Published December 26, 2022
| Version v1
Journal article
Open
Comparative Analysis of Complete Mitogenomes of Two Oxyurichthys Gobies and Their Phylogenetic Implication
Authors/Creators
- 1. Institute of Marine Environment and Resources, Vietnam Academy of Science and Technology, Haiphong, Vietnam.
- 2. Department of Biotechnology, Sangmyung University, Seoul 03016, South Korea.
- 3. Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX 78412-5806, USA. & Florida Museum of Natural History, University of Florida, Gainesville, FL 32611-7800, USA
Description
Nguyen, Quan Van, Pham, Chien Van, Nguyen, Thanh Xuan, Kim, Jung-Il, Pezold, Frank L., Nguyen, The Duc, Le, Hiep Minh, Kim, Chang-Bae, Dang, Viet Do Hung, Do, Thinh Dinh (2022): Comparative Analysis of Complete Mitogenomes of Two Oxyurichthys Gobies and Their Phylogenetic Implication. Zoological Studies 61 (88): 1-14, DOI: 10.6620/ZS.2022.61-88, URL: http://dx.doi.org/10.5281/zenodo.12827569
Files
source.pdf
Linked records
Additional details
Identifiers
- LSID
- urn:lsid:plazi.org:pub:CF3B532EFF900A2CFFF9FF93FFF70A67
References
- Adrian-Kalchhauser I, Svensson O, Kutschera VE, Rosenblad MA, Pippel M, Winkler S, Schloissnig S, Blomberg A, Burkhardt- Holm P. 2017. The mitochondrial genome sequences of the round goby and the sand goby reveal patterns of recent evolution in gobiid fish. BMC Genom 18:177. doi:10.1186/s12864-017- 3550-8.
- Agorreta A, San Mauro D, Schliewen U, Van Tassell JL, Kovacic M, Zardoya R, Ruber L. 2013. Molecular phylogenetics of Gobioidei and phylogenetic placement of European gobies. Mol Phyl Evol 69(3):619-633. doi:10.1016/j.ympev.2013.07.017.
- Akihito, Iwata A, Kobayashi T, Ikeo K, Imanishi T, Ono H, Umehara Y, Hamamatsu C, Sugiyama K, Ikeda Y, Sakamoto K, Fumihito A, Ohno S, Gojobori T. 2000. Evolutionary aspects of gobioid fishes based upon a phylogenetic analysis of mitochondrial cytochrome b genes. Gene 259(1-2):5-15. doi:10.1016/S0378- 1119(00)00488-1.
- Bell KNI. 1999. An overview of goby-fry fisheries. Naga, ICLARM Quarterly 22(4):30-36.
- Bernt M, Donath A, Juhling F, Externbrink F, Florentz C, Fritzsch G, Putz J, Middendorf M, Stadler PF. 2013. MITOS: improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol 69(2):313-319. doi:10.1016/j.ympev.2012.08. 023.
- Betancur RR, Wiley EO, Arratia G, Acero A, Bailly N, Miya M, Lecointre G, Orti G. 2017. Phylogenetic classification of bony fishes. BMC Evol Biol 17(1):1-40. doi:10.1186/s12862-017- 0958-3.
- Castresana J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Phylogenet Evol 17(4):540-552. doi:10.1093/oxfordjournals.molbev. a026334.
- Chan PP, Lowe TM. 2019. tRNAscan-SE: Searching for tRNA Genes in Genomic Sequences. Methods Mol Biol 1962:1-14. doi:10.1007/978-1-4939-9173-0_1.
- Cheng YZ, Xu TJ, Jin XX, Tang D, Wei T, Sun YY, Meng FQ, Shi G, Wang RX. 2012. Universal primers for amplification of the complete mitochondrial control region in marine fish species. Mol Biol 46(5):727-730. doi:10.1134/S0026893312040024.
- Clayton DA. 1991. Replication and transcription of vertebrate mitochondrial DNA. Ann Rev Cell Biol 7:453-478. doi:10.1146/ annurev.cb.07.110191.002321.
- Gilbert CR, Randall JE. 1979. Two new western Atlantic species of the gobiid fish genus Gobionellus, with remarks on characteristics of the genus. Northeast Gulf Sci 3(1):27-47. doi:10.18785/negs.0301.03.
- Hoese DF. 1986. Family 240: Gobiidae. In: Smith MM, Heemstra PC (eds.) Smith's Sea Fishes. Springer-Verlag, New York, pp. 774-807.
- Iwasaki W, Fukunaga T, Isagozawa R, Yamada K, Maeda Y, Satoh TP, Sado T, Mabuchi K, Takeshima H, Miya M, Nishida M. 2013. MitoFish and MitoAnnotator: a mitochondrial genome database of fish with an accurate and automatic annotation pipeline. Mol Biol Evol 30(11):2531-2540. doi:10.1093/molbev/mst141.
- Jin XX, Wang RX, Wei T, Tang D, Xu TJ. 2015. Complete mitochondrial genome sequence of Tridentiger bifasciatus and Tridentiger barbatus (Perciformes, Gobiidae): a mitogenomic perspective on the phylogenetic relationships of Gobiidae. Mol Biol Rep 42(1):253-265. doi:10.1007/s11033-014-3768-3.
- Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30(4):772-780. doi:10.1093/molbev/mst010.
- Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Meintjes P, Drummond A. 2012. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28(12):1647- 1649. doi:10.1093/bioinformatics/bts199.
- Kumar S, Stecher G, Li M, Knyaz C, Tamura K. 2018. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35(6):1547-1549. doi:10.1093/molbev/ msy096.
- Lanfear R, Frandsen PB, Wright AM, Senfeld T, Calcott B. 2017. PartitionFinder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Mol Biol Evol 34(3):772-773. doi:10.1093/molbev/ msw260.
- Larson HK, Jaafar Z, Lim KKP. 2008. An annotated checklist of the gobioid fishes of Singapore. Raffles Bull Zool 56(1):135-155. doi:10.5281/zenodo.5354604.
- Lee W, Conroy J, Howell WH, Kocher TD. 1995. Structure and evolution of teleost mitochondrial control regions. J Mol Evol 41:54-66. doi:10.1007/BF00174041.
- Lee WJ, Kocher TD. 1995. Complete sequence of a sea Lamprey (Petromyzon marinus) mitochondrial genome: early establishment of the vertebrate genome organization. Genetics 139(2):873-887. doi:10.1093/genetics/139.2.873.
- Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, Von Haeseler A, Lanfear R. 2020. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol 37(5):1530-1534. doi:10.1093/molbev/msaa015.
- Patzner RA, Van Tassell JL, Kovacic M, Kapoor BG (eds). 2011. The Biology of Gobies. Science Publishers, Enfield, USA.
- Perna NT, Kocher TD. 1995. Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. J Mol Evol 41(3):353-358. doi:10.1007/BF00186547.
- Pezold F. 1991. The status of the gobioid genus Paroxyurichthys. Japan J Ich 37:344-353. doi:10.11369/jji1950.37.344.
- Pezold F. 1998. Three new species of Oxyurichthys (Teleostei: Gobiidae) from the Indian and Pacific Oceans. Copeia 1998(3):687-695. doi:10.2307/1447798.
- Pezold F. 2004. Phylogenetic analysis of the genus Gobionellus (Teleostei: Gobiidae). Copeia 2004(2):260-280. doi:10.1643/CI-02-218R3.
- Pezold FL, Larson HK. 2015.A revision of the fish genus Oxyurichthys (Gobioidei: Gobiidae) with descriptions of four new species. Zootaxa 3988(1):1. doi:10.11646/zootaxa.3988.1.1.
- Rambaut A. 2018. FigTree, Version 1.4.4. Available at: https://tree. bio.ed.ac.uk/softw are/figtr ee/. Accessed 20 Feb. 2022.
- Rambaut A, Drummond AJ, Xie D, Baele G, Suchard MA. 2018. Posterior summarisation in Bayesian phylogenetics using Tracer 1.7. Syst Biol 67(5):901-904. doi:10.1093/sysbio/syy032.
- Ronquist F, Teslenko M, Van Der Mark P, Ayres DL, Darling A, Hohna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP. 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 61(3):539- 542. doi:10.1093/sysbio/sys029.
- Satoh TP, Miya M, Mabuchi K, Nishida M. 2016. Structure and variation of the mitochondrial genome of fishes. BMC Genomics 17:719. doi:10.1186/s12864-016-3054-y.
- Shadel GS, Clayton DA. 1997. Mitochondrial DNA maintenance in vertebrates. Ann Rev Biochem 66:409-435. doi:10.1146/annurev. biochem.66.1.409.
- Sun YN, Jin XX, Zhao SL, Liu XZ. 2013. Mitochondrial genome of Cryptocentrus yatsui (Perciformes, Gobioidei) and phylogenetic consideration within the genus Cryptocentrus. Mitochondrial DNA 24(4):376-378. doi:10.3109/19401736.2013.763236.
- Thacker CE. 2003. Molecular phylogeny of the gobioid fishes (Teleostei: Perciformes: Gobioidei). Mol Phylogenet Evol 26(3):354-368. doi:10.1016/S1055-7903(02)00361-5.
- Thacker CE. 2009. Phylogeny of Gobioidei and placement within Acanthomorpha, with a new classification and investigation of diversification and character evolution. Copeia 2009(1):93-104. doi:10.1643/CI-08-004.
- Thacker CE. 2015. Biogeography of goby lineages (Gobiiformes: Gobioidei): origin, invasions and extinction throughout the Cenozoic. Jour Biogeogr 42(9):1615-1625. doi:10.1111/jbi. 12545.
- Thacker CE, Roje DM. 2011. Phylogeny of Gobiidae and identification of gobiid lineages. Syst Biodivers 9(4):329-347. doi:10.1080/14772000.2011.629011.
- Tornabene L, Chen Y, Pezold F. 2013. Gobies are deeply divided: phylogenetic evidence from nuclear DNA (Teleostei: Gobioidei: Gobiidae). Syst Biod 11(3):345-361. doi:10.1080/14772000.201 3.818 589.
- Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, Rozen SG. 2012. Primer3-new capabilities and interfaces. Nucleic Acids Res 40(15):e115. doi:10.1093/nar/gks596.
- Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PDN. 2005. DNA barcoding Australia's fish species. Philos Trans R Soc Lond B Biol Sci 360(1462):1847-1857. doi:10.1098/rstb.2005.1716.
- Yokoo T, Kanou K, Moteki M, Kohno H, Tongnunui P, Kurokura H. 2012. Assemblage structures and spatial distributions of small gobioid fishes in a mangrove estuary, southern Thailand. Fish Sci 78:237-247. doi:10.1007/s12562-011-0447-3.
- Yu P, Zhou L, Yang WT, Miao LJ, Li Z, Zhang XJ, Wang Y, Gui JF. 2021. Comparative mitogenome analyses uncover mitogenome features and phylogenetic implications of the subfamily cobitinae. BMC Genomics 22(1):50. doi:10.1186/s12864-020-07360-w.
- Zarev V, Apostolou A, Velkov B, Vassilev M. 2013. Bulgarian black sea gobies as important object in the commercial fishing. Bulg J Agric Sci 19(2):233-236.
- Zuker M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31(13):3406-3415. doi:10.1093/nar/gkg595.