Phylogenetics of native conifer species in Vietnam based on two chloroplast gene regions rbcL and matK

Pham M.P., Tran V.H., Vu D.D., Nguyen Q.K., Shah S.N.M. (2021): Phylogenetics of native conifer species in Vietnam based on two chloroplast gene regions rbcL and matK. Czech J. Genet. Plant Breed., 57: 58−66.

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We used two chloroplast gene regions (matK and rbcL) as a tool for the identification of 33 local conifer species. All 136 sequences, 101 newly generated (14 species for gene matK; 16 species for gene rbcL) and 35 retrieved from the GenBank, were used in the analysis. The highest genetic distance (matK region) was recorded between the species in Cupressaceae with an average of 5% (0.1–8.5), Podocarpaceae with an average of 6% (0–8.5), Taxaceae with an average of 5% (0.2–0.5) and Pinaceae with an average of 20.4% (0.8–54.1). The rbcL region showed a low genetic distance between the species in Cupressaceae 2% (0–3.3), Podocarpaceae 3% (0.6–3.4), Taxaceae 1% (0–2.1) and Pinaceae 1.2% (0–5.82). The phylogenetic analyses using the Maximum likelihood (ML) and Bayesian inference (BI) bootstrap values obtained at the branching nodes of each species ranged from 62 to 100% (Maximum likelihood bootstrap – MLBS and Bayesian posterior probabilities – BPP) for the matK gene; from 66 to 100% (MLBS) and 60 to 100% (BPP) for the rbcL region. The rbcL region was not identified between the species of Taxaceae and Cephalotaxaceae. The matK gene region was very clear in the different species among the families (Cupressaceae, Podocarpaceae, and Cephalotaxaceae) and unsuitable for identifying closely related species in Amentotaxus (Taxaceae) and Pinus (Pinaceae). The gene (matK) is a useful tool as a barcode in the identification of conifer species of Cupressaceae, Podocarpaceae, and Cephalotaxaceae in Vietnam.

Asaf S., Khan A.L., Khan M.A., Shahzad R., Kang S.M., Al-Harrasi A., Al-Rawahi A., Lee I.-J. (2018): Complete chloroplast genome sequence and comparative analysis of loblolly pine (Pinus taeda L.) with related species. PLoS One, 13: e0192966.
Bafeel S.O., Arif I.A., Bakir M.A., Khan H.A., Al Farhan A.H., Al Homaidan A.A., Ahamed A., Thomas J. (2011): Comparative evaluation of PCR success with universal primers of maturase K (matK) and ribulose-1, 5-bisphosphate carboxylase oxygenase large subunit (rbcL) for barcoding of some arid plants. Plant Omics, 4: 195.
Bui X.P., Do H.T., Shah S.N.M., Nguyen P.D.N., Pham Q.M., Nguyen H.M., Dao M.D., Bui L.M., Vu D.D. (2019): Molecular identification of Boletus speciosus (Boletaceae) using nuclear ribosomal internal transcribed spacer region in Vietnam. Research Journal of Biotechnology, 14: 53–67.
Burgess K.S., Fazekas A.J., Kesanakurti P.R., Graham S.W., Husband B.C., Newmaster S.G., Percy D.M., Hajibabaei M., Barrett S.C. (2011): Discriminating plant species in a local temperate flora using the rbcL+ matK DNA barcode. Methods in Ecology and Evolution, 2: 333–340.
Chase M.W., Salamin N., Wilkinson M., Dunwell J.M., Kesanakurthi R.P., Haidar N., Savolainen V. (2005): Land plants and DNA barcodes: short-term and long-term goals. Philosophical Transactions of the Royal Society B: Biological Sciences, 360: 1889–1895.
Chase M.W., Cowan R.S., Hollingsworth P.M., van den Berg C., Madriñán S., Petersen G., Seberg O., Jørgsen-sen T., Cameron K.M., Carine M. (2007): A proposal for a standardised protocol to barcode all land plants. Taxon, 56: 295–299.
Contreras-Medina R., Vega I.L. (2002): On the distribution of gymnosperm genera, their areas of endemism and cladistic biogeography. Australian Systematic Botony, 15: 193–204.
Cowan R.S., Chase M.W., Kress W.J., Savolainen V. (2006): 300 000 species to identify: problems, progress, and prospects in DNA barcoding of land plants. Taxon, 55: 611–616.
de Vere N., Rich T.C., Ford C.R., Trinder S.A., Long C., Moore C.W., Satterthwaite D., Davies H., Allainguillaume J., Ronca S. (2012): DNA barcoding the native flowering plants and conifers of Wales. PLoS One, 7: e37945.
Doyle J.J., Doyle J.L. (1990): Isolation ofplant DNA from fresh tissue. Focus, 12: 39–40.
Fazekas A.J., Kuzmina M.L., Newmaster S.G., Hollingsworth P.M. (2012): DNA barcoding methods for land plants. In: DNA Barcodes. Methods in Molecular Biology (Methods and Protocols). Totowa, Humana Press: 223–252.
Forest F., Moat J., Baloch E., Brummitt N.A., Bachman S.P., Ickert-Bond S., Hollingsworth P.M., Liston A., Little D.P., Mathews S. (2018): Gymnosperms on the EDGE. Scientific Reports, 8: 1–11.
Hall T.A. (1999): BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. In: Nucleic Acids Symposium Series. London, Information Retrieval Ltd.: 95–98.
Hebert P.D., Cywinska A., Ball S.L., Dewaard J.R. (2003): Biological identifications through DNA barcodes. Proceedings of the Royal Society of London. Series B: Biological Sciences, 270: 313–321.
Hiep N.T., Loc P.K., Luu N.D.T., Thomas P., Farjon A., Averyanov L.V., Regalado Jr. J. (2005): Viet Nam Conifers: Conservation Status Review 2004. Hanoi, Fauna & Flora International, Vietnam Programme.
Hiep N.T., Khang N.S., Loc P.K. (2015): Gymnosperms of Indochina. St. Petersburg, Komarov Botanical Institute of the Russian Academy of Sciences.
Hollingsworth P.M., Forrest L.L., Spouge J.L., Hajibabaei M., Ratnasingham S., van der Bank M., Chase M.W., Cowan R.S., Erickson D.L., Fazekas A.J., Graham S.W., James K.E., Kim K.-J., Kress W.J., Schneider H., van AlphenStahl J., Barrett S.C.H., van den Berg C., Bogarin D., Burgess K.S., Cameron K.M., Carine M., Chacón J., Clark A., Clarkson J.J., Conrad F., Devey D.S., Ford C.S., Hedderson T.A.J., Hollingsworth M.L., Husband B.C., Kelly L.J., Kesanakurti P.R., Kim J.S., Kim Y.-D., Lahaye R., Lee H.-L., Long D.G., Madriñán S., Maurin O., Meusnier I., Newmaster S.G., Park C.-W., Percy D.M., Petersen G., Richardson J.E., Salazar G.A., Savolainen V., Seberg O., Wilkinson M.J., Yi D.-K., Little D.P. (2009): A DNA barcode for land plants. Proceding of National Academy of Sciences, 106: 12794–12797.
Jobb G. (2011): TREEFINDER Manual. Version of March 2011. Munich. Available at
Kang H.-I., Lee H.O., Lee I.H., Kim I.S., Lee S.-W., Yang T.J., Shim D. (2019): Complete chloroplast genome of Pinus densiflora Siebold & Zucc. and comparative analysis with five pine trees. Forests, 10: 600.
Kress W.J., Erickson D.L. (2007): A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region. PLoS One, 2: e508.
Kress W.J., Wurdack K.J., Zimmer E.A., Weigt L.A., Janzen D.H. (2005): Use of DNA barcodes to identify flowering plants. Proceding of National Academy of Sciences, 102: 8369–8374.
Kress W.J., García-Robledo C., Uriarte M., Erickson D.L. (2015): DNA barcodes for ecology, evolution, and conservation. Trends in Ecology and Evolotion, 30: 25–35.
Kumar S., Stecher G., Tamura K. (2016): MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33: 1870–1874.
Lahaye R., Van der Bank M., Bogarin D., Warner J., Pupulin F., Gigot G., Maurin O., Duthoit S., Barraclough T.G., Savolainen V. (2008): DNA barcoding the floras of biodiversity hotspots. Proceding of National Academy of Sciences. 105: 2923–2928.
Little D.P., Knopf P., Schulz C. (2013): DNA barcode identification of Podocarpaceae – the second largest conifer family. PLoS One, 8: e81008.
Loc P.K., Long P., Regalado J., Averyanov L., Maslin B. (2017): Native conifers of Vietnam – A review. Pakistan Journal of Botany, 49: 2037–2068.
MOST and VAST (2007): Vietnam Red Data Book. Part II. Plants. Hanoi, Natural Science and Technology Publishing House.
Newmaster S., Fazekas A., Ragupathy S. (2006): DNA barcoding in land plants: evaluation of rbcL in a multigene tiered approach. Canadian Journal of Botany, 84: 335–341.
Pennisi E. (2007): Taxonomy. Wanted: a barcode for plants. Science, 318: 190–191.
Phong D.T., Hien V.T.T., Lieu T.T. (2018): Nucleotide diversity of 15 conifer species in Vietnam’s central highlands based on the analysis of ITS, trnH-psbA, matK, trnL and rpoC1 gene regions. Vietnam Journal of Science and Technology, 56: 47.
Ronquist F., Huelsenbeck J.P. (2003): MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19: 1572–1574.
Tanabe A.S. (2011): Kakusan4 and Aminosan: two programs for comparing nonpartitioned, proportional and separate models for combined molecular phylogenetic analyses of multilocus sequence data. Molecular Ecology Resources, 11: 914–921.
Trias-Blasi A., Vorontsova M. (2015): Plant identification is key to conservation. Nature, 521: 161–161.
Wu F., Li M., Liao B., Shi X., Xu Y. (2019): DNA barcoding analysis and phylogenetic relation of mangroves in Guangdong Province, China. Forests, 10: 56.
Zheng W., Chen J., Hao Z., Shi J. (2016): Comparative analysis of the chloroplast genomic information of Cunninghamia lanceolata (Lamb.) Hook with sibling species from the Genera Cryptomeria D. Don, Taiwania Hayata, and Calocedrus Kurz. Intenational Journal of Molecular Science, 17: 1084.
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