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United States Department of Agriculture

Agricultural Research Service

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Research Project: Production of A Draft Genome Sequence Assembly for Channel Catfish

Location: Warmwater Aquaculture Research Unit

2011 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.

3. Progress Report
The objective of this Reimbursible Agreement is the production of genomic DNA sequence for channel catfish as part of an overall whole genome sequence assembly. The ADODR communicates with the cooperator through monthly telephone and email correspondence. Genomic DNA was isolated from a homozygous, doubled haploid catfish produced at the Catfish Genetics Research Unit. This fish was used in order to remove DNA sequence variation between alleles that could complicate accurate sequence assembly. Genomic DNA libraries were produced by random shearing to 400-500 base pair fragments and these fragments were sequenced using Illumina 2nd generation sequencing technology. To date, > 650 million DNA sequences have been produced. An initial sequence assembly has been produced using the ABySS assembly software. This assembly includes approximately 255,000 contigs that total approximately 77% of the size of the catfish genome. Further assembly is limited by repetitive elements in the genome so work is ongoing to produce DNA sequences from the ends of larger fragments in order to span the repetitive regions and place the contigs in order.

4. Accomplishments

Last Modified: 10/18/2017
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