DNA barcode of Metroxylon sagu and others palm species using matK gene
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Abstract. Abbas B, Kabes RJ, Mawikere NL, Ruimassa RMR, Maturbong RA. 2020. DNA barcode of Metroxylon sagu and other palm species using matK gene. Biodiversitas 21: 4047-4057. Palm family encompasses numerous species, and they disperse broadly across tropical and subtropical countries. The palm family is generally used as an ornamental plant, food, oil, and industrial raw materials. Species of palm that accumulate large amount carbohydrate in the trunk is sago palm (Metroxylon sagu Rottb). The objectives of this study were to explore the plastid sequence associated with matK genes in the palm family and to reveal DNA barcode of 16 genera and 28 species of the palm. Plant materials used in the studies were derived from Sago Research Center (SRC), and other palm sequences were retrieved from the GenBank, NCBI accessions. The PCR product was sequenced by the 1st Base Asia, Singapore. Sequences of the matK gene that were observed in the plastid genome of M. sagu were registered into the NCBI GenBank as DNA barcode of M. sagu. Percent query cover of Blast analysis range from 98% to 100%, and identity range from 97.70% to 100%. Plastid nucleotides associated with matK genes in the chloroplast genome of palm family were shown substantial differences in inter-genera and small differences in inter-species. Genetic distance among palm family range from 0 to 0.026 with nucleotide variation observed was of 0.008822 value. The result of molecular phylogenetic analysis showed that the palm family separated into three clades and three sub-clades based on the plastid matK gene. Species of M. sagu and M. warburgii were considered closely related as compared to other palm species. The matK gene barcoding method is one powerful tool for identification inter-genera and inter-species of the palm.
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References
Abbas B, Bintoro MH, Sudarosono, Surahman M, Ehara H. 2009. Genetic relationship of sago palm (Metroxylon sagu Rottb.) in Indonesiabased on RAPD markers. Biodiversitas 10 (4): 168-174. DOI: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 11 (3): 112-17. DOI: 10.13057/biodiv/d110302.
Abbas B. 2015. Sago commodity as a pillar of food sovereignty that needs to be managed and developed wisely as well as sustainably for community welfare. Scientific Oration for inauguration of Professor in the University of Papua, Manokwari [Indonesian].
Abbas B, Paisey EK, Dailami M, Munarti. 2017. Assessment of genetic arrangement of sago palm collection based on mitochondrial nad2 gene Marker. Proceeding of the 13th International Sago Symposium, Kuching Sarawak, Malaysia, 2-6 Oktober 2017.
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://doi.org/10.1007/978-981-10-5269-9_5.
Abbas B, Tjolli I, Dailami M, Munarti. 2019. Phylogenetic of sago palm (Metroxylon sagu) and others monocotyledon based on mitochondrial nad2 gene markers. Biodiversitas 20(8):2249-2256. DOI: 10.13057/biodiv/d200820.
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(1):219-225. DOI: 10.13057/biodiv/d2101 28
Asmussen,C.B., Dransfield,J., Deichmann,V., Barfod,A.S., Pintaud,J.C. and Baker,W.J. 2006. A new subfamily classification of the palm family (Arecacee): Evidence from plastid DNA phylogeny Bot. J. Linn. Soc. 151 (1):15-38.
Anoja K, Anoop BS, Dev SA, Muralidharan EM. 2012. Calamus palustris maturase K (matK) gene, partial cds; chloroplast. Kerala Forest Research Institute, Peechi 680 653, Trichur, Kerala 680653, Indias and shrubs of two major gardens 1:46-55.
Barrett CF, Baker WJ, Comer JR, Conran JG, Lahmeyer SC, Leebens-Mack JH, Li J, Lim GS, Mayfield-Jones DR, Perez L, Medina J, Pires JC, Santos C, Wm Stevenson,D, Zomlefer WB, Davis JI. 2016. Plastid genomes reveal support for deep phylogenetic relationships and extensive rate variation among palms and other commelinid monocots. New Phytol. 209 (2):855-870.
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.
Chen ZD, Yang T, Lin L, Lu LM, Li HL, Sun M, Liu B, Chen M, Niu YT, Ye JF, Cao ZY, Liu H, Wang XM, Wang W, Zhang JB, Meng Z, Cao W, Li JH, Wu SD, Zhao HL, Liu ZJ, Du ZY, Wang QF, Guo J, Tan XX, Su JX, Zhang LJ, Yang LL, Liao YY, Li MH, Zhang GQ, Chung SW, Zhang J, Xiang KL, Li RQ, Soltis DE, Soltis PS, Zhou SL, Ran JH, Wang XQ, Jin XH, Chen YS, Gao TG, Li JH, Zhang SZ, Lu AM. 2016. Tree of life for the genera of Chinese vascular plants. J. Syst Evol. 54 (4): 277-306
Christenhusz MJM, Byng JW. 2016. The number of known plants species in the world and its annual increase. Phytotaxa 261 (3): 201–217.
Claverie J, Notredame C. 2003. Bioinformatics for dummies. Willey Publishing. Indianapolis, USA.
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.
Elansary HO. 2013. Towards a DNA barcode library for Egyptian flora, with a preliminary focus on ornamental tree. DNA Barcodes (Berlin) 1: 46-55
Felsenstein J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39: 783-791.
Freire JAP, Barros KBNT, Lima LKF, Martins JM, Araujo YDC, Oliveira GLDS, Aquino JDS, Ferreir PMP. 2016. Phytochemistry profile, Nutritional Properties and pharmacological activities of Mauritia flexuosa. J. Food Science 81(11):2611-2622.
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 Biol 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. DOI: 10.13057/biodiv/d190340.
Hilu KW, Borsch T, Muller K, Soltis DE, Soltis PS, Savolainen V, Chase MW, Powell MP, Alice LA, Evans R, Sauquet H, Neinhuis C, Slotta TA, Rohwer JG, Campbell CS, Chatrou LW. 2003. Angiosperm Phylogeny Based on matK Sequence Information. American Journal of Botany. 90(12):1758–1776.
Hollingsworth PM, Graham SW, Little DP. 2011. Choosing and Using a Plant DNA Barcode. PLoS ONE. 6 (5): 1 -13.
Jones A, Del Vecchio DS, Savolainen V. 2010. Retispatha dumetosa chloroplast partial matK pseudogene, specimen voucher. https://www.ncbi.nlm.nih.gov/nuccore/FR832823.1
Kar P, Goyal A, Sen A. 2015. Maturase K gene in plant DNA barcoding and phylogenetics. Lambert Academic Publishing, Saarbruken.
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. Proc Natl Acad Sci 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. Proc Natl Acad Sci USA 102: 8369-8374.
Kumar S, Stecher G, Tamura K. 2016. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870-1874.
Kurian A, Dev SA, Sreekumar VB, Muralidharan EM. 2018. Limitations of the Recommended DNA Barcode Regions in Slow Evolving Plants: A Case Study of Rattans in the Western Ghats of India. J. Bamboo and Rattan 17(1):1 -10.
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. Proc Natl Acad Sci USA 105 (8):2761 -2762.
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.
Maurin,O., Davies,J.T., Yessoufou,K., Daru,B.H., Bezeng,S.B., Mankga,L. and Van der Bank,M. 2012. Human population density correlates with the phylogenetic diversity of trees in southern Africa. https://www.ncbi.nlm.nih.gov/nuccore/JX517810.1.
Morgulis A, Coulouris G, Raytselis Y, Madden TL, Agarwala R, Schäffer AA. 2008. Database indexing for production MegaBLAST searches, Bioinformatics 24: 1757-1764.
Nei M, Gojobori T. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 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. DOI: 10.13057/biodiv/d190241.
Riyanto R, Widodo I, Abbas B. 2018. Morphology, growth and genetic variations of sago palm (Metroxylon sagu) seedlings derived from seeds. Biodiversitas 19 (2): 602-608.
Rzhetsky A, Nei M. 1992. A simple method for estimating and testing minimum evolution trees. Mol Biol Evol 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. Mol Biol Evol 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 Arch 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 Res 35 (3): 1 -8. DOI: 10.1093/nar/gkl938.
Tajima F. 1989. Statistical methods to test for nucleotide mutation hypothesis by DNA polymorphism. Genetics 123 (3): 585-595.
Tamura K, Nei M. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512-526.
Tamura K, Nei M, Kumar S. 2004. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci 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.
Yamamoto Y. 2011. State of the art sago research in Asia Pacific. Proceeding of the 10th International Sago Symposium, October 29-30, 2011, Bogor, Indonesia.
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. DOI: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. DOI: 10.13057/biodiv/d2011 38.
Zhang Z, Schwartz S, Wagner L, Miller W. 2000. A greedy algorithm for aligning DNA sequences, J Comput Biol 2000 7 (1 -2): 203-214.
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 11 (3): 112-17. DOI: 10.13057/biodiv/d110302.
Abbas B. 2015. Sago commodity as a pillar of food sovereignty that needs to be managed and developed wisely as well as sustainably for community welfare. Scientific Oration for inauguration of Professor in the University of Papua, Manokwari [Indonesian].
Abbas B, Paisey EK, Dailami M, Munarti. 2017. Assessment of genetic arrangement of sago palm collection based on mitochondrial nad2 gene Marker. Proceeding of the 13th International Sago Symposium, Kuching Sarawak, Malaysia, 2-6 Oktober 2017.
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://doi.org/10.1007/978-981-10-5269-9_5.
Abbas B, Tjolli I, Dailami M, Munarti. 2019. Phylogenetic of sago palm (Metroxylon sagu) and others monocotyledon based on mitochondrial nad2 gene markers. Biodiversitas 20(8):2249-2256. DOI: 10.13057/biodiv/d200820.
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(1):219-225. DOI: 10.13057/biodiv/d2101 28
Asmussen,C.B., Dransfield,J., Deichmann,V., Barfod,A.S., Pintaud,J.C. and Baker,W.J. 2006. A new subfamily classification of the palm family (Arecacee): Evidence from plastid DNA phylogeny Bot. J. Linn. Soc. 151 (1):15-38.
Anoja K, Anoop BS, Dev SA, Muralidharan EM. 2012. Calamus palustris maturase K (matK) gene, partial cds; chloroplast. Kerala Forest Research Institute, Peechi 680 653, Trichur, Kerala 680653, Indias and shrubs of two major gardens 1:46-55.
Barrett CF, Baker WJ, Comer JR, Conran JG, Lahmeyer SC, Leebens-Mack JH, Li J, Lim GS, Mayfield-Jones DR, Perez L, Medina J, Pires JC, Santos C, Wm Stevenson,D, Zomlefer WB, Davis JI. 2016. Plastid genomes reveal support for deep phylogenetic relationships and extensive rate variation among palms and other commelinid monocots. New Phytol. 209 (2):855-870.
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.
Chen ZD, Yang T, Lin L, Lu LM, Li HL, Sun M, Liu B, Chen M, Niu YT, Ye JF, Cao ZY, Liu H, Wang XM, Wang W, Zhang JB, Meng Z, Cao W, Li JH, Wu SD, Zhao HL, Liu ZJ, Du ZY, Wang QF, Guo J, Tan XX, Su JX, Zhang LJ, Yang LL, Liao YY, Li MH, Zhang GQ, Chung SW, Zhang J, Xiang KL, Li RQ, Soltis DE, Soltis PS, Zhou SL, Ran JH, Wang XQ, Jin XH, Chen YS, Gao TG, Li JH, Zhang SZ, Lu AM. 2016. Tree of life for the genera of Chinese vascular plants. J. Syst Evol. 54 (4): 277-306
Christenhusz MJM, Byng JW. 2016. The number of known plants species in the world and its annual increase. Phytotaxa 261 (3): 201–217.
Claverie J, Notredame C. 2003. Bioinformatics for dummies. Willey Publishing. Indianapolis, USA.
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.
Elansary HO. 2013. Towards a DNA barcode library for Egyptian flora, with a preliminary focus on ornamental tree. DNA Barcodes (Berlin) 1: 46-55
Felsenstein J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39: 783-791.
Freire JAP, Barros KBNT, Lima LKF, Martins JM, Araujo YDC, Oliveira GLDS, Aquino JDS, Ferreir PMP. 2016. Phytochemistry profile, Nutritional Properties and pharmacological activities of Mauritia flexuosa. J. Food Science 81(11):2611-2622.
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 Biol 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. DOI: 10.13057/biodiv/d190340.
Hilu KW, Borsch T, Muller K, Soltis DE, Soltis PS, Savolainen V, Chase MW, Powell MP, Alice LA, Evans R, Sauquet H, Neinhuis C, Slotta TA, Rohwer JG, Campbell CS, Chatrou LW. 2003. Angiosperm Phylogeny Based on matK Sequence Information. American Journal of Botany. 90(12):1758–1776.
Hollingsworth PM, Graham SW, Little DP. 2011. Choosing and Using a Plant DNA Barcode. PLoS ONE. 6 (5): 1 -13.
Jones A, Del Vecchio DS, Savolainen V. 2010. Retispatha dumetosa chloroplast partial matK pseudogene, specimen voucher. https://www.ncbi.nlm.nih.gov/nuccore/FR832823.1
Kar P, Goyal A, Sen A. 2015. Maturase K gene in plant DNA barcoding and phylogenetics. Lambert Academic Publishing, Saarbruken.
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. Proc Natl Acad Sci 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. Proc Natl Acad Sci USA 102: 8369-8374.
Kumar S, Stecher G, Tamura K. 2016. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870-1874.
Kurian A, Dev SA, Sreekumar VB, Muralidharan EM. 2018. Limitations of the Recommended DNA Barcode Regions in Slow Evolving Plants: A Case Study of Rattans in the Western Ghats of India. J. Bamboo and Rattan 17(1):1 -10.
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. Proc Natl Acad Sci USA 105 (8):2761 -2762.
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.
Maurin,O., Davies,J.T., Yessoufou,K., Daru,B.H., Bezeng,S.B., Mankga,L. and Van der Bank,M. 2012. Human population density correlates with the phylogenetic diversity of trees in southern Africa. https://www.ncbi.nlm.nih.gov/nuccore/JX517810.1.
Morgulis A, Coulouris G, Raytselis Y, Madden TL, Agarwala R, Schäffer AA. 2008. Database indexing for production MegaBLAST searches, Bioinformatics 24: 1757-1764.
Nei M, Gojobori T. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 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. DOI: 10.13057/biodiv/d190241.
Riyanto R, Widodo I, Abbas B. 2018. Morphology, growth and genetic variations of sago palm (Metroxylon sagu) seedlings derived from seeds. Biodiversitas 19 (2): 602-608.
Rzhetsky A, Nei M. 1992. A simple method for estimating and testing minimum evolution trees. Mol Biol Evol 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. Mol Biol Evol 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 Arch 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 Res 35 (3): 1 -8. DOI: 10.1093/nar/gkl938.
Tajima F. 1989. Statistical methods to test for nucleotide mutation hypothesis by DNA polymorphism. Genetics 123 (3): 585-595.
Tamura K, Nei M. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512-526.
Tamura K, Nei M, Kumar S. 2004. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci 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.
Yamamoto Y. 2011. State of the art sago research in Asia Pacific. Proceeding of the 10th International Sago Symposium, October 29-30, 2011, Bogor, Indonesia.
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. DOI: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. DOI: 10.13057/biodiv/d2011 38.
Zhang Z, Schwartz S, Wagner L, Miller W. 2000. A greedy algorithm for aligning DNA sequences, J Comput Biol 2000 7 (1 -2): 203-214.
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- BARAHIMA ABBAS, YANUARIUS RENWARIN, MUHAMMAD HASIM BINTORO, SUDARSONO SUDARSONO, MEMEN SURAHMAN2, HIROSHI EHARA, Genetic diversity of sago palm in Indonesia based on chloroplast DNA (cpDNA) markers , Biodiversitas Journal of Biological Diversity: Vol. 11 No. 3 (2010)
- BARAHIMA ABBAS, IHWAN TJOLLI, MUHAMMAD DAILAMI, MUNARTI, Phylogenetic of sago palm (Metroxylon sagu) and others monocotyledon based on mitochondrial nad2 gene markers , Biodiversitas Journal of Biological Diversity: Vol. 20 No. 8 (2019)
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