Comparative analyses of complete plastid genomes from seven representative species of Convallarioideae (Asparagaceae)

Abstract

Abstract Background Convallarioideae is a subfamily of Asparagaceae, a morphologically diverse group comprising 7 tribes (i.e., Eriospermeae, Rusceae, Dracaeneae, Nolineae, Convallarieae, Ophiopogoneae, and Polygonateae) and two unclassified genera. Methods and Results In this study, we conducted comparative chloroplast genomic and phylogenetic analyses on seven species, representing seven lineages of the tribe. The results showed that all genomes exhibited a conserved quadripartite structure with two inverted repeat regions (26,261 − 26,522 bp) separated by a large single-copy region (83,007–85,692 bp) and a small single-copy region (18,205 − 18,707 bp). Each genome contains 137 unique genes, including 87 protein-coding genes, 38 transfer RNA, and 8 ribosomal RNA genes. Furthermore, we detected 33–61 simple sequence repeats in six categories and 39–57 long repeats in four categories. We selected eleven divergent hotspots for potential molecular markers. Phylogenetic analysis revealed that all the tribes are strongly supported except for Polygonateae, but weak supports were observed among the main lineages within the subfamily. Conclusions The use of the complete chloroplast genomes provides useful implications for a better understanding on the chloroplast evolution on Convallarioideae.