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Munarti

Judul : Phylogenetic of sago palm (Metroxylon sagu) and others monocotyledon based on mitochondrial nad2 gene markers

Abstrak :
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.

Tahun : 2019 Media Publikasi : Jurnal Internasional

Kategori : Jurnal No/Vol/Tahun : 08 / 20 / 2019

ISSN/ISBN : 1412-033X

PTN/S : Universitas Pakuan Program Studi : PENDIDIKAN BIOLOGI

Bibliography :
Abbas B, Bintoro MH, Sudarsono, Surahman M, Ehara H. 2009. Genetic relationship of sago palm (Metroxylon sagu Rottb.) in Indonesia based on RAPD markers. Biodiversitas 10 (4): 168-174.
Abbas 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. Afr J Plant Sci 6 (12): 314-320.
Abbas B, Listyorini FH, 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. [Indonesian]
Abbas B, Paisey EK, Bachri S, Edowai DN, Ehara H.2014. Genetic diversities of sago palm forest in South Sorong, West Papua, Indonesia based on RAPD markers. Conf Soc Sago Palm Stud 23: 31-32.
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, Rauf AW, Listyorini FH, Munarti. 2014. Brief description of aspects of biology, ecology, agronomy, and prospects for development of sago palm. Eur J Sci Res 120 (2): 221-229.
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. 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. 2017. Dimensions of development sago commodities in the perspective of 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. [Indonesian]
Abbas B. 2018. Sago palm genetic resource diversity in Indonesia. In: Ehara H, Toyoda Y, Johnson D. (eds) Sago Palm. Springer, Singapore.
Barr CM, Keller SR, Ingvarsson PK, Sloan DB, Taylor DR. 2007. Variation in mutation rate and polymorphism among mitochondrial gene of Silene vulgaris. Mol Biol Evol 24 (8): 1783-1791.
Bintoro HMHD, Pratama AJ. 2015. Transformation of sago to agroindustry plantation through development of Science Park. Bogor Agricultural University. Paper presented at Science Park Seminar in Manokwari, November 25, 2015. [Indonesian]
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. [Indonesian]

Blacker TS, Duchen MR. 2016. Investigating mitochondrial redox state using NADH and NADPH autofluorescence. Free Radic Biol Med 100: 53-65.
Boesch P, Ibrahim N, Paulus F, Cosset A, Tarasenko V, Dietrich A. 2009. Plant mitochondria possess a short-patch base excision DNA repair pathway. Nucleic Acids Res 37 (17): 5690-5700.
Bujang K. 2008. Potential of bioenergy from the sago industries in Malaysia. Biotechnology 14: 1-8.
Castro JA, Picornel A, Ramon M. 1998. Mitochondrial DNA: a tool for population genetic studies. Intl Microb 1:327-332
Chen Z, Zhao N, Li S, Grover CE, Nie H, Wendel JF, Hua J. 2017. Plant mitochondrial genome evolution and cytoplasmic male sterility. Crit Rev Plant Sci 36 (1): 55-69.
Christensen AC. 2013. Plant mitochondrial genome evolution can be explained by DNA repair mechanisms. Genome Biol Evol 5 (6): 1079-1086.
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
Dewi RK, Bintoro MH, Sudrajat. 2016. Karakter morfologi dan potensi produksi beberapa aksesi sagu (Metroxylon spp.) di Kabupaten Sorong Selatan, Papua Barat. J Agron Indonesia 44:91-97. [Indonesian]
Duminil J, Pomonge MH, Petit RJ. 2002. A set of 35 consensus primer pairs amplifying genes and introns of plant mitochondrial DNA. Mol Ecol 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, 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, 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.
Kitazaki K, Kubo T. 2010. Cost of having the largest mitochondrial genome: Evolutionary mechanism of plant mitochondrial genome. J Bot. DOI: 10.1155/2010/620137
McClatchey W, Manner HI, Elevitch CR. 2005. Metroxylon amicarum, M. paulcoxii, M. sagu, M. salomonense, M. vitiense, and M. warburgii (sago palm). Species Profiles for Pacific Island Agroforestry. Permanent Agriculture Resources-UH Press, Hawaii
Morgulis A, Coulouris G, Raytselis Y, Madden TL, Agarwala R, Schäffer AA. 2008. Database indexing for production MegaBLAST searches, Bioinformatics 24: 1757-1764.
Morley SA, Nielsen BL. 2017. Plant mitochondrial DNA. Front Biosci 1 (22): 1023-1032.
Mower JP, Tauzet P, Gummow J, Delph LF, Palmer JD. 2007. Extensive variation in synonymous substitution rates in mitochondrial genes of seed plants. BMC Evol Biol 7 (135): 1-14.
Pervaiz T, Sun X, Zhang Y, Tao R, Zhang J. 2015. Association between chloroplast and mitochondrial DNA sequences in Chinese Prunus genotypes (Prunus persica, Prunus domestica, and Prunus avium). BMC Plant Biol 15: 4. DOI 10.1186/s12870-014-0402-4.
Petit RJ, Duminil J, Fineschi S, Hampe A, Salvini D, Vendramin GG. 2005. Comparative organization of chloroplast, mitochondrial, and nuclear diversity in plant populations. Mol Ecol 14: 689-701.
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.
Schuiling DL. 1995. The variability of the sago palm and the need and possibilities for its conservation. In: Subhadrabandhu S, Sdoodee S (eds.). Fifth International Sago Symposium. Hat Yai, Songkhla, Thailand, 27-29 January 1994. ISHS Acta Hort 38 (9)..
Sneath PHA, Sokal RR. 1973. Numerical Taxonomy. Freeman. San Francisco.
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 (30): 11030-11035.
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: Molecular Evolutionary Genetics Analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739.
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 30: 2725-2729.
Touzet P, 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, 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.
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

URL : DOI: 10.13057/biodiv/d200820

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Judul	:	Phylogenetic of sago palm (Metroxylon sagu) and others monocotyledon based on mitochondrial nad2 gene markers
Abstrak	:	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.
Tahun	:	2019	Media Publikasi	:	Jurnal Internasional
Kategori	:	Jurnal	No/Vol/Tahun	:	08 / 20 / 2019
ISSN/ISBN	:	1412-033X
PTN/S	:	Universitas Pakuan	Program Studi	:	PENDIDIKAN BIOLOGI
Bibliography	:	Abbas B, Bintoro MH, Sudarsono, Surahman M, Ehara H. 2009. Genetic relationship of sago palm (Metroxylon sagu Rottb.) in Indonesia based on RAPD markers. Biodiversitas 10 (4): 168-174. Abbas 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. Afr J Plant Sci 6 (12): 314-320. Abbas B, Listyorini FH, 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. [Indonesian] Abbas B, Paisey EK, Bachri S, Edowai DN, Ehara H.2014. Genetic diversities of sago palm forest in South Sorong, West Papua, Indonesia based on RAPD markers. Conf Soc Sago Palm Stud 23: 31-32. 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, Rauf AW, Listyorini FH, Munarti. 2014. Brief description of aspects of biology, ecology, agronomy, and prospects for development of sago palm. Eur J Sci Res 120 (2): 221-229. 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. 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. 2017. Dimensions of development sago commodities in the perspective of 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. [Indonesian] Abbas B. 2018. Sago palm genetic resource diversity in Indonesia. In: Ehara H, Toyoda Y, Johnson D. (eds) Sago Palm. Springer, Singapore. Barr CM, Keller SR, Ingvarsson PK, Sloan DB, Taylor DR. 2007. Variation in mutation rate and polymorphism among mitochondrial gene of Silene vulgaris. Mol Biol Evol 24 (8): 1783-1791. Bintoro HMHD, Pratama AJ. 2015. Transformation of sago to agroindustry plantation through development of Science Park. Bogor Agricultural University. Paper presented at Science Park Seminar in Manokwari, November 25, 2015. [Indonesian] 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. [Indonesian] Blacker TS, Duchen MR. 2016. Investigating mitochondrial redox state using NADH and NADPH autofluorescence. Free Radic Biol Med 100: 53-65. Boesch P, Ibrahim N, Paulus F, Cosset A, Tarasenko V, Dietrich A. 2009. Plant mitochondria possess a short-patch base excision DNA repair pathway. Nucleic Acids Res 37 (17): 5690-5700. Bujang K. 2008. Potential of bioenergy from the sago industries in Malaysia. Biotechnology 14: 1-8. Castro JA, Picornel A, Ramon M. 1998. Mitochondrial DNA: a tool for population genetic studies. Intl Microb 1:327-332 Chen Z, Zhao N, Li S, Grover CE, Nie H, Wendel JF, Hua J. 2017. Plant mitochondrial genome evolution and cytoplasmic male sterility. Crit Rev Plant Sci 36 (1): 55-69. Christensen AC. 2013. Plant mitochondrial genome evolution can be explained by DNA repair mechanisms. Genome Biol Evol 5 (6): 1079-1086. 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 Dewi RK, Bintoro MH, Sudrajat. 2016. Karakter morfologi dan potensi produksi beberapa aksesi sagu (Metroxylon spp.) di Kabupaten Sorong Selatan, Papua Barat. J Agron Indonesia 44:91-97. [Indonesian] Duminil J, Pomonge MH, Petit RJ. 2002. A set of 35 consensus primer pairs amplifying genes and introns of plant mitochondrial DNA. Mol Ecol 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, 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, 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. Kitazaki K, Kubo T. 2010. Cost of having the largest mitochondrial genome: Evolutionary mechanism of plant mitochondrial genome. J Bot. DOI: 10.1155/2010/620137 McClatchey W, Manner HI, Elevitch CR. 2005. Metroxylon amicarum, M. paulcoxii, M. sagu, M. salomonense, M. vitiense, and M. warburgii (sago palm). Species Profiles for Pacific Island Agroforestry. Permanent Agriculture Resources-UH Press, Hawaii Morgulis A, Coulouris G, Raytselis Y, Madden TL, Agarwala R, Schäffer AA. 2008. Database indexing for production MegaBLAST searches, Bioinformatics 24: 1757-1764. Morley SA, Nielsen BL. 2017. Plant mitochondrial DNA. Front Biosci 1 (22): 1023-1032. Mower JP, Tauzet P, Gummow J, Delph LF, Palmer JD. 2007. Extensive variation in synonymous substitution rates in mitochondrial genes of seed plants. BMC Evol Biol 7 (135): 1-14. Pervaiz T, Sun X, Zhang Y, Tao R, Zhang J. 2015. Association between chloroplast and mitochondrial DNA sequences in Chinese Prunus genotypes (Prunus persica, Prunus domestica, and Prunus avium). BMC Plant Biol 15: 4. DOI 10.1186/s12870-014-0402-4. Petit RJ, Duminil J, Fineschi S, Hampe A, Salvini D, Vendramin GG. 2005. Comparative organization of chloroplast, mitochondrial, and nuclear diversity in plant populations. Mol Ecol 14: 689-701. 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. Schuiling DL. 1995. The variability of the sago palm and the need and possibilities for its conservation. In: Subhadrabandhu S, Sdoodee S (eds.). Fifth International Sago Symposium. Hat Yai, Songkhla, Thailand, 27-29 January 1994. ISHS Acta Hort 38 (9).. Sneath PHA, Sokal RR. 1973. Numerical Taxonomy. Freeman. San Francisco. 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 (30): 11030-11035. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: Molecular Evolutionary Genetics Analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 30: 2725-2729. Touzet P, 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, 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. 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
URL	:	DOI: 10.13057/biodiv/d200820