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
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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