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New Goat Genome Assembly Breaks Continuity Record, Expands Breeding Tools

Tuesday, March 21, 2017, PACBIO 
Efforts to produce a reference-grade goat genome assembly for improved breeding programs have paid off. A new Nature Genetics publication reports a high-quality, highly contiguous assembly that can be used to develop genotyping tools for quick, reliable analysis of traits such as milk and meat quality or adaptation to harsh environments. The program also offers a look at how different scaffolding approaches perform with SMRT Sequencing data.

The project was motivated by a clear need to develop methods for high-quality livestock genome assemblies to benefit breeding communities. Goat offers a particular boost to developing countries, where these animals are a primary source of textile fiber, milk, and meat.

They chose SMRT Sequencing because its long reads could characterize even the most difficult genomic regions. “Initial assembly of the PacBio data alone resulted in a contig NG50 ... of 3.8 Mb,” the team reports. PacBio contigs were then connected with optical mapping and Hi-C data to create extremely long scaffolds in the final 2.92 Gb assembly. “These combined technologies produced what is, to our knowledge, the most continuous de novo mammalian assembly to date, with chromosome-length scaffolds and only 649 gaps,” they write. The assembly is 400 times more continuous than the previous short-read assembly.

Source: PACBIO 


 

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