Abstract
The yellowtail rasbora (Rasbora tornieri) is a miniature ray-finned fish categorized under the genus Rasbora in the family of Cyprinidae. In this study, a complete mitogenome sequence of R. tornieri was sequenced using four primers targeting two halves of the mitogenome with overlapping flanking regions. The size of mitogenome was 16,573 bp, housing 22 transfer RNA genes, 13 protein-coding genes, two ribosomal RNA genes and a putative control region. Identical gene organization was detected between this species and other members of Rasbora genus. The heavy strand encompassed 28 genes while the light strand accommodated the other nine genes. Most protein-coding genes execute ATG as start codon, excluding COI and ND3 genes, which utilized GTG instead. The central conserved sequence blocks (CSB-E, CSB-F and CSB-D), variable sequence blocks (CSB-1, CSB-3 and CSB-2) as well as the terminal associated sequence (TAS) were conserved within the control region. The maximum likelihood phylogenetic family tree revealed the divergence of R. tornieri from the basal region of the Rasbora clade, where its evolutionary relationships with other Rasbora members are poorly resolved as indicated by the low bootstrap values. This work acts as window for further population genetics and molecular evolution studies of Rasbora genus in future.
Similar content being viewed by others
References
Bankevich A., Nurk S., Antipov D., Gurevich A. A., Dvorkin M., Kulikov A. S. et al. 2012 SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455–477.
Brittan M. R. 1954 A revision of the Indo-Malayan fresh-water fish genus Rasbora. Monographs of the Institute of Science and Technology, p. 224. T.F.H. Publications, Manila, Philippines.
Chang C. H., Tsai C. L. and Jang-Liaw N. H. 2012 Complete mitochondrial genome of the Chinese rasbora Rasbora steineri (Teleostei, Cyprinidae). Mitochondrial DNA 24, 183–185.
Chung H. H. 2018 Real-time polymerase chain reaction (RT-PCR) for the authentication of raw meats. Int. Food Res. J. 25, 632–638.
Chung H. H., Lim L. W. K., Liao Y., Lam T. T. Y. and Chong Y. L. 2020a Sequencing and characterisation of complete mitochondrial DNA genome for Trigonopoma pauciperforatum (Cypriniformes: Cyprinidae: Danioninae) with phylogenetic consideration. Trop. Life Sci. Res. 31, 107–121.
Chung H. H., Kamar C. K. A., Lim L. W. K., Liao Y., Lam T. T. Y. and Chong Y. L. 2020b Sequencing and characterization of complete mitochondrial DNA genome for Rasbora hobelmani (Cypriniformes: Cyprinidae: Rasbora) with phylogenetic consideration. J. Ichthyol. 60, 90–98.
Cui J., Xu J., Li Q., Wang K., Xu P. and Sun X. 2013 The complete mitochondrial genome of Cobitis lutheri (Cypriniformes: Cobitidae: Cobitis). Mitochondrial DNA 26, 875–876.
Eschmeyer W. N. 2015 Catalog of fishes: genera, species, references. California Academy of Sciences, San Francisco.
Ho C. W., Liu M. Y. and Chen M. H. 2014 Complete mitochondrial genome of Rasbora trilineata (Cypriniformes, Cyprinidae). Mitochondrial DNA 27, 1755–1757.
Iwasaki W., Fukunaga T., Isagozawa R., Yamada K., Maeda Y., Satoh T. P. et al. 2013 MitoFish and MitoAnnotator: a mitochondrial genome database of fish with an accurate annotation pipeline. Mol. Biol. Evol. 30, 2531–2540.
Kottelat M. 2005 Rasbora notura, a new species of cypinid fish from the Malay Peninsula. Ichthyol. Explor. Freshw. 16, 265–270.
Kottelat M. and Vidthayanon C. 1993 Boraras micros, a new genus and species of minute freshwater fish from Thailand (Teleostei: Cyprinidae). Ichthyol. Explor. Freshw. 4, 161–176.
Kottelat M., Whitten A. J., Kartikasari S. N. and Wirjoatmodjo S. 1993 Freshwater fishes of Western Indonesia and Sulawesi, pp. 221. Periplus Editions, Hong Kong, China.
Kumar S., Stecher G. and Tamura K. 2016 MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 33, 1870–1874.
Kusuma W. E. and Kumazawa Y. 2015 Complete mitochondrial genome sequences of two Indonesian rasboras (Rasbora aprotaenia and Rasbora lateristriata). Mitochondrial DNA A DNA Mapp. Seq. Anal. 27, 4222–4223.
Kusuma W. E., Ratmuangkhwang S. and Kumazawa Y. 2016 Molecular phylogeny and historical biogeography of the Indonesian freshwater fish Rasbora lateristriata species complex (Actinopterygii: Cyprinidae): Cryptic species and west-to-east divergences. Mol. Phylogenet. Evol. 105, 212–223.
Kusuma W. E., Samuel P. D., Wiadnya D. G. R., Hariati A. M. and Kumazawa Y. 2017 Complete mitogenome sequence of Rasbora argyrotaenia (Actinopterygii: Cyprinidae). Mitochondrial DNA Part B 2, 373–374.
Liao T. Y., Kullander S. O. and Fang F. 2010 Phylogenetic analysis of the genus Rasbora (Teleostei: Cyprinidae). Ichthyol. Explor. Freshw. 23, 37–44.
Lim L. W. K., Tan H. Y., Aminan A. W., Jumaan A. Q., Moktar M. Z., Tan S. Y. et al. 2018 Phylogenetic and expression of ATP-binding cassette transporter genes in Rasbora sarawakensis. Pertanika J. Trop. Agric. Sci. 41, 1341–1354.
Lim L. W. K., Roja J. S., Kamar C. K., Chung H. H., Liao Y., Lam T. T. Y. et al. 2019 Sequencing and characterization of complete mitochondrial DNA genome for Rasbora myersi (Cypriniformes: Cyprinidae: Rasbora) and its evolutionary significance. Gene Rep. 17, 100499.
Lowe T. M. and Chan P. P. 2016 tRNAscan-SE on-line: search and contextual analysis of transfer RNA genes. Nucleic Acids Res. 44, 54–57.
Martin M. 2011 Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. J. 17, 10–12.
Miya M. 2009 Whole mitochondrial genome sequences in Cypriniformes. Unpublished manuscript, Natural History Museum & Institute, Chiba, Japan.
Miya M. and Nishida M. 2000 Use of mitogenic information in teleostean molecular phylogenetics: A tree-based exploration under the maximum-parsimony optimality criterion. Mol. Phylogenet. Evol. 17, 437–455.
Ojala D., Montoya J. and Attardi G. 1981 tRNA punctuation model of RNA processing in human mitochondrial. Nature 290, 470–474.
Reuter J. S. and Mathews D. H. 2010 RNAstructure: Software for RNA secondary structure prediction and analysis. BMC Bioinformatics 11, 129.
Siebert D. J. and Guiry S. 1996 Rasbora johannae (Teleostei: Cyprinidae), a new species of the R. trifasciata-complex from Kalimantan, Indonesia. Cybium 20, 395–404.
Tang K. L. Agnew M. K., Hirt M. V., Sado T., Schneider L. M., Freyhof J. et al. 2010 Systematics of the subfamily Danioninae (Teleostei: Cypriniformes: Cyprinidae). Mol. Phylogenet. Evol. 57, 189–214.
Wijeyaratne W. M. D. N. and Pathiratne A. 2006 Acetylcholinesterase inhibition and gill lesions in Rasbora caverii, an indigenous fish inhabiting rice field associated water bodies in Sri Lanka. Ecotoxicology 15, 609.
Zhang S., Cui J., Li C. Y., Mahboob S., Al-Ghanim K., Xu P. and Sun J. 2014 The complete mitochondrial genome of Rasbora borapetensis (Cypriniformes: Cyprinidae: Rasbora). Mitochondrial DNA 27, 1–2.
Acknowledgement
This research was supported by Fundamental Research Grant Scheme with Grant Number F07/FRGS/1872/2019 awarded to H. H. Chung by The Ministry of Education Malaysia.
Author information
Authors and Affiliations
Corresponding authors
Additional information
Corresponding editor: H. A. Ranganath
Rights and permissions
About this article
Cite this article
Chung, H.H., Kamar, C.K.A., Lim, L.W.K. et al. Sequencing and characterization of complete mitogenome DNA of Rasbora tornieri (Cypriniformes: Cyprinidae: Rasbora) and its evolutionary significance. J Genet 99, 67 (2020). https://doi.org/10.1007/s12041-020-01221-x
Received:
Revised:
Accepted:
Published:
DOI: https://doi.org/10.1007/s12041-020-01221-x