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

Changhong Li; Yu Liu; Furong Lin; Yongqi Zheng; Ping Huang

doi:10.7717/peerj.13570

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

PeerJ. 2022 Jul 1:10:e13570. doi: 10.7717/peerj.13570. eCollection 2022.

Authors

Changhong Li^#¹, Yu Liu^#^{1

2}, Furong Lin¹, Yongqi Zheng¹, Ping Huang¹

Affiliations

¹ State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.
² Key Laboratory of Resource Plant Innovation and Utilization, Institute of Subtropical Crops of Zhejiang Province, Zhejiang Academy of Agricultural Sciences, Wenzhou, Zhejiang, China.

^# Contributed equally.

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.

Keywords: Chloroplast genome; Dalbergia genus; Gene selective pressure; Phylogenetic relationship; Sequence diversity.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Dalbergia* / genetics
Fabaceae* / genetics
Genome, Chloroplast* / genetics
Photosynthesis
Phylogeny

Grants and funding

This work was supported by the National Natural Science Foundation of China (No.31761143002, No. 32071783) and Special Funds for the Laboratory of Forest Silviculture and Tree Cultivation, National Forestry and Grassland Administration (No. ZDRIF201713); we also thank plant material supports from National Center for Forestry and Grassland Genetic resources (Beijing, China). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.