桃儿七叶绿体比较基因组学分析

为探究桃儿七（Sinopodophyllum hexandrum）不同叶绿体基因组特征，本研究以桃儿七5个叶绿体基因组为研究对象，借助生物信息学工具进行基因组图谱构建、重复序列分析、密码子偏好分析、反向重复序列区（inverted repeat，IR）/单拷贝区（single-copy，SC）边界分析、基因组序列比较分析及系统发育分析。结果表明：桃儿七5个叶绿体基因组全长为157 203–157 940 bp，为典型的叶绿体四分体结构，共注释出133–137个基因，说明桃儿七叶绿体基因组具有多样性。桃儿七不同叶绿体基因组简单重复序列（simple sequence repeat，SSR）位点不同，单核苷酸A/T占主要优势，散在重复序列包括正向重复、回文重复和反向重复3类。密码子偏好分析显示有效密码子（effective number of codon，ENc）值为51.14–51.17，密码子偏好性弱，GC与GC3s所占比例小于50%，密码子偏向使用A和U碱基并且以A和U碱基结尾。桃儿七5个叶绿体基因组IR/SC边界和基因组序列均比较保守。系统发育分析结果表明桃儿七和北美桃儿七亲缘关系最近。本研究获取了桃儿七5个叶绿体基因组信息与进化关系，为桃儿七资源开发利用与保护、品种鉴定和遗传进化研究奠定了科学基础。

Comparative genomics on chloroplasts of Sinopodophyllum hexandrum

To explore the different chloroplast genome characteristics of Sinopodophyllum hexandrum, five chloroplast genome sequences of S. hexandrum were compared. Its genome map, repeat sequence, codon preference, inverted repeat (IR)/single-copy (SC) boundary, alignment of chloroplast genome sequences and phylogenetic were analyzed using bioinformatics tools. The results showed that:the total length of five chloroplast genomes of S. hexandrum, with a typical tetrad structure, were 157 203-157 940 bp, and a total of 133-137 genes were annotated, reflecting the diversity of chloroplast genomes of S. hexandrum. Different chloroplast genomes of S. hexandrum has different simple sequence repeat (SSR), where simple repeat of single nucleotide of A/T were the majority among the SSR detected. The interspersed repetitive sequences included direct, palindromic and inverted repeats. The value of effective number of codon(ENc) which was analyzed by using codon bias was 51.14~51.17, the proportion of GC and GC3s was less than 50%, the codon usage pattern tended towards frequently use of A/U-ending bases. Genome sequences and the IR/SC boundaries of five chloroplast genomes of S. hexandrum were relatively conservative. Phylogenetic analysis showed that S. hexandrum and Podophyllum pettatum had the closest genetic relationship. In summary, the chloroplast genome characteristics and evolutionary relationship of different chloroplast genomes of S. hexandrum were obtained, which may facilitate the utilization, protection, variety identification and genetic evolution of S. hexandrum resources.