Identification of structural variation in chimpanzee using optical mapping and nanopore sequencing
About Daniela Soto
Daniela Soto is a Ph.D. candidate in the Integrative Genetics and Genomics program at University of California, Davis, and a Chilean Fulbright fellow. She is part of the Dennis Lab at UC Davis Genome Center. The focus of her research is using long-read sequencing technologies to unveil the variability landscape of complex genomic regions in great apes and explore their impact in evolution and disease.
Structural variation comprises a larger proportion of genetic differences between and within great apes, making them an important yet understudied source of trait divergence. We used nanopore sequencing and optical mapping to identify structural variants ≥10kbp in two Pan troglodytes individuals, finding 425 deletions and 59 inversion, where 88 and 36 were novel. Compared to humans, we found an enrichment of chimpanzee genes differentially expressed within deletions and near inversion breakpoints, and a depletion of putatively disrupted domains. Finally, we evaluated nanopore sequencing and optical mapping as tools for de novo assembly and scaffolding of a chimpanzee genome, achieving N50≥80Mbp.