Production of A Draft Genome Sequence Assembly for Channel Catfish
Warmwater Aquaculture Research Unit
2012 Annual Report
1a.Objectives (from AD-416):
The objective of this research is the production of a draft genome sequence assembly for channel catfish, Ictalurus punctatus.
1b.Approach (from AD-416):
The investigators and collaborators will utilize second generation DNA sequencing technology to produce sufficient amounts of DNA sequence from a homozygous catfish to permit efficient reassembly to recapitulate the original genome sequence. Existing sequence resources will be used to annotate and validate the assembly. The raw data and assembled genome will be placed in public databases.
Long DNA sequences were produced from the channel catfish reference genome using Pacific Biosciences single molecule sequencing technology. Approximately 10-fold coverage of the genome was produced with an average read length of 3,000 base pairs(BP). We are working with bioinformatic cooperators to use existing catfish DNA sequence to increase the base quality of these long sequences. Paired Illumina sequencing reads from long fragment libraries (3,000 bp, 8,000 bp, 36,000 bp) were also produced to assist in scaffolding assembled sequence contigs. Sufficient DNA sequence has been produced for a draft assembly and the project is now focused on bioinformatics such as using Celera Assembler 7 to produce the channel catfish genome sequence assembly, in cooperation with the USDA, ARS, Genomics and Bioinformatics Research Unit. Production of genomic DNA sequence also began for the blue catfish genome assembly and is ongoing.