Improvement of the Alpaca Reference Genome to Chromosome Level with Comprehensive Gene Annotation and Variant Database

Principal investigators:

Brian W. Davis and Terje Raudsepp
Texas A&M University, College Station Texas
January 1, 2023 – December 31, 2024
$37,999

A reference genome is the most essential asset to modern genetics research. This singular community resource has the power to shape every aspect of species investigations including population structure and health, evolution, morphological variation, and heritable disease. Additionally, an understanding of the genetic variation within a species is extremely important for identifying variation associated with phenotypes and disease by comparing affected individuals to the entire population. The current alpaca reference has been helpful but is extremely fragmented, existing in 204,000 small individual segments that are stitched together into ~77,000 regions with unknown gaps between each region. No database of genetic variation exists for alpaca at the genome level, and very little information as to the placement of genes in the genome exists.

The proposed work seeks to correct all three of these deficiencies by using cutting-edge genomic technologies and computational methods to construct a chromosome-level genome that rivals that of other important agricultural species. We will then characterize genomic variation across all publicly available and privately held alpaca sequence data (see letters of support) and perform an “annotation” to unambiguously identify the location and structure of genes in alpaca. This work will follow similar approaches used in many other species by the PI and co-PI and will utilize resources already available in their labs. The finished deliverables will be provided to the research community immediately upon completion.