title: In Silico Mining of Conserved miRNAs of Indian Catfish Clarias batrachus (Linnaeus, 1758) from the Contigs, ESTs, and BAC End Sequences.
abstract: MicroRNAs are small non-coding RNAs which play significant role in RNA interference. The present work deals with mining of the conserved miRNA and their target genes from the contigs, ESTs, and BAC end sequences of commercially important catfish, Clarias batrachus, from India. A total of 138, 1 and 1 conserved pre-miRNA sequences, were mined from the contigs, ESTs, and BAC end sequences, respectively. The analysis of families of the conserved pre-miRNA revealed conservation of the fish-specific family mir-430 and other important families, such as mir-455, let-7, mir-133, and mir-137. The mir-455 is involved in hypoxia signaling, let-7 family represents potential anti-tumor molecules involved in human cancer therapy, whereas mir-133 and mir-137 have high therapeutic potentials. Using an alternate computational in silico approach, mining of mature miRNAs resulted in identification of 210 mature miRNAs from contigs, 1 from EST, and 2 each from forward as well as reverse BAC end sequences. Target prediction of these putative miRNAs resulted in the identification of 66,758 and 18,747 target genes in C. batrachus and Danio rerio, respectively. Functional annotation of these miRNAs indicated their involvement in diverse biological functions. The findings of the present study can serve as a valuable resource for further functional genomics studies in C. batrachus.
authors.affiliation: Division of Molecular Biology and Biotechnology, ICAR- National Bureau of Fish Genetic Resources, Canal Ring Road, Lucknow, Uttar Pradesh, 226 002, India.|AMITY University Uttar Pradesh, Lucknow Campus, Lucknow, Uttar Pradesh, 226 028, India.
authors.forename: Suyash
authors.initials: S
authors.lastname: Agarwal
authors.affiliation: Division of Molecular Biology and Biotechnology, ICAR- National Bureau of Fish Genetic Resources, Canal Ring Road, Lucknow, Uttar Pradesh, 226 002, India.
authors.forename: N S
authors.initials: NS
authors.lastname: Nagpure
authors.affiliation: AMITY University Uttar Pradesh, Lucknow Campus, Lucknow, Uttar Pradesh, 226 028, India.
authors.forename: Prachi
authors.initials: P
authors.lastname: Srivastava
authors.affiliation: Division of Molecular Biology and Biotechnology, ICAR- National Bureau of Fish Genetic Resources, Canal Ring Road, Lucknow, Uttar Pradesh, 226 002, India.
authors.forename: Ravindra
authors.initials: R
authors.lastname: Kumar
authors.affiliation: Division of Molecular Biology and Biotechnology, ICAR- National Bureau of Fish Genetic Resources, Canal Ring Road, Lucknow, Uttar Pradesh, 226 002, India.
authors.forename: Manmohan
authors.initials: M
authors.lastname: Pandey
authors.affiliation: Division of Molecular Biology and Biotechnology, ICAR- National Bureau of Fish Genetic Resources, Canal Ring Road, Lucknow, Uttar Pradesh, 226 002, India.
authors.forename: Shreya
authors.initials: S
authors.lastname: Srivastava
authors.affiliation: Division of Molecular Biology and Biotechnology, ICAR- National Bureau of Fish Genetic Resources, Canal Ring Road, Lucknow, Uttar Pradesh, 226 002, India.
authors.forename: J K
authors.initials: JK
authors.lastname: Jena
authors.affiliation: ICAR- Central Institute of Freshwater Aquaculture, Kausalyanga, Bhubaneswar, Odisha, 751 002, India.
authors.forename: P
authors.initials: P
authors.lastname: Das
authors.affiliation: Division of Molecular Biology and Biotechnology, ICAR- National Bureau of Fish Genetic Resources, Canal Ring Road, Lucknow, Uttar Pradesh, 226 002, India. basdeo.scientist@gmail.com.
authors.forename: Basdeo
authors.initials: B
authors.lastname: Kushwaha
mesh_terms: D000818:Animals; D002397:Catfishes / Q000235:genetics*; D003198:Computer Simulation; D020224:Expressed Sequence Tags; D006801:Humans; D035683:MicroRNAs / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D035683:MicroRNAs
keywords: C. batrachus; In silico mining; MicroRNAs (miRNAs); Putative genes; Target prediction