Degradome comparison between wild and cultivated rice identifies differential targeting by miRNAs
Abstract Background Small non-coding (s)RNAs are involved in the negative regulation of gene expression, playing critical roles in genome integrity, development and metabolic pathways. Targeting of RNAs by ribonucleoprotein complexes of sRNAs bound to Argonaute (AGO) proteins results in cleaved RNAs...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2022-01-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-021-08288-5 |
| _version_ | 1798026544351805440 |
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| author | Chenna Swetha Anushree Narjala Awadhesh Pandit Varsha Tirumalai P. V. Shivaprasad |
| author_facet | Chenna Swetha Anushree Narjala Awadhesh Pandit Varsha Tirumalai P. V. Shivaprasad |
| author_sort | Chenna Swetha |
| collection | DOAJ |
| description | Abstract Background Small non-coding (s)RNAs are involved in the negative regulation of gene expression, playing critical roles in genome integrity, development and metabolic pathways. Targeting of RNAs by ribonucleoprotein complexes of sRNAs bound to Argonaute (AGO) proteins results in cleaved RNAs having precise and predictable 5` ends. While tools to study sliced bits of RNAs to confirm the efficiency of sRNA-mediated regulation are available, they are sub-optimal. In this study, we provide an improvised version of a tool with better efficiency to accurately validate sRNA targets. Results Here, we improvised the CleaveLand tool to identify additional micro (mi)RNA targets that belong to the same family and also other targets within a specified free energy cut-off. These additional targets were otherwise excluded during the default run. We employed these tools to understand the sRNA targeting efficiency in wild and cultivated rice, sequenced degradome from two rice lines, O. nivara and O. sativa indica Pusa Basmati-1 and analyzed variations in sRNA targeting. Our results indicate the existence of multiple miRNA-mediated targeting differences between domesticated and wild species. For example, Os5NG4 was targeted only in wild rice that might be responsible for the poor secondary wall formation when compared to cultivated rice. We also identified differential mRNA targets of secondary sRNAs that were generated after miRNA-mediated cleavage of primary targets. Conclusions We identified many differentially targeted mRNAs between wild and domesticated rice lines. In addition to providing a step-wise guide to generate and analyze degradome datasets, we showed how domestication altered sRNA-mediated cascade silencing during the evolution of indica rice. |
| first_indexed | 2024-04-11T18:37:02Z |
| format | Article |
| id | doaj.art-f451ac952b894a7fbbc3ba9f3adcea85 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-11T18:37:02Z |
| publishDate | 2022-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-f451ac952b894a7fbbc3ba9f3adcea852022-12-22T04:09:13ZengBMCBMC Genomics1471-21642022-01-0123111710.1186/s12864-021-08288-5Degradome comparison between wild and cultivated rice identifies differential targeting by miRNAsChenna Swetha0Anushree Narjala1Awadhesh Pandit2Varsha Tirumalai3P. V. Shivaprasad4National Centre for Biological Sciences, Tata Institute of Fundamental ResearchNational Centre for Biological Sciences, Tata Institute of Fundamental ResearchNational Centre for Biological Sciences, Tata Institute of Fundamental ResearchNational Centre for Biological Sciences, Tata Institute of Fundamental ResearchNational Centre for Biological Sciences, Tata Institute of Fundamental ResearchAbstract Background Small non-coding (s)RNAs are involved in the negative regulation of gene expression, playing critical roles in genome integrity, development and metabolic pathways. Targeting of RNAs by ribonucleoprotein complexes of sRNAs bound to Argonaute (AGO) proteins results in cleaved RNAs having precise and predictable 5` ends. While tools to study sliced bits of RNAs to confirm the efficiency of sRNA-mediated regulation are available, they are sub-optimal. In this study, we provide an improvised version of a tool with better efficiency to accurately validate sRNA targets. Results Here, we improvised the CleaveLand tool to identify additional micro (mi)RNA targets that belong to the same family and also other targets within a specified free energy cut-off. These additional targets were otherwise excluded during the default run. We employed these tools to understand the sRNA targeting efficiency in wild and cultivated rice, sequenced degradome from two rice lines, O. nivara and O. sativa indica Pusa Basmati-1 and analyzed variations in sRNA targeting. Our results indicate the existence of multiple miRNA-mediated targeting differences between domesticated and wild species. For example, Os5NG4 was targeted only in wild rice that might be responsible for the poor secondary wall formation when compared to cultivated rice. We also identified differential mRNA targets of secondary sRNAs that were generated after miRNA-mediated cleavage of primary targets. Conclusions We identified many differentially targeted mRNAs between wild and domesticated rice lines. In addition to providing a step-wise guide to generate and analyze degradome datasets, we showed how domestication altered sRNA-mediated cascade silencing during the evolution of indica rice.https://doi.org/10.1186/s12864-021-08288-5DegradomemiRNAO. nivaraO. sativa indica Pusa Basmati-1Domestication |
| spellingShingle | Chenna Swetha Anushree Narjala Awadhesh Pandit Varsha Tirumalai P. V. Shivaprasad Degradome comparison between wild and cultivated rice identifies differential targeting by miRNAs BMC Genomics Degradome miRNA O. nivara O. sativa indica Pusa Basmati-1 Domestication |
| title | Degradome comparison between wild and cultivated rice identifies differential targeting by miRNAs |
| title_full | Degradome comparison between wild and cultivated rice identifies differential targeting by miRNAs |
| title_fullStr | Degradome comparison between wild and cultivated rice identifies differential targeting by miRNAs |
| title_full_unstemmed | Degradome comparison between wild and cultivated rice identifies differential targeting by miRNAs |
| title_short | Degradome comparison between wild and cultivated rice identifies differential targeting by miRNAs |
| title_sort | degradome comparison between wild and cultivated rice identifies differential targeting by mirnas |
| topic | Degradome miRNA O. nivara O. sativa indica Pusa Basmati-1 Domestication |
| url | https://doi.org/10.1186/s12864-021-08288-5 |
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