Isolation and characterization of hypoxia inducible gene connective tissue growth factor (CTGF) in Labeo rohita
The connective tissue growth factor gene plays important role in several biological processes and also responsive to hypoxia stress in fishes. The freshwater fish, Labeo rohita, highly cultured in Indian subcontinent for food, is reported as hypoxia sensitive but annotation and sequences of nuclear genes were not available for this species so far in the public domain, except some transcripts. In this study, an attempt was made for isolation and annotation of the CTGF gene in L. rohita using information of zebrafish from the same family. The CTGF gene sequence was obtained by aligning assembled genome of L. rohita, (NCBI BioProject ID: PRJNA437789), with the CTGF protein of zebrafish. Eight overlapping sets of forward and reverse primers from aligned region were designed for amplification of around 600 bp long successive overlapping fragments of CTGF gene in L. rohita. Assembly and annotation of overlapping fragments confirmed a complete 2421 bp long CTGF gene sequence with a full coding region that comprised of five exons between 308 and 1921 positions. This annotated CTGF gene sequence was submitted to GenBank (Acc. No. KY940466). Characterization of CTGF will be an initiative in identification of hypoxia response genes in L. rohita which may further help in understanding the mechanism of hypoxia tolerability in this species.
KeywordsDatabase HIF HRE Hypoxia Promoter Transcription
Connective tissue growth factor
Hypoxia ancillary sequence
Hypoxia inducible factors
Hypoxia response element
Transcription start site
Authors are thankful to the Director, ICAR-NBFGR, Lucknow, for providing necessary facilities to carry out this work. Authors are also thankful to the CABin Scheme of ICAR and CABin Division of ICAR-IASRI, New Delhi, for financial assistance and guidance. First author is thankful to Dr. Satarudra Prakash Singh and Dr. Vineet Awasthi, Amity University Uttar Pradesh, Lucknow, for their continued suggestions.
Compliance with ethical standards
Conflict of interest
The authors declare no conflict of interest.
- 3.Diaz R, Rosenberg R (1995) Marine benthic hypoxia: a review of its ecological effects and the behavioral responses of benthic macro fauna. Oceanogr Mar Biol Annu Rev 33:245–303Google Scholar
- 7.Whitworth KL, Baldwin DS, Kerr JL (2012) Drought, floods and water quality: Drivers of a severe hypoxic blackwater event in a major river system (the southern Murray–Darling Basin, Australia). J Hydrol 450–451, 190–198Google Scholar
- 8.Padmavathy P, Ramanathan N, Francis T (2003) Glucose, lactate and pyruvate metabolism in Labeo rohita with reference to ambient oxygen. Asian Fish Sci 16:51–58Google Scholar
- 11.Varghese T, Pal AK, Mishal P, Sahu NP, Dasgupta S (2017) Physiological and molecular responses of a bottom dwelling carp, Cirrhinus mrigala to short-term environmental hypoxia. Tur J Fish Aqua Sci 18:483–490Google Scholar
- 12.Froese R, Pauly D (2017) FishBase. World Wide Web electronic publication. http://www.fishbase.org, version (June 2017)
- 14.Jena JK (2006) Cultured aquatic species information programme. Labeo rohita. FAO Fisheries and Aquaculture Department [online]. Rome. Updated 21 February 2006. [Cited 20 December 2018]Google Scholar
- 15.Das S, Chhottaray C, Das Mahapatra K, Saha JN, Baranski M, Robinson N, Sahoo PK (2014) Analysis of immune-related ESTs and differential expression analysis of few important genes in lines of rohu (Labeo rohita) selected for resistance and susceptibility to Aeromonas hydrophila infection. Mol Biol Rep 41(11):7361–7371CrossRefGoogle Scholar
- 24.Wenger RH, Stiehl DP, Camenisch G (2005) Integration of oxygen signaling at the consensus HRE. Sci STKE 2005(306):re12Google Scholar
- 36.Solovyev V, Kosarev P, Seledsov I, Vorobyev D (2006) Automatic annotation of eukaryotic genes, pseudogenes and promoters. Genome Biol S10:1–12Google Scholar
- 38.Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011.MEGA5: molecular evolutionary genetics analysis using maximum likelihood,evolutionary distance, and maximum parsimony methods. MolBiolEvol. 28:2731–2739Google Scholar
- 43.Ratnasingham S, Hebert PD (2007) BOLD: the barcode of life data system. Mol Ecol Notes 7:355–364. http://www.barcodinglife.org
- 48.Kimura H, Weisz A, Ogura T, Hitomi Y, Kurashima Y, Hashimoto K, D’Acquisto F, Makuuchi M, Esumi H (2001) Identification of hypoxia-inducible factor 1 ancillary sequence and its function in vascular endothelial growth factor gene induction by hypoxia and nitric oxide. J Biol Chem 276:2292–2298CrossRefGoogle Scholar