Lamothe, L. | Search bioRxiv

bioRxiv2026

Taming the Genetic Fire: Transposable Element diversity across thermal environments in polychaetes

Genetic variation plays a central role in enabling organisms to adapt to ever-changing environments. Transposable elements (TEs) are key drivers of genetic variation and adaptation, partly due to their ability to respond to environmental changes, such as thermal variability, through transcriptional activation, potentially leading to insertion events. The new copies will eventually accumulate mutations, increasing the TE diversity in the genome. In this study, we investigated how the TE diversity varies across environments, contrasted by their average temperature and their thermal variability profile, using polychaete annelids as a model system. These primarily benthic organisms occupy a wide range of habitats, from polar waters to hydrothermal vents and temperate shores. TE diversity varied substantially among polychaete species, with significantly lower diversity observed in species inhabiting unstable habitats, such as those associated with hydrothermal vents. This link between TE diversity and environment was statistically consistent across the different TE orders, except for DIRS-like elements in Errantia polychaetes, that display a surprisingly high diversity. Our results suggest that TE diversity may be selected to balance the level of TE activation, linked to thermal variability, to maintain a sustainable mutation rate at the whole genome level. In unstable environments, high TE diversity may not be sustainable due to the accumulation of deleterious mutations, caused by a higher rate of stress-induced transposition compared to other habitats. These findings highlight the influence of environmental conditions on the long-term dynamics governing TE-host interactions and underscore the role of TEs in evolution.

evolutionary biology↗

bioRxiv2023

Improved gene annotation of the fungal wheat pathogen Zymoseptoria tritici based on combined Iso-Seq and RNA-Seq evidence

Despite large omics datasets, the establishment of a reliable gene annotation is still challenging for eukaryotic genomes. Here, we used the reference genome of the major fungal wheat pathogen Zymoseptoria tritici (isolate IPO323) as a case study to develop methods to improve eukaryotic gene prediction. Four previous IPO323 annotations identified 10,933 to 13,260 gene models, but only one third of these coding sequences (CDS) have identical structures. To resolve these discrepancies and improve gene models, we generated full-length transcripts using long-read sequencing. This dataset was used together with other evidence (RNA-Seq transcripts and protein sequences) to generate novel ab initio gene models. The selection of the best structure among novel and existing gene models was performed according to transcript and protein evidence using InGenAnnot, a novel bioinformatics suite. Overall, 13,414 re-annotated gene models (RGMs) were predicted, including 671 new genes among which 53 encoded effector candidates. This process corrected many of the errors (15%) observed in previous gene models (coding sequence fusions, false introns, missing exons). While fungal genomes have poor annotations of untranslated regions (UTRs), our Iso-Seq long-read sequences outlined 5 and 3UTRs for 73% of the RGMs. Alternative transcripts were identified for 13% of RGMs, mostly due to intron retention (75%), likely corresponding to unprocessed pre-mRNAs. A total of 353 genes displayed alternative transcripts with combinations of previously predicted or novel exons. Long non-coding transcripts (lncRNAs) and double-stranded RNAs from two fungal viruses were also identified. Most lncRNAs corresponded to antisense transcripts of genes (52%). lncRNAs that were up or down regulated during infection were enriched in antisense transcripts (70%), suggesting their involvement in the control of gene expression. Our results showed that combining different ab initio gene predictions and evidence-driven curation using InGenAnnot improved the quality of gene annotations of a compact eukaryotic genome. Our analysis also provided new insights into the transcriptional landscape of Z. tritici, helping develop an increasingly complex picture of its biology.

genomics↗