In silico identification of conserved miRNAs and their selective target gene prediction in indicine (Bos indicus) cattle.
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 c...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2018-01-01
|
| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC6203363?pdf=render |
| _version_ | 1819013916419686400 |
|---|---|
| author | Quratulain Hanif Muhammad Farooq Imran Amin Shahid Mansoor Yi Zhang Qaiser Mahmood Khan |
| author_facet | Quratulain Hanif Muhammad Farooq Imran Amin Shahid Mansoor Yi Zhang Qaiser Mahmood Khan |
| author_sort | Quratulain Hanif |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-21T02:07:33Z |
| format | Article |
| id | doaj.art-978f3a037ced471bb68bed9f7001dcaf |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-21T02:07:33Z |
| publishDate | 2018-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-978f3a037ced471bb68bed9f7001dcaf2022-12-21T19:19:27ZengPublic Library of Science (PLoS)PLoS ONE1932-62032018-01-011310e020615410.1371/journal.pone.0206154In silico identification of conserved miRNAs and their selective target gene prediction in indicine (Bos indicus) cattle.Quratulain HanifMuhammad FarooqImran AminShahid MansoorYi ZhangQaiser Mahmood KhanThe 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.http://europepmc.org/articles/PMC6203363?pdf=render |
| spellingShingle | Quratulain Hanif Muhammad Farooq Imran Amin Shahid Mansoor Yi Zhang Qaiser Mahmood Khan In silico identification of conserved miRNAs and their selective target gene prediction in indicine (Bos indicus) cattle. PLoS ONE |
| title | In silico identification of conserved miRNAs and their selective target gene prediction in indicine (Bos indicus) cattle. |
| title_full | In silico identification of conserved miRNAs and their selective target gene prediction in indicine (Bos indicus) cattle. |
| title_fullStr | In silico identification of conserved miRNAs and their selective target gene prediction in indicine (Bos indicus) cattle. |
| title_full_unstemmed | In silico identification of conserved miRNAs and their selective target gene prediction in indicine (Bos indicus) cattle. |
| title_short | In silico identification of conserved miRNAs and their selective target gene prediction in indicine (Bos indicus) cattle. |
| title_sort | in silico identification of conserved mirnas and their selective target gene prediction in indicine bos indicus cattle |
| url | http://europepmc.org/articles/PMC6203363?pdf=render |
| work_keys_str_mv | AT quratulainhanif insilicoidentificationofconservedmirnasandtheirselectivetargetgenepredictioninindicinebosindicuscattle AT muhammadfarooq insilicoidentificationofconservedmirnasandtheirselectivetargetgenepredictioninindicinebosindicuscattle AT imranamin insilicoidentificationofconservedmirnasandtheirselectivetargetgenepredictioninindicinebosindicuscattle AT shahidmansoor insilicoidentificationofconservedmirnasandtheirselectivetargetgenepredictioninindicinebosindicuscattle AT yizhang insilicoidentificationofconservedmirnasandtheirselectivetargetgenepredictioninindicinebosindicuscattle AT qaisermahmoodkhan insilicoidentificationofconservedmirnasandtheirselectivetargetgenepredictioninindicinebosindicuscattle |