Genomics & Informatics

Korea Genome Organization (한국유전체학회)
권호 표지
DOI QR코드

DOI QR Code

Sequencing and annotation of the complete mitochondrial genome of a threatened labeonine fish, Cirrhinus reba

  • Islam, Mohammad Nazrul (Department of Biotechnology, Sher-e-Bangla Agricultural University) ;
  • Sultana, Shirin (Fisheries Biotechnology Division, National Institute of Biotechnology) ;
  • Alam, Md. Jobaidul (Department of Fisheries, Ministry of Fisheries and Livestock)
  • Received : 2020.06.01
  • Accepted : 2020.09.01
  • Published : 2020.09.30
Download PDF
⟨ Previous Next ⟩

Abstract

The mitochondrial genome of a species is an essential resource for its effective conservation and phylogenetic studies. In this article, we present sequencing and characterization of the complete mitochondrial genome of a threatened labeonine fish, Cirrhinus reba collected from Khulna region of Bangladesh. The complete mitochondrial genome was 16,597 bp in size, which formed a circular double-stranded DNA molecule containing a total of 37 mitochondrial genes (13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes) with two non-coding regions, an origin of light strand replication (OL) and a displacement loop (D-loop), similar structure with other fishes of Teleostei. The phylogenetic tree demonstrated its close relationship with labeonine fishes. The complete mitogenome of Cirrhinus reba (GenBank no. MN862482) showed 99.96% identity to another haplotype of Cirrhinus reba (AP013325), followed by 90.18% identity with Labeo bata (AP011198).

Keywords

References

  1. Sultana S, Hasan MM, Hossain MS, Islam MR, Salimullah M, Sarder MR, et al. Cryogenic preservation of critically endangered Cirrhinus reba fish sperm. Int J Fish Aquat Stud 2017;5:334-339.
  2. Ethin R, Hossain MS, Roy A, Rutegwa M. Stock identification of minor carp, Cirrhinus reba, Hamilton 1822 through landmark-based morphometric and meristic variations. Fish Aquat Sci 2019;22:12. https://doi.org/10.1186/s41240-019-0128-1
  3. International Union for Conservation of Nature. Bangladesh: Red Book of Threatened Fishes of Bangladesh. Gland: International Union for Conservation of Nature, 2015.
  4. Sarkar UK, Negi RS, Deepak PK, Singh SP, Srivastava SM, Roy D. Captive breeding of vulnerable Indian carp Cirrhinus reba with Ovaprim for conservation of wild populations. Aquac Asia 2004;9:5-7.
  5. Rahman MA, Zaher M, Azimuddin KM. Development of fingerling production techniques in nursery ponds for the critically endangered reba carp, Cirrhinus ariza (Hamilton, 1807). Turk J Fish Aquat Sci 2009;9:165-172.
  6. Artuso L, Romano A, Verri T, Domenichini A, Argenton F, Santorelli FM, et al. Mitochondrial DNA metabolism in early development of zebrafish (Danio rerio). Biochim Biophys Acta 2012;1817:1002-1011. https://doi.org/10.1016/j.bbabio.2012.03.019
  7. Anderson S, Bankier AT, Barrell BG, de Bruijn MH, Coulson AR, Drouin J, et al. Sequence and organization of the human mitochondrial genome. Nature 1981;290:457-465. https://doi.org/10.1038/290457a0
  8. Giles RE, Blanc H, Cann HM, Wallace DC. Maternal inheritance of human mitochondrial DNA. Proc Natl Acad Sci U S A 1980;77:6715-6719. https://doi.org/10.1073/pnas.77.11.6715
  9. Brown WM, George M Jr, Wilson AC. Rapid evolution of animal mitochondrial DNA. Proc Natl Acad Sci U S A 1979;76:1967-1971. https://doi.org/10.1073/pnas.76.4.1967
  10. Ingman M, Gyllensten U. mtDB: Human Mitochondrial Genome Database, a resource for population genetics and medical sciences. Nucleic Acids Res 2006;34:D749-D751. https://doi.org/10.1093/nar/gkj010
  11. Macey JR, Papenfuss TJ, Kuehl JV, Fourcade HM, Boore JL. Phylogenetic relationships among amphisbaenian reptiles based on complete mitochondrial genomic sequences. Mol Phylogenet Evol 2004;33:22-31. https://doi.org/10.1016/j.ympev.2004.05.003
  12. Meusnier I, Singer GA, Landry JF, Hickey DA, Hebert PD, Hajibabaei M. A universal DNA mini-barcode for biodiversity analysis. BMC Genomics 2008;9:214. https://doi.org/10.1186/1471-2164-9-214
  13. Saxena N, Taneja N, Shome P, Mani S. Mitochondrial donation: a boon or curse for the treatment of incurable mitochondrial diseases. J Hum Reprod Sci 2018;11:3-9. 29681709 https://doi.org/10.4103/jhrs.JHRS_54_17
  14. Handy SM, Deeds JR, Ivanova NV, Hebert PD, Hanner RH, Ormos A, et al. A single-laboratory validated method for the generation of DNA barcodes for the identification of fish for regulatory compliance. J AOAC Int 2011;94:201-210. https://doi.org/10.1093/jaoac/94.1.201
  15. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, et al. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 2012;28:1647-1649. https://doi.org/10.1093/bioinformatics/bts199
  16. Laslett D, Canback B. ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences. Bioinformatics 2008;24:172-175. https://doi.org/10.1093/bioinformatics/btm573
  17. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 2016;33:1870-1874. https://doi.org/10.1093/molbev/msw054
  18. Cheng J, Ma GQ, Song N, Gao TX. Complete mitochondrial genome sequence of bighead croaker Collichthys niveatus (Perciformes, Sciaenidae): a mitogenomic perspective on the phylogenetic relationships of Pseudosciaeniae. Gene 2012;491:210-223. https://doi.org/10.1016/j.gene.2011.09.020
  19. Alam MJ, Andriyono S, Eunus AT, Rahman MM, Kim HW. Mitochondrial genome of Mola carplet, Amblypharyngodon mola (Hamilton, 1822) and its evolutional relationship in subfamily Danioninae. Mitochondrial DNA B Resour 2019;4:650-651. https://doi.org/10.1080/23802359.2018.1553525
  20. Satoh TP, Miya M, Mabuchi K, Nishida M. Structure and variation of the mitochondrial genome of fishes. BMC Genomics 2016;17:719. https://doi.org/10.1186/s12864-016-3054-y
  21. Ojala D, Montoya J, Attardi G. tRNA punctuation model of RNA processing in human mitochondria. Nature 1981;290:470-474. https://doi.org/10.1038/290470a0
  22. Miya M, Nishida M. Organization of the mitochondrial genome of a deep-sea fish, Gonostoma gracile (Teleostei: Stomiiformes): first example of transfer RNA gene rearrangements in bony fishes. Mar Biotechnol (NY) 1999;1:416-426. https://doi.org/10.1007/PL00011798
  23. Zhao L, Gao T, Lu W. Complete mitochondrial DNA sequence of the endangered fish (Bahaba taipingensis): mitogenome characterization and phylogenetic implications. Zookeys 2015;181-195.
  24. Yang H, Xia J, Zhang JE, Yang J, Zhao H, Wang Q, et al. Characterization of the complete mitochondrial genome sequences of three croakers (Perciformes, Sciaenidae) and novel insights into the phylogenetics. Int J Mol Sci 2018;19:3646. https://doi.org/10.3390/ijms19113646
  25. Boore JL. Animal mitochondrial genomes. Nucleic Acids Res 1999;27:1767-1780. https://doi.org/10.1093/nar/27.8.1767