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Cloning and validation of novel miRNA from basmati rice indicates cross talk between abiotic and biotic stresses

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Abstract

Most of the physiological processes are controlled by the small RNAs in several organisms including plants. A huge database exists on one type of small RNA, i.e., microRNAs (miRs) identified from diverse species. However, the processes of data-mining of miRs in most of the species are still incomplete. Rice feeds the hungry trillions and hence understanding its developmental processes as well as its stress biology, which might be largely controlled by the small RNA pathways, is certainly a worthwhile task. Here, we report the cloning and identification of ~40 new putative miRs from local basmati rice variety in accordance to the annotation suggested by Meyers et al. (Plant Cell 20:3186–3190, 2008). About 23 sequences were derived from rice exposed to salt stress while 18 were derived from rice infected with tungro virus. A few of these putative miRs were common to both. Our data showed that at least two of these miRs were up-regulated in response to both abiotic and biotic stresses. The miR target predictions indicate that most of the putative miRs target specific metabolic processes. The up-regulation of similar miRs in response to two entirely different types of stresses suggests a converging functional role of miRs in managing various stresses. Our findings suggest that more rice miRs need to be identified and a thorough understanding of the function of such miRs will help unravel the mysteries of rice stress biology.

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Acknowledgments

This research was supported by grants from Department of Science and Technology and Department of Biotechnology, New Delhi, India.

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Authors and Affiliations

  1. International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India

    Neeti Sanan-Mishra, Vikash Kumar, Sudhir K. Sopory & Sunil K. Mukherjee

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  1. Neeti Sanan-Mishra
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  2. Vikash Kumar
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  3. Sudhir K. Sopory
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  4. Sunil K. Mukherjee
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Correspondence to Sunil K. Mukherjee.

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Communicated by A. Tyagi.

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Table 1 List of the cloned sequences that are homologous with the already known miRs from rice (XLS 32 kb)

438_2009_478_MOESM2_ESM.xls

Supplemental material Table 2 Homology of the cloned small RNA sequences with the rice genome sequence available in the GenBank accessions with NCBI. The table lists the small RNA sequence, physiology of the tissue from which it was isolated along with the details of accession number, clone name, nucleotide positions, polarity of the homologous rice genomic or cDNA regions. The 5’-3’ strand is designated as the + strand while the complementary 3’-5’ strand is designated as the – strand (XLS 56 kb)

438_2009_478_MOESM3_ESM.xls

Supplemental Table 3 Homology of the cloned small RNA sequences with the mature miR sequences in the Sanger’s database. The table lists the small RNA sequence, tissue and physiology from which it was isolated along with the details of homologous miR including expect (E) value, accession number and genomic coordinates, number of predicted targets and polarity of the strand. The 5’-3’ strand is designated as the + strand while the complementary 3’-5’ strand is designated as the – strand (XLS 78 kb)

438_2009_478_MOESM4_ESM.xls

Supplemental Table 4 Predicted precursors of the 44 small RNA sequences having 0-3 mismatches with the available rice genome. The table lists the cultivar of rice and accession number from which the precursor was predicted. The length, sequence and free energy (dG) of the putative precursor is mentioned (XLS 57 kb)

438_2009_478_MOESM5_ESM.xls

Supplemental Table 5 Predicted targets of the putative miR sequences determined by using miRU software. The table lists accession number, sequence and function of the predicted target region. The maximum score and prediction parameters are mentioned in the table (XLS 58 kb)

438_2009_478_MOESM6_ESM.xls

Supplemental Table 6 Homologs of putative miR sequences identified in plant species other than rice. The summarized presentation of homologs of putative miR sequences identified in plant species other than rice using nucleotide BLAST search. The sequences specific to rice genome have been separately highlighted (XLS 47 kb)

438_2009_478_MOESM7_ESM.ppt

Supplemental Figure 1 Foldback structures. Foldback structures of the putative precursors of the 44 small RNA sequences having 0-3 mismatches with the available rice genome. The sequences are numbered starting from the 5’end, so the top strand represents the 5’ arm while the bottom strand represents the 3’ arm. The putative miR sequence is highlighted in green colour. dG indicates the free energy of the folded precursort (PPT 3205 kb)

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Sanan-Mishra, N., Kumar, V., Sopory, S.K. et al. Cloning and validation of novel miRNA from basmati rice indicates cross talk between abiotic and biotic stresses. Mol Genet Genomics 282, 463–474 (2009). https://doi.org/10.1007/s00438-009-0478-y

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