Abstract
Lack of complete genomic information concerning Vicia sepium (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. V. sepium 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 V. sepium genome length occurred in protein-coding regions. In these regions, some genes and introns were lost or gained; for example, ycf4, clpP intron, and rpl16 intron deletions and rpl20 and ORF292 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 Vicia species exhibit additional interesting characteristics including positive selection of ccsA, clpP, rpl32, rpl33, rpoC1, rps15, rps2, rps4, and rps7, and the evolutionary rates of atpA, accD, and rps2 in Vicia are significantly accelerated. These genes are important candidate genes for understanding the evolutionary strategies of Vicia and other genera in Fabeae. The phylogenetic analysis showed that Vicia and Lens are included in the same clade and that Vicia is paraphyletic. These results provide evidence regarding the evolutionary history of the chloroplast genome.
Highlights
Complete chloroplast sequences are indispensable for analyzing genome evolution and phylogenetics (Sabir et al, 2014; Moner et al, 2018)
The results showed that the nucleotide variability rate ranged from 0.001 to 0.248 (L. sativus vs C. arietinum)
Upon comparing the four neighbor joining (NJ) trees, we found that V. sepium, V. sativa, and V. faba were located in the same evolutionary branch with support rates of 100% in the protein-coding sequence tree, 99% in the matK tree, and 49% in the rbcL tree
Summary
Complete chloroplast sequences are indispensable for analyzing genome evolution and phylogenetics (Sabir et al, 2014; Moner et al, 2018) These sequences offer two advantages over genomic ones, namely, a high degree of conservation and a relatively compact gene alignment, resulting from symbiotic horizontal transfer (Timmis et al, 2004). That is not to say that we oppose the use of one or a few genes in evolutionary studies, but we instead suggest the investigation of conflicts between complete chloroplast genomes and analyses of one or a few genes that may indicate crucial evolutionary events Another advantage of the chloroplast genome is that it contributes to structural diversity at low taxonomic levels and among basal lineages. With the development of high-throughput sequencing, more than 800 complete chloroplast genomes have been made available in the National Center for Biotechnology Information (NCBI) database (Asaf et al, 2017a)
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