Comparative genomics on chloroplasts of <i>Sinopodophyllum hexandrum</i>.

Luhua MA; Jiaqi Ning; Yongjie Wang; Min Zhao; Yikang LI; Huakun Zhou

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Comparative genomics on chloroplasts of Sinopodophyllum hexandrum.

Author: Luhua MA ¹ ; Jiaqi NING ² ; Yongjie WANG ² ; Min ZHAO ¹ ; Yikang LI ¹ ; Huakun ZHOU ¹
Author Information

1. Institute of Northwest Plateau Biology Chinese Academy of Science, Xining 810008, Qinghai, China.
2. Qinghai Minzu University, Xining 810007, Qinghai, China.
Publication Type:Journal Article
Keywords: Sinopodophyllum hexandrum; chloroplast genome; phylogenetic analysis; structural characteristics
MeSH: Phylogeny; Genome, Chloroplast; Chloroplasts/genetics*; Genomics; Evolution, Molecular
From: Chinese Journal of Biotechnology 2022;38(10):3695-3712
CountryChina
Language:Chinese
Abstract: 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.