A complete genome for the common marmoset

Area of Science:

• Genomics
• Primate Evolution
• Comparative Genomics

Background:

• The common marmoset is a crucial model organism for primate evolution and human disease research.
• Previous genome assemblies had limitations in resolving complex genomic regions.

Purpose of the Study:

• To generate a high-quality, telomere-to-telomere (T2T) reference genome assembly for the common marmoset.
• To resolve previously inaccessible genomic regions, including centromeres and sex chromosomes.
• To identify novel genes and understand primate genome evolution.

Main Methods:

• Telomere-to-telomere (T2T) sequencing and assembly.
• Analysis of complex genomic regions such as centromeres, sex chromosomes, and satellite DNA.
• Identification and characterization of lineage-specific genes and transcript models.

Main Results:

• A complete T2T reference assembly and three near-T2T haplotypes for the common marmoset were generated.
• Previously unresolved regions, including centromeres, sex chromosomes, and the MHC, were resolved.
• Marmoset centromeres feature chromosomal-specific dimeric alpha satellites, with inactive ancestral remnants.
• Gene-poor, satellite-rich acrocentric chromosome short arms were assembled, harboring rDNA and sharing pseudo-homolog regions (PHRs).
• Over 500 marmoset-lineage-specific transcribed genes with novel transcript models or expansions were identified.

Conclusions:

• The T2T reference genome significantly enhances the common marmoset's utility as a model organism.
• This resource provides critical insights into primate genome evolution, particularly concerning centromere structure and evolution.
• The identification of novel genes and genomic features advances our understanding of marmoset biology and its relevance to human disease.