Hairpin in a haystack: In silico identification and characterization of plant-conserved microRNA in Rafflesiaceae
Rafflesiaceae is a family of endangered plants whose members are solely parasitic to the tropical grape vine Tetrastigma (Vitaceae). Currently, the genetics of their crosstalk with the host remains unexplored. In this study, we use homology-based in silico approaches to characterize micro-RNAs (miRN...
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De Gruyter
2025-01-01
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| Series: | Open Life Sciences |
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| Online Access: | https://doi.org/10.1515/biol-2022-1033 |
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| author | Wicaksono Adhityo Meitha Karlia Wan Kiew-Lian Mat Isa Mohd Noor Parikesit Arli Aditya Molina Jeanmaire |
| author_facet | Wicaksono Adhityo Meitha Karlia Wan Kiew-Lian Mat Isa Mohd Noor Parikesit Arli Aditya Molina Jeanmaire |
| author_sort | Wicaksono Adhityo |
| collection | DOAJ |
| description | Rafflesiaceae is a family of endangered plants whose members are solely parasitic to the tropical grape vine Tetrastigma (Vitaceae). Currently, the genetics of their crosstalk with the host remains unexplored. In this study, we use homology-based in silico approaches to characterize micro-RNAs (miRNAs) expressed by Sapria himalayana and Rafflesia cantleyi from published omics data. Derived from secondary structures or hairpins, miRNAs are small regulators of gene expression. We found that some plant-conserved miRNA still exists in Rafflesiaceae. Out of 9 highly conserved miRNA families in plants, 7 families (156/157, 159/319, 160, 165/166, 171, 172, 390) were identified with a total of 22 variants across Rafflesiaceae. Some miRNAs were missing endogenous targets and may have evolved to target host miRNA, though this requires experimental verification. Rafflesiaceae miRNA promoters are mostly inducible by ethylene that mediates stress response in the host but could be perceived by the parasites as a signal for growth. This study provides evidence that certain miRNAs with ancient origins in land plants still exist in Rafflesiaceae, though some may have been coopted by parasites to target host genes. |
| format | Article |
| id | doaj-art-c535ec5d80e547d58b4cfb051d794495 |
| institution | Kabale University |
| issn | 2391-5412 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | De Gruyter |
| record_format | Article |
| series | Open Life Sciences |
| spelling | doaj-art-c535ec5d80e547d58b4cfb051d7944952025-02-02T15:44:51ZengDe GruyterOpen Life Sciences2391-54122025-01-0120179380310.1515/biol-2022-1033Hairpin in a haystack: In silico identification and characterization of plant-conserved microRNA in RafflesiaceaeWicaksono Adhityo0Meitha Karlia1Wan Kiew-Lian2Mat Isa Mohd Noor3Parikesit Arli Aditya4Molina Jeanmaire5Genomik Solidaritas Indonesia (GSI) Lab, Jl. Sultan Agung no. 29, Guntur, Jakarta, 12980, IndonesiaResearch group of Genetics and Molecular Biology, School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha no. 10, Bandung, 40132, IndonesiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, 43600, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, 43600, MalaysiaDepartment of Bioinformatics, School of Life Sciences, Indonesia International Institute for Life Sciences, Jl. Pulomas Barat Kav. 88, Jakarta, 13210, IndonesiaDepartment of Biology, Pace University, One Pace Plaza, 3rd Floor, New York, 10038, NY, United States of AmericaRafflesiaceae is a family of endangered plants whose members are solely parasitic to the tropical grape vine Tetrastigma (Vitaceae). Currently, the genetics of their crosstalk with the host remains unexplored. In this study, we use homology-based in silico approaches to characterize micro-RNAs (miRNAs) expressed by Sapria himalayana and Rafflesia cantleyi from published omics data. Derived from secondary structures or hairpins, miRNAs are small regulators of gene expression. We found that some plant-conserved miRNA still exists in Rafflesiaceae. Out of 9 highly conserved miRNA families in plants, 7 families (156/157, 159/319, 160, 165/166, 171, 172, 390) were identified with a total of 22 variants across Rafflesiaceae. Some miRNAs were missing endogenous targets and may have evolved to target host miRNA, though this requires experimental verification. Rafflesiaceae miRNA promoters are mostly inducible by ethylene that mediates stress response in the host but could be perceived by the parasites as a signal for growth. This study provides evidence that certain miRNAs with ancient origins in land plants still exist in Rafflesiaceae, though some may have been coopted by parasites to target host genes.https://doi.org/10.1515/biol-2022-1033ncrnagene regulationmalpighialessmall rnarnai |
| spellingShingle | Wicaksono Adhityo Meitha Karlia Wan Kiew-Lian Mat Isa Mohd Noor Parikesit Arli Aditya Molina Jeanmaire Hairpin in a haystack: In silico identification and characterization of plant-conserved microRNA in Rafflesiaceae Open Life Sciences ncrna gene regulation malpighiales small rna rnai |
| title | Hairpin in a haystack: In silico identification and characterization of plant-conserved microRNA in Rafflesiaceae |
| title_full | Hairpin in a haystack: In silico identification and characterization of plant-conserved microRNA in Rafflesiaceae |
| title_fullStr | Hairpin in a haystack: In silico identification and characterization of plant-conserved microRNA in Rafflesiaceae |
| title_full_unstemmed | Hairpin in a haystack: In silico identification and characterization of plant-conserved microRNA in Rafflesiaceae |
| title_short | Hairpin in a haystack: In silico identification and characterization of plant-conserved microRNA in Rafflesiaceae |
| title_sort | hairpin in a haystack in silico identification and characterization of plant conserved microrna in rafflesiaceae |
| topic | ncrna gene regulation malpighiales small rna rnai |
| url | https://doi.org/10.1515/biol-2022-1033 |
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