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DNA Barcoding of the Cymbidium Species (Orchidaceae) in Thailand

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DNA Barcoding of the Cymbidium Species (Orchidaceae) in Thailand ` African Journal of Agricultural Research Vol. 7(3), pp. 393-404, 19 January, 2012 Available online at http://www.academicjournals.org/AJAR DOI: 10.5897/AJAR11.1434 ISSN 1991-637X ©2012 Academic Journals Full Length Research Paper DNA barcoding of the Cymbidium species (Orchidaceae) in Thailand Pornarong SIRIPIYASING1, Kobsukh KAENRATANA2, Piya MOKKAMUL3, Tawatchai TANEE4, Runglawan SUDMOON1 and Arunrat CHAVEERACH1* 1Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand. 2Pakkret Floriculture Company, 46/6 Moo 1, Tiwanond Road, Bangplud Subdistrict, Pakkret District, Nonthaburi 11120, Thailand. 3Department of Biology, Faculty of Science, Mahasarakham Rajabhat University, Mahasarakham 44000, Thailand. 4Faculty of Environment and Resource Studies, Mahasarakham University, Mahasarakham 44000, Thailand. Accepted 28 November, 2011 The objective of the research is to achieve molecular markers for an economical, ornamental plant group in agriculture worldwide. These plants, Cymbidium aloifolium, Cymbidium atropurpureum, Cymbidium bicolor, Cymbidium chloranthum, Cymbidium dayanum, Cymbidium devonianum, Cymbidium ensifolium, Cymbidium finlaysonianum, Cymbidium haematodes, Cymbidium insigne, Cymbidium lancifolium, Cymbidium lowianum, Cymbidium mastersii, Cymbidium munronianum, Cymbidium rectum, Cymbidium roseum, Cymbidium sinense, Cymbidium tigrinum, and Cymbidium tracyanum in Thailand have been explored, collected and identified. DNA barcoding for a species specific marker was performed in order to provide further rapid, accurate, and automatable species identification for plants lacking flowers or having incomplete morphological characteristics and for the young plants that are massively grown on orchid cutting flower farms. The sequences of four standard regions as barcodes were tested for genetic distances. The genetic distances, means nucleotide variations in tag sequences based on rpoB, rpoC1, matK, and trnH-psbA spacer region sequences of the 19 species ranging from 0.012 to 0.546, 0.018 to 0.546, 0.052 to 0.385, and 0.026 to 0.528, respectively. DNA barcoding shows promise for molecular-based identification of Cymbidium species. The sequences have been deposited in GenBank. Key words: Cymbidium, matK, rpoB, rpoC1, species diversity, trnH-psbA. INTRODUCTION Cymbidium Sw. is a popular group of orchids with 2006). Cymbidium haematodes Lindl. was once classified significant commercial importance. Their flowers can to be a subspecies of Cymbidium ensifolium (L.) Sw. by come in all shades of colors with varying attractive Du Puy and Cribb (1988). Currently, it is recognized as a shapes, and can be of long lasting quality and of large species, Cymbidium haematodes by Liu et al. (2009). size (Obara-Okeyo and Kako, 1998). The members of Also, Cymbidium siamense Rolfe and Downie was this genus have a range of distribution from Northwest rearranged to be C. ensifolium by Du Puy and Cribb India to China and Japan, south through the Malay (1988), but was included to be C. haematodes by Liu et Peninsula to Northern and Eastern Australia (Choi et al., al. (2009). Many people have reported that 20 Cymbidium species can be found in Thailand. They are namely Cymbidium aloifolium (L.) Sw., Cymbidium atropurpureum (Lindl.) Rolfe, C. bicolor Lindl., Cymbidium *Corresponding author. E-mail: [email protected]. Tel: 66 chloranthum Lindl., Cymbidium cyperifolium . and Lindl., 4334-2908. Fax: 66 4336-4169. Cymbidium dayanum Rchb.f., Cymbidium devonianum ` 394 Afr. J. Agric. Res. Paxton., C. ensifolium (L.) Sw., Cymbidium sequence analysis. The DNA barcoding was done following rpoB, finlaysonianum Lindl., Cymbidium insigne Rolfe, rpoC1, matK, and trnH-psbA spacer regions allowing for two Cymbidium lancifolium Hook., Cymbidium lowianum options: Rchb.f., Cymbidium macrorhizon Lindl., Cymbidium 1) rpoC1, matK, and trnH-psbA spacer regions, and mastersii Griffith and Lindl., Cymbidium rectum Ridl., 2) rpoB, matK, and trnH-psbA spacer regions following Chase et al. Cymbidium roseum J.J. Sm., Cymbidium sinense (Jacks) (2007). Willd.,Cymbidium tigrinum Parish and Hook., Cymbidium tracyanum L. Castle, Cymbidium wadae Yukawa DNA extraction (Vaddhanaphuti, 1992; Thaithong, 2000; Yukawa, 2002; Sitthisatjadham, 2006; Kaenratana, 2009). Total genomic DNA was extracted using the Plant Genomic DNA DNA barcoding is a popular method for species Extraction Kit (RBC Bioscience). Extracted DNA was run on a 0.8% identification that can be used in samples which have a agarose gel electrophoresis stained with ethidium bromide. The short region of reliable DNA or even in those samples quality and quantity of DNA samples were determined by a gel that have highly degraded DNA such as those found in documenting instrument. DNA samples were diluted to a final concentration of 20 ng/µl, and these dilutions were used as DNA processed foods, in fossil remains, or herbarium templates in the PCR reactions. specimens. However, Taberlet et al. (2006) have claimed that this study in most cases only allows for the identification of specimens to a family, but does not allow DNA barcode amplification for the identification of genera or species. Nevertheless, there have been many studies of the DNA barcoding in For DNA barcoding of the species-specific samples quoted earlier, PCR were performed using primer pairs 5′- plants (Hebert et al., 2003). Since then there have been AAGTGCATTGTTGGAACTGG-3′ and 5′- many studies that have tested standard regions in plant CCGTATGTGAAAAGAAGTATA-3′ of rpoB, 5′- groups aiming to provide rapid, accurate, and GTGGATACACTTCTTGATAATGG-3′ and 5′- automatable species identification by using a TGAGAAAACATAAGTAAACGGGC-3′ of rpoC1, 5′- standardized DNA region as a tag (Hebert et al., 2005). TAATTTACGATCAATTCATTC-3′ and 5′- GTTCTAGCACAAGAAAGTCG-3′ of matK, and 5′- Chase et al. (2007) proposed to use two options, the GTTATGCATGAACGTAATGCTC-3′ and 5′- three regions combined for a standard protocol for CGCGCATGGTGGATTCACAATCC-3′ of trnH-psbA barcoding all land plants namely rpoB, rpoC1, matK, and (http://www.kew.org/barcoding/update.html; 28 January 2009). The trnH-psbA spacer regions. Newmaster et al. (2008) reaction mixture was done in 25 l consisting of GoTaq Green proposed to use matK and trnH-psbA to identify plants in Master mix (Promega), 0.25 μM each primer, and 10 ng DNA Myristicaceae. template. The reaction mixture was incubated at 94°C for 1 min and amplification was performed with the following thermal cycles: 35 Finally, Hollingsworth et al. (2009) at the Consortium cycles of denaturation for 30 s at 94°C, 40 s annealing temperature for the Barcode of Life (CBOL), the plant working group, at 53°C, 40 s extension at 72°C, and 5 min final extension at 72°C. recommended rbcL and matK to be used as the core The amplified products were detected by 1.2% agarose gel DNA barcode for land plants. We performed DNA electrophoresis in TAE buffer and were visualized with ethidium barcoding on species of the genus Cymbidium in bromide staining. Thailand. DNA barcodes with rpoB, rpoC1, matK, and trnH-psbA spacer regions of each species were DNA sequence analysis performed to further test rapid, accurate, and automatable species identification in the plants that lack The amplified specific fragments of the studied samples were flowers or have incomplete morphological characteristics sequenced and the sequences were submitted to the GenBank and in immature plants. database. Sequence alignment was done by using MEGA software Version 5 (Tamura et al., 2011) and the genetic distances were calculated by this software. MATERIALS AND METHODS RESULTS Plant materials Cymbidium species were explored, collected and identified Investigation and identification following Du Puy and Cribb (1988), Kaenratana (2009), and Liu et al. (2009). Short descriptions are given and photos are All Cymbidium species are used ornamentally. From the demonstrated. Voucher specimens were prepared and kept at BK. investigation, 19 species were identified. The total number of voucher specimens has been deposited at BK Molecular performing as collector numbers A. Chaveerach 701 to 719. The list of taxa and GenBank accession numbers are shown in All collected samples were field grown and were studied with DNA Table 1. Concise descriptions including short morpho- extraction, DNA barcoding amplification, and DNA barcoding logical characteristics, habits, habitats, and distribution ` Siripiyasing et al. 395 Table 1. GenBank accession numbers of the four barcoding regions of all studied Cymbidium species. GenBank accession no. Plants Voucher number rpoB rpoC1 mat K trnH - psbA C. aloifolium A. Chaveerach 701 HM137074 HM053600 HM137055 FJ527771 C. atropurpureum A. Chaveerach 702 HM137080 HM053606 HM137061 HM008994 C. bicolor A. Chaveerach 703 HM137066 GU990532 GU990531 FJ527762 C. chloranthum A. Chaveerach 704 HM137065 HM053592 HM137047 FJ527761 C. dayanum A. Chaveerach 705 HM137064 HM053591 HM137046 FJ527760 C. devonianum A. Chaveerach 706 HM137072 HM053598 HM137053 FJ527769 C. ensifolium A. Chaveerach 707 HM137069 HM053595 HM137050 FJ527765 C. finlaysonianum A. Chaveerach 708 HM137067 HM053593 HM137048 FJ527763 C. haematodes A. Chaveerach 709 HM137082 HM053608 HM137063 HM008996 C. haematodes (C. siamense) A. Chaveerach 709 JN412744 JN412743 JN412742 JN412741 C. insigne A. Chaveerach 710 HM137071 HM053597 HM137052 FJ527768 C. lancifolium A. Chaveerach 711 HM137077 HM053603 HM137058 HM008991 C. lowianum A. Chaveerach 712 HM137076 HM053602 HM137057 HM008990 C. mastersii A.
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