Section: Genomics
Topic: Biophysics and computational biology, Genetics/genomics
Conference: JOBIM

GrAnnoT, a tool for efficient and reliable annotation transfer through pangenome graph

Marthe, Nina1  ; Zytnicki, Matthias2 ; Sabot, François1  
1 DIADE unit, UM, Cirad, IRD, Montpellier, France
2 MIAT, INRAE, Auzeville-Tolosane, France

Corresponding author(s): Marthe, Nina (nina.marthe@ird.fr); Sabot, François (francois.sabot@ird.fr)

10.24072/pcjournal.651 - Peer Community Journal, Volume 5 (2025), article no. e133

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The increasing availability of genome sequences has highlighted the limitations of using a single reference genome to represent the diversity within a species. Pangenomes, encompassing the genomic information from multiple genomes, thus offer a more comprehensive representation of intraspecific diversity. However, pangenomes in form of a variation graph often lack annotation information and tools for manipulating it, which limits their utility for downstream analyses. We introduce here GrAnnoT, a tool designed for an efficient and reliable integration of annotation information in such variation graphs. It projects existing annotations from a source genome to the variation graph and subsequently to other embedded genomes. GrAnnoT was benchmarked against state-of-the-art tools on pangenome variation graphs and linear genomes from Asian rice, and tested on human and E. coli data. The results demonstrate that GrAnnoT is consensual, conservative, and fast. It provides informative outputs, such as presence-absence matrices for genes, and alignments of transferred features between source and target genomes, helping in the study of genomic variations and evolution. GrAnnoT’s robustness and replicability across different species make it a valuable tool for enhancing pangenome analyses. GrAnnoT is available under the GNU GPLv3 licence at https://forge.ird.fr/diade/dynadiv/grannot.

Published online:
DOI: 10.24072/pcjournal.651
Type: Research article
Keywords: Pangenome, graph, annotation transfer

Marthe, Nina 1; Zytnicki, Matthias 2; Sabot, François 1

1 DIADE unit, UM, Cirad, IRD, Montpellier, France
2 MIAT, INRAE, Auzeville-Tolosane, France
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights 
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Marthe, N.; Zytnicki, M.; Sabot, F. GrAnnoT, a tool for efficient and reliable annotation transfer through pangenome graph. Peer Community Journal, Volume 5 (2025), article  no. e133. https://doi.org/10.24072/pcjournal.651

PCI peer reviews and recommendation, and links to data, scripts, code and supplementary information: 10.24072/pci.genomics.100432

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

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