Wheat Long Noncoding RNAs from Organelle and Nuclear Genomes Carry Conserved microRNA Precursors Which May Together...

Area of Science:

• Plant Molecular Biology
• Genomics
• Transcriptomics

Background:

• Long noncoding RNAs (lncRNAs) are critical regulatory molecules in eukaryotes, but their identification and annotation are challenging due to poor sequence conservation.
• Wheat, a vital global food crop, faces significant threats from insect pests, necessitating research into its genetic defense mechanisms.
• Understanding noncoding RNA roles in plant-pest interactions can reveal novel strategies for crop improvement.

Purpose of the Study:

• To identify and characterize long noncoding RNAs (lncRNAs) in wheat varieties with differing resistance to insect pests.
• To investigate potential functional interactions between lncRNAs and microRNAs (miRNAs) in wheat.
• To explore the origin of lncRNAs, including potential contributions from organellar genomes.

Main Methods:

• Deep sequencing technologies were employed to identify putative lncRNAs from durum and bread wheat varieties.
• Bioinformatic analyses were used for annotation, including prediction of miRNA precursor and target sites within lncRNAs.
• Sequence conservation analysis was performed for both lncRNAs and associated miRNAs.

Main Results:

• Putative lncRNAs were identified in wheat varieties differing in stem solidness (resistance to wheat stem sawfly) and in bread wheat resistant/susceptible to orange wheat blossom midge.
• Several lncRNAs showed potential precursor and target regions for miRNAs, suggesting regulatory networks.
• While lncRNAs showed limited conservation, miRNAs with precursors within lncRNAs were highly conserved.
• Some lncRNAs exhibited strong matches to organellar genomes, indicating a potential source of noncoding transcripts.

Conclusions:

• This study provides a valuable resource of lncRNAs in wheat, contributing to the understanding of noncoding RNA roles in plant defense.
• The identified lncRNA-miRNA interactions suggest complex regulatory mechanisms in wheat's response to insect pests.
• The findings highlight the potential involvement of organellar genomes in generating the cellular noncoding transcript pool in plants.