ARS Units Collaborate to Develop Novel Genome Assembly Method, January 2015
USDA ARS researchers from the Beltsville Agricultural Research Center with US Meat Animal Research Center worked closely with collaborators from the Department of Homeland Security and University of Maryland to develop a strategy based on third-generation DNA sequencing technology from Pacific Biosciences (PacBio). This technology generates much longer fragments of DNA sequence than established methods, but the sequence error rate is much higher. To compensate for these random errors, many copies of the genome were sequenced and a consensus of these multiple copies was taken to be the true sequence. A major challenge in assembling large genomes is the existence of repetitive, non-unique sequence patterns scattered across genome. The increased length of PacBio fragments enabled researchers to span across the repetitive elements and anchor the fragment on both sides of repeats. This new approach assembled much larger fragments of the genome into a reference assembly. Researchers generated a high-quality de novo genome assembly for the goat (Capra hircus), and the new strategy may enable creation of new reference assemblies for many species. Current approaches are complex and laborious, requiring a large amounts of data generated from a variety of sequencing libraries as well as cytogenetic surveys to better understand the chromosomal landscape. This research provided dramatically improved tools to perform goat genetic conservation, enhancement, and breeding research. Scientists in the Animal Genomics and Improvement Laboratory in Beltsville are leading an international partnership under Feed the Future (FtF) initiative to characterize and improve productivity of African goats and enhance food security for small holders. The new reference assembly guided this work and informed conservation and breeding programs.