Description

This track displays gene annotations for the marmoset genome. These annotations include protein-coding genes and their exon/intron structures predicted from genome assembly and transcriptomics data. Gene annotations were generated through the CAT (Comparative Annotation Toolkit) pipeline and validated against transcriptomic evidence.

Display Conventions and Configuration

Genes are displayed in the GenePred format with exons shown as thicker blocks and introns as connecting lines. Genes are colored by biotype (blue for protein coding, green for lncRNA, pink for pseudogenes, and purple for novel isoforms and genes). Individual gene features can be searched by name or identifier. Labels display the primary gene name when available.

Methods

Gene annotations were generated using the Comparative Annotation Toolkit (CAT) pipeline, which uses comparative genomics, pairwise alignments (including minimap2, miniprot, and liftoff) and Iso-seq evidence to predict gene structures. Novel genes and isoforms were predicted using available transcriptomics data (See IsoSeq bams).

Credits

Gene annotations were generated by Prajna Hebbar of UC Santa Cruz.

References

• Fiddes IT, Armstrong J, Diekhans M, Nachtweide S, Kronenberg ZN, Underwood JG, Gordon D, Earl D, Keane T, Eichler EE et al. Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation. Genome Res. 2018 Jul;28(7):1029-1038. PMID: 29884752
• Stanke M, Diekhans M, Baertsch R, Haussler D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics. 2008 Mar 1;24(5):637-44. PMID: 18218656
• Stanke M, Steinkamp R, Waack S, Morgenstern B. AUGUSTUS: a web server for gene finding in eukaryotes. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W309-12. PMID: 15215400
• Armstrong J, Hickey G, Diekhans M, Fiddes IT, Novak AM, Deran A, Fang Q, Xie D, Feng S, Stiller J et al. Progressive Cactus is a multiple-genome aligner for the thousand-genome era. Nature. 2020 Nov;587(7833):246-251. PMID: 33177663
• Shumate A, Salzberg SL. Liftoff: accurate mapping of gene annotations. Bioinformatics. 2020 Dec 15;. PMID: 33320174
• Li, H. (2018). Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics, 34:3094-3100
• Li, H. (2021). New strategies to improve minimap2 alignment accuracy. Bioinformatics, 37:4572-4574
• Li, H. (2023) Protein-to-genome alignment with miniprot. Bioinformatics, 39, btad014; PMID: 36648328