Complete chloroplast genome of a spring ephemeral plant Alyssum desertorum and its implications for the phylogenetic position of the tribe Alysseae within the Brassicaceae
7 August 2017
Li, Yan; Lv, Guanghui; He, Xuemin; Zhang, Xueni; Yang, Xiaodong‖Alyssum desertorum (Alysseae, Brassicaceae) is an annual spring ephemeral plant whose life cycle is only 2-3 months. It typically has high photosynthetic capacity and a high growth rate. However, little is known about the chloroplast (cp) genome structure of this species. Furthermore, the phylogenetic position of the tribe Alysseae relative to other tribes in the Brassicaceae has not been determined due to inconsistences in different DNA markers. This study is the first report on a cp genome of the genus Alyssum and discusses the phylogenetic relationships of the tribe Alysseae relative to other tribes in the family. The complete cp genome of A. desertorum was 151,677 bp in size and is the smallest cp genome in the Brassicaceae sequenced to date. The genome includes a large single-copy region of 81,551 bp, a small single-copy region of 17,804 bp, and two inverted repeats of 26,161 bp each. The genome contains 132 genes, including 86 protein-coding genes (PCGs), 38 tRNA genes and 8 rRNA genes. A total of 16 genes contained introns, including 10 PCGs and 6 tRNA genes; the ycf3 and clpP genes contained two introns, and the remaining genes each contained one. Compared to the cp genomes of 21 other species, the cp genome of Alyssum desertorum was the smallest, which was due to variations in gene content and gene length, such as a lack of the rps16 gene and the deletion of some coding genes. Additionally, deletions of introns and intergenic spacers were observed, but their total length was not significantly shorter than those of other taxa. Phylogenetic analysis at the tribal level based on a cp genome dataset revealed that the tribe Alysseae is an early-diverging lineage and is sister to other species within subclade B of clade Ⅱ.