Complete mitochondrial genome of Devario shanensis (Cypriniformes: Danionidae: Danioninae): genome characterization and phylogenetic consideration

References

• Alam MJ, Andriyono S, Eunus ATM, Rahman MM, Kim HW. 2018. Mitochondrial genome of Mola carplet, Amblypharyngodon mola (Hamilton, 1822) and its evolutional relationship in subfamily danioninae. Mitochondrial DNA Part B Resour. 4(1):650–651. doi:10.1080/23802359.2018.1553525.
   Web of Science ®Google Scholar
• Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 30(15):2114–2120. doi:10.1093/bioinformatics/btu170.
   PubMed Web of Science ®Google Scholar
• Chu XL. 1981. A preliminary revision of fishes of the genus Danio from China. Zool. Res. 2:145–156.
   Google Scholar
• Chen XJ, Liu WZ, Song L, Liu HX. 2023. Assembly and phylogenetic analysis of the complete mitogenome of Devario interruptus (Teleostei, Cypriniformes, Danionidae). Mitochondrial DNA Part B Resour. 8(2):187–191. doi:10.1080/23802359.2022.2151831.
   PubMed Web of Science ®Google Scholar
• Darriba D, Taboada GL, Doallo R, Posada D. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nat Methods. 9(8):772–772. doi:10.1038/nmeth.2109.
   PubMed Web of Science ®Google Scholar
• Fang F. 2000. Barred Danio species from the Irrawaddy River drainage (Teleostei, Cyprinidae). Ichthyological Res. 47:13–26. doi:10.1007/BF02674309.
   Web of Science ®Google Scholar
• Fang F, Noren M, Liao TY, Kallersjo M, Kullander SO. 2010. Molecular phylogenetic interrelationships of the south Asian cyprinid genera Danio, Devario and Microrasbora (Teleostei, Cyprinidae, Danioninae). Zool Scr. 38(3):237–256. doi:10.1111/j.1463-6409.2008.00373.x.
   Web of Science ®Google Scholar
• Grant JR, Stothard P. 2008. The CGView server: a comparative genomics tool for circular genomes. Nucleic Acids Res. 36(Web Server issue):W181–W184. doi:10.1093/nar/gkn179.
   PubMedGoogle Scholar
• Huang Q, Ji X, Wang K. 2016. The complete mitochondrial genome of dwarf danio, Danio nigrofasciatus. Mitochondrial DNA Part A Resour. 27:2854–2855. doi:10.3109/19401736.2015.1053126.
   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
• Kumar S, Stecher G, Tamura K. 2016. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 33(7):1870–1874. doi:10.1093/molbev/msw054.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 25(14):1754–1760. doi:10.1093/bioinformatics/btp324.
   PubMed Web of Science ®Google Scholar
• Liu L, Chen L, Wu YN, Wang XQ, Liao FC, Wang DW, Huang XQ, Deng SM, Liu LL. 2016. Base composition of the Danio chrysotaenitus complete mitochondrial genome. Mitochondrial DNA Part A Resour. 27(5):3370–3371. doi:10.3109/19401736.2015.1018225.
   PubMed Web of Science ®Google Scholar
• Liu WZ, Song L, Chen XJ, Liu HX. 2023. The complete mitochondrial genome of Rhinogobius szechuanensis (Gobiiformes: ggobiidae: gobionellinae). Mitochondrial DNA Part B Resour. 8(2):192–196. doi:10.1080/23802359.2023.2167473.
   PubMed Web of Science ®Google Scholar
• Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. 2017. MetaSPAdes: a new versatile metagenomic assembler. Genome Res. 27(5):824–834. doi:10.1101/gr.213959.116.
   PubMed Web of Science ®Google Scholar
• Norén M, Kullander S. 2018. The enigmatic Betadevario ramachandrani (Teleostei: cyprinidae: danioninae): phylogenetic position resolved by mitogenome analysis, with remarks on the prevalence of chimeric mitogenomes in GenBank. Cogent Biol. 4(1):1525857. doi:10.1080/23312025.2018.1525857.
   Web of Science ®Google Scholar
• 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: effi-cient Bayesian phylogenetic inference and model choice across a large model space. Systemat Biol. 61(3):539–542. doi:10.1093/sysbio/sys029.
   PubMed Web of Science ®Google Scholar
• Sen N. 2007. Description of a new species of Brachydanio weber and de beaufort, 1916 (Pisces: Cypriniformes: Cyprinidae) from Meghalaya, north east India with a note on comparative studies of other known species. Rec. Zool. Surv. India. 107(4):27–31.
   Google Scholar
• Song L, Chen XJ, Han XP, Gu YW. 2022. Complete mitochondrial genome and phylogenetic analysis of Danio roseus (Teleostei, Cypriniformes, Danionidae.). Mitochondrial DNA Part B Resour. 7(2):350–352. doi:10.1080/23802359.2022.2030257.
   PubMed Web of Science ®Google Scholar
• Song L, Chen XJ, Zhang S, Wang Q. 2022. Complete mitochondrial genome of Devario kakhienensis (Cypriniformes: Danionidae: Danioninae): genome characterization and phylogenetic consideration. Mitochondrial DNA Part B. 7(9):1685–1687. doi:10.1080/23802359.2022.2122749.
   PubMed Web of Science ®Google Scholar
• Tang KL, Agnew MK, Hirt MV, Sado T, Schneider LM, Freyhof J, Sulaiman Z, Swartz E, Vidthayanon C, Miya M, et al. 2010. Systematics of the subfamily Danioninae (Teleostei: Cypriniformes: Cyprinidae). Mol Phylogenet Evol. 57(1):189–214. doi:10.1016/j.ympev.2010.05.021.
   PubMed Web of Science ®Google Scholar