Nature Genetics features Ponce de León goat de novo genome benefits
Department of Animal Science Molecular Genetics Professor Emeritus Abel Ponce de León coauthored a study just published in Nature Genetics detailing strides taken in genome sequence assembly. The research team's results demonstrate the current state of the art for de novo genome assembly using the domestic goat.
"Sequencing of the three billion base pairs of the human genome started 26 years ago, cost about $3 billion, and involved numerous labs and researchers. Now the combination of several newly available technologies helped to generate a more complete assembly of the goat genome that is about 400 times more contiguous than the previous published assembly at a significantly lower cost of approximately $100,000," Ponce de León says.
"Once you generate sequence information of a species genome then you need to assemble it so you can read it, and this has been done at a much slower pace due to genome complexities and lack of algorithms to do the work. Most of the sequenced genomes have different levels of ordering precision and contiguity. To date the human genome is the best-assembled genome and possibly the goat genome is now the second best assembled genome.
"Our attempt here was to use high resolution technologies in a synergistic way to be able to produce a more complete genome that is more contiguous across all chromosomes of this specie. What we have achieved is a more precise and more reliable model," he says. These technologies should help improve the assemblies of other genomes and enhance the precision of comparative genomic studies across species.
Ponce de Leon's contribution to the research was on the Y chromosome of the goat. His contribution entails a comparative genomic analysis of the goat and bull Y-chromosomes. The latter has been part of his work on farm animals since the early 90s, "so the genomic information we have generated for the bovine sex chromosomes became a valuable resource for this de novo genome assembly."
Read more in Nature Genetics.