Characterization of the complete chloroplast genome sequence of Dalbergia species and its phylogenetic implications

Yun Song,Jin Xu,Yongjiang Zhang,Weimin Li,Mingfu Li

doi:10.1038/s41598-019-56727-x

Yun Song, Jin Xu + Show 3 more

Open Access

https://doi.org/10.1038/s41598-019-56727-x

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Abstract

The pantropical plant genus Dalbergia comprises approximately 250 species, most of which have a high economic and ecological value. However, these species are among the most threatened due to illegal logging and the timber trade. To enforce protective legislation and ensure effective conservation of Dalbergia species, the identity of wood being traded must be accurately validated. For the rapid and accurate identification of Dalbergia species and assessment of phylogenetic relationships, it would be highly desirable to develop more effective DNA barcodes for these species. In this study, we sequenced and compared the chloroplast genomes of nine species of Dalbergia. We found that these chloroplast genomes were conserved with respect to genome size, structure, and gene content and showed low sequence divergence. We identified eight mutation hotspots, namely, six intergenic spacer regions (trnL-trnT, atpA-trnG, rps16-accD, petG-psaJ, ndhF-trnL, and ndhG-ndhI) and two coding regions (ycf1a and ycf1b), as candidate DNA barcodes for Dalbergia. Phylogenetic analyses based on whole chloroplast genome data provided the best resolution of Dalbergia, and phylogenetic analysis of the Fabaceae showed that Dalbergia was sister to Arachis. Based on comparison of chloroplast genomes, we identified a set of highly variable markers that can be developed as specific DNA barcodes.

Highlights

The pantropical plant genus Dalbergia comprises approximately 250 species, most of which have a high economic and ecological value
All the Dalbergia species are protected by international trade regulations under the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) Appendix II, among which 86 species are included in the Red List drawn up by the International Union for Conservation of Nature (IUCN)
On the basis of BLAST searches, the contigs mapped to D. odorifera chloroplast genome sequence were used for reconstructing the chloroplast genomes of the nine examined Dalbergia species

Summary

Introduction

The pantropical plant genus Dalbergia comprises approximately 250 species, most of which have a high economic and ecological value. Angiosperm chloroplast genomes typically range in size from 115 to 165 kb and contain approximately 130 genes, among which there are 80 protein-coding genes, four rRNA genes, and 30 tRNA genes Owing to their slower evolution than that of nuclear genomes, lack of recombination, and general uniparental inheritance, chloroplast genome sequences are a primary source of data for species identification and inferring plant phylogenies[13,14]. Most relevant studies have revealed that chloroplast genomes are characterized by distinct clusters of mutations, known as “hotspots,” or highly variable regions, which can serve as DNA markers for the accurate identification of plant species. We reasoned that a comparative study of the chloroplast genomes of Dalbergia species might provide potentially useful insights for developing DNA barcodes that could be applied to facilitate the reliable identification of these species

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