The complete mitochondrial genome and phylogenetic position of Schizothorax argentatus (Cyprinomorpha: Crypriniformes: Cyprinidae)

References

• Avise JC. 2000. Phylogeography: the history and formation of species. Cambridge (MA): Harvard University Press.
   Google Scholar
• Baeza JA. 2022. An introduction to the special section on crustacean mitochondrial genomics: improving the assembly, annotation, and characterization of mitochondrial genomes using user-friendly and open-access bioinformatics tools, with decapod crustaceans as an example. J Crustac Biol. 42(1):1–4. doi: 10.1093/jcbiol/ruac012.
   Web of Science ®Google Scholar
• Benson G. 1999. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27(2):573–580. doi: 10.1093/nar/27.2.573.
   PubMed Web of Science ®Google Scholar
• Boore JL. 1999. Animal mitochondrial genomes. Nucleic Acids Res. 27(8):1767–1780. doi: 10.1093/nar/27.8.1767.
   PubMed Web of Science ®Google Scholar
• Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu C-H, Xie D, Suchard MA, Rambaut A, Drummond AJ. 2014. Beast 2: a software platform for Bayesian evolutionary analysis. PLoS Comput Biol. 10(4):e1003537. doi: 10.1371/journal.pcbi.1003537.
   PubMed Web of Science ®Google Scholar
• Cao W, Chen Y, Wu Y, et al. 1981. The origin and evolution of the fissiparous fish and its relationship with the uplift of the Qinghai-Tibet Plateau. In: The age, magnitude, and form of the uplift of the Qinghai-Tibet Plateau. Beijing: Science Press, p. 118–130.
   Google Scholar
• Chan PP, Lin BY, Mak AJ, Lowe TM. 2021. tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes. Nucleic Acids Res. 49(16):9077–9096. doi: 10.1093/nar/gkab688.
   PubMed Web of Science ®Google Scholar
• Chen X, Yue P, Lin R. 1984. Major groups the family Cyprinidae and their phylogenetic relationships. Acta Zootaxon Sin. 9(4):424–440.
   Google Scholar
• Cheng H, Zha Y, Gao D, et al. 2020. Study on methods of DNA extraction from different muscle tissues in animal. J Northwest Minzu Univ (Nat Sci Ed). 41(2):73–79.
   Google Scholar
• Dierckxsens N, Mardulyn P, Smits G. 2017. Novoplasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Res. 45(4):e18. doi: 10.1093/nar/gkw955.
   PubMed Web of Science ®Google Scholar
• Drummond AJ, Suchard MA, Xie D, Rambaut A. 2012. Bayesian phylogenetics with Beauti and the Beast 1.7. Mol Biol Evol. 29(8):1969–1973. doi: 10.1093/molbev/mss075.
   PubMed Web of Science ®Google Scholar
• Grauer D, Li WH. 2000. Fundamentals of molecular evolution. Sunderland (MA): Sinauer.
   Google Scholar
• Gruber AR, Lorenz R, Bernhart SH, Neuböck R, Hofacker IL. 2008. The Vienna RNA Websuite. Nucleic Acids Res. 36(Web Server issue):W70–W74. doi: 10.1093/nar/gkn188.
   PubMed Web of Science ®Google Scholar
• Guo Y, Cai L, Zhang R, et al. 1999. The native fisher distributed and made of evolution in the Yili River (China’s section). Arid Zone Res. 16(2):31–35.
   Google Scholar
• He D, Chen Y. 2006. Biogeography and molecular phylogeny of the genus Schizothorax (Teleostei: Cyprinidae) in China inferred from cytochrome b sequences. J Biogeogr. 33(8):1448–1460. doi: 10.1111/j.1365-2699.2006.01510.x.
   Web of Science ®Google Scholar
• He D, Chen Y. 2007. Molecular phylogeny and biogeography of the highly specialized grade schizothoracine fishes (Teleostei: Cyprinidae) inferred from cytochrome b sequences. Chin Sci Bull. 52(6):777–788. doi: 10.1007/s11434-007-0123-2.
   Google Scholar
• He D, Chen Y, Chen Y, Chen Z. 2004. Molecular phylogeny of the specialized schizothoracine fishes (Teleostei: Cyprinidae), with their implications for the uplift of the Qinghai-Tibetan Plateau. Chin Sci Bull. 49(1):39–48. doi: 10.1360/03wc0212.
   Google Scholar
• Hillis D, Bull J. 1993. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst Biol. 42(2):182–192. doi: 10.2307/2992540.
   Web of Science ®Google Scholar
• Hou Z, Xie Y, Zeng P, et al. 2006. Metallogenesis in Tibetan collosional orogenic belt: II. Mineralization in late-collisional transformation setting. Min Depos. 25(5):23.
   Google Scholar
• Huelsenbeck JP, Rannala B. 2004. Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. Syst Biol. 53(6):904–913. doi: 10.1080/10635150490522629.
   PubMed Web of Science ®Google Scholar
• Iwasaki W, Fukunaga T, Isagozawa R, Yamada K, Maeda Y, Satoh TP, Sado T, Mabuchi K, Takeshima H, Miya M, et al. 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.
   PubMed Web of Science ®Google Scholar
• Jin J-J, Yu W-B, Yang J-B, Song Y, dePamphilis CW, Yi T-S, Li D-Z. 2020. Getorganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol. 21(1):1–31. doi: 10.1186/s13059-020-02154-5.
   Web of Science ®Google Scholar
• Kerpedjiev P, Hammer S, Hofacker IL. 2015. Forna (force-directed RNA): simple and effective online RNA secondary structure diagrams. Bioinformatics. 31(20):3377–3379. doi: 10.1093/bioinformatics/btv372.
   PubMed Web of Science ®Google Scholar
• Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, et al. 2007. Clustal W and clustal X version 2.0. Bioinformatics. 23(21):2947–2948. doi: 10.1093/bioinformatics/btm404.
   PubMed Web of Science ®Google Scholar
• Lee WJ, Conroy J, Howell WH, Kocher TD. 1995. Structure and evolution of teleost mitochondrial control regions. J Mol Evol. 41(1):54–66. doi: 10.1007/BF00174041.
   PubMed Web of Science ®Google Scholar
• Levinson G, Gutman GA. 1987. Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol Biol Evol. 4(3):203–221.
   PubMed Web of Science ®Google Scholar
• Mamilov N. 2020. Schizothorax argentatus. The IUCN red list of threatened species 2020: e.T156744412A156744418. IUCN.
   Google Scholar
• Minh BQ, Nguyen MA, von Haeseler A. 2013. Ultrafast approximation for phylogenetic bootstrap. Mol Biol Evol. 30(5):1188–1195. doi: 10.1093/molbev/mst024.
   PubMed Web of Science ®Google Scholar
• Nardi F, Carapelli A, Frati F. 2012. Repeated regions in mitochondrial genomes: distribution, origin and evolutionary significance. Mitochondrion. 12(5):483–491. doi: 10.1016/j.mito.2012.07.105.
   PubMed Web of Science ®Google Scholar
• Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. 2015. IQ-tree: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 32(1):268–274. doi: 10.1093/molbev/msu300.
   PubMed Web of Science ®Google Scholar
• Ojala D, Montoya J, Attardi G. 1981. tRNA punctuation model of RNA processing in human mitochondria. Nature. 290(5806):470–474. doi: 10.1038/290470a0.
   PubMed Web of Science ®Google Scholar
• Perna N, Kocher T. 1995. Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. J Mol Evol. 41(3):353–358. doi: 10.1007/BF01215182.
   PubMed Web of Science ®Google Scholar
• Qi D, Guo SC, Zhao X. 2006. Molecular systematics of two enigmatic fishes in the genus Schizopygopsis in the Qinghai-Tibetan Plateau. Acta Zool Sin Engl Ed. 52(6):1058–1066.
   Google Scholar
• Qi J-W, Shi L-Y, Lin Y-Q, Han J. 2019. The complete mitochondrial genomes of three species in the genus Macridiscus Dall, 1902 (Bivalvia: Veneridae) and their phylogenetic implications. J Molluscan Stud. 85(2):271–279. doi: 10.1093/mollus/eyz009.
   Google Scholar
• Rambaut A, Drummond AJ, Xie D, Baele G, Suchard MA. 2018. Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Syst Biol. 67(5):901–904. doi: 10.1093/sysbio/syy032.
   PubMed Web of Science ®Google Scholar
• Ranwez V, Harispe S, Delsuc F, Douzery EJP. 2011. MACSE: multiple alignment of coding sequences accounting for frameshifts and stop codons. PLoS One. 6(9):e22594. doi: 10.1371/journal.pone.0022594.
   PubMed Web of Science ®Google Scholar
• Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 19(12):1572–1574. doi: 10.1093/bioinformatics/btg180.
   PubMed Web of Science ®Google Scholar
• Rustam D, Yuan X, Zhang Q, et al. 2022. Study on the phylogeny of schizothoracids based on complete mitochondrial genome. J Fish Sci China. 29(6):781–791.
   Google Scholar
• Saccone C, De Giorgi C, Gissi C, Pesole G, Reyes A. 1999. Evolutionary genomics in Metazoa: the mitochondrial DNA as a model system. Gene. 238(1):195–209. doi: 10.1016/s0378-1119(99)00270-x.
   PubMed Web of Science ®Google Scholar
• Satoh TP, Miya M, Mabuchi K, Nishida M. 2016. Structure and variation of the mitochondrial genome of fishes. BMC Genom 17(1):719. doi: 10.1186/s12864-016-3054-y.
   PubMed Web of Science ®Google Scholar
• Talavera G, Castresana J. 2007. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol. 56(4):564–577. doi: 10.1080/10635150701472164.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• van Dijk EL, Auger H, Jaszczyszyn Y, Thermes C. 2014. Ten years of next-generation sequencing technology. Trends Genet. 30(9):418–426. doi: 10.1016/j.tig.2014.07.001.
   PubMed Web of Science ®Google Scholar
• Wang C, Song Y, Zi F, Ge J, Chen S. 2022. The mitochondrial genome of Schizothorax argentatus from Northern Xinjiang and its phylogenetic analysis. Mitochondrial DNA B Resour. 7(10):1834–1836. doi: 10.1080/23802359.2022.2133555.
   PubMed Web of Science ®Google Scholar
• Wang D, Zhang Y, Zhang Z, Zhu J, Yu J. 2010. KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies. Genom Proteom Bioinf. 8(1):77–80. doi: 10.1016/S1672-0229(10)60008-3.
   PubMedGoogle Scholar
• Wilcox TP, Zwickl DJ, Heath TA, Hillis DM. 2002. Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support. Mol Phylogenet Evol. 25(2):361–371. doi: 10.1016/s1055-7903(02)00244-0.
   PubMed Web of Science ®Google Scholar
• Wu Y. 1984. Systematic studies on the cyprinid fishes of the subfamily Schizothoracinae from China. Acta Biol Plateau Sin. 3:119–140.
   Google Scholar
• Yang L, Sado T, Vincent Hirt M, Pasco-Viel E, Arunachalam M, Li J, Wang X, Freyhof J, Saitoh K, Simons AM, et al. 2015. Phylogeny and polyploidy: resolving the classification of cyprinine fishes (Teleostei: Cypriniformes). Mol Phylogenet Evol. 85:97–116. doi: 10.1016/j.ympev.2015.01.014.
   PubMed Web of Science ®Google Scholar
• Yue P. 2000. Fanuna sinaica (osteichthyes): cypriniformes, III. Beijing (China): Science Press.
   Google Scholar
• Zhang D, Gao F, Jakovlić I, Zou H, Zhang J, Li WX, Wang GT. 2020. PhyloSuite: an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. Mol Ecol Resour. 20(1):348–355. doi: 10.1111/1755-0998.13096.
   PubMed Web of Science ®Google Scholar
• Zhang K, Wang G, Hong H, et al. 2013. The study of the cenozoic uplift in the Tibetan Plateau: a review. Geol Bull China. 32(1):1–18.
   Google Scholar