PUBLICATION
In Silico Mining of Conserved miRNAs of Indian Catfish Clarias batrachus (Linnaeus, 1758) from the Contigs, ESTs, and BAC End Sequences
- Authors
- Agarwal, S., Nagpure, N.S., Srivastava, P., Kumar, R., Pandey, M., Srivastava, S., Jena, J.K., Das, P., Kushwaha, B.
- ID
- ZDB-PUB-161224-19
- Date
- 2017
- Source
- Applied Biochemistry and Biotechnology 182(3): 956-966 (Journal)
- Registered Authors
- Keywords
- C. batrachus, In silico mining, MicroRNAs (miRNAs), Putative genes, Target prediction
- MeSH Terms
-
- Animals
- Catfishes/genetics*
- Computer Simulation*
- Expressed Sequence Tags*
- Humans
- MicroRNAs/genetics*
- Sequence Analysis, DNA/methods*
- PubMed
- 28004230 Full text @ Appl. Biochem. Biotechnol.
Citation
Agarwal, S., Nagpure, N.S., Srivastava, P., Kumar, R., Pandey, M., Srivastava, S., Jena, J.K., Das, P., Kushwaha, B. (2017) In Silico Mining of Conserved miRNAs of Indian Catfish Clarias batrachus (Linnaeus, 1758) from the Contigs, ESTs, and BAC End Sequences. Applied Biochemistry and Biotechnology. 182(3):956-966.
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.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping