Candidate miRNAs from <i>Oryza sativa</i> for Silencing the Rice Tungro Viruses
Rice tungro disease (RTD), caused by <i>Rice tungro bacilliform virus</i> (RTBV) and <i>Rice tungro spherical virus</i> (RTSV) is one of the most prominent viral diseases in Asian countries. This virus disease problem seems to have been accentuated in those countries by causi...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2023-03-01
|
| Series: | Agriculture |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2077-0472/13/3/651 |
| _version_ | 1797614104517541888 |
|---|---|
| author | Noor Amni Mohamed Nik Muhammad Faris Nazmie Che Ngah Azlan Abas Noraini Talip Murni Nazira Sarian Hamizah Shahirah Hamezah Sarahani Harun Hamidun Bunawan |
| author_facet | Noor Amni Mohamed Nik Muhammad Faris Nazmie Che Ngah Azlan Abas Noraini Talip Murni Nazira Sarian Hamizah Shahirah Hamezah Sarahani Harun Hamidun Bunawan |
| author_sort | Noor Amni Mohamed |
| collection | DOAJ |
| description | Rice tungro disease (RTD), caused by <i>Rice tungro bacilliform virus</i> (RTBV) and <i>Rice tungro spherical virus</i> (RTSV) is one of the most prominent viral diseases in Asian countries. This virus disease problem seems to have been accentuated in those countries by causing a series of outbreaks over the years after being first reported in International Rice Research Institute (IRRI), Philippines, in 1963. One of the effective ways to combat viruses is through RNA silencing. microRNA is an important player in the RNA silencing mechanism. Genome sequences analysis shows RTBV-SP isolate (8 Kb) is composed of four open reading frames (ORF 1, ORF 2, ORF 3, and ORF 4), meanwhile, RTSV-SP (12 Kb) consists of one open reading frame encoded by seven different polyproteins (P1, CP1, CP2, CP3, NTP, Pro, and Rep). Therefore, this study investigated possible rice-encoded miRNAs targeted on RTBV and RTSV using in silico analysis. Five bioinformatics tools were employed using five different prediction algorithms: miRanda, RNA22, RNAhybrid, Tapirhybrid, and psRNATarget. The results revealed each RTBV and RTSV can be silenced by three potentially best candidate rice-encoded miRNA. For RTBV, osa-miR5510 (accession no. MIMAT0022143), osa-miR3980a-3p (accession no. MIMAT0019676), and osa-miR3980b-3p (accession no. MIMAT0019678) are being predicted by all five algorithms. Meanwhile, for RTSV, three miRNAs predicted are osa-miR414 (accession no. MIMAT0001330), osa-miR5505 (accession no. MIMAT00221138) and osa-miR167a-3p (accession no. MIMAT0006780). The predicted data provide useful material for developing RTBV and RTSV-resistant rice varieties. |
| first_indexed | 2024-03-11T07:04:30Z |
| format | Article |
| id | doaj.art-ea8bae8cbf5048d9b62bb1677943e783 |
| institution | Directory Open Access Journal |
| issn | 2077-0472 |
| language | English |
| last_indexed | 2024-03-11T07:04:30Z |
| publishDate | 2023-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Agriculture |
| spelling | doaj.art-ea8bae8cbf5048d9b62bb1677943e7832023-11-17T09:01:31ZengMDPI AGAgriculture2077-04722023-03-0113365110.3390/agriculture13030651Candidate miRNAs from <i>Oryza sativa</i> for Silencing the Rice Tungro VirusesNoor Amni Mohamed0Nik Muhammad Faris Nazmie Che Ngah1Azlan Abas2Noraini Talip3Murni Nazira Sarian4Hamizah Shahirah Hamezah5Sarahani Harun6Hamidun Bunawan7Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, MalaysiaInstitute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, MalaysiaCenter for Research in Development, Social and Environment (SEEDS), Faculty of Social Sciences and Humanities, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, MalaysiaDepartment of Biotechnology and Biological Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, MalaysiaInstitute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, MalaysiaInstitute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, MalaysiaInstitute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, MalaysiaInstitute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, MalaysiaRice tungro disease (RTD), caused by <i>Rice tungro bacilliform virus</i> (RTBV) and <i>Rice tungro spherical virus</i> (RTSV) is one of the most prominent viral diseases in Asian countries. This virus disease problem seems to have been accentuated in those countries by causing a series of outbreaks over the years after being first reported in International Rice Research Institute (IRRI), Philippines, in 1963. One of the effective ways to combat viruses is through RNA silencing. microRNA is an important player in the RNA silencing mechanism. Genome sequences analysis shows RTBV-SP isolate (8 Kb) is composed of four open reading frames (ORF 1, ORF 2, ORF 3, and ORF 4), meanwhile, RTSV-SP (12 Kb) consists of one open reading frame encoded by seven different polyproteins (P1, CP1, CP2, CP3, NTP, Pro, and Rep). Therefore, this study investigated possible rice-encoded miRNAs targeted on RTBV and RTSV using in silico analysis. Five bioinformatics tools were employed using five different prediction algorithms: miRanda, RNA22, RNAhybrid, Tapirhybrid, and psRNATarget. The results revealed each RTBV and RTSV can be silenced by three potentially best candidate rice-encoded miRNA. For RTBV, osa-miR5510 (accession no. MIMAT0022143), osa-miR3980a-3p (accession no. MIMAT0019676), and osa-miR3980b-3p (accession no. MIMAT0019678) are being predicted by all five algorithms. Meanwhile, for RTSV, three miRNAs predicted are osa-miR414 (accession no. MIMAT0001330), osa-miR5505 (accession no. MIMAT00221138) and osa-miR167a-3p (accession no. MIMAT0006780). The predicted data provide useful material for developing RTBV and RTSV-resistant rice varieties.https://www.mdpi.com/2077-0472/13/3/651rice tungro diseasebioinformaticsmiRNA<i>Oryza sativa</i> |
| spellingShingle | Noor Amni Mohamed Nik Muhammad Faris Nazmie Che Ngah Azlan Abas Noraini Talip Murni Nazira Sarian Hamizah Shahirah Hamezah Sarahani Harun Hamidun Bunawan Candidate miRNAs from <i>Oryza sativa</i> for Silencing the Rice Tungro Viruses Agriculture rice tungro disease bioinformatics miRNA <i>Oryza sativa</i> |
| title | Candidate miRNAs from <i>Oryza sativa</i> for Silencing the Rice Tungro Viruses |
| title_full | Candidate miRNAs from <i>Oryza sativa</i> for Silencing the Rice Tungro Viruses |
| title_fullStr | Candidate miRNAs from <i>Oryza sativa</i> for Silencing the Rice Tungro Viruses |
| title_full_unstemmed | Candidate miRNAs from <i>Oryza sativa</i> for Silencing the Rice Tungro Viruses |
| title_short | Candidate miRNAs from <i>Oryza sativa</i> for Silencing the Rice Tungro Viruses |
| title_sort | candidate mirnas from i oryza sativa i for silencing the rice tungro viruses |
| topic | rice tungro disease bioinformatics miRNA <i>Oryza sativa</i> |
| url | https://www.mdpi.com/2077-0472/13/3/651 |
| work_keys_str_mv | AT nooramnimohamed candidatemirnasfromioryzasativaiforsilencingthericetungroviruses AT nikmuhammadfarisnazmiechengah candidatemirnasfromioryzasativaiforsilencingthericetungroviruses AT azlanabas candidatemirnasfromioryzasativaiforsilencingthericetungroviruses AT norainitalip candidatemirnasfromioryzasativaiforsilencingthericetungroviruses AT murninazirasarian candidatemirnasfromioryzasativaiforsilencingthericetungroviruses AT hamizahshahirahhamezah candidatemirnasfromioryzasativaiforsilencingthericetungroviruses AT sarahaniharun candidatemirnasfromioryzasativaiforsilencingthericetungroviruses AT hamidunbunawan candidatemirnasfromioryzasativaiforsilencingthericetungroviruses |