Characterization and Phylogenetic Analyses of the Complete Chloroplast Genome Sequence in <i>Arachis</i> Species
Xiaona Yu | Tianzhu Liang | Yi Guo | Yan Liang | Xiaoxia Zou | Tong Si | Yu Ni | Xiaojun Zhang
Peanut is an important oilseed and a widely cultivated crop worldwide. Knowledge of the phylogenetic relationships and information on the chloroplast genomes of wild and cultivated peanuts is crucial for the evolution of peanuts. In this study, we sequenced and assembled 14 complete chloroplast genomes of <i>Arachis</i>. The total lengths varied from 156,287 bp to 156, 402 bp, and the average guanine–cytosine content was 36.4% in 14 <i>Arachis</i> species. A total of 85 simple sequence repeats (SSRs) loci were detected, including 3 dinucleotide and 82 polynucleotide SSRs. Based on 110 complete chloroplast genomes of <i>Arachis</i>, a phylogenetic tree was constructed, which was divided into two groups (I and II). A total of 79 different genes were identified, of which six double-copy genes (<i>ndhB</i>, <i>rpl2</i>, <i>rpl23</i>, <i>rps7</i>, <i>ycf1</i>, and <i>ycf2</i>) and one triple-copy gene (<i>rps12</i>) are present in all 14 <i>Arachis</i> species, implying that these genes may be critical for photosynthesis. The dN/dS ratios for four genes (<i>rps18</i>, <i>accD</i>, <i>clpP</i>, <i>ycf1</i>) were larger than 1, indicating that these genes are subject to positive selection. These results not only provided rich genetic resources for molecular breeding but also candidate genes for further functional gene research.
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