In silico identification of conserved miRNAs and their selective target gene prediction in indicine (Bos indicus) cattle
Autor: | Shahid Mansoor, Imran Amin, Qaiser M. Khan, Yi Zhang, Quratulain Hanif, Muhammad Farooq |
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Rok vydání: | 2018 |
Předmět: |
0301 basic medicine
lcsh:Medicine Biochemistry Genome Homology (biology) Conserved sequence Medicine and Health Sciences Copy-number variation lcsh:Science Conserved Sequence Mammals Genetics Mammalian Genomics Multidisciplinary Chromosome Mapping Eukaryota Agriculture Genomics Ruminants Phenotype Copy Number Variation Nucleic acids Animals Domestic Vertebrates Research Article Livestock DNA Copy Number Variations In silico Immunology Biology Genome Complexity Polymorphism Single Nucleotide 03 medical and health sciences Bovines Animals Computer Simulation Non-coding RNA Gene Natural antisense transcripts Sequence Assembly Tools Biology and life sciences lcsh:R Organisms Immunity Computational Biology Genome Analysis Gene regulation MicroRNAs 030104 developmental biology Gene Expression Regulation Animal Genomics Amniotes RNA Cattle lcsh:Q Gene expression |
Zdroj: | PLoS ONE, Vol 13, Iss 10, p e0206154 (2018) PLoS ONE |
ISSN: | 1932-6203 |
Popis: | The modern cattle was domesticated from aurochs, sharing its physiological traits into two subspecies Bos taurus and Bos indicus. MicroRNAs (miRNAs) are a class of non-coding short RNAs of ~22nt which have a key role in the regulation of many cellular and physiological processes in the animal. The current study was aimed to predict and annotate the potential mutations in indicine miRNAs throughout the genome using de novo and homology-based in silico approaches. Genome-wide mapping was performed in available indicine assembly by the homology-based approach and 768 miRNAs were recovered out of 808 reported taurine miRNAs belonging to 521 unique mature miRNA families. While 42 precursors were dropped due to lack of secondary miRNA structure, increasing stringency or decreasing similarity between the two genomes’ miRNA. Increasing tendency of miRNAs incidence was observed on chr5, chr7, chr8, chr12 and chr21 with 19 polycistronic miRNA within 1-kilobase distance throughout the indicine genome. Notably, 12 miRNAs showed copy number variation. Eighteen miRNAs showed a mutation in their mature sequences in which eight were found in their seed region. Whilst in de novo based approach, 12 novel potential miRNAs on Y chromosome in indicine cattle along with a new miRNA (bind-miR-1264) on chrX were found. The final data set is annotated and explains the impending target genes that are responsible for enhanced immunity, heat tolerance and disease tolerance regulation in indicine. The study conforms to better understanding and perceptive approach towards indicine genome. |
Databáze: | OpenAIRE |
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