Characterization of the complete chloroplast genome sequences of six <i>Dalbergia</i> species and its comparative analysis in the subfamily of Papilionoideae (Fabaceae)

Abstract

<i>Dalbergia</i> spp. are numerous and widely distributed in pantropical areas in Asia, Africa and America, and most of the species have important economic and ecological value as precious timber. In this study, we determined and characterized six complete chloroplast genomes of <i>Dalbergia</i> species (<i>Dalbergia obtusifolia</i>, <i>D. hupeana</i>, <i>D. mimosoides</i>, <i>D. sissoo</i>, <i>D. hancei</i>, <i>D. balansae</i>), which displayed the typical quadripartite structure of angiosperms. The sizes of the genomes ranged from 155,698 bp (<i>D. hancei</i>) to 156,419 bp (<i>D. obtusifolia</i>). The complete chloroplast genomes of <i>Dalbergia</i> include 37 tRNA genes, eight rRNA genes and 84 protein-coding genes. We analysed the sequence diversity of <i>Dalberigia</i> chloroplast genomes coupled with previous reports. The results showed 12 noncoding regions (<i>rps16-accD</i>, <i>trnR-UCU-trnG-UCC</i>, <i>ndhE-ndhG</i>, <i>trnG-UCC-psbZ</i>, <i>rps8-rpl14</i>, <i>trnP-UGG-psaJ</i>, <i>ndhH-rps15</i>, <i>trnQ-UUG-rps16</i>, <i>trnS-GCU-psbI</i>, <i>rps12-clpP</i>, <i>psbA-trnK-UUU</i>, t<i>rnK-UUU-intron)</i>, and four coding regions (<i>rps16</i>, <i>ycf1</i>, <i>rps15</i> and <i>ndhF</i>) showed many nucleotide variations that could be used as potential molecular markers. Based on a site-specific model, we analysed the selective pressure of chloroplast genes in <i>Dalbergia</i> species. Twenty-two genes with positively selected sites were detected, involving the photosynthetic system (<i>ndhC</i>, <i>adhD</i>, <i>ndhF</i>, <i>petB</i>, <i>psaA</i>, <i>psaB</i>, <i>psbB</i>, <i>psbC</i>, <i>psbK</i> and <i>rbcL</i>), self-replication category of genes (<i>rpoA</i>, <i>rpoC2</i>, <i>rps3</i>, <i>rps12</i> and <i>rps18</i>) and others (<i>accD</i>, <i>ccsA</i>, <i>cemA</i>, <i>clpP</i>, <i>matK</i>, <i>ycf1 and ycf2</i>). Additionally, we identified potential RNA editing sites that were relatively conserved in the genus <i>Dalbergia</i>. Furthermore, the comparative analysis of cp genomes of Dalbergieae species indicated that the boundary of IRs/SSC was highly variable, which resulted in the size variation of cp genomes. Finally, phylogenetic analysis showed an inferred phylogenetic tree of Papilionoideae species with high bootstrap support and suggested that Amorpheae was the sister of the clade Dalbergieae. Moreover, three genera of the <i>Pterocarpus</i> clade showed a nested evolutionary relationship. These complete cp genomes provided valuable information for understanding the genetic variation and phylogenetic relationship of <i>Dalbergia</i> species with their relatives.