AUTHOR=Li Chaoyang , Zhao Yunlin , Xu Zhenggang , Yang Guiyan , Peng Jiao , Peng Xiaoyun 

TITLE=Initial Characterization of the Chloroplast Genome of Vicia sepium, an Important Wild Resource Plant, and Related Inferences About Its Evolution

JOURNAL=Frontiers in Genetics

VOLUME=11

YEAR=2020

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2020.00073

DOI=10.3389/fgene.2020.00073

ISSN=1664-8021

ABSTRACT=<p>Lack of complete genomic information concerning <italic>Vicia sepium</italic> (Fabaceae: Fabeae) precludes investigations of evolution and populational diversity of this perennial high-protein forage plant suitable for cultivation in extreme conditions. Here, we present the complete and annotated chloroplast genome of this important wild resource plant. <italic>V. sepium</italic> chloroplast genome includes 76 protein-coding genes, 29 tRNA genes, 4 rRNA genes, and 1 pseudogene. Its 124,095 bp sequence has a loss of one inverted repeat (IR). The GC content of the whole genome, the protein-coding, intron, tRNA, rRNA, and intergenic spacer regions was 35.0%, 36.7%, 34.6%, 52.3%, 54.2%, and 29.2%, respectively. Comparative analyses with plastids from related genera belonging to Fabeae demonstrated that the greatest variation in the <italic>V. sepium</italic> genome length occurred in protein-coding regions. In these regions, some genes and introns were lost or gained; for example, <italic>ycf4</italic>, <italic>clpP</italic> intron, and <italic>rpl16</italic> intron deletions and <italic>rpl20</italic> and <italic>ORF292</italic> insertions were observed. Twelve highly divergent regions, 66 simple sequence repeats (SSRs) and 27 repeat sequences were also found in these regions. Detailed evolutionary rate analysis of protein-coding genes showed that <italic>Vicia</italic> species exhibit additional interesting characteristics including positive selection of <italic>ccsA</italic>, <italic>clpP</italic>, <italic>rpl32</italic>, <italic>rpl33</italic>, <italic>rpoC1</italic>, <italic>rps15</italic>, <italic>rps2, rps4</italic>, and <italic>rps7</italic>, and the evolutionary rates of <italic>atpA</italic>, <italic>accD</italic>, and <italic>rps2</italic> in <italic>Vicia</italic> are significantly accelerated. These genes are important candidate genes for understanding the evolutionary strategies of <italic>Vicia</italic> and other genera in Fabeae. The phylogenetic analysis showed that <italic>Vicia</italic> and <italic>Lens</italic> are included in the same clade and that <italic>Vicia</italic> is paraphyletic. These results provide evidence regarding the evolutionary history of the chloroplast genome.</p>