Ma Luhua, Ning Jiaqi, Wang Yongjie, Zhao Min, Li Yikang, Zhou Huakun
Institute of Northwest Plateau Biology Chinese Academy of Science, Xining 810008, Qinghai, China.
University of Chinese Academy of Sciences, Beijing 100049, China.
Sheng Wu Gong Cheng Xue Bao. 2022 Oct 25;38(10):3695-3712. doi: 10.13345/j.cjb.220386.
To explore the different chloroplast genome characteristics of , five chloroplast genome sequences of . 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 . , 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 . . Different chloroplast genomes of . 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 . were relatively conservative. Phylogenetic analysis showed that . and had the closest genetic relationship. In summary, the chloroplast genome characteristics and evolutionary relationship of different chloroplast genomes of . were obtained, which may facilitate the utilization, protection, variety identification and genetic evolution of . resources.
为探究[具体物种名称]的不同叶绿体基因组特征，对[具体物种名称]的五个叶绿体基因组序列进行了比较。利用生物信息学工具分析了其基因组图谱、重复序列、密码子偏好、反向重复（IR）/单拷贝（SC）边界、叶绿体基因组序列比对及系统发育。结果表明：[具体物种名称]的五个叶绿体基因组全长157203 - 157940 bp，具有典型的四分体结构，共注释出133 - 137个基因，反映了[具体物种名称]叶绿体基因组的多样性。[具体物种名称]不同的叶绿体基因组具有不同的简单序列重复（SSR），其中在检测到的SSR中，A/T单核苷酸的简单重复占多数。散布重复序列包括正向、回文和反向重复。通过密码子偏好性分析得到的有效密码子数（ENc）值为51.14~51.17，GC和GC3s的比例小于50%，密码子使用模式倾向于频繁使用以A/U结尾的碱基。[具体物种名称]的五个叶绿体基因组序列及其IR/SC边界相对保守。系统发育分析表明，[具体物种名称]与[另一具体物种名称]具有最密切的亲缘关系。综上所述，获得了[具体物种名称]不同叶绿体基因组的叶绿体基因组特征及进化关系，这可能有助于[具体物种名称]资源的利用、保护、品种鉴定及遗传进化。
