Comparative Analyses of 35 Complete Chloroplast Genomes from the Genus <i>Dalbergia</i> (Fabaceae) and the Identification of DNA Barcodes for Tracking Illegal Logging and Counterfeit Rosewood
The genus <i>Dalbergia</i> contains more than 200 species, several of which are trees that produce traditional medicines and extremely high-value timber commonly referred to as rosewood. Due to the rarity of these species in the wild, the high value of the timber, and a growing internati...
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MDPI AG
2022-04-01
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| Online Access: | https://www.mdpi.com/1999-4907/13/4/626 |
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| author | Zhou Hong Wenchuang He Xiaojing Liu Luke R. Tembrock Zhiqiang Wu Daping Xu Xuezhu Liao |
| author_facet | Zhou Hong Wenchuang He Xiaojing Liu Luke R. Tembrock Zhiqiang Wu Daping Xu Xuezhu Liao |
| author_sort | Zhou Hong |
| collection | DOAJ |
| description | The genus <i>Dalbergia</i> contains more than 200 species, several of which are trees that produce traditional medicines and extremely high-value timber commonly referred to as rosewood. Due to the rarity of these species in the wild, the high value of the timber, and a growing international illicit trade, CITES (Convention on International Trade in Endangered Species of Wild Fauna and Flora) has listed the entire genus in appendix II and the species <i>Dalbergia nigra</i> in appendix I because species in this genus are considered at risk of extinction. Given this, and the fact that species or even genus level determination is nearly impossible from cut timber morphology, alternative molecular methods are needed to identify and track intercepted rosewood. To better identify rosewood using molecular methods, we sequenced and assembled eight chloroplast genomes including <i>D. nigra</i> as well as conducted comparative analyses with all other available chloroplast genomes in <i>Dalbergia</i> and closely related lineages. From these analyses, numerous repeats including simple sequence repeats (SSR) and conserved nucleotide polymorphisms unique to subclades within the genus were detected. From phylogenetic analysis based on the CDS from 77 chloroplast genes, the groups Siam rosewood and scented rosewood resolved as monophyletic, supporting the morphological traits used to delimit these species. In addition, several instances of paraphyly and polyphyly resulting from mismatches between taxonomic determinations and phylogenetic tree topology were identified. Ultimately, the highly variable regions in the chloroplast genomes will provide useful plastid markers for further studies regarding the identification, phylogeny, and population genetics of <i>Dalbergia</i> species, including those frequently intercepted in illegal trade. |
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| last_indexed | 2024-03-10T04:09:15Z |
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| spelling | doaj.art-7b6568e5c2604deea66442f30e5509fc2023-11-23T08:15:05ZengMDPI AGForests1999-49072022-04-0113462610.3390/f13040626Comparative Analyses of 35 Complete Chloroplast Genomes from the Genus <i>Dalbergia</i> (Fabaceae) and the Identification of DNA Barcodes for Tracking Illegal Logging and Counterfeit RosewoodZhou Hong0Wenchuang He1Xiaojing Liu2Luke R. Tembrock3Zhiqiang Wu4Daping Xu5Xuezhu Liao6State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, ChinaShenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, ChinaState Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, ChinaDepartment of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USAShenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, ChinaState Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, ChinaShenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, ChinaThe genus <i>Dalbergia</i> contains more than 200 species, several of which are trees that produce traditional medicines and extremely high-value timber commonly referred to as rosewood. Due to the rarity of these species in the wild, the high value of the timber, and a growing international illicit trade, CITES (Convention on International Trade in Endangered Species of Wild Fauna and Flora) has listed the entire genus in appendix II and the species <i>Dalbergia nigra</i> in appendix I because species in this genus are considered at risk of extinction. Given this, and the fact that species or even genus level determination is nearly impossible from cut timber morphology, alternative molecular methods are needed to identify and track intercepted rosewood. To better identify rosewood using molecular methods, we sequenced and assembled eight chloroplast genomes including <i>D. nigra</i> as well as conducted comparative analyses with all other available chloroplast genomes in <i>Dalbergia</i> and closely related lineages. From these analyses, numerous repeats including simple sequence repeats (SSR) and conserved nucleotide polymorphisms unique to subclades within the genus were detected. From phylogenetic analysis based on the CDS from 77 chloroplast genes, the groups Siam rosewood and scented rosewood resolved as monophyletic, supporting the morphological traits used to delimit these species. In addition, several instances of paraphyly and polyphyly resulting from mismatches between taxonomic determinations and phylogenetic tree topology were identified. Ultimately, the highly variable regions in the chloroplast genomes will provide useful plastid markers for further studies regarding the identification, phylogeny, and population genetics of <i>Dalbergia</i> species, including those frequently intercepted in illegal trade.https://www.mdpi.com/1999-4907/13/4/626forensic biologyphylogenyCITESendangered speciesforest conservation |
| spellingShingle | Zhou Hong Wenchuang He Xiaojing Liu Luke R. Tembrock Zhiqiang Wu Daping Xu Xuezhu Liao Comparative Analyses of 35 Complete Chloroplast Genomes from the Genus <i>Dalbergia</i> (Fabaceae) and the Identification of DNA Barcodes for Tracking Illegal Logging and Counterfeit Rosewood Forests forensic biology phylogeny CITES endangered species forest conservation |
| title | Comparative Analyses of 35 Complete Chloroplast Genomes from the Genus <i>Dalbergia</i> (Fabaceae) and the Identification of DNA Barcodes for Tracking Illegal Logging and Counterfeit Rosewood |
| title_full | Comparative Analyses of 35 Complete Chloroplast Genomes from the Genus <i>Dalbergia</i> (Fabaceae) and the Identification of DNA Barcodes for Tracking Illegal Logging and Counterfeit Rosewood |
| title_fullStr | Comparative Analyses of 35 Complete Chloroplast Genomes from the Genus <i>Dalbergia</i> (Fabaceae) and the Identification of DNA Barcodes for Tracking Illegal Logging and Counterfeit Rosewood |
| title_full_unstemmed | Comparative Analyses of 35 Complete Chloroplast Genomes from the Genus <i>Dalbergia</i> (Fabaceae) and the Identification of DNA Barcodes for Tracking Illegal Logging and Counterfeit Rosewood |
| title_short | Comparative Analyses of 35 Complete Chloroplast Genomes from the Genus <i>Dalbergia</i> (Fabaceae) and the Identification of DNA Barcodes for Tracking Illegal Logging and Counterfeit Rosewood |
| title_sort | comparative analyses of 35 complete chloroplast genomes from the genus i dalbergia i fabaceae and the identification of dna barcodes for tracking illegal logging and counterfeit rosewood |
| topic | forensic biology phylogeny CITES endangered species forest conservation |
| url | https://www.mdpi.com/1999-4907/13/4/626 |
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