Vertebrate genomics is heading into an era where the release of hundreds of new reference genomes a year is going to be the norm. If we are to effectively engage with the new biology, we need to be able to annotate genes on these genomes in an accurate and efficient manner. Unfortunately, the current state of gene annotation software requires the use of multiple tools and hours of manual curation. In order to remedy this, I am working on CAT2.0, an improved version of the Comparative Annotation Toolkit. CAT2.0 performs both evidence-based and de novo gene annotation. It can simultaneously annotate many closely related genomes using an annotated reference genome while incorporating information like RNA-seq/Iso-seq data or transcripts and protein homology. CAT2.0. was used to perform gene annotation of protein-coding and non-coding genes for all the non-human primate (NHP) assemblies. We also plan to use CAT2.0 to annotate genomes for several large-scale genome projects- such as the Human Pangenome and Vertebrate Genomes Projects. In my talk, I will present current developments in the tool and also some results from previous projects. In the last part of my talk, I will also present exciting new updates on the Telomere-to-Telomere Common Marmoset project- which will be the first complete genome assembly for a New World Monkey species. This genome will enable increased power for comparative analyses among available primate genomes and will also facilitate biomedical research application.
Prajna Hebbar is a third year PhD student in the Department of Biomolecular Engineering at the University of California Santa Cruz under the supervision of Dr Benedict Paten. She is extremely interested in developing methods for comparative and pan- genomics, with a focus on gene annotation. Her most recent efforts have been to assemble and annotate the complete T2T genome of the common marmoset. She also is currently working on annotating the human pangenome. She also previously annotated the complete T2T genomes of the primates from the T2T Primates project.