DNA barcoding of endangered Paphiopedilum species (Orchidaceae) of Peninsular Malaysia
In this study, the efficacy of four DNA markers and their combinations (rbcL, matK, ITS, trnH-psbA) as barcode markers were tested across the endangered Paphiopedilum species from Peninsular Malaysia. Four species of Paphiopedilum were sampled and barcoded. The DNA barcodes reliabilities were evalua...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Magnolia Press
2019
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| Online Access: | http://psasir.upm.edu.my/id/eprint/79424/ http://psasir.upm.edu.my/id/eprint/79424/1/DNA%20barcoding%20of%20endangered%20Paphiopedilum%20species%20.pdf |
| _version_ | 1848858674947162112 |
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| author | Rajaram, Micheal Charles Yong, Christina Seok Yien Gansau, Jualang Azlan Go, Rusea |
| author_facet | Rajaram, Micheal Charles Yong, Christina Seok Yien Gansau, Jualang Azlan Go, Rusea |
| author_sort | Rajaram, Micheal Charles |
| building | UPM Institutional Repository |
| collection | Online Access |
| description | In this study, the efficacy of four DNA markers and their combinations (rbcL, matK, ITS, trnH-psbA) as barcode markers were tested across the endangered Paphiopedilum species from Peninsular Malaysia. Four species of Paphiopedilum were sampled and barcoded. The DNA barcodes reliabilities were evaluated using NCBI BLASTn program, phylogenetic tree via Neighbour-Joining method with 1000 bootstrap replicates in MEGA 6 and barcoding gap assessment. matK is the most promising barcode with high sequence quality (100%), high accuracy in BLASTn (100%), clear resolution of species in Neighbour-Joining phylogenetic tree (100%) and a distinct barcoding gap followed by ITS, trnH-psbA and rbcL. The combination of barcode regions revealed the lack of variation in rbcL and trnH-psbA but they are still useful for preliminary identification followed up by matK for accurate identification. |
| first_indexed | 2025-11-15T12:17:12Z |
| format | Article |
| id | upm-79424 |
| institution | Universiti Putra Malaysia |
| institution_category | Local University |
| language | English |
| last_indexed | 2025-11-15T12:17:12Z |
| publishDate | 2019 |
| publisher | Magnolia Press |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | upm-794242021-04-05T22:12:53Z http://psasir.upm.edu.my/id/eprint/79424/ DNA barcoding of endangered Paphiopedilum species (Orchidaceae) of Peninsular Malaysia Rajaram, Micheal Charles Yong, Christina Seok Yien Gansau, Jualang Azlan Go, Rusea In this study, the efficacy of four DNA markers and their combinations (rbcL, matK, ITS, trnH-psbA) as barcode markers were tested across the endangered Paphiopedilum species from Peninsular Malaysia. Four species of Paphiopedilum were sampled and barcoded. The DNA barcodes reliabilities were evaluated using NCBI BLASTn program, phylogenetic tree via Neighbour-Joining method with 1000 bootstrap replicates in MEGA 6 and barcoding gap assessment. matK is the most promising barcode with high sequence quality (100%), high accuracy in BLASTn (100%), clear resolution of species in Neighbour-Joining phylogenetic tree (100%) and a distinct barcoding gap followed by ITS, trnH-psbA and rbcL. The combination of barcode regions revealed the lack of variation in rbcL and trnH-psbA but they are still useful for preliminary identification followed up by matK for accurate identification. Magnolia Press 2019 Article PeerReviewed text en http://psasir.upm.edu.my/id/eprint/79424/1/DNA%20barcoding%20of%20endangered%20Paphiopedilum%20species%20.pdf Rajaram, Micheal Charles and Yong, Christina Seok Yien and Gansau, Jualang Azlan and Go, Rusea (2019) DNA barcoding of endangered Paphiopedilum species (Orchidaceae) of Peninsular Malaysia. Phytotaxa, 387 (2). pp. 94-104. ISSN 1179-3155; ESSN: 1179-3163 https://www.biotaxa.org/Phytotaxa/article/view/phytotaxa.387.2.2 10.11646/phytotaxa.387.2.2 |
| spellingShingle | Rajaram, Micheal Charles Yong, Christina Seok Yien Gansau, Jualang Azlan Go, Rusea DNA barcoding of endangered Paphiopedilum species (Orchidaceae) of Peninsular Malaysia |
| title | DNA barcoding of endangered Paphiopedilum species (Orchidaceae) of Peninsular Malaysia |
| title_full | DNA barcoding of endangered Paphiopedilum species (Orchidaceae) of Peninsular Malaysia |
| title_fullStr | DNA barcoding of endangered Paphiopedilum species (Orchidaceae) of Peninsular Malaysia |
| title_full_unstemmed | DNA barcoding of endangered Paphiopedilum species (Orchidaceae) of Peninsular Malaysia |
| title_short | DNA barcoding of endangered Paphiopedilum species (Orchidaceae) of Peninsular Malaysia |
| title_sort | dna barcoding of endangered paphiopedilum species (orchidaceae) of peninsular malaysia |
| url | http://psasir.upm.edu.my/id/eprint/79424/ http://psasir.upm.edu.my/id/eprint/79424/ http://psasir.upm.edu.my/id/eprint/79424/ http://psasir.upm.edu.my/id/eprint/79424/1/DNA%20barcoding%20of%20endangered%20Paphiopedilum%20species%20.pdf |