Identification of Conserved and Novel MicroRNAs with their Targets in Garden Pea ( L.) Leaves by High-Throughput Sequencing
MicroRNAs (miRNAs) are single-stranded, endogenous, non-coding RNAs of 20–24 nucleotides that play a significant role in post-transcriptional gene regulation. Various conserved and novel miRNAs have been characterized, especially from the plant species whose genomes were well-characterized; however,...
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| Format: | Article |
| Language: | English |
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SAGE Publishing
2023-03-01
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| Series: | Bioinformatics and Biology Insights |
| Online Access: | https://doi.org/10.1177/11779322231162777 |
| _version_ | 1797776133630984192 |
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| author | Qurshid Hasan Khan |
| author_facet | Qurshid Hasan Khan |
| author_sort | Qurshid Hasan Khan |
| collection | DOAJ |
| description | MicroRNAs (miRNAs) are single-stranded, endogenous, non-coding RNAs of 20–24 nucleotides that play a significant role in post-transcriptional gene regulation. Various conserved and novel miRNAs have been characterized, especially from the plant species whose genomes were well-characterized; however, information on miRNA in economically important plants such as pea ( Pisum sativum L.) is limited. In this study, I have identified conserved and novel miRNA in garden pea plant leaves samples along with their targets by analyzing the next generation sequencing (NGS) data. The raw data obtained from NGS were processed and 1.38 million high-quality non-redundant reads were retained for analysis, this tremendous quantity of reads indicates a large and diverse small RNA population in pea leaves. After analyzing the deep sequencing data, 255 conserved and 11 novel miRNAs were identified in the garden pea leaves sample. Utilizing psRNATarget tool, the miRNA targets of conserved and novel miRNA were predicted. Further, the functional annotation of the miRNA targets were performed using blast2Go software and the target gene products were predicted. The miRNA target gene products along with GO_ID (Gene Ontology Identifier) were categorized into biological processes, cellular components, and molecular functions. The information obtained from this study will provide genomic resources that will help in understanding miRNA-mediated post-transcriptional gene regulation in garden peas. |
| first_indexed | 2024-03-12T22:45:37Z |
| format | Article |
| id | doaj.art-d2cd7254e3ef446faa9e92940558541a |
| institution | Directory Open Access Journal |
| issn | 1177-9322 |
| language | English |
| last_indexed | 2024-03-12T22:45:37Z |
| publishDate | 2023-03-01 |
| publisher | SAGE Publishing |
| record_format | Article |
| series | Bioinformatics and Biology Insights |
| spelling | doaj.art-d2cd7254e3ef446faa9e92940558541a2023-07-21T06:03:21ZengSAGE PublishingBioinformatics and Biology Insights1177-93222023-03-011710.1177/11779322231162777Identification of Conserved and Novel MicroRNAs with their Targets in Garden Pea ( L.) Leaves by High-Throughput SequencingQurshid Hasan KhanMicroRNAs (miRNAs) are single-stranded, endogenous, non-coding RNAs of 20–24 nucleotides that play a significant role in post-transcriptional gene regulation. Various conserved and novel miRNAs have been characterized, especially from the plant species whose genomes were well-characterized; however, information on miRNA in economically important plants such as pea ( Pisum sativum L.) is limited. In this study, I have identified conserved and novel miRNA in garden pea plant leaves samples along with their targets by analyzing the next generation sequencing (NGS) data. The raw data obtained from NGS were processed and 1.38 million high-quality non-redundant reads were retained for analysis, this tremendous quantity of reads indicates a large and diverse small RNA population in pea leaves. After analyzing the deep sequencing data, 255 conserved and 11 novel miRNAs were identified in the garden pea leaves sample. Utilizing psRNATarget tool, the miRNA targets of conserved and novel miRNA were predicted. Further, the functional annotation of the miRNA targets were performed using blast2Go software and the target gene products were predicted. The miRNA target gene products along with GO_ID (Gene Ontology Identifier) were categorized into biological processes, cellular components, and molecular functions. The information obtained from this study will provide genomic resources that will help in understanding miRNA-mediated post-transcriptional gene regulation in garden peas.https://doi.org/10.1177/11779322231162777 |
| spellingShingle | Qurshid Hasan Khan Identification of Conserved and Novel MicroRNAs with their Targets in Garden Pea ( L.) Leaves by High-Throughput Sequencing Bioinformatics and Biology Insights |
| title | Identification of Conserved and Novel MicroRNAs with their Targets in Garden Pea ( L.) Leaves by High-Throughput Sequencing |
| title_full | Identification of Conserved and Novel MicroRNAs with their Targets in Garden Pea ( L.) Leaves by High-Throughput Sequencing |
| title_fullStr | Identification of Conserved and Novel MicroRNAs with their Targets in Garden Pea ( L.) Leaves by High-Throughput Sequencing |
| title_full_unstemmed | Identification of Conserved and Novel MicroRNAs with their Targets in Garden Pea ( L.) Leaves by High-Throughput Sequencing |
| title_short | Identification of Conserved and Novel MicroRNAs with their Targets in Garden Pea ( L.) Leaves by High-Throughput Sequencing |
| title_sort | identification of conserved and novel micrornas with their targets in garden pea l leaves by high throughput sequencing |
| url | https://doi.org/10.1177/11779322231162777 |
| work_keys_str_mv | AT qurshidhasankhan identificationofconservedandnovelmicrornaswiththeirtargetsingardenpealleavesbyhighthroughputsequencing |