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

Abstract

Dalbergia 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 Dalbergia species (Dalbergia obtusifolia, D. hupeana, D. mimosoides, D. sissoo, D. hancei, D. balansae), which displayed the typical quadripartite structure of angiosperms. The sizes of the genomes ranged from 155,698 bp (D. hancei) to 156,419 bp (D. obtusifolia). The complete chloroplast genomes of Dalbergia include 37 tRNA genes, eight rRNA genes and 84 protein-coding genes. We analysed the sequence diversity of Dalberigia chloroplast genomes coupled with previous reports. The results showed 12 noncoding regions (rps16-accD, trnR-UCU-trnG-UCC, ndhE-ndhG, trnG-UCC-psbZ, rps8-rpl14, trnP-UGG-psaJ, ndhH-rps15, trnQ-UUG-rps16, trnS-GCU-psbI, rps12-clpP, psbA-trnK-UUU, trnK-UUU-intron), and four coding regions (rps16, ycf1, rps15 and ndhF) 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 Dalbergia species. Twenty-two genes with positively selected sites were detected, involving the photosynthetic system (ndhC, adhD, ndhF, petB, psaA, psaB, psbB, psbC, psbK and rbcL), self-replication category of genes (rpoA, rpoC2, rps3, rps12 and rps18) and others (accD, ccsA, cemA, clpP, matK, ycf1 and ycf2). Additionally, we identified potential RNA editing sites that were relatively conserved in the genus Dalbergia. 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 Pterocarpus clade showed a nested evolutionary relationship. These complete cp genomes provided valuable information for understanding the genetic variation and phylogenetic relationship of Dalbergia species with their relatives.

Comparative chloroplast genome analysis of Ficus (Moraceae): Insight into adaptive evolution and mutational hotspot regions

“…Hence, positive selection in this gene may help explain the radiation of Ficus into diverse ecological niches. The rbcL gene, which is a photosynthesis-related gene encoding the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), is commonly under positive selection in terrestrial plants but not in algae ( Kapralov and Filatov, 2007 ; Li et al, 2022 ), possibly due to more unstable thermal regimes on land ( Kapralov and Filatov, 2007 ). For example, rbcL is under positive selection in shade-tolerant Oryza species, probably in response to adaptive evolution associated with sunlight and thermal conditions ( Gao et al, 2019b ).…”

Chloroplast genome structure analysis of Equisetum unveils phylogenetic relationships to ferns and mutational hotspot region

“…During our analysis were subjected to positive selection of 12 plastid genes ( rpoB, ycf1, psaA, psaM, psbH, psbD, rbcL, ndhF, matK, accD, rps18 and ycf2 ), indicating that they may have contributed to environmental adaptation in Equisetum . Remarkably, the photosynthesis-related gene rbcL encoding the RuBisco’s large subunit, which displayed particularly pronounced indications, is commonly under positive selection in terrestrial plants but not in water plant ( Li et al., 2022 ), possibly due to more unstable thermal regimes on land ( Kapralov and Filatov, 2007 ). In this study, we collected Equisetum from habitats with diverse sunlight exposure, and thus rbcL may be probably in response to adaptive evolution associated with sunlight and thermal conditions.…”

Thirteen complete chloroplast genomes of the costaceae family: insights into genome structure, selective pressure and phylogenetic relationships

“…Lastly, ycf1 encodes unknown proteins and is competent in identification at genus and species level of orchids [ 46 ]. Recent studies have revealed that these eight genes with positive selection in flowering plants are common [ 27 – 31 , 33 , 35 , 47 , 48 ]. For example, ndhF has been reported as a positive selection in the Aroideae species [ 30 ]; clpP and ycf1 have been reported as positive selections in the Polystachya species [ 31 ]; ndhA and clpP have been reported as positive selections in the Hoya species [ 35 ]; ndhA , clpP , rps12 and ycf1 have been reported as positive selections in the Zingiber species [ 33 , 47 ]; and cemA , clpP , ndhF , petB , rps12 and ycf1 have been reported as positive selections in the Dalbergia species [ 48 ].…”

“…Recent studies have revealed that these eight genes with positive selection in flowering plants are common [ 27 – 31 , 33 , 35 , 47 , 48 ]. For example, ndhF has been reported as a positive selection in the Aroideae species [ 30 ]; clpP and ycf1 have been reported as positive selections in the Polystachya species [ 31 ]; ndhA and clpP have been reported as positive selections in the Hoya species [ 35 ]; ndhA , clpP , rps12 and ycf1 have been reported as positive selections in the Zingiber species [ 33 , 47 ]; and cemA , clpP , ndhF , petB , rps12 and ycf1 have been reported as positive selections in the Dalbergia species [ 48 ]. Among the analyzed species of Costaceae, they possessed diversity of ecological habitats, such as shade under the woods, forest margins, moist places in valleys, roadsides and ditch sides [ 1 , 7 ].…”