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. 2022 Apr 20;11(9):1109.
doi: 10.3390/plants11091109.

Comparative Analysis of Chloroplast Genomes of Dalbergia Species for Identification and Phylogenetic Analysis

Hoi-Yan Wu  1 , Kwan-Ho Wong  2   3 , Bobby Lim-Ho Kong  1   3 , Tin-Yan Siu  2   4 , Grace Wing-Chiu But  3 , Stacey Shun-Kei Tsang  3 , David Tai-Wai Lau  2 , Pang-Chui Shaw  1   3   5
Affiliations

Comparative Analysis of Chloroplast Genomes of Dalbergia Species for Identification and Phylogenetic Analysis

Hoi-Yan Wu et al. Plants (Basel). .

Abstract

Dalbergia L.f. is a pantropical genus consisting of 269 species of trees, shrubs, and woody lianas. This genus is listed in CITES Appendices because of illegal logging and trafficking driven by the high economic value of its heartwood. Some species are also used medicinally. Species identification of Dalbergia timber and herbs is challenging but essential for CITES implementation. Molecular methods had been developed for some timber species, mostly from Madagascar and Southeast Asia, but medicinal species in south China were usually not included in those studies. Here, we sequenced and assembled the chloroplast genomes of five Dalbergia species native to Hong Kong, four of which are medicinal plants. Our aim is to find potential genetic markers for the identification of medicinal Dalbergia species based on divergence hotspots detected in chloroplast genomes after comparative and phylogenetic analysis. Dalbergia chloroplast genomes displayed the typical quadripartite structure, with the 50 kb inversion found in most Papilionoideae lineages. Their sizes and gene content are well conserved. Phylogenetic tree of Dalbergia chloroplast genomes showed an overall topology similar to that of ITS sequences. Four divergence hotspots (trnL(UAA)-trnT(UGU), ndhG-ndhI, ycf1a and ycf1b) were identified and candidate markers for identification of several Dalbergia species were suggested.

Keywords: Dalbergia; chloroplast genomes; molecular authentication; phylogenetic analysis.

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Conflict of interest statement

The authors declare no conflict of interest. The funders/donors had no role in the design of the study, in the collection, analyses, or interpretation of data, in the writing of the manuscript, or in the decision to publish the results.

Figures

Figure 1
Figure 1
Genome maps of the five Dalbergia chloroplast genomes.
Figure 2
Figure 2
Analysis of repeats in the five Dalbergia chloroplast genomes. (a) Number of SSRs in different regions of Dalbergia cp genomes. (b) Frequency of SSRs classified by the types of repeats. (c) Frequency of different SSR motifs. (d) Number of different types of long sequence repeats.
Figure 3
Figure 3
Comparison of the junction regions of the cp genomes of the five Dalbergia species. (JLB: junction between LSC and IRB; JSB: junction between SSC and IRB; JSA: junction between SSC and IRA; JLA: junction between LSC and IRA).
Figure 4
Figure 4
Sliding window analysis of 46 Dalbergia cp genomes.
Figure 5
Figure 5
Maximum likelihood tree of 46 chloroplast genomes of 26 Dalbergia species, with Glycine max as an outgroup. Species included in the phylogenetic study based on ITS sequences by Vatanparast et al. [15] were marked with an asterisk, followed by the clade number assigned in that study. ֍1: Extension of ycf68 gene. ֍2: Loss of ycf68 gene because of internal stop codon.
See this image and copyright information in PMC

References

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