Arthur Durante, a PhD researcher at INRAE France, and an active member of EU-LI-PHE Working Group 2: Genome-to-Phenome Integration, realized a successful STSM recently.
Arthur carried out a 3-month research visit (January–April 2025) at the Roslin Institute in the UK, where he contributed to the annotation of the upcoming Telomere-to-Telomere (T2T) pig genome assembly, which includes haplotypes from Hampshire, Large White, and Landrace pig breeds.
During his STSM, Arthur worked with transcriptomic data from 12 tissues of male and female pig fetuses. He applied a combination of advanced sequencing approaches to identify high-confidence long-read isoforms using the FLAIR pipeline. This involved defining isoforms and splice junctions, correcting misalignments, and validating transcription start sites. The pipeline was complemented with TAMA to integrate tissue-specific annotations into a unified transcriptome view.
The project resulted in the identification of 22,540 genes and 359,614 isoforms, a significant expansion compared to the current Sus scrofa annotation, which contains 32,988 genes and 57,741 isoforms. Many of the newly identified elements may represent previously unannotated features, underscoring the value of de novo approaches in genome research.
“EU-LI-PHE funding covered the majority of the expenses for my STSM, allowing me to fully focus on the research and collaborate closely with experts in my field. This experience has not only enriched my PhD work, but also helped me build long-term professional connections that I hope to maintain well beyond this project.”, said Arthur about his experience.
We congratulate Arthur on his outstanding work and look forward to future collaborations stemming from this visit.
