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. 2022 Apr 7;23(1):41-49.
doi: 10.2174/1389202923666211223122305.

Novel MicroRNAs and their Functional Targets from Phytophthora infestans and Phytophthora cinnamomi

Binta Varghese  1 , Ravisankar Valsalan  1 , Deepu Mathew  1
Affiliations

Novel MicroRNAs and their Functional Targets from Phytophthora infestans and Phytophthora cinnamomi

Binta Varghese et al. Curr Genomics. .

Abstract

Background: Even though miRNAs play vital roles in developmental biology by regulating the translation of mRNAs, they are poorly studied in oomycetes, especially in the plant pathogen Phytophthora.

Objective: The study aimed to predict and identify the putative miRNAs and their targets in Phytophthora infestans and Phytophthora cinnamomi.

Methods: The homology-based comparative method was used to identify the unique miRNA sequences in P. infestans and P. cinnamomi with 148,689 EST and TSA sequences of these species. Secondary structure prediction of sRNAs for the 76 resultant sequences has been performed with the MFOLD tool, and their targets were predicted using psRNATarget.

Results: Novel miRNAs, miR-8210 and miR-4968, were predicted from P. infestans and P. cinnamomi, respectively, along with their structural features. The newly identified miRNAs were identified to play important roles in gene regulation, with few of their target genes predicted as transcription factors, tumor suppressor genes, stress-responsive genes, DNA repair genes, etc.

Conclusion: The miRNAs and their targets identified have opened new interference and editing targets for the development of Phytophthora resistant crop varieties.

Keywords: Data mining; fungus; genome annotation; miRNA; oomycete; siRNA; target prediction.

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Figures

Fig. (1)
Fig. (1)
Strategy followed to search for the putative miRNAs in Phytophthora genomes.
Fig. (2)
Fig. (2)
Structure of pre-miRNA miR-8210 in P. infestans.
Fig. (3)
Fig. (3)
Structure of pre-miRNA miR-4968 in P. cinnamomi.
See this image and copyright information in PMC

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References

    1. Fry W. Phytophthora infestans: The plant (and R gene) destroyer. Mol. Plant Pathol. 2008;9(3):385–402. doi: 10.1111/j.1364-3703.2007.00465.x. - DOI - PMC - PubMed
    1. Mathew D., Anju P.S., Tom A., Johnson N., George M.L., Davis S.P., Ravisankar V., Asha K.N. Genome-wide microsatellites and species specific markers in genus Phytophthora revealed through whole genome analysis. 3 Biotech. 2020;10:442. doi: 10.1007/s13205-020-02430-y. - DOI - PMC - PubMed
    1. Moore N., Barrett S., Bowen B., Shearer B., Hardy G. The role of fire on Phytophthora dieback caused by the root pathogen Phytophthora cinnamomi in the Stirling Range National Park, Western Australia.; In: Proc. 11th International Mediterranean Ecosystems (MEDECOS) Conference; 2007 Sep 2-5; Perth, Western Australia. pp. 165–166.
    1. Scott P., Bader M.K., Burgess T., Hardy G., Williams N. Global biogeography and invasion risk of the plant pathogen genus Phytophthora. Environ. Sci. Policy. 2019;101:175–182. doi: 10.1016/j.envsci.2019.08.020. - DOI
    1. Axtell M.J. Classification and comparison of small RNAs from plants. Annu. Rev. Plant Biol. 2013;64:137–159. doi: 10.1146/annurev-arplant-050312-120043. - DOI - PubMed