Mitochondrial DNA of CO1 and 16S rRNA genes for diversity and phylogenetic analysis of sardine (Sardinella spp.) from the Lombok Straits, Indonesia
##plugins.themes.bootstrap3.article.sidebar##
Issue
Section
Articles
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
##plugins.themes.bootstrap3.article.main##
Abstract
Abstract. Mahrus H, Idrus AA, Syukur A. 2024. Mitochondrial DNA of CO1 and 16S rRNA genes for diversity and phylogenetic analysis of sardine (Sardinella spp.) from the Lombok Straits, Indonesia. Biodiversitas 25: 3500-3509. Sardines in Indonesia consist of six species from around 21 species- world, having many similarities and difficulty distinguishing between one species and others caused the taxonomy of the Sardines species is still ambiguous affected the same names in two different species and the different names in one species because of morphological similarities. The most effective method for identifying animal species and subspecies is the molecular method using sequences of the cytochrome c oxidase subunit 1 (CO1) gene and the 16S rRNA gene. The study aims to determine the molecular characteristics, genetic diversity, and phylogenetic relationships of sardines in the Lombok Strait using a sequence of CO1 and 16S rRNA genes. The study has significant practical implications as it can potentially inform conservation efforts and fisheries management. The sardine samples were collected from the Lombok Strait by small-scale fishermen. The sampling method was random. It takes 55 individuals as a sample. Initially, the sardine samples were grouped based on morphological characteristics. Subsequently, DNA from the two genes of 20 sardine samples were separated and amplified using two pairs of primers. The DNA amplification yielded 671 bp for the CO1 gene and 625 bp for the 16S rRNA gene. The sequence data from the two genes were analyzed using Molecular Evolutionary Genetics Analysis Version 11 (MEGA 11). The CO1 gene sequence revealed that sardines from the Lombok Strait could be determined more accurately than the 16S rRNA. CO1 rRNA genes of 12 individuals indicated a close genetic relationship between sardines of Lombok Strait and Sardinella aurita Valenciennes 1847, and the 16S rRNA gene placed sardines from Lombok Strait as an out-group. It empirically demonstrates that the CO1 gene is more effective than the 16S rRNA gene in identifying and determining molecular characteristics, genetic diversity, and phylogenetic relationships of sardines in Lombok Strait.
##plugins.themes.bootstrap3.article.details##
References
Azevedo RS, Bitencourt A, Silva DA, Amorim A, Mazzoni R, Carvalho EF, Amaral CR. 2017. Genetic diversity of Geophagus brasiliensis from the South American Atlantic Rainforest. Forensic Sci Intl Genet Suppl Ser 26: e433-e434. DOI: 10.1016/j.fsigss.2017.09.149.
Barrientos-Villalobos J, Schmitter-Soto JJ. 2019. Phylogeography of the Mayan cichlid Mayaheros urophthalmus (Teleostei: Cichlidae) in the Yucatan peninsula based on mitochondrial markers CYTB and COI. Environ Biol Fish 102: 1461-1472. DOI: 10.1007/s10641-019-00920-4.
Bemis KE, Girard MG, Santos MD, Carpenter KE, Deeds JR, Pitassy DE, Flores NA, Hunter ES, Driskell AC, Macdonald III KS, Weigt LA. 2023. Biodiversity of Philippine marine fishes: A DNA barcode reference library based on voucher specimens. Sci Data 10 (1): 411. DOI: 10.1038/s41597-023-02306-9.
Bingpeng X, Heshan L, Zhilan Z, Chunguang W, Yanguo W, Jianjun W. 2018. DNA barcoding for identification of fish species in the Taiwan Strait. PLoS One 13: e0198109. DOI: 10.1371/journal.pone.0198109.
Birge TL, Ralph GM, Di Dario F, Munroe TA, Bullock RW, Maxwell SM, Santos MD, Hata H, Carpenter KE. 2021. Global conservation status of the world's most prominent forage fishes (Teleostei: Clupeiformes). Biol Conserv 253: 108903-2021-01. DOI: 1016/j.biocon.2020.108903.
Buckwalter J, Angermeier PL, Argentina J, Wolf S, Floyd S, Hallerman EM. 2019. The drift of larval darters (Family Percidae) in the upper Roanoke River basin, USA, characterized using phenotypic and DNA barcoding markers. Fishes 4 (4): 59. DOI: 10.3390/fishes4040059.
Chan KO, Hertwig ST, Neokleous DN, Flury JM, Brown RM. 2022. Widely used, short 16S rRNA mitochondrial gene fragments yield poor and erratic results in phylogenetic estimation and species delimitation of amphibians. BMC Ecol Evol 22: 37. DOI: 10.1186/s12862-022-01994-y.
Chen C, Ding Y, Jiang Z, Jiang H, Lu C, Zhang L, Chen Z, Zhu C. 2021. DNA barcoding of yellow croakers (Larimichthys spp.) and morphologically similar fish species for authentication. Food Control 127: 108087. DOI: 10.1016/j.foodcont.2021.108087.
Choi EH, Kim G, Cha SH, Lee JS, Ryu SH, Suk HY, Lee YS, Baek SY, Hwang UW. 2020. Molecular phylogenetic, population genetic, and demographic studies of Nodularia douglasiae and Nodularia breviconcha based on CO1 and 16S rRNA. Sci Rep 10 (1): 16572. DOI: 10.1038/s41598-020-72015-5.
Devanand TN, Anjanayappa HN, Kumar G, Naveen Kumar BT, Gopan A, Panda K. 2020a. A comparative study of COI and 16S rRNA genes for DNA barcoding of Indian marine clupeids. J Exp Zool India 23 (2): 1439-1444.
Devanand TN, Kumar G, Anjanayappa HN, Naveen Kumar BT, Soman C, Panda K. 2020b. Identification of Coilia dussumieri and Sardinella gibbosa from Mangaluru waters using 16S rRNA gene. J Exp Zool India 23 (2): 1355-1360.
Devanand TN, Naveenkumar BT, Soman C, Anjanayappa HN, Naik M, Sathish RP, Kagalgomb A. 2018. DNA barcoding of Coilia dussumieri and Sardinella gibbosa using Cytochrome C oxidase sub unit I (CO1): A mitochondrial gene. J Exp Zool India 21: 1207-1211.
Dogan ?, Dogan N. 2016. Genetic distance measures. Turkiye Klinikleri J Biostat 8 (1): 87-93. DOI: 10.5336/biostatic.2015-49517.
Dong D, Gan Z, Li X. 2021. Descriptions of eleven new species of squat lobsters (Crustacea: Anomura) from seamounts around the Yap and Mariana Trenches with notes on DNA barcodes and phylogeny. Zool J Linn Soc 192 (2): 306-355. DOI: 10.1093/zoolinnean/zlab003.
Durand JD, Diatta MA, Diop K, Trape S. 2010. Multiplex 16S rRNA haplotype?specific PCR, a rapid and convenient method for fish species identification: An application to West African Clupeiform larvae. Mol Ecol Resour 10 (3): 568-72. DOI: 10.1111/j.1755-0998.2009.02776.x.
Eisele MH, Madrigal?Mora SM. 2021. Drivers of reef fish assemblages in an upwelling region from the Eastern Tropical Pacific Ocean. J Fish Biol 98 (4): 1074-1090. DOI: 10.1111/jfb.14639.
Eviasta IW, Boer M, Butet NA. 2018. Kajian stok ikan teri (Stolephorus commersonnii Lacepede, 1803) di Teluk Palabuhanratu, Sukabumi, Jawa Barat. J Trop Fish Manag 2 (2): 61. DOI: 10.29244/jppt.v2i2.26322. [Indonesian]
Fachrul M, Karkey A, Shakya M, Judd LM, Harshegyi T, Sim KS, Tonks S, Dongol S, Shrestha R, Salim A. 2023. Direct inference and control of genetic population structure from RNA sequencing data. Commun Biol 6 (1): 804. DOI: 10.1038/s42003-023-05171-9.
Findra MN, Setyobudiandi I, Butet NA, Solihin DD. 2017. Genetic profile assessment of giant clam genus Tridacna as a basis for resource management at Wakatobi National Park Waters. Ilmu Kelautan: Indones J Mar Sci 22 (2): 67-74. DOI: 10.14710/ik.ijms.22.2.67-74.
Gong S, Ding Y, Wang Y, Jiang G, Zhu C. 2018. Advances in DNA barcoding of toxic marine organisms. Intl J Mol Sci 19 (10): 2931. DOI: 10.3390/ijms19102931.
Hellberg RS, Kawalek MD, Van KT, Shen Y, Williams-Hill DM. 2014. Comparison of DNA extraction and PCR setup methods for use in high-throughput DNA barcoding of fish species. Food Anal Methods 7: 1950-1959. DOI: 10.1007/s12161-014-9865-z.
Hendiari IG, Sartimbul A, Arthana IW, Kartika GR. 2020. Keragaman genetik ikan lemuru (Sardinella lemuru) di wilayah perairan Indonesia. Acta Aquatica: Aquat Sci 7: 28-36. DOI: 10.29103/aa.v7i1.2405. [Indonesian]
Hunnam K, Carlos I, Hammer MP, Dos Reis Lopes J, Mills DJ, Stacey N. 2021. Untangling tales of tropical sardines: Local knowledge from fisheries in Timor-Leste. Front Mar Sci 8: 673173. DOI: 10.3389/fmars.2021.673173.
Hunnam K. 2021. The biology and ecology of tropical marine sardines and herrings in Indo-West Pacific fisheries: A review. Rev Fish Biol Fish 31 (3): 449-84. DOI: 10.1007/s11160-021-09649-9.
Jakab E, Bücs S, Jére C, Csösz I, Jakab RI, Szodoray-Parádi F, Popescu O. 2021. Low population structure and genetic diversity in Rhinolophus blasii at the northern limit of its European range: Are there undiscovered colonies?. Acta Chiropterol 23 (2): 301-311. DOI: 10.3161/15081109ACC2021.23.2.003.
Jaonalison H, Durand JD, Mahafina J, Valade P, Collet A, Cerqueira F, Ponton D. 2022. Application of DNA barcoding for monitoring Madagascar fish biodiversity in coastal areas. Diversity 14 (5): 377. DOI: 10.3390/d14050377.
Jaya I, Satria F, Nugroho D, Sadiyah L, Buchary EA, White AT, Franklin EC, Courtney CA, Green G, Green SJ. 2022. Are the working principles of fisheries management at work in Indonesia?. Mar Pol 140 (2-3): 105047. DOI: 10.1016/j.marpol.2022.105047.
Kartika GR, Sartimbul A, Widodo W. 2017. Varian genetik Sardinella lemuru di perairan Selat Bali. Jurnal Kelautan: Indones J Mar Sci 10 (1): 21-28. DOI: 10.21107/jk.v10i1.1615.
Katoh K, Rozewicki J, Yamada KD. 2019. MAFFT online service: Multiple sequence alignment, interactive sequence choice and visualization. Brief Bioinform 20 (4): 1160-1166. DOI: 10.1093/bib/bbx108.
Keat-Chuan Ng C, Aun-Chuan Ooi P, Wong WL, Khoo G. 2017. A review of fish taxonomy conventions and species identification techniques. J Surv Fish Sci 4 (1): 54-93. DOI: 10.17762/sfs.v4i1.140.
Khandan-Barani H, Alavi-Yeganeh MS. 2022. First record of white sardine Escualosa thoracata (Valenciennes, 1847) (Clupeiformes: Clupeidae) from the Oman Sea. Acta Zool Bulg 74 (1): 147-150.
Kombong CB, Arisuryanti T. 2018. The 16S and COI mitochondrial DNA nucleotide composition of stripped snakehead (Channa striata Bloch, 1793) from Lake Sentani, Jayapura, Papua. Jurnal Perikanan Universitas Gadjah Mada 20 (2): 57-62. DOI: 10.22146/jfs.35551.
Labrador K, Agmata A, Palermo JD, Ravago-Gotanco R, Pante MJ. 2021. Mitochondrial DNA reveals genetically structured haplogroups of Bali sardinella (Sardinella lemuru) in Philippine waters. Reg Stud Mar Sci 41: 101588. DOI: 10.1016/j.rsma.2020.101588.
Lavoué S, Miya M, Saitoh K, Ishiguro NB, Nishida M. 2007. Phylogenetic relationships among anchovies, sardines, herrings and their relatives (Clupeiformes), inferred from whole mitogenome sequences. Mol Phylogenet Evol 43 (3): 1096-105. DOI: 10.1016/j.ympev.2006.09.018.
Mahboob S, Al-Ghanim KA, Al-Misned F, Al-Balawi HA, Ashraf A, Al-Mulhim NM. 2019. Genetic diversity in tilapia populations in a freshwater reservoir assayed by randomly amplified polymorphic DNA markers. Saudi J Biol Sci 26 (2): 363-367. DOI: 10.1016/j.sjbs.2018.11.015.
Mahrus H, Al Idrus AG, Zulkifli L. 2022. Molecular phylogeny of anchovy (Clupeiformes: Clupeidae) from southern waters of Lombok using mitochondrial DNA CO1 gene sequences. Biodiversitas 23 (5): 2433-2443. DOI: 10.13057/biodiv/d230522.
Mahrus, Sumitro SB, Utomo DH, Sartimbul A, Toha AH, Widodo N. 2012. Genetic relationship of Sardinella lemuru from Lombok Strait with fish rich in omega-3 fatty acid. Bioinformation 8 (25): 1271-1276. DOI: 10.6026/97320630081271.
Mallik AK, Achyuthan NS, Ganesh SR, Pal SP, Vijayakumar SP, Shanker K. 2019. Discovery of a deeply divergent new lineage of vine snake (Colubridae: Ahaetuliinae: Proahaetulla gen. nov.) from the southern Western Ghats of Peninsular India with a revised key for Ahaetuliinae. PLoS One 14 (7): e0218851. DOI: 10.1371/journal.pone.0218851.
Martínez-Huitle CA, Panizza M. 2018. Electrochemical oxidation of organic pollutants for wastewater treatment. Curr Opin Electrochem 11: 62-71. DOI: 10.1016/j.coelec.2018.07.010.
Miya S, Takahashi H, Nakagawa M, Kuda T, Igimi S, Kimura B. 2015. Genetic characteristics of Japanese clinical Listeria monocytogenes isolates. PLoS One 10: e0122902. DOI: 10.1371/journal.pone.0122902.
Mohanty M, Jayasankar P, Sahoo L, Das P. 2015. A comparative study of COI and 16 S rRNA genes for DNA barcoding of cultivable carps in India. Mitochondrial DNA 26 (1): 79-87. DOI: 10.3109/19401736.2013.823172.
Nuryanto A, Dewi RE, Pramono H. 2019. Genetic homogeneity of commerson's anchovy (Stolephorus commersonnii) in Segara Anakan Cilacap Central Java Inferred from PCR-RFLP Marker. Biogenesis 7 (1): 14-23. DOI: 10.24252/bio.v7i1.6352.
Pereira LL, Damasceno JD, Leandro ED. 2016. Comparison of DNA extraction protocols for different marine fish tissues. Pan-Am J Aquat Sci 11 (2): 135-142.
Phillips JD, Gillis DJ, Hanner RH. 2019. Incomplete estimates of genetic diversity within species: Implications for DNA barcoding. Ecol Evol 9 (5): 2996-3010. DOI: 10.1002/ece3.4757.
Queiroz CD, Souza RF, Silva SS, de Mattos Dias CA, Fecury AA, de Oliveira E, da Cunha DB, Schneider H, Sampaio I. 2020. Molecular phylogeny of Clupeiformes and the placement of some Western Atlantic and Amazonian taxa. Biota Amazônia 10 (2): 14-19. DOI: 10.18561/2179-5746/biotaamazonia.v10n2p14-19.
Quilang JP, Santos BS, Ong PS, Basiao ZU, Fontanilla IK, Cao EP. 2011. DNA barcoding of the Philippine endemic freshwater sardine Sardinella tawilis (Clupeiformes: Clupeidae) and its marine relatives. Philipp Agric Sci 94 (3): 248-257.
Rahayu DA, Jannah M. 2019. DNA barcode hewan dan tumbuhan Indonesia. Yayasan Inspirasi Ide Berdaya. DOI: 10.17605/OSF.IO/TY7E5. [Indonesian]
Rosselló-Móra R, Amann R. 2015. Past and future species definitions for Bacteria and Archaea. Syst Appl Microbiol 38 (4): 209-216. DOI: 10.1016/j.syapm.2015.02.001.
Rozas J, Ferrer-Mata A, Sánchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos-Onsins SE, Sánchez-Gracia A. 2017. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Mol Evol 34 (12): 3299-302. DOI: 10.1093/molbev/msx248.
Saher NU, Niazi RM, Qureshi NA. 2018. Occurrence and abundance of commercially important fish species of family Clupeidae and Engraulidae in the MianiHor, Sonmiani Bay, Balochistan. Indian J Geo-Mar Sci 47 (03): 702-711.
Sartimbul A, Nakata H, Herawati EY, Rohadi E, Yona D, Harlyan LI, Putri AD, Winata VA, Khasanah RI, Arifin Z, Susanto RD. 2023. Monsoonal variation and its impact on the feeding habit of Bali Sardinella (S. lemuru Bleeker, 1853) in Bali Strait. Deep-Sea Res PT II 211: 105317. DOI: 10.1016/j.dsr2.2023.105317.
Sartimbul A, Rohadi E, Ikhsani SN, Listiyaningsih D. 2018. Morphometric and meristic variations among five populations of Sardinella lemuru Bleeker, 1853 from waters of Bali Strait, northern and southern-east Java and their relation to the environment. AACL Bioflux 11 (3): 744-752.
Shirk AJ, Landguth EL, Cushman SA. 2017. A comparison of individual?based genetic distance metrics for landscape genetics. Mol Ecol Resour 17 (6): 1308-1317. DOI: 10.1111/1755-0998.12684.
Sidiq M, Ahmed I, Bakhtiyar Y. 2021. Length-weight relationship, morphometric characters, and meristic counts of the coldwater fish (Heckel) from Dal Lake. Fish Aquat Life 29 (1): 29-34. DOI: 10.2478/aopf-2021-0003.
Suherman AS, Boesono H, Kurohman F, Muzakir AK. 2020. Kinerja Pelabuhan Perikanan Nusantara (PPN) Pengambengan Jembrana Bali. Indones J Fish Sci Technol 16 (2): 123-131. DOI: 10.14710/ijfst.16.2.123-131. [Indonesian]
Sukumaran S, Sebastian W, Gopalakrishnan A. 2016. Population genetic structure of Indian oil sardine, Sardinella longiceps along Indian coast. Gene 576 (1): 372-378. DOI: 10.1016/j.gene.2015.10.043.
Symonová R, Suh A. 2019. Nucleotide composition of transposable elements likely contributes to AT/GC compositional homogeneity of teleost fish genomes. Mobile DNA 10: 1-8. DOI: 10.1186/s13100-019-0195-y.
Tamura K, Stecher G, Kumar S. 2021. MEGA11: Molecular Evolutionary Genetics Analysis version 11. Mol Biol Evol 38 (7): 3022-3027. DOI: 10.1093/molbev/msab120.
Thomas Jr RC, Willette DA, Carpenter KE, Santos MD. 2014. Hidden diversity in sardines: Genetic and morphological evidence for cryptic species in the goldstripe sardinella, Sardinella gibbosa (Bleeker, 1849). PLoS One 9: e84719. DOI: 10.1371/journal.pone.0084719.
Tinungki GM, Sirajang N. 2019. The dynamic system analysis of lemuru fishery in Bali strait by using biological parameter yield of some surplus production models. IOP Conf Ser: Earth Environ Sci 279 (1): 012054. DOI: 10.1088/1755-1315/279/1/012054.
Tovar Verba J, Stow A, Bein B, Pennino MG, Lopes PF, Ferreira BP, Mortier M, Maia Queiroz Lima S, Pereira RJ. 2023. Low population genetic structure is consistent with high habitat connectivity in a commercially important fish species (Lutjanus jocu). Mar Biol 170: 5. DOI: 10.1007/s00227-022-04149-1.
Turan C, Uyan A, Atalay MA, Dogdu SA, Ayas D, Erguden D, Turan F, Gokoglu M, Gurlek M. 2023. Genetic differentiation of round sardinella Sardinella aurita (Clupeidae) populations from the Northeastern Mediterranean. J Ichthyol 63 (5): 962-968. DOI: 10.1134/S0032945223050119.
Wang ZL, Yang XQ, Wang T Z, Yu X. 2018. Assessing the effectiveness of mitochondrial COI and 16S rRNA genes for DNA barcoding of farmland spiders in China. Mitochondrial DNA Part A 29 (5): 695-702. DOI: 10.1080/24701394.2017.1350949.
Yang CH, Wang TW, Ng PK, Chan TY, Lin YY, Chan BK. 2022. Population genetic differentiation on the hydrothermal vent crabs Xenograpsus testudinatus along depth and geographical gradients in the Western pacific. Diversity 14 (3): 162. DOI: 10.3390/d14030162.
Yang L, Tan Z, Wang D, Xue L, Guan MX, Huang T, Li R. 2014. Species identification through mitochondrial rRNA genetic analysis. Sci Rep 4 (1): 4089. DOI: 10.1038/srep04089.
Zulfikar, Arisoesilaningsih E, Indriani S, Fernandes AAR. 2020. Community structure of fruit tree species on successful marginal land conservation in Jombang Regency, East Java Province, Indonesia. J Phys Conf Ser 1563: 012025. DOI: 10.1088/1742-6596/1563/1/012025.