Newly reported chloroplast genome of Sinosenecio albonervius Y. Liu & Q. E. Yang and comparative analyses with other Sinosenecio species

• Published in: BMC genomics 2022-09, Vol.23 (1), p.1-639, Article 639
• Main Authors: Peng, Jing-Yi, Zhang, Xiao-Shuang, Zhang, Dai-Gui, Wang, Yi, Deng, Tao, Huang, Xian-Han, Kuang, Tian-Hui, Zhou, Qiang
• Format: Article
• Language: English
• Subjects: Amino acids; Chloroplasts; Codons; Comparative analysis; Comparison of the chloroplast genome; Compositae; Deoxyribonucleic acid; Divergence; DNA; Editing; Gene sequencing; Genes; Genetic aspects; Genomes; Genomics; Identification and classification; Interspecific relationships; Inverted repeat; Metabolism; Nucleotide sequence; Phylogenetic analysis; Phylogenetics; Phylogeny; Phylogeny (Botany); Proteins; Ribonucleic acid; RNA; RNA editing; Simple sequence repeats; Sinosenecio; Species; Taxonomy; Transfer RNA; Varieties
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-022-08872-3

Sinosenecio B. Nordenstam (Asteraceae) currently comprises 44 species. To investigate the interspecific relationship, several chloroplast markers, including ndhC-trnV, rpl32-trnL, matK, and rbcL, are used to analyze the phylogeny of Sinosenecio. However, the chloroplast genomes of this genus have not been thoroughly investigated. We sequenced and assembled the Sinosenecio albonervius chloroplast genome for the first time. A detailed comparative analysis was performed in this study using the previously reported chloroplast genomes of three Sinosenecio species. The results showed that the chloroplast genomes of four Sinosenecio species exhibit a typical quadripartite structure. There are equal numbers of total genes, protein-coding genes and RNA genes among the annotated genomes. Per genome, 49-56 simple sequence repeats and 99 repeat sequences were identified. Thirty codons were identified as RSCU values greater than 1 in the chloroplast genome of S. albonervius based on 54 protein-coding genes, indicating that they showed biased usage. Among 18 protein-coding genes, 46 potential RNA editing sites were discovered. By comparing these chloroplast genomes' structures, inverted repeat regions and coding regions were more conserved than single-copy and non-coding regions. The junctions among inverted repeat and single-copy regions showed slight difference. Several hot spots of genomic divergence were detected, which can be used as new DNA barcodes for species identification. Phylogenetic analysis of the whole chloroplast genome showed that the four Sinosenecio species have close interspecific relationships. The complete chloroplast genome of Sinosenecio albonervius was revealed in this study, which included a comparison of Sinosenecio chloroplast genome structure, variation, and phylogenetic analysis for related species. These will help future research on Sinosenecio taxonomy, identification, origin, and evolution to some extent.