New insights into genome annotation in Podospora anserina through re-exploiting multiple RNA-seq data

Area of Science:

• Genomics
• Molecular Biology
• Fungal Biology

Background:

• Publicly available RNA-seq datasets can improve eukaryotic genome functional annotation.
• Filamentous fungi genomes, like Podospora anserina, require enhanced annotation for cis-regulatory elements.
• Current P. anserina annotation lacks promoters, transcription start sites, and terminators.

Purpose of the Study:

• To leverage RNA-seq data for comprehensive functional annotation of the P. anserina genome.
• To identify cis-regulatory elements and alternative splicing events.
• To discover novel transcriptionally active regions (nTARs) in unannotated genomic areas.

Main Methods:

• Utilized 37 RNA-seq experiments across diverse developmental and physiological conditions.
• Analyzed transcriptional signal starts and end sites.
• Detected alternative splicing events and identified novel transcriptionally active regions.

Main Results:

• Defined 5' and 3' untranslated regions (UTRs) for 7554 genes, with 3328 showing differential transcriptional start/end sites.
• Identified alternative splicing in 2350 genes, primarily at alternative 3' splice sites.
• Discovered 1732 novel transcriptionally active regions (nTARs) in previously unannotated genomic locations.

Conclusions:

• Provides a comprehensive genome-wide functional annotation for P. anserina, including UTRs, alternative splicing, and non-coding transcription.
• Enhances understanding of gene regulation strategies in compact filamentous fungal genomes.
• Opens avenues for discovering new genes, alternative peptides, and regulatory non-coding RNAs through characterization of alternative transcripts and nTARs.