Improvement of the Threespine Stickleback Genome Using a Hi-C-Based Proximity-Guided Assembly.

ABSTRACT: Scaffolding genomes into complete chromosome assemblies remains challenging even with the rapidly increasing sequence coverage generated by current next-generation sequence technologies. Even with scaffolding information, many genome assemblies remain incomplete. The genome of the threespine stickleback (Gasterosteus aculeatus), a fish model system in evolutionary genetics and genomics, is not completely assembled despite scaffolding with high-density linkage maps. Here, we first test the ability of a Hi-C based proximity-guided assembly (PGA) to perform a de novo genome assembly from relatively short contigs. Using Hi-C based PGA, we generated complete chromosome assemblies from a distribution of short contigs (20-100 kb). We found that 96.40% of contigs were correctly assigned to linkage

SUBMITTER: Peichel CL 

PROVIDER: S-EPMC5892396 | biostudies-literature | 2017 Sep

REPOSITORIES: biostudies-literature