Cargando…

Wheat Long Noncoding RNAs from Organelle and Nuclear Genomes Carry Conserved microRNA Precursors Which May Together Comprise Intricate Networks in Insect Responses

Long noncoding RNAs (lncRNAs) are a diverse class of noncoding RNAs that are typically longer than 200 nucleotides but lack coding potentials. Advances in deep sequencing technologies enabled a better exploration of this type of noncoding transcripts. The poor sequence conservation, however, complic...

Descripción completa

Detalles Bibliográficos
Autores principales: Akpinar, Bala Ani, Muslu, Tugdem, Reddy, Gadi V. P., Dogramaci, Munevver, Budak, Hikmet
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9917100/
https://www.ncbi.nlm.nih.gov/pubmed/36768565
http://dx.doi.org/10.3390/ijms24032226
_version_ 1784886288505110528
author Akpinar, Bala Ani
Muslu, Tugdem
Reddy, Gadi V. P.
Dogramaci, Munevver
Budak, Hikmet
author_facet Akpinar, Bala Ani
Muslu, Tugdem
Reddy, Gadi V. P.
Dogramaci, Munevver
Budak, Hikmet
author_sort Akpinar, Bala Ani
collection PubMed
description Long noncoding RNAs (lncRNAs) are a diverse class of noncoding RNAs that are typically longer than 200 nucleotides but 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 both biotic and abiotic stressors. Here, we identified putative lncRNAs from durum wheat varieties that differ in stem solidness, a major source of defense 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 contained 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 themselves, 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.
format Online
Article
Text
id pubmed-9917100
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-99171002023-02-11 Wheat Long Noncoding RNAs from Organelle and Nuclear Genomes Carry Conserved microRNA Precursors Which May Together Comprise Intricate Networks in Insect Responses Akpinar, Bala Ani Muslu, Tugdem Reddy, Gadi V. P. Dogramaci, Munevver Budak, Hikmet Int J Mol Sci Article Long noncoding RNAs (lncRNAs) are a diverse class of noncoding RNAs that are typically longer than 200 nucleotides but 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 both biotic and abiotic stressors. Here, we identified putative lncRNAs from durum wheat varieties that differ in stem solidness, a major source of defense 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 contained 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 themselves, 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. MDPI 2023-01-23 /pmc/articles/PMC9917100/ /pubmed/36768565 http://dx.doi.org/10.3390/ijms24032226 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Akpinar, Bala Ani
Muslu, Tugdem
Reddy, Gadi V. P.
Dogramaci, Munevver
Budak, Hikmet
Wheat Long Noncoding RNAs from Organelle and Nuclear Genomes Carry Conserved microRNA Precursors Which May Together Comprise Intricate Networks in Insect Responses
title Wheat Long Noncoding RNAs from Organelle and Nuclear Genomes Carry Conserved microRNA Precursors Which May Together Comprise Intricate Networks in Insect Responses
title_full Wheat Long Noncoding RNAs from Organelle and Nuclear Genomes Carry Conserved microRNA Precursors Which May Together Comprise Intricate Networks in Insect Responses
title_fullStr Wheat Long Noncoding RNAs from Organelle and Nuclear Genomes Carry Conserved microRNA Precursors Which May Together Comprise Intricate Networks in Insect Responses
title_full_unstemmed Wheat Long Noncoding RNAs from Organelle and Nuclear Genomes Carry Conserved microRNA Precursors Which May Together Comprise Intricate Networks in Insect Responses
title_short Wheat Long Noncoding RNAs from Organelle and Nuclear Genomes Carry Conserved microRNA Precursors Which May Together Comprise Intricate Networks in Insect Responses
title_sort wheat long noncoding rnas from organelle and nuclear genomes carry conserved microrna precursors which may together comprise intricate networks in insect responses
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9917100/
https://www.ncbi.nlm.nih.gov/pubmed/36768565
http://dx.doi.org/10.3390/ijms24032226
work_keys_str_mv AT akpinarbalaani wheatlongnoncodingrnasfromorganelleandnucleargenomescarryconservedmicrornaprecursorswhichmaytogethercompriseintricatenetworksininsectresponses
AT muslutugdem wheatlongnoncodingrnasfromorganelleandnucleargenomescarryconservedmicrornaprecursorswhichmaytogethercompriseintricatenetworksininsectresponses
AT reddygadivp wheatlongnoncodingrnasfromorganelleandnucleargenomescarryconservedmicrornaprecursorswhichmaytogethercompriseintricatenetworksininsectresponses
AT dogramacimunevver wheatlongnoncodingrnasfromorganelleandnucleargenomescarryconservedmicrornaprecursorswhichmaytogethercompriseintricatenetworksininsectresponses
AT budakhikmet wheatlongnoncodingrnasfromorganelleandnucleargenomescarryconservedmicrornaprecursorswhichmaytogethercompriseintricatenetworksininsectresponses