Researchers from the Vertebrate Genomes Project have produced a chromosome-level, fully haplotype-resolved diploid genome assembly for the common marmoset (Callithrix jacchus), an important primate model for a broad range of biomedical research such as neuroscience, stem cell biology, and regenerative medicine.
Two common marmosets (Callithrix jacchus). Image credit: Dario Sanches.
The genome includes two sets of chromosomes, one inherited from the mother, the other from the father.
In traditional genome sequencing efforts including the human genome project, the sequencing only produced a mosaic reference genome mixing randomly with sequences from the maternal or paternal chromosomes.
University of Copenhagen researcher Guojie Zhang and colleagues used a new strategy to produce completed assemblies of the two sets of the marmoset genomes independently into chromosomal level.
“The two parental genomes in our cell are not completely identical but have different nucleotide compositions,” Dr. Zhang said.
“These differences can affect the function of genes and also our health. Some of these differences in men, for examples, the X chromosome from our mother and Y chromosome from our father have different structures and harbor genes with intensified sexual conflicts.”
The scientists sequenced a trio — the mother, father and a male offspring — of the common marmosets.
Taking advance of the long reads sequencing technology, they now can distinguish the two parental genomic sequences in the male offspring based on the genomic features from the mother and father.
“This allows us to detect large genomic variations between the parental genomes,” said Chentao Yang, a Ph.D. student at the University of Copenhagen.
“Surprisingly, we found the heterozygosity level in the diploid genome is 10 times higher than that can be revealed by previous method.”
The diploid assembly enabled the authors to discover a recent expansion of the sex differentiated region and unique evolutionary changes in the marmoset Y chromosome.
Additionally, they identified many genes with signatures of positive selection that might have contributed to the evolution of biological features in the common marmoset.
“We compared 2,533 genes related to brain development and neurodegenerative diseases, and found that the majority are highly conserved between marmoset and human in both sequence and copy numbers,” they explained.
“However, we detected 24 genes showing copy number variations and 8 genes under diversification selection between the two species. These may be associated with brain differences between human and marmoset.”
“Brain related genes were highly conserved between marmosets and humans, though several genes experienced lineage-specific copy number variations or diversifying selection, providing important implications for the application of marmosets as a model system.”
The findings are published in the journal Nature.
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C. Yang et al. Evolutionary and biomedical insights from a marmoset diploid genome assembly. Nature, published online April 28, 2021; doi: 10.1038/s41586-021-03535-x
