DNA barcoding of razor clam Solen spp. (Solinidae, Bivalva) in Indonesian beaches
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Abstract. Trisyani N, Rahayu DA. 2020. DNA barcoding of razor clam Solen spp. (Solinidae, Bivalva) in Indonesian beaches. Biodiversitas 21: 478-484. Solen spp. are shells with various morphological characteristics with a wide distribution of tropical and subtropical beaches, including Indonesia. The identification of Solen spp. is generally based on its morphological characteristics. This method is very problematic due to specimens share similarity in morphology and color. This study was using DNA barcode as a molecular identification tool. The bivalve COI sequence was amplified using PCR and molecular phylogenetic analysis using the Neighbor-Joining method. The amplified COI gene has a length of about 665 bp. The purpose of this study was to evaluate genetic variation and compare the phylogenetic Solen spp. in Indonesian waters. The composition of the nucleotide bases of Solen spp. the comparative species are A = 26.79%, C = 23.16%, G = 19.17% and T = 30.93%. The total nucleotide base A + T was 57.72%, while G + C was 42.33%. The results of phylogenetic analysis showed that Solen spp. Cirebon and Jambi are in one clade with Solen regularis with genetic distance 0.000 - 0.002. Solen spp. Surabaya, Bangkalan, Pamekasan, and Sumenep are in separate clades and are related to Solen grandis, Solen stricus and Solen lamarckii with genetic distance from 0.146 - 0.156. The diversity of nucleotide was 0.9780 and was divided into 12 haplotypes.
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References
Alcantara SG, Yambot AV. 2014. DNA barcoding of commercially important grouper species (Perciformes, Serranidae) in the Philippines. Mitochondrial DNA, Part A: DNA Mapping Sequencing and Analysis 27: 3837-3845.
Asphama AI. 2014. Analysis of complex genetic diversity of Portunus pelagicus (Linnaeus, 1758) species in Barru waters based on morphological and DNA characteristics. Tesis. Makassar: Program PascaSarjana Universitas Hasanuddin Makassar [Indonesian]
Bandelts HJ, Forster P, Rohl A. 1999. Median joining networks for inferring intraspesific phylogenies. Molecular Biological Evolution (16): 37-48.
Bensasson D, Zhang DX, Hartl DL, Hewitt GM. 2001. Mitochondrial pseudogenes: evolution’s misplaced witnesses. Trends Ecol Evol 16 (6): 314-321.
Buhay JE. 2009. “COI-like” Sequences are becoming problematic in molecular systematic and DNA barcoding studies. J Crustacean Biol 29 (1): 96-110.
Byun SO, Fang Q, Zhou H, Hickford JG. 2009. An effective method for silver-staining DNA in large numbers of polyacrylamide gels. Analytical Biochemistry 385: 174-175.
Cosel RV. 1990. An introduction to the razor shells (Bivalvia: Solenacea). In the bivalvia. Proceedings of a memorial symposium in honour of Sir Charles Maurice Yonge, Edinburgh, 1986, edited by B.S. Morton. Hong Kong, HongKong University, pp. 283-311.
Esa BY, Siti Shapor S, Siti Khalijah D, Khairul, Adha AR, Jeffrine RR, Soon GT. 2008. Mitochondrial DNA diversity of Tor Tambraides Valenciennes (Cyprinidae) from five natural populations in Malaysia. Zoological Studies 47(3): 360-367
Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R. 1994. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology 3(5): 294-299.
Habeeb SKM, Sanjayan KP. 2011. Sequencing and phylogenetic analysis of the mitochondrial cytochrome c oxidase subunit I of Oxycarenus laetus (Hemiptera: Lygaeidae). International Journal of Plant, Animal and Environmental Science IJPAES 1: 85-92.
Hebert PDN, Cywinska A, Ball SL, Waard JR. 2003. Biological identifications through DNA barcodes. Proceedings Biological Science 270: 313-321.
Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM. 2004. Identification of birds through DNA barcodes. PloS Biology 2: 1657-1663.
Hesterberg T, Monaghan S, Moore DS, Clipson A, Epstein R. 2003. Bootstrap methods and permutation tests. W. H. Freeman and Company, New York.
Hmida L, Fassatoui C, Ayed D, Ayache N, Romdhane MS. 2012. Genetic characterization of the razor clam Solen marginatus (Mollusca: Bivalvia: Solenidae) in Tunisian coasts based on isozyme markers. Journal Biochemical Systematics and Ecology 40: 146–155
Huang BX, Peakall R, Hanna PJ. 2000. Analysis of genetic structure of blacklip abalone (Haliotis rubra) populations using RAPD, minisatellite and microsatellite markers. Marine Biology 136: 207-216.
Hubert N. 2008. Identifying Canadian freshwater fishes through DNA Barcodes. PloS One 3: 2490.
Kimura. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16 (2): 111-20.
McCully KM. 2013. Uncharted waters: bivalves of midway atoll and integrating mathematics into biology education. Electronic theses and dissertations UC Santa Cruz.
Nugroho ED, Nawir D, Amin M, Lestari U. 2017. DNA barcoding of nomei fish (Synodontidae: Harpadon sp.) in Tarakan Island, Indonesia. AACL Bioflux 10(6): 1466-1474.
Nurjanah, Kustiariyah, Rusyadi S. 2008. Nutritional characteristics and potential development of the razor clams (Solen spp.) in the waters of Pamekasan, Madura. Jurnal Perikanan dan Kelautan 13(1): 41-51. [Indonesian]
Parenrengi A. 2001. Genetic variability of grouper (Epinephelus spp) from Indo Malaysian water using FCR/RAPD analysis. Tesis. Trenggano: Faculty Sience and Technology University Putra Malaysia Trenggano.
Park KY and Oh CW. 2002. Length-weight relationship of bivalves from coastal Wwters of Korea. Naga, The ICLARM Quarterly 25(1): 21-22
Rahayu DA, Nugroho ED. 2015. Molecular biology (in conservation perspective). Penerbit Plantaxia. Jogjakarta 185 pp. [Indonesian]
Ramadhan MF, Nasution S, Efriyeld. 2017. Characteristics of habitat and population of bamboo shells (Solen lamarckii) in the intertidal zone of Teluk Lancar Village, Bantan District, Bengkalis Regency. Jurnal perikanan dan kelautan 22(1): 36-43 [Indonesian]
Rinyod AMR, Rahim SAKA. 2011. Reproductive cycle of the razor clam Solen regularis Dunker, 1862 in the western part of Sarawak, Malaysia, based on gonadal condition index. Journal of Sustainability Science and Management 6: 10-18.
Saeedi H, Raad SP, Ardalan AA, Kamrani E, Kiabi BH. 2009. Growth and production of Solen dactylus (Bivalvia: Solen sp.idae) on northern coast of the Persian Gulf (Iran). Journal of the Marine Biological Association of the United Kingdom 89(8): 1635–1642.
Sarkar IN, Thornton JW, Planet PJ. 2002. An automated phylogenetic key for classifying homeoboxes. Mol Phylogenet Evol 24: 388-399.
Schmidt H. 2003. Phylogenetic trees from large datasets. Inaugural-Dissertation, Dusseldorf University.
Simone LRL. 2009. Anatomical description of cf. exiguus Dunker from Thailand (Bivalvia: Solenidae). Arch. Molluskenkunde 138 (2): 113–122
Subiyanto, Hartoko A, Umah K. 2013. Sediment structure and knife clam (Solen lamarckii) distribution in Kejawanan coast, Cirebon, west Java. Jurnal Manajemen Sumberdaya Perairan 2(3): 65-73. [Indonesian]
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
Trisyani N. 2018. Fishing technique and environmental factors affecting the size of razor clam Solen sp. in Indonesia coast. AACL Bioflux 11(1): 29-36.
Trisyani N, Herawati E Y, Widodo MS, Setyohadi D. 2016a. The length-weight correlation and population dynamics of razor clams (Solen regularis) in Surabaya east coast, Indonesia. Biodiversitas 17(2): 808-813.
Trisyani N, Herawati EY, Widodo MS, Setyohadi D. 2016b. Genetic relationship of razor clams (Solen sp.) in the Surabaya and Pamekasan coastal area, Indonesia. AACL Bioflux 9(5): 1113-1120
Trisyani N, Budiman K. 2015. Genetic diversity of razor clam (Solen sp.) at Pamekasan beaches and Surabaya east coast Indonesia based on RAPD markers. J Biod Environ Sci 7(6): 267-274
Trisyani N, Irawan B. 2008. Abundance of razor clam (Solen sp.) in east coast of Surabaya. Jurnal Ilmu Kelautan 13(2): 67-72. [Indonesian]
Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PDN. 2005. DNA barcoding Australia’s fish species. Philosophical Transaction of the Royal Society of London. Series B, Biological Sciences, 360: 1847-1857.
Waugh J. 2007. DNA barcoding in animal species: progress, potential and pitfalls. BioEssays 29: 188-197.
Wong EH, Shivji MS, Hanner RH. 2009. Identifying sharks with DNA barcodes: Assessing the utility of a nucleotide diagnostic approach. Mol Ecol Resour 9: 243-256
Wong EHK, Hanner RH. 2008. DNA barcoding detects market substitution in North American seafood. Food Res Intl 41: 828-837
Yoon JM. 2018. Genetic variations of intra- and between-razor clam Solen corneus population identified by PCR analysis. Dev. Reprod. 22(2): 193~198,
Yuan Y, Li Qi, Kong L, Yu H. 2012. The complete mitochondrial genome of Solen strictus (Bivalvia: Solen sp.idae). Mitochondrial DNA 23(2): 112–114
Zhang JB, Hanner R. 2011. DNA barcoding is a useful tool for the identification of marine fishes from Japan. Biochemistry Systematics and Ecology 39: 31-42.
Asphama AI. 2014. Analysis of complex genetic diversity of Portunus pelagicus (Linnaeus, 1758) species in Barru waters based on morphological and DNA characteristics. Tesis. Makassar: Program PascaSarjana Universitas Hasanuddin Makassar [Indonesian]
Bandelts HJ, Forster P, Rohl A. 1999. Median joining networks for inferring intraspesific phylogenies. Molecular Biological Evolution (16): 37-48.
Bensasson D, Zhang DX, Hartl DL, Hewitt GM. 2001. Mitochondrial pseudogenes: evolution’s misplaced witnesses. Trends Ecol Evol 16 (6): 314-321.
Buhay JE. 2009. “COI-like” Sequences are becoming problematic in molecular systematic and DNA barcoding studies. J Crustacean Biol 29 (1): 96-110.
Byun SO, Fang Q, Zhou H, Hickford JG. 2009. An effective method for silver-staining DNA in large numbers of polyacrylamide gels. Analytical Biochemistry 385: 174-175.
Cosel RV. 1990. An introduction to the razor shells (Bivalvia: Solenacea). In the bivalvia. Proceedings of a memorial symposium in honour of Sir Charles Maurice Yonge, Edinburgh, 1986, edited by B.S. Morton. Hong Kong, HongKong University, pp. 283-311.
Esa BY, Siti Shapor S, Siti Khalijah D, Khairul, Adha AR, Jeffrine RR, Soon GT. 2008. Mitochondrial DNA diversity of Tor Tambraides Valenciennes (Cyprinidae) from five natural populations in Malaysia. Zoological Studies 47(3): 360-367
Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R. 1994. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology 3(5): 294-299.
Habeeb SKM, Sanjayan KP. 2011. Sequencing and phylogenetic analysis of the mitochondrial cytochrome c oxidase subunit I of Oxycarenus laetus (Hemiptera: Lygaeidae). International Journal of Plant, Animal and Environmental Science IJPAES 1: 85-92.
Hebert PDN, Cywinska A, Ball SL, Waard JR. 2003. Biological identifications through DNA barcodes. Proceedings Biological Science 270: 313-321.
Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM. 2004. Identification of birds through DNA barcodes. PloS Biology 2: 1657-1663.
Hesterberg T, Monaghan S, Moore DS, Clipson A, Epstein R. 2003. Bootstrap methods and permutation tests. W. H. Freeman and Company, New York.
Hmida L, Fassatoui C, Ayed D, Ayache N, Romdhane MS. 2012. Genetic characterization of the razor clam Solen marginatus (Mollusca: Bivalvia: Solenidae) in Tunisian coasts based on isozyme markers. Journal Biochemical Systematics and Ecology 40: 146–155
Huang BX, Peakall R, Hanna PJ. 2000. Analysis of genetic structure of blacklip abalone (Haliotis rubra) populations using RAPD, minisatellite and microsatellite markers. Marine Biology 136: 207-216.
Hubert N. 2008. Identifying Canadian freshwater fishes through DNA Barcodes. PloS One 3: 2490.
Kimura. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16 (2): 111-20.
McCully KM. 2013. Uncharted waters: bivalves of midway atoll and integrating mathematics into biology education. Electronic theses and dissertations UC Santa Cruz.
Nugroho ED, Nawir D, Amin M, Lestari U. 2017. DNA barcoding of nomei fish (Synodontidae: Harpadon sp.) in Tarakan Island, Indonesia. AACL Bioflux 10(6): 1466-1474.
Nurjanah, Kustiariyah, Rusyadi S. 2008. Nutritional characteristics and potential development of the razor clams (Solen spp.) in the waters of Pamekasan, Madura. Jurnal Perikanan dan Kelautan 13(1): 41-51. [Indonesian]
Parenrengi A. 2001. Genetic variability of grouper (Epinephelus spp) from Indo Malaysian water using FCR/RAPD analysis. Tesis. Trenggano: Faculty Sience and Technology University Putra Malaysia Trenggano.
Park KY and Oh CW. 2002. Length-weight relationship of bivalves from coastal Wwters of Korea. Naga, The ICLARM Quarterly 25(1): 21-22
Rahayu DA, Nugroho ED. 2015. Molecular biology (in conservation perspective). Penerbit Plantaxia. Jogjakarta 185 pp. [Indonesian]
Ramadhan MF, Nasution S, Efriyeld. 2017. Characteristics of habitat and population of bamboo shells (Solen lamarckii) in the intertidal zone of Teluk Lancar Village, Bantan District, Bengkalis Regency. Jurnal perikanan dan kelautan 22(1): 36-43 [Indonesian]
Rinyod AMR, Rahim SAKA. 2011. Reproductive cycle of the razor clam Solen regularis Dunker, 1862 in the western part of Sarawak, Malaysia, based on gonadal condition index. Journal of Sustainability Science and Management 6: 10-18.
Saeedi H, Raad SP, Ardalan AA, Kamrani E, Kiabi BH. 2009. Growth and production of Solen dactylus (Bivalvia: Solen sp.idae) on northern coast of the Persian Gulf (Iran). Journal of the Marine Biological Association of the United Kingdom 89(8): 1635–1642.
Sarkar IN, Thornton JW, Planet PJ. 2002. An automated phylogenetic key for classifying homeoboxes. Mol Phylogenet Evol 24: 388-399.
Schmidt H. 2003. Phylogenetic trees from large datasets. Inaugural-Dissertation, Dusseldorf University.
Simone LRL. 2009. Anatomical description of cf. exiguus Dunker from Thailand (Bivalvia: Solenidae). Arch. Molluskenkunde 138 (2): 113–122
Subiyanto, Hartoko A, Umah K. 2013. Sediment structure and knife clam (Solen lamarckii) distribution in Kejawanan coast, Cirebon, west Java. Jurnal Manajemen Sumberdaya Perairan 2(3): 65-73. [Indonesian]
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
Trisyani N. 2018. Fishing technique and environmental factors affecting the size of razor clam Solen sp. in Indonesia coast. AACL Bioflux 11(1): 29-36.
Trisyani N, Herawati E Y, Widodo MS, Setyohadi D. 2016a. The length-weight correlation and population dynamics of razor clams (Solen regularis) in Surabaya east coast, Indonesia. Biodiversitas 17(2): 808-813.
Trisyani N, Herawati EY, Widodo MS, Setyohadi D. 2016b. Genetic relationship of razor clams (Solen sp.) in the Surabaya and Pamekasan coastal area, Indonesia. AACL Bioflux 9(5): 1113-1120
Trisyani N, Budiman K. 2015. Genetic diversity of razor clam (Solen sp.) at Pamekasan beaches and Surabaya east coast Indonesia based on RAPD markers. J Biod Environ Sci 7(6): 267-274
Trisyani N, Irawan B. 2008. Abundance of razor clam (Solen sp.) in east coast of Surabaya. Jurnal Ilmu Kelautan 13(2): 67-72. [Indonesian]
Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PDN. 2005. DNA barcoding Australia’s fish species. Philosophical Transaction of the Royal Society of London. Series B, Biological Sciences, 360: 1847-1857.
Waugh J. 2007. DNA barcoding in animal species: progress, potential and pitfalls. BioEssays 29: 188-197.
Wong EH, Shivji MS, Hanner RH. 2009. Identifying sharks with DNA barcodes: Assessing the utility of a nucleotide diagnostic approach. Mol Ecol Resour 9: 243-256
Wong EHK, Hanner RH. 2008. DNA barcoding detects market substitution in North American seafood. Food Res Intl 41: 828-837
Yoon JM. 2018. Genetic variations of intra- and between-razor clam Solen corneus population identified by PCR analysis. Dev. Reprod. 22(2): 193~198,
Yuan Y, Li Qi, Kong L, Yu H. 2012. The complete mitochondrial genome of Solen strictus (Bivalvia: Solen sp.idae). Mitochondrial DNA 23(2): 112–114
Zhang JB, Hanner R. 2011. DNA barcoding is a useful tool for the identification of marine fishes from Japan. Biochemistry Systematics and Ecology 39: 31-42.