Comparative Analyses on the Chloroplast Genome of Three Sympatric Atraphaxis Species
Received date: 2022-04-08
Accepted date: 2022-09-19
Online published: 2022-09-27
Atraphaxis spinosa, A. jrtyschensis, and A. decipiens are three species with sympatric distribution in northern Xinjiang, China. In this study, their chloroplast genomes were assembled and annotated with the second-generation high-throughput sequencing technology (NGS). We compared the nucleotide sequences of the chloroplast (cp) genomes of these three Atraphaxis species and carried out the phylogenetic analysis. The results showed that the cp genomes of the three species ranged from 164 106 bp to 164 216 bp, similar to that of other green plants, all including a pair of inverted repeats separated by a large single-copy and a small single-copy region. We detected a total of 48-49 tandem repeats and 59-63 simple sequence repeats (SSRs) from the three cp genomes. The mean value of nucleotide diversity of the three species was 0.000 96, the average score of Ka/Ks ratio was 0.030 3, and the mean genetic distance value was 0.001 0. A comparative analysis showed that the coding regions were more conserved than the non-coding regions. The phylogenetic analysis showed that the three species were closely related. This study reveals the phylogenetic relationships among the three sympatric distribution species of Atraphaxis based on complete chloroplast genomes, and the phylogenetic position of Atraphaxis in the family Polygonaceae. This work may provide a reference for taxonomic, systematic and biogeographical studies of Atraphaxis.
Zhenzhou Chu, Gulbar Yisilam, Zezhong Qu, Xinmin Tian . Comparative Analyses on the Chloroplast Genome of Three Sympatric Atraphaxis Species[J]. Chinese Bulletin of Botany, 2023 , 58(3) : 417 -432 . DOI: 10.11983/CBB22065
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