Genetic diversity of sago palm (Metroxylon sagu) accessions based on plastid cpDNA matK gene as DNA barcoding
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Abstract. Abbas B, Tjolli I, Munarti. 2020. Genetic diversity of sago palm (Metroxylon sagu) accessions based on plastid cpDNA matK gene as DNA barcoding. Biodiversitas 21: 219-225. Metroxylon sagu Rottb is one of the plant species including in the Palmae family that deposits starch in the trunk. Sago palm was reported has high capability to produce a large amount of starch and large variation starch qualities which were mostly influenced by genetic factors. The objectives of this study are revealed sequence chloroplast DNA (cpDNA) associated with matK genes for the genetic diversity identification of sago palm accessions. Plant materials used in the studies were derived from Sago Research Center (SRC) collection. DNA extraction has adopted the procedure of Plant Genomic DNA Mini Kit. Polymerase chain reaction (PCR) was performed by using primer sets of MatK-1RKIM-f and MatK-3FKIM-r. DNA PCR product was sequenced by the 1st Base Asia, Singapore. Results of the study showed that the cpDNA sequence associated with matK genes in the genome of sago palm showed differences among accessions. Molecular diversities of sago palm accessions based on matK gene showed sago palm accessions separated into two genotypes. Genotype-1 incorporated of ten individuals of 15 accessions and genotype-2 incorporated five individuals of 15 accessions. A mutation site and deletion site occurred in the sequences of matK gene of the Genotype-2. Ten of the 15 sequences of the matK gene (belong to Genotype-1) were registered in the GenBank, NCBI as DNA barcoding and authenticity of sago palm germplasm from Papua islands, Indonesia territorials.
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References
Abbas B, Bintoro MH, Sudarosono, Surahman M, Ehara H. 2009. Genetic Relationship of Sago Palm (Metroxylon Sagu Rottb.) in Indonesia Based on RAPD Markers. Biodiversitas, Journal of Biological Diversity 10 (4): 168–74. https://doi.org/10.13057/biodiv/d100402.
Abbas B, Renwarin Y, Bintoro MH, Sudarsono, Surahman M, Ehara H. 2010. Genetic Diversity of Sago Palm in Indonesia Based on Chloroplast DNA (CpDNA) Markers. Biodiversitas, Journal of Biological Diversity 11 (3): 112–17. https://doi.org/10.13057/biodiv/d110302.
Abbas B, Tjolli I, Dailami M, Munarti. 2019. Phylogenetic of Sago Palm ( Metroxylon Sagu ) and Others Monocotyledon Based on Mitochondrial Nad2 Gene Markers. Biodiversitas, Journal of Biological Diversity 20(8): 2249–2256. https://doi.org/10.13057/biodiv/d200820.
Abbas B. 2018. Sago Palm Genetic Resource Diversity in Indonesia. In: Ehara H, Toyoda Y, Johnson D. (eds) Sago Palm: Multiple Contributions to Food Security and Sustainable Livelihoods. Springer, Singapore. https://rd.springer.com/book/10.1007/978-981-10-5269-9
Beccari O. 1918. Asiatic palms. Lepidocaryeae. Ann. Roy. Bot. Gard., Calcutta. 12:156-195.
Chase MW, Cowan RS, Hollingsworth PM, Berg CVD, Madrin’an S, Petersen G, Seberg O, Jorsensen T, Cameron KM, Carine M, Pedersen N, Hedderson TAJ, Conrad F, Salazar GA, Richardson JE, Hollingsworth ML, Barraclough TG, Kelly L, Wilkinson M. 2007. A proposal for a standardized protocol to barcode all land plants. Taxon 56: 295–299.
Darracq A, Varre JS, Drouard LM, Courseaux A, Castric V, Laprade PS, Oztas S, Lenoble P, Barbe B, Touzet P. 2011. Structural and content diversity of mitochondrial genome in beet: A comparative genomic analysis. Genome Biol Evol 3: 723-736
Felsenstein J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791.
Genievskaya Y , Abugalieva S , Zhubanysheva A, Turuspekov Y. 2017. Morphological description and DNA barcoding study of sand rice (Agriophyllum squarrosum, Chenopodiaceae) collected in Kazakhstan. BMC Plant Biology, 17(1):177-185 . DOI 10.1186/s12870-017-1132-1.
Harnelly E, Thomy Z, Fathiya N. 2018. Phylogenetic analysis of Dipterocarpaceae in Ketambe Research Station, Gunung Leuser National Park (Sumatra, Indonesia) based on rbcL and matK genes. Biodiversitas 19: 1074-1080. https://doi.org/10.13057/biodiv/d190340.
Hollingsworth PM, Graham SW, Little DP. 2011. Choosing and Using a Plant DNA Barcode. PLoS ONE. 6(5):1-13.
Karim AA, Pei-Lang Tie A, Manan DMA, Zaidul ISM. 2008. Starch from the sago (Metroxylon sagu) palm tree-properties, prospects and challenges as a source for food and other uses. Compr Rev Food Sci Food Saf 7: 215-228.
Kress WJ, Erickson DL. 2008. DNA DNA barcoding: Genes, genomics, and bioinformatics. Proceedings of the National Academy of Sciences USA, 105:2761–2762.
Kress W J, Erickson DL. 2007. A two-locus global DNA barcode for land plants: The coding rbcL gene complements the noncoding trnH-psbA spacer region. PLoS ONE 2: e508. doi: 10.1371/journal.pone.0000508.
Kress WJ, Wurdack KJ, Zimmer EA, Weigt LA, Janzen DH. 2005. Use of DNA barcodes to identify flowering plants. Proceedings of the National Academy of Sciences USA, 102: 8369–8374.
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.
Kuzmina ML, Johnson KL, Barron HR, Herbert PDN. 2012. Identification of vascular plants of Churchill, Manitoba, using a DNA barcode library. BMC Ecology 12(25):1-11. Doi:10.1186/1472-6785-12-25.
Lahaye R, Bank MVD, Bogarin D, Warner J, Pupulin F, Gigot G, Maurin O, Duthoit S, Barraclough TG, Savolainen V. 2008. DNA barcoding the floras of biodiversity hotspots. Proceedings of the National Academy of Sciences USA, 105: www.pnas.org_cgi_doi_ 10.1073_ pnas.0709936105.
Liston A. 1992. Variation in the chloroplast genes RPOC1 and RPOC2 of the genus Astragalus (Fabaceae): Evidence from restriction site mapping of a PCR amplified fragment. Am J Bot 79: 953-961.
Nei M, Gojobori T. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Molecular Biology and Evolution 3:418-426.
Nei M, Kumar S. 2000. Molecular Evolution and Phylogenetics. Oxford University Press, New York.
Provan J, Soranzo N, Wilson NJ, Goldstein DB, Powel W. 1999. A low mutation rate for chloroplast microsatellites. Genetics 153: 943-947.
Riyanto R, Widodo I, Abbas B. 2018. Morphology, growth and genetic variations of sago palm (Metroxylon sagu) seedlings derived from seeds. Biodiversitas 19: 602-608.
Rzhetsky A, Nei M. 1992. A simple method for estimating and testing minimum evolution trees. Molecular Biology and Evolution 9:945-967.
Saddhe AA , Jamdade AR, Kumar K. 2016. Assessment of mangroves from Goa, west coast India using DNA barcode. SpringerOpen 5:1554-1564. DOI 10.1186/s40064-016-3191-4.
Saitou N, Nei M. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4:406-425.
Savolainen V, Corbaz R, Moncousin C, Spchiger R, Manen JF. 1995. Chloroplast DNA variation and parentage analysis in 55 apples. Theor Appl Genet 90: 1138-1141.
Selvaraj D, Sarma RK, Sathishkumar R. 2008. Phylogenetic analysis of chloroplast matK gene from Zingiberaceae for plant DNA barcoding. Bioinformation 3(1): 24-27.
Singh J, Banerjee S. 2018. Utility of DNA barcoding tools for conservation and molecular identification of intraspecies of rice genotypes belonging to Chhattisgarh using rbcL and matK gene sequences. Plant Archives 18: 69-75.
Taberlet P, Coissac E, Pompanon F, Gielly L, Miquel C, Valentini A, Vermat T, Corthier, Brochmann C, Willerslev E. 2007. Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding. Nucleic Acids Research. 35(3):1-8. doi:10.1093/nar/gkl938
Tajima F. 1989. Statistical methods to test for nucleotide mutation hypothesis by DNA.
Tamura K, Nei M. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution 10:512-526.
Tamura K, Nei M, Kumar S. 2004. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proceedings of the National Academy of Sciences (USA) 101:11030-11035.
Tsumura Y, Yoshimura K, Tomaru N, Ohba K. 1995. Molecular phylogeny of conifer using RFLP analysis of PCR-amplified specific chloroplast genes. Theor Appl Genet 91: 1222-1236.
Viard F, El-Kassaby YA, Ritland A. 2001. Diversity and genetic structure in populations of Pseudotsuga menziesii (Pinaceae) at chloroplast microsatellite loci. Genome 44: 336-344.
Yater T, Tubur HW, Meliala C, Abbas B. 2019. Short Communication: A comparative study of phenotypes and starch production in sago palm (Metroxylon sagu) growing naturally in temporarily inundated and non-inundated areas of South Sorong, Indonesia. Biodiversitas 20: 1121-1126. https://doi.org/10.13057/biodiv/d200425.
Zebua LI, Gunaedi T, Budi IM, Lunga N. 2019. The DNA barcode of red fruit pandan (Pandanaceae) cultivar from Wamena, Papua Province, Indonesia based on matK gene. Biodiversitas 20: 3405-3412. https://doi.org/10.13057/biodiv/d2011 38.
Abbas B, Renwarin Y, Bintoro MH, Sudarsono, Surahman M, Ehara H. 2010. Genetic Diversity of Sago Palm in Indonesia Based on Chloroplast DNA (CpDNA) Markers. Biodiversitas, Journal of Biological Diversity 11 (3): 112–17. https://doi.org/10.13057/biodiv/d110302.
Abbas B, Tjolli I, Dailami M, Munarti. 2019. Phylogenetic of Sago Palm ( Metroxylon Sagu ) and Others Monocotyledon Based on Mitochondrial Nad2 Gene Markers. Biodiversitas, Journal of Biological Diversity 20(8): 2249–2256. https://doi.org/10.13057/biodiv/d200820.
Abbas B. 2018. Sago Palm Genetic Resource Diversity in Indonesia. In: Ehara H, Toyoda Y, Johnson D. (eds) Sago Palm: Multiple Contributions to Food Security and Sustainable Livelihoods. Springer, Singapore. https://rd.springer.com/book/10.1007/978-981-10-5269-9
Beccari O. 1918. Asiatic palms. Lepidocaryeae. Ann. Roy. Bot. Gard., Calcutta. 12:156-195.
Chase MW, Cowan RS, Hollingsworth PM, Berg CVD, Madrin’an S, Petersen G, Seberg O, Jorsensen T, Cameron KM, Carine M, Pedersen N, Hedderson TAJ, Conrad F, Salazar GA, Richardson JE, Hollingsworth ML, Barraclough TG, Kelly L, Wilkinson M. 2007. A proposal for a standardized protocol to barcode all land plants. Taxon 56: 295–299.
Darracq A, Varre JS, Drouard LM, Courseaux A, Castric V, Laprade PS, Oztas S, Lenoble P, Barbe B, Touzet P. 2011. Structural and content diversity of mitochondrial genome in beet: A comparative genomic analysis. Genome Biol Evol 3: 723-736
Felsenstein J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791.
Genievskaya Y , Abugalieva S , Zhubanysheva A, Turuspekov Y. 2017. Morphological description and DNA barcoding study of sand rice (Agriophyllum squarrosum, Chenopodiaceae) collected in Kazakhstan. BMC Plant Biology, 17(1):177-185 . DOI 10.1186/s12870-017-1132-1.
Harnelly E, Thomy Z, Fathiya N. 2018. Phylogenetic analysis of Dipterocarpaceae in Ketambe Research Station, Gunung Leuser National Park (Sumatra, Indonesia) based on rbcL and matK genes. Biodiversitas 19: 1074-1080. https://doi.org/10.13057/biodiv/d190340.
Hollingsworth PM, Graham SW, Little DP. 2011. Choosing and Using a Plant DNA Barcode. PLoS ONE. 6(5):1-13.
Karim AA, Pei-Lang Tie A, Manan DMA, Zaidul ISM. 2008. Starch from the sago (Metroxylon sagu) palm tree-properties, prospects and challenges as a source for food and other uses. Compr Rev Food Sci Food Saf 7: 215-228.
Kress WJ, Erickson DL. 2008. DNA DNA barcoding: Genes, genomics, and bioinformatics. Proceedings of the National Academy of Sciences USA, 105:2761–2762.
Kress W J, Erickson DL. 2007. A two-locus global DNA barcode for land plants: The coding rbcL gene complements the noncoding trnH-psbA spacer region. PLoS ONE 2: e508. doi: 10.1371/journal.pone.0000508.
Kress WJ, Wurdack KJ, Zimmer EA, Weigt LA, Janzen DH. 2005. Use of DNA barcodes to identify flowering plants. Proceedings of the National Academy of Sciences USA, 102: 8369–8374.
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.
Kuzmina ML, Johnson KL, Barron HR, Herbert PDN. 2012. Identification of vascular plants of Churchill, Manitoba, using a DNA barcode library. BMC Ecology 12(25):1-11. Doi:10.1186/1472-6785-12-25.
Lahaye R, Bank MVD, Bogarin D, Warner J, Pupulin F, Gigot G, Maurin O, Duthoit S, Barraclough TG, Savolainen V. 2008. DNA barcoding the floras of biodiversity hotspots. Proceedings of the National Academy of Sciences USA, 105: www.pnas.org_cgi_doi_ 10.1073_ pnas.0709936105.
Liston A. 1992. Variation in the chloroplast genes RPOC1 and RPOC2 of the genus Astragalus (Fabaceae): Evidence from restriction site mapping of a PCR amplified fragment. Am J Bot 79: 953-961.
Nei M, Gojobori T. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Molecular Biology and Evolution 3:418-426.
Nei M, Kumar S. 2000. Molecular Evolution and Phylogenetics. Oxford University Press, New York.
Provan J, Soranzo N, Wilson NJ, Goldstein DB, Powel W. 1999. A low mutation rate for chloroplast microsatellites. Genetics 153: 943-947.
Riyanto R, Widodo I, Abbas B. 2018. Morphology, growth and genetic variations of sago palm (Metroxylon sagu) seedlings derived from seeds. Biodiversitas 19: 602-608.
Rzhetsky A, Nei M. 1992. A simple method for estimating and testing minimum evolution trees. Molecular Biology and Evolution 9:945-967.
Saddhe AA , Jamdade AR, Kumar K. 2016. Assessment of mangroves from Goa, west coast India using DNA barcode. SpringerOpen 5:1554-1564. DOI 10.1186/s40064-016-3191-4.
Saitou N, Nei M. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4:406-425.
Savolainen V, Corbaz R, Moncousin C, Spchiger R, Manen JF. 1995. Chloroplast DNA variation and parentage analysis in 55 apples. Theor Appl Genet 90: 1138-1141.
Selvaraj D, Sarma RK, Sathishkumar R. 2008. Phylogenetic analysis of chloroplast matK gene from Zingiberaceae for plant DNA barcoding. Bioinformation 3(1): 24-27.
Singh J, Banerjee S. 2018. Utility of DNA barcoding tools for conservation and molecular identification of intraspecies of rice genotypes belonging to Chhattisgarh using rbcL and matK gene sequences. Plant Archives 18: 69-75.
Taberlet P, Coissac E, Pompanon F, Gielly L, Miquel C, Valentini A, Vermat T, Corthier, Brochmann C, Willerslev E. 2007. Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding. Nucleic Acids Research. 35(3):1-8. doi:10.1093/nar/gkl938
Tajima F. 1989. Statistical methods to test for nucleotide mutation hypothesis by DNA.
Tamura K, Nei M. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution 10:512-526.
Tamura K, Nei M, Kumar S. 2004. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proceedings of the National Academy of Sciences (USA) 101:11030-11035.
Tsumura Y, Yoshimura K, Tomaru N, Ohba K. 1995. Molecular phylogeny of conifer using RFLP analysis of PCR-amplified specific chloroplast genes. Theor Appl Genet 91: 1222-1236.
Viard F, El-Kassaby YA, Ritland A. 2001. Diversity and genetic structure in populations of Pseudotsuga menziesii (Pinaceae) at chloroplast microsatellite loci. Genome 44: 336-344.
Yater T, Tubur HW, Meliala C, Abbas B. 2019. Short Communication: A comparative study of phenotypes and starch production in sago palm (Metroxylon sagu) growing naturally in temporarily inundated and non-inundated areas of South Sorong, Indonesia. Biodiversitas 20: 1121-1126. https://doi.org/10.13057/biodiv/d200425.
Zebua LI, Gunaedi T, Budi IM, Lunga N. 2019. The DNA barcode of red fruit pandan (Pandanaceae) cultivar from Wamena, Papua Province, Indonesia based on matK gene. Biodiversitas 20: 3405-3412. https://doi.org/10.13057/biodiv/d2011 38.
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