Analysis of Homologous Regions of Small RNAs <i>MIR397</i> and <i>MIR408</i> Reveals the Conservation of Microsynteny among Rice Crop-Wild Relatives
<i>MIRNAs</i> are small non-coding RNAs that play important roles in a wide range of biological processes in plant growth and development. <i>MIR397</i> (involved in drought, low temperature, and nitrogen and copper (Cu) starvation) and <i>MIR408</i> (differential...
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MDPI AG
2022-11-01
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| author | Prasanta K. Dash Payal Gupta Sharat Kumar Pradhan Ajit Kumar Shasany Rhitu Rai |
| author_facet | Prasanta K. Dash Payal Gupta Sharat Kumar Pradhan Ajit Kumar Shasany Rhitu Rai |
| author_sort | Prasanta K. Dash |
| collection | DOAJ |
| description | <i>MIRNAs</i> are small non-coding RNAs that play important roles in a wide range of biological processes in plant growth and development. <i>MIR397</i> (involved in drought, low temperature, and nitrogen and copper (Cu) starvation) and <i>MIR408</i> (differentially expressed in response to environmental stresses such as copper, light, mechanical stress, dehydration, cold, reactive oxygen species, and drought) belong to conserved <i>MIRNA</i> families that either negatively or positively regulate their target genes. In the present study, we identified the homologs of <i>MIR397</i> and <i>MIR408</i> in <i>Oryza sativa</i> and its six wild progenitors, three non-<i>Oryza</i> species, and one dicot species. We analyzed the 100 kb segments harboring <i>MIRNA</i> homologs from 11 genomes to obtain a comprehensive view of their community evolution around these loci in the farthest (distant) relatives of rice. Our study showed that mature <i>MIR397</i> and <i>MIR408</i> were highly conserved among all <i>Oryza</i> species. Comparative genomics analyses also revealed that the microsynteny of the 100 kb region surrounding <i>MIRNAs</i> was only conserved in <i>Oryza</i> spp.; disrupted in <i>Sorghum,</i> maize, and wheat; and completely lost in <i>Arabidopsis</i>. There were deletions, rearrangements, and translocations within the 100 kb segments in <i>Oryza</i> spp., but the overall microsynteny of the region was maintained. The phylogenetic analyses of the precursor regions of all <i>MIRNAs</i> under study revealed a bimodal clade of common origin. This comparative analysis of miRNA involved in abiotic stress tolerance in plants provides a powerful tool for future <i>Oryza</i> research. Crop wild relatives (CWRs) offer multiple traits with potential to decrease the amount of yield loss owing to biotic and abiotic stresses. Using a comparative genomics approach, the exploration of CWRs as a source of tolerance to these stresses by understanding their evolution can be further used to leverage their yield potential. |
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| spelling | doaj.art-9b49d46186a047d1a5a569c738ad843d2023-11-24T04:09:09ZengMDPI AGCells2073-44092022-11-011121346110.3390/cells11213461Analysis of Homologous Regions of Small RNAs <i>MIR397</i> and <i>MIR408</i> Reveals the Conservation of Microsynteny among Rice Crop-Wild RelativesPrasanta K. Dash0Payal Gupta1Sharat Kumar Pradhan2Ajit Kumar Shasany3Rhitu Rai4ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, IndiaICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, IndiaICAR-National Rice Research Institute, Cuttack 753006, IndiaICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, IndiaICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India<i>MIRNAs</i> are small non-coding RNAs that play important roles in a wide range of biological processes in plant growth and development. <i>MIR397</i> (involved in drought, low temperature, and nitrogen and copper (Cu) starvation) and <i>MIR408</i> (differentially expressed in response to environmental stresses such as copper, light, mechanical stress, dehydration, cold, reactive oxygen species, and drought) belong to conserved <i>MIRNA</i> families that either negatively or positively regulate their target genes. In the present study, we identified the homologs of <i>MIR397</i> and <i>MIR408</i> in <i>Oryza sativa</i> and its six wild progenitors, three non-<i>Oryza</i> species, and one dicot species. We analyzed the 100 kb segments harboring <i>MIRNA</i> homologs from 11 genomes to obtain a comprehensive view of their community evolution around these loci in the farthest (distant) relatives of rice. Our study showed that mature <i>MIR397</i> and <i>MIR408</i> were highly conserved among all <i>Oryza</i> species. Comparative genomics analyses also revealed that the microsynteny of the 100 kb region surrounding <i>MIRNAs</i> was only conserved in <i>Oryza</i> spp.; disrupted in <i>Sorghum,</i> maize, and wheat; and completely lost in <i>Arabidopsis</i>. There were deletions, rearrangements, and translocations within the 100 kb segments in <i>Oryza</i> spp., but the overall microsynteny of the region was maintained. The phylogenetic analyses of the precursor regions of all <i>MIRNAs</i> under study revealed a bimodal clade of common origin. This comparative analysis of miRNA involved in abiotic stress tolerance in plants provides a powerful tool for future <i>Oryza</i> research. Crop wild relatives (CWRs) offer multiple traits with potential to decrease the amount of yield loss owing to biotic and abiotic stresses. Using a comparative genomics approach, the exploration of CWRs as a source of tolerance to these stresses by understanding their evolution can be further used to leverage their yield potential.https://www.mdpi.com/2073-4409/11/21/3461comparative genomics<i>Oryza</i>crop wild relatives<i>MIRNAs</i><i>MIR397</i><i>MIR408</i> |
| spellingShingle | Prasanta K. Dash Payal Gupta Sharat Kumar Pradhan Ajit Kumar Shasany Rhitu Rai Analysis of Homologous Regions of Small RNAs <i>MIR397</i> and <i>MIR408</i> Reveals the Conservation of Microsynteny among Rice Crop-Wild Relatives Cells comparative genomics <i>Oryza</i> crop wild relatives <i>MIRNAs</i> <i>MIR397</i> <i>MIR408</i> |
| title | Analysis of Homologous Regions of Small RNAs <i>MIR397</i> and <i>MIR408</i> Reveals the Conservation of Microsynteny among Rice Crop-Wild Relatives |
| title_full | Analysis of Homologous Regions of Small RNAs <i>MIR397</i> and <i>MIR408</i> Reveals the Conservation of Microsynteny among Rice Crop-Wild Relatives |
| title_fullStr | Analysis of Homologous Regions of Small RNAs <i>MIR397</i> and <i>MIR408</i> Reveals the Conservation of Microsynteny among Rice Crop-Wild Relatives |
| title_full_unstemmed | Analysis of Homologous Regions of Small RNAs <i>MIR397</i> and <i>MIR408</i> Reveals the Conservation of Microsynteny among Rice Crop-Wild Relatives |
| title_short | Analysis of Homologous Regions of Small RNAs <i>MIR397</i> and <i>MIR408</i> Reveals the Conservation of Microsynteny among Rice Crop-Wild Relatives |
| title_sort | analysis of homologous regions of small rnas i mir397 i and i mir408 i reveals the conservation of microsynteny among rice crop wild relatives |
| topic | comparative genomics <i>Oryza</i> crop wild relatives <i>MIRNAs</i> <i>MIR397</i> <i>MIR408</i> |
| url | https://www.mdpi.com/2073-4409/11/21/3461 |
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