Phylogenomics and plastome evolution of Indigofera (Fabaceae)

作者：Sheng-Mao Zhou, Fang Wang, Si-Yuan Yan, Zhang-Ming Zhu, Xin‐Fen Gao, Xueli Zhao · 发表于：Frontiers in Plant Science · 年份：2023 · DOI：10.3389/fpls.2023.1186598 · 被引用次数：17 · 研究领域：Genomics and Phylogenetic Studies、Plant and Fungal Species Descriptions、Plant Diversity and Evolution

Introduction Indigofera L. is the third largest genus in Fabaceae and includes economically important species that are used for indigo dye-producing, medicinal, ornamental, and soil and water conservation. The genus is taxonomically difficult due to the high level of overlap in morphological characters of interspecies, fewer reliability states for classification, and extensive adaptive evolution. Previous characteristic-based taxonomy and nuclear ITS-based phylogenies have contributed to our understanding of Indigofera taxonomy and evolution. However, the lack of chloroplast genomic resources limits our comprehensive understanding of the phylogenetic relationships and evolutionary processes of Indigofera . Methods Here, we newly assembled 18 chloroplast genomes of Indigofera . We performed a series of analyses of genome structure, nucleotide diversity, phylogenetic analysis, species pairwise Ka/Ks ratios, and positive selection analysis by combining with allied species in Papilionoideae. Results and discussion The chloroplast genomes of Indigofera exhibited highly conserved structures and ranged in size from 157,918 to 160,040 bp, containing 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Thirteen highly variable regions were identified, of which trn K- rbc L, ndh F- trn L, and ycf 1 were considered as candidate DNA barcodes for species identification of Indigofera . Phylogenetic analysis using maximum likelihood (ML) and Bayesian inference (BI) methods based on...