Wheat long noncoding RNAs from organelle and nuclear genomes carry conserved microRNA precursors which may together comprise intricate networks in insect responses

Authors: AKPINAR, BALA - MONTANA BIOAGRICULTURE INC.; MUSLU, TUGDEM - MONTANA BIOAGRICULTURE INC.; OZTURK-GOKCE, ZAHIDE - NIGDE UNIVERSITY; Reddy, Gadi V.P.; Dogramaci, Munevver; BUDAK, HIKMET - MONTANA BIOAGRICULTURE INC.

Submitted to: International Journal of Molecular Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/20/2023
Publication Date: 1/23/2023
Citation: Akpinar, B.A., Muslu, T., Ozturk-Gokce, Z.N., Reddy, G.V., Dogramaci, M., Budak, H. 2023. Wheat long noncoding RNAs from organelle and nuclear genomes carry conserved microRNA precursors which may together comprise intricate networks in insect responses. International Journal of Molecular Sciences. 24(3). Article 2226. https://doi.org/10.3390/ijms24032226.
DOI: https://doi.org/10.3390/ijms24032226

Interpretive Summary: Wheat is among the leading food crops worldwide, whose production is threatened by both biotic and abiotic stressors. In recent years, deep sequencing technologies have enabled a better exploration of plant responses. They helped determine the roles and complex interactions of different types of molecules/fragments (such as microRNAs, and long non-coding RNAs) generated in the cell under stress based on the genetic make-up of the plants. In this study, we incorporated state-of-the-art methods to identify fundamental molecular mechanisms regulating defense responses using durum and bread wheat varieties known to be resistant or susceptible to certain pests. Overall, our results highlight the roles of specific RNA fragments and their functional networks for defense responses in durum and bread wheat. We also identified that some of these RNA fragments were common between durum and bread wheat varieties highlighting the conservation of genetic code for particular defense responses in the wheat family. Our results also suggest that organellar genomes may contribute to the noncoding transcript pool of the cell.

Technical Abstract: Long noncoding RNAs (lncRNAs) are a diverse class of noncoding RNAs that are typically longer than 200 nucleotides but that lack coding potentials. Advances in deep sequencing technologies enabled a better exploration of this type of noncoding transcripts. The poor sequence conservation, however, complicates the identification and annotation of lncRNAs at a large scale. Wheat is among the leading food staples worldwide, whose production is threatened by biotic and abiotic stressors. Here, we identified putative lncRNAs from durum wheat varieties that differ in stem solidness, a significant defense source against wheat stem sawfly, a devastating insect pest. We also analyzed and annotated LncRNAs from two bread wheat varieties, resistant and susceptible to another destructive pest, orange wheat blossom midge, with and without infestation. Several putative lncRNAs were found to contain potential precursor sequences and/or target regions for microRNAs, another type of regulatory noncoding RNAs, which may indicate functional networks. Interestingly, in contrast to lncRNAs, microRNAs with potential precursors within the lncRNA sequences appeared to be highly conserved at the sequence and family levels. We also observed a few putative lncRNAs that have perfect to near-perfect matches to organellar genomes, supporting the recent observations that organellar genomes may contribute to the noncoding transcript pool of the cell.