780 bp，由88 205 bp的大单拷贝区(Large Single Copy，LSC)、30 747 bp 的反向重复区(Inverted Repeat，IR)A、12 081 bp的小单拷贝区(Small Single Copy，SSC)和30 747 bp的反向重复区B(IRB)排列而成，含有131个基因；共有28 757个密码子，偏好使用以A或T结尾的密码子；存在67个简单重复序列(Simple Sequence Repeat，SSR)，并以A/T单核苷酸重复居多。五爪金龙与近缘植物在IRB-SSC边界之间存在较为明显的变异，与同属三裂叶薯I.triloba、番薯I.batatas等的亲缘关系更近。本研究报道了五爪金龙叶绿体基因组的结构和序列组成，并分析其特征，为五爪金龙的物种鉴定、遗传进化及开发利用提供了基因组信息。

Abstract:

To clarify the chloroplast genome features of Ipomoea cairica,this study used a kit to extract DNA from the leaves of I.cairica and then constructed the sequence library.The next-generation sequencing was employed for high-throughput organelle sequencing,and then bioinformatics tools were used to assemble and analyze the sequences.The results showed that the chloroplast genome of I.cairica was a circular quadripartite structure with a total length of 161 780 bp,which was composed of a Large Single Copy (LSC,88 205 bp),an Inverted Repeat A (IRA,30 747 bp),a Small Single Copy (SSC,12 081 bp),and an Inverted Repeat B (IRB,30 747 bp).A total of 131 genes were embodied in the chloroplast genome.The genome contained 28 757 codons,among which those ended with A/T were frequently used.There were 67 Simple Sequence Repeats (SSR),which were dominated by the mononucleotide repeat A/T.I.cairica showed significant variations with related species at the boundary between IRB and SSC and shared close relationship with I.triloba and I.batatas.This work reports and characterizes the chloroplast genome of I.cairica,which will provide genome data for species identification, phylogenetic relationship research,and development and utilization of this herbal medicine.