Phylogenetic of sago palm (Metroxylon sagu) and others monocotyledon based on mitochondrial nad2 gene markers
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Abstract. 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: 2249-2256. Sago palm forest and sago palm semi cultivated are found in the Papua islands as well as Ambon and Seram islands. The diversity center of sago palm is found in the Papua Islands. The objectives of this study are revealed sequence DNA mitochondrial associated with nad2 genes in sago palm accessions and molecular phylogenetic of sago palm and other monocotyledon plants. Plant materials used in the studies were derived from Sago Research Center (SRC) and sequencing and other monocotyledon were retrieved from the GenBank, NCBI accessions. Young fresh leaflets were derived from the experimental field of SRC and DNA extraction by following the procedure of Plant Genomic DNA Mini Kit and then PCR performed by using nad2 primer sets. Thereafter, DNA PCR product was sequenced by Macrogen Inc., Seoul, Korea. Sequences of nad2 genes in sago palm accessions from Papua, Indonesia were registered by GenBank NCBI for further used in the future as biological authenticity from the certain location. Mitochondrial DNA sequences associated with nad2 genes in the genome of sago palm were shown no differences among sago palm accessions. Molecular phylogenetic of sago palm and others monocotyledon based on nad2 gene markers showed the sago palm and others monocotyledon incorporated into two major clades and five subclades. Sago palm, coconut, and date palm were described as close related and being in the same subclades.
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References
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Abbas B. 2017. Dimensions of Development Sago Commodities in the Perspective Local Resource-Based Development. Scientific Oration that presented at the Open Senate Meeting in the framework of Graduation of Master Program, Bachelor and Diploma, University of Papua. Manokwari, 60p (Indonesian).
Abbas B, Paisey EK, Dailami M, and 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. 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, Listyorini FH, and Munarti. 2015. Genetic diversity of eleven sago palm accessions from SRC’s Germplasm Based on Mitochondrial atp-6-2 gene and intron. The 12th International Sago Symposium, Rikkyo University, Tokyo, Japan, 15-17th, September, 2015
Abbas B, Rauf AW, Listyorini FH, and Munarti. 2014. Brief Description of Aspects of Biology , Ecology , Agronomy , and Prospects for Development of Sago Palm. European Journal of Scientific Research, 120(2), 221–229.
Abba B, Ehara H. 2012. Assessment Genetic Variation and Relationship of Sago Palm (Metroxylon sagu Rottb.) in Indonesia Based on Specific Expression Gene (Wx genes) Markers. African Journal of Plant Science Vol. 6(12):314-320.
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: 112-117.
Abbas B, Bintoro MH, Sudarsono, Surahman M, and Ehara H. 2009. Genetic relationship of sago palm (Metroxylon Sagu Rottb.) in Indonesia based on RAPD markers. Journal of Biological Diversity Vol. 10(4):168-174
Abbas B, Bintoro MH, Surahman M, Ehara H, and Sudarsono. 2007. Genetic diversity of sago palm in Indonesia based on genes encoding starch biosynthesis (Waxy genes). Proceeding of the 9th International sago Symposium in Philippines. July 19-21, 2007
Barr, C.M., S.R. Keller, P.K. Ingvarsson, D.B. Sloan, D.R. Taylor. 2007. Variatiaon in mutation rate and polymorphism among mitochondrial gene of Silene vulgaris. Mol.Biol. Evol. 24(8)1783-1791.
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Boesch P, Ibrahim N, Paulus F, Cosset A, Tarasenko V, and Dietrich A. 2009. Plant mitochondria possess a short-patch base excision DNA repair pathway. Nucleic Acids Research 37(17): 5690-5700.
Bujang K. 2008. Potential of bioenergy from the Sago industries in Malaysia. Biotechnology 14: 8p
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Chen Z, Zhao N, Li S, Grover CE, Nie H, Wendel JF, and Hua J. 2017. Plant Mitochon-drial Genome Evolution and Cytoplasmic Male Sterility, Critical Reviews in Plant Sciences, 36:1, 55-69, DOI:10.1080/07352689.2017.132776
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Dewi RK, Bintoro MH, and Sudrajat. 2016. Karakter morfologi dan potensi produksi beberapa aksesi sagu (Metroxylon spp.) di Kabupaten Sorong Selatan, Papua Barat. J. Agron. Indonesia 44:91-97.
Darracq A, Varre JS, Drouard LM, Courseaux A, Castric V, Laprade PS, Oztas S, Lenoble P, Barbe B, and Touzet P. 2011. Struktural and content diversity of mitochondrial genome in beet: A comparative genomic analysis. Genom Biol. Evol. 3:723-736
Duminil J, Pomonge MH, and Petit RJ. 2002. A set of 35 consensus primer pairs amplifying genes and introns of plant mitochondrial DNA. Molecular Ecology Notes 2:428-430
Flach M. 1997. Sago Palm Metroxylon sagu Rottb. Promoting the Conservation and Used of Under-Utilized and Neglected Crops. 13. Institute of Plant Genetics and Crop Plant Research, Gatersleben/Internasional Plant Genetic Resources Institute (IPGRI), Rome, Italy
Ishizuka K, Hisajima S, and Macer DRJ. 1996. Traditional technology for environmental conservation and sustainable development in the Asian- Pacific Region. Proceedings of UNESCO. University of Tsukuba, Japan.
Karim AA, Tie APL, Manan DMA, and Zaidul ISM. 2008. Starch from the Sago (Metroxylon sagu) Palm tree-properties, prospects and challenges as a source for food and other uses. Comprehensive Reviews in Food Science and Food Safety 7:215-228.
Kitazaki K and Kubo T. 2010. Cost of Having the Largest Mitochondrial Genome: Evolutionary Mechanism of Plant Mitochondrial Genome. Journal of Botany, Vol. 2010:1-12, http://dx.doi.org/10.1155/2010/620137
McClatchey W, Manner HI, and Elevitch CR. 2005. Metroxylon amicarum, M. paulcoxii, M. sagu, M. salomonense, M. vitiense, and M. warburgii (sago palm). Species Profiles for Pacific Island Agroforestry. www.traditionaltree. Org.
Morgulis A, Coulouris G, Raytselis Y, Madden TL, Agarwala R, and Schäffer AA. 2008. Database Indexing for Production MegaBLAST Searches", Bioinformatics 24:1757-1764.
Morley SA and Nielsen BL. 2017. Plant mitochondrial DNA. Front Biosci.1(22):1023-1032.
Mower JP, Tauzet P, Gummow J, Delph LF, and Palmer JD. 2007. Extensive variation in synonymous substitution rates in mitochondrial genes of seed plants. BMC Evolutionary Biology Vol. 7:135
Pervaiz T, Sun X, Zhang Y, Tao R, and Zhang J, 2015. Association between chloroplast and mitochondrial DNA sequences in Chinese Prunus genotypes (Prunus persica, Prunus domestica, and Prunus avium). BMC Plant Biology. Vol 15(4):
Petit RJ, Duminil J, Fineschi S, Hampe A, Salvini D, and Vendramin GG. 2005. Comparative organization of chloroplast, mitochondrial, and nuclear diversity in plant populations. Molecular Ecology 14:689-701
Riyanto R, Widodo I, and Abbas B. 2018. Morphology, growth and genetic variations of sago palm (Metroxylon sagu) seedlings derived from seeds. Biodiversitas 19(2):602-608. DOI: 10.13057/biodiv/d190241
Schuiling DL. 1995. The variability of the sago palm and the need and possibilities for its conservation. ISHS Acta Horticulturae http://www. actahort.org/books/389.
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, and Kumar S. 2011. MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution 28: 2731-2739.
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. Evolution 30:2725-2729.
Touzet P and Delph LF. 2009. The effect of breeding system on polymorphism in mitochondrial genes of sine. Genetics 181:631-664
Yamamoto Y. 2011. State of the art sago research in Asia Pacific. Proceeding of the 10th International Sago Symposium. Held in October 29-30, 2011, Bogor, Indonesia
Zhang Z, Schwartz S, Wagner L, Miller W. 2000. A greedy algorithm for aligning DNA sequences, J Comput Biol 2000; 7(1-2):203-14.
Abbas B. 2017. Dimensions of Development Sago Commodities in the Perspective Local Resource-Based Development. Scientific Oration that presented at the Open Senate Meeting in the framework of Graduation of Master Program, Bachelor and Diploma, University of Papua. Manokwari, 60p (Indonesian).
Abbas B, Paisey EK, Dailami M, and 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. 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, Listyorini FH, and Munarti. 2015. Genetic diversity of eleven sago palm accessions from SRC’s Germplasm Based on Mitochondrial atp-6-2 gene and intron. The 12th International Sago Symposium, Rikkyo University, Tokyo, Japan, 15-17th, September, 2015
Abbas B, Rauf AW, Listyorini FH, and Munarti. 2014. Brief Description of Aspects of Biology , Ecology , Agronomy , and Prospects for Development of Sago Palm. European Journal of Scientific Research, 120(2), 221–229.
Abba B, Ehara H. 2012. Assessment Genetic Variation and Relationship of Sago Palm (Metroxylon sagu Rottb.) in Indonesia Based on Specific Expression Gene (Wx genes) Markers. African Journal of Plant Science Vol. 6(12):314-320.
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: 112-117.
Abbas B, Bintoro MH, Sudarsono, Surahman M, and Ehara H. 2009. Genetic relationship of sago palm (Metroxylon Sagu Rottb.) in Indonesia based on RAPD markers. Journal of Biological Diversity Vol. 10(4):168-174
Abbas B, Bintoro MH, Surahman M, Ehara H, and Sudarsono. 2007. Genetic diversity of sago palm in Indonesia based on genes encoding starch biosynthesis (Waxy genes). Proceeding of the 9th International sago Symposium in Philippines. July 19-21, 2007
Barr, C.M., S.R. Keller, P.K. Ingvarsson, D.B. Sloan, D.R. Taylor. 2007. Variatiaon in mutation rate and polymorphism among mitochondrial gene of Silene vulgaris. Mol.Biol. Evol. 24(8)1783-1791.
Bintoro MH. 2011 . Progress of sago research in Indonesia. In: Siregar IZ, Sudaryanto T, Ehara H, Suwardi, Lubis I, Ardie SW (eds.) Sago for food security, Bio-energy, and Industry, from research to market. Proceeding of the 1 0th International Sago. Symposium. IPB International Convention Center, Bogor, Indonesia, October 29-31 , 2011 .
Blacker TS and Duchen MR. 2016. Investigating mitochondrial redox state using NADH and NADPH autoflourescene. Free Radical Biology and Medicine, 100:53-65
Boesch P, Ibrahim N, Paulus F, Cosset A, Tarasenko V, and Dietrich A. 2009. Plant mitochondria possess a short-patch base excision DNA repair pathway. Nucleic Acids Research 37(17): 5690-5700.
Bujang K. 2008. Potential of bioenergy from the Sago industries in Malaysia. Biotechnology 14: 8p
Castro JA, Picornel A, and Ramon M. 1998. Mitochondrial DNA: a tool for population genetic studies. Internal Microbial Vol. 1:327-332
Claverie J and Notredame C. 2003. Bioinformatics for dummies . Willey Publishing, Indiana polis, USA.
Chen Z, Zhao N, Li S, Grover CE, Nie H, Wendel JF, and Hua J. 2017. Plant Mitochon-drial Genome Evolution and Cytoplasmic Male Sterility, Critical Reviews in Plant Sciences, 36:1, 55-69, DOI:10.1080/07352689.2017.132776
Christensen AC. 2013. Plant mitochondrial genome evolution can be explained by DNA repair mechanisms. Genome Biol. Evol. 5(6):1079–1086. doi:10.1093/gbe/evt069
Dewi RK, Bintoro MH, and Sudrajat. 2016. Karakter morfologi dan potensi produksi beberapa aksesi sagu (Metroxylon spp.) di Kabupaten Sorong Selatan, Papua Barat. J. Agron. Indonesia 44:91-97.
Darracq A, Varre JS, Drouard LM, Courseaux A, Castric V, Laprade PS, Oztas S, Lenoble P, Barbe B, and Touzet P. 2011. Struktural and content diversity of mitochondrial genome in beet: A comparative genomic analysis. Genom Biol. Evol. 3:723-736
Duminil J, Pomonge MH, and Petit RJ. 2002. A set of 35 consensus primer pairs amplifying genes and introns of plant mitochondrial DNA. Molecular Ecology Notes 2:428-430
Flach M. 1997. Sago Palm Metroxylon sagu Rottb. Promoting the Conservation and Used of Under-Utilized and Neglected Crops. 13. Institute of Plant Genetics and Crop Plant Research, Gatersleben/Internasional Plant Genetic Resources Institute (IPGRI), Rome, Italy
Ishizuka K, Hisajima S, and Macer DRJ. 1996. Traditional technology for environmental conservation and sustainable development in the Asian- Pacific Region. Proceedings of UNESCO. University of Tsukuba, Japan.
Karim AA, Tie APL, Manan DMA, and Zaidul ISM. 2008. Starch from the Sago (Metroxylon sagu) Palm tree-properties, prospects and challenges as a source for food and other uses. Comprehensive Reviews in Food Science and Food Safety 7:215-228.
Kitazaki K and Kubo T. 2010. Cost of Having the Largest Mitochondrial Genome: Evolutionary Mechanism of Plant Mitochondrial Genome. Journal of Botany, Vol. 2010:1-12, http://dx.doi.org/10.1155/2010/620137
McClatchey W, Manner HI, and Elevitch CR. 2005. Metroxylon amicarum, M. paulcoxii, M. sagu, M. salomonense, M. vitiense, and M. warburgii (sago palm). Species Profiles for Pacific Island Agroforestry. www.traditionaltree. Org.
Morgulis A, Coulouris G, Raytselis Y, Madden TL, Agarwala R, and Schäffer AA. 2008. Database Indexing for Production MegaBLAST Searches", Bioinformatics 24:1757-1764.
Morley SA and Nielsen BL. 2017. Plant mitochondrial DNA. Front Biosci.1(22):1023-1032.
Mower JP, Tauzet P, Gummow J, Delph LF, and Palmer JD. 2007. Extensive variation in synonymous substitution rates in mitochondrial genes of seed plants. BMC Evolutionary Biology Vol. 7:135
Pervaiz T, Sun X, Zhang Y, Tao R, and Zhang J, 2015. Association between chloroplast and mitochondrial DNA sequences in Chinese Prunus genotypes (Prunus persica, Prunus domestica, and Prunus avium). BMC Plant Biology. Vol 15(4):
Petit RJ, Duminil J, Fineschi S, Hampe A, Salvini D, and Vendramin GG. 2005. Comparative organization of chloroplast, mitochondrial, and nuclear diversity in plant populations. Molecular Ecology 14:689-701
Riyanto R, Widodo I, and Abbas B. 2018. Morphology, growth and genetic variations of sago palm (Metroxylon sagu) seedlings derived from seeds. Biodiversitas 19(2):602-608. DOI: 10.13057/biodiv/d190241
Schuiling DL. 1995. The variability of the sago palm and the need and possibilities for its conservation. ISHS Acta Horticulturae http://www. actahort.org/books/389.
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, and Kumar S. 2011. MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution 28: 2731-2739.
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. Evolution 30:2725-2729.
Touzet P and Delph LF. 2009. The effect of breeding system on polymorphism in mitochondrial genes of sine. Genetics 181:631-664
Yamamoto Y. 2011. State of the art sago research in Asia Pacific. Proceeding of the 10th International Sago Symposium. Held in October 29-30, 2011, Bogor, Indonesia
Zhang Z, Schwartz S, Wagner L, Miller W. 2000. A greedy algorithm for aligning DNA sequences, J Comput Biol 2000; 7(1-2):203-14.
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