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Wu HY, Wong KH, Kong BLH, Siu TY, But GWC, Tsang SSK, Lau DTW, Shaw PC. Comparative Analysis of Chloroplast Genomes of Dalbergia Species for Identification and Phylogenetic Analysis. PLANTS 2022; 11:plants11091109. [PMID: 35567110 PMCID: PMC9104903 DOI: 10.3390/plants11091109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/12/2022] [Accepted: 04/12/2022] [Indexed: 11/16/2022]
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.
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Affiliation(s)
- Hoi-Yan Wu
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China; (H.-Y.W.); (B.L.-H.K.)
| | - Kwan-Ho Wong
- Shiu-Ying Hu Herbarium, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China; (K.-H.W.); (T.-Y.S.); (D.T.-W.L.)
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China; (G.W.-C.B.); (S.S.-K.T.)
| | - Bobby Lim-Ho Kong
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China; (H.-Y.W.); (B.L.-H.K.)
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China; (G.W.-C.B.); (S.S.-K.T.)
| | - Tin-Yan Siu
- Shiu-Ying Hu Herbarium, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China; (K.-H.W.); (T.-Y.S.); (D.T.-W.L.)
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Grace Wing-Chiu But
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China; (G.W.-C.B.); (S.S.-K.T.)
| | - Stacey Shun-Kei Tsang
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China; (G.W.-C.B.); (S.S.-K.T.)
| | - David Tai-Wai Lau
- Shiu-Ying Hu Herbarium, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China; (K.-H.W.); (T.-Y.S.); (D.T.-W.L.)
| | - Pang-Chui Shaw
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China; (H.-Y.W.); (B.L.-H.K.)
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China; (G.W.-C.B.); (S.S.-K.T.)
- State Key Laboratory of Research on Bioactivities and Clinical Applications of Medicinal Plants (The Chinese University of Hong Kong) and Institute of Chinese Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Correspondence:
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Development of Genomic SSR for the Subtropical Hardwood Tree Dalbergia hupeana and Assessment of Their Transferability to Other Related Species. FORESTS 2021. [DOI: 10.3390/f12060804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Dalbergia hupeana Hance (D. hupeana) is a precious hardwood tree of the genus Dalbergia. It is one of the few species widely distributed within subtropical areas and is important for timber production and forest restoration. At present, there is little published genetic information on D. hupeana. Therefore, we performed a genome survey using next generation sequencing (NGS) and developed a set of novel genomic SSR (gSSR) markers from the assembled data, and assessed the transferability of these markers to other Dalbergia species in Asia. The results of the genome survey show the genome size of D. hupeana to be about 664 Mb and highly heterozygous. The assembly of sequencing data produced 2,431,997 contigs, and the initial assembly of the NGS data alone resulted in contig N50 of 393 kb with a total of 720 Mb. A total of 127,742 perfect SSR markers were found in the assembled contigs. A total of 37 highly polymorphic and easily genotyped gSSR markers were developed in D. hupeana, while the majority of gSSR markers could be successfully transferred to nine other Dalbergia species in Asia. The transferability rate of gSSR markers was highest in D. balansae, which is more closely related to D. hupeana. Seven gSSR markers were able to be amplified in all tested species. In addition, a preliminary assessment of the genetic diversity of three tree species in the Dalbergia genus suggested a high level of genetic diversity within populations distributed in the subtropical area in China. However, the determination of the global status of their genetic variation still requires further and more comprehensive assessment. Our findings will enable further studies on the genetic diversity, phylogenetics, germplasm characterization, and taxonomy of various Dalbergia species.
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Moraes BÁLCDE, Borges DB, Souza-Alves JP, Boubli JP, Bezerra B. Microsatellite Markers for Bearded Capuchins (Sapajus libidinosus): Transferability and Characterization. AN ACAD BRAS CIENC 2021; 93:e20190802. [PMID: 33470383 DOI: 10.1590/0001-3765202120190802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 11/07/2019] [Indexed: 11/22/2022] Open
Abstract
Natural Sapajus libidinosus populations are in continuous decline due to fragmentation, habitat loss, and the illegal pet trade. They live in Caatinga scrub forests, which already lost over 50% of their original cover. The lack of studies on S. libidinosus population genetics means that we do not know how they are being affected by this striking habitat loss and other anthropogenic disturbances. Polymorphic markers are not available for the study of S. libidinosus diversity and population genetics. Thus, here we aimed to test the transferability of 14 microsatellite markers to S. libidinosus. These microsatellites were previously isolated from Cebus capucinus (white-faced capuchin), species belonging to the same subfamily (Cebinae) as the study species. We found that six of the tested microsatellite markers (tetra-nucleotide) were cross-amplified in our target species. All loci were polymorphic. The number of alleles varied from 4 to 7, and the expected heterozygosity ranged from 0.588 to 0.869. The microsatellite markers transferred to S. libidinosus and characterised in our study will be valuable tools to evaluate the genetic variability of both wild and captive populations. They will considerably reduce the costs of microsatellite isolations, helping to prioritise currently limited research and conservation budgets in Brazil.
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Affiliation(s)
- BÁrbara L C DE Moraes
- Universidade Federal de Pernambuco, Programa de Pós-Graduação em Biologia Animal, Laboratório de Ecologia Comportamento e Conservação, Departamento de Zoologia, Centro de Biociências, Av. Prof. Moraes Rego, 1235, Cidade Universitária, 50670-901 Recife, PE, Brazil.,University of Salford, School of Environment and Life Sciences, Peel Building, Salford Western Gateway, Salford M5 4WX, United Kingdom
| | - Daniela B Borges
- Universidade Estadual de Santa Cruz, Laboratório de Marcadores Moleculares, Departamento de Biologia, Campus Soane Nazaré de Andrade, Rodovia Ilhéus-Itabuna, s/n, Km 16, 45662-900 Ilhéus, BA, Brazil.,University of Salford, School of Environment and Life Sciences, Peel Building, Salford Western Gateway, Salford M5 4WX, United Kingdom
| | - JoÃo Pedro Souza-Alves
- Universidade Federal de Pernambuco, Programa de Pós-Graduação em Biologia Animal, Laboratório de Ecologia Comportamento e Conservação, Departamento de Zoologia, Centro de Biociências, Av. Prof. Moraes Rego, 1235, Cidade Universitária, 50670-901 Recife, PE, Brazil
| | - Jean Phillipe Boubli
- University of Salford, School of Environment and Life Sciences, Peel Building, Salford Western Gateway, Salford M5 4WX, United Kingdom
| | - Bruna Bezerra
- Universidade Federal de Pernambuco, Programa de Pós-Graduação em Biologia Animal, Laboratório de Ecologia Comportamento e Conservação, Departamento de Zoologia, Centro de Biociências, Av. Prof. Moraes Rego, 1235, Cidade Universitária, 50670-901 Recife, PE, Brazil
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Song Y, Zhang Y, Xu J, Li W, Li M. Characterization of the complete chloroplast genome sequence of Dalbergia species and its phylogenetic implications. Sci Rep 2019; 9:20401. [PMID: 31892714 PMCID: PMC6938520 DOI: 10.1038/s41598-019-56727-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 12/13/2019] [Indexed: 11/09/2022] Open
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.
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Affiliation(s)
- Yun Song
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, 100176, China
| | - Yongjiang Zhang
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, 100176, China
| | - Jin Xu
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, 100176, China
| | - Weimin Li
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, 100176, China
| | - MingFu Li
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, 100176, China.
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