October 2026 talk of the monthly meeting of the #animal-genomics special interest group.

We are happy to introduce Marco Sollitto (University of Florence, Italy). Dr. Marco Sollitto is a researcher at the University of Florence working in comparative and evolutionary genomics. He has undertaken a visiting research period at the Vertebrate Genome Laboratory at The Rockefeller University, where he contributed to large-scale vertebrate genome projects, including genome annotation and comparative genomics.

The Vertebrate Genomes Project Phase I: From reference genomes to standardized gene annotation

The Vertebrate Genomes Project (VGP) aims to generate high-quality reference genomes for all extant vertebrate species, establishing a standardized genomic foundation for comparative, evolutionary, conservation, and biomedical research. Phase I represents the first major milestone toward this goal, delivering reference genomes spanning approximately 97% of vertebrate orders. Alongside improvements in genome contiguity and completeness, a key component of this resource is the generation of consistent, evidence-supported gene annotations that enable meaningful comparisons across highly divergent vertebrate lineages.

For the main VGP Phase I comparative dataset, we use annotations generated with the NCBI Eukaryotic Genome Annotation Pipeline (EGAP) and the publicly available EGAPx workflow. Among these genomes, 298 were annotated with NCBI EGAP and 269 with EGAPx. Both approaches integrate genomic sequence with complementary biological evidence, including short- and long-read transcriptomic data and protein sequences from related species, to reconstruct transcripts, resolve exon-intron structures, identify protein-coding genes and alternative isoforms, and assign functional annotations. This evidence-driven strategy produced highly complete annotation sets, with most reaching 90–100% BUSCO completeness.

EGAPx is implemented as a reproducible and scalable Nextflow workflow, enabling standardized annotation across hundreds of genomes and efficient deployment on high-performance computing environments. Applying closely related annotation strategies across the VGP dataset reduces methodological heterogeneity among species and makes differences in gene content and structure more interpretable in an evolutionary context. Together, chromosome-scale genome assemblies and standardized gene annotations provide a foundation for investigating gene conservation, duplication and loss, lineage-specific innovations, and other aspects of vertebrate genome evolution at an unprecedented phylogenetic scale.