ArticleGenome biology2023
GET_PANGENES: calling pangenes from plant genome alignments confirms presence-absence variation.
Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers, 1 of them a synthesis that pooled it.
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Who cites it
11 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-Analysis of Rice Phosphoproteomics Data to Understand Variation in Cell Signaling Across the Rice Pan-Genome.Journal of proteome research · 2024Pooled it
- Vernalization regulatory network identifies potential novel functions for genes in the HvVRN2 locus.The New phytologist · 2026Article
- Assessment of genome evolution inmSystems · 2026Article
- Ubiquitin-like SUMO protease expansion in rice (Oryza sativa L.).The plant genome · 2026Article
- Pangenomics in the Mimulus guttatus Species Complex.Molecular ecology resources · 2026Article
- Comparative genomics profiling of Citrus species reveals the diversity and disease responsiveness of the GLP pangenes family.BMC plant biology · 2025Article
- PangenePro: an automated pipeline for rapid identification and classification of gene family members.Bioinformatics advances · 2025Article
- Pandagma: a tool for identifying pan-gene sets and gene families at desired evolutionary depths and accommodating whole-genome duplications.Bioinformatics (Oxford, England) · 2024Article
- Technological Development and Advances for Constructing and Analyzing Plant Pangenomes.Genome biology and evolution · 2024Review
- Genetic control of root/shoot biomass partitioning in barley seedlings.Frontiers in plant science · 2024Article
- A meta-analysis of rice phosphoproteomics data to understand variation in cell signalling across the rice pan-genome.bioRxiv : the preprint server for biology · 2023Article
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Authors and funding
8 authors.
Funding
Abstract
Crop pangenomes made from individual cultivar assemblies promise easy access to conserved genes, but genome content variability and inconsistent identifiers hamper their exploration. To address this, we define pangenes, which summarize a species coding potential and link back to original annotations. The protocol get_pangenes performs whole genome alignments (WGA) to call syntenic gene models based on coordinate overlaps. A benchmark with small and large plant genomes shows that pangenes recapitulate phylogeny-based orthologies and produce complete soft-core gene sets. Moreover, WGAs support lift-over and help confirm gene presence-absence variation. Source code and documentation: https://github.com/Ensembl/plant-scripts .
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