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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Research Project #438288

Research Project: High-quality Reference Assembly And Annotation Of The Rainbow Trout Genome

Location: Cool and Cold Water Aquaculture Research

Project Number: 8082-31000-013-07-R
Project Type: Reimbursable Cooperative Agreement

Start Date: Apr 1, 2020
End Date: Mar 31, 2021

Objective:
Aquaculture is the world’s fastest-growing agri-food business. Rainbow trout is the most cultivated cold-water fish in the US. The US aquaculture industry needs applications of genomics in breeding programs to define genetic and phenotypic parameters that control complex traits such as disease resistance and feed efficiency. The FAASG consortium "Functional Analysis of All Salmonid Genomes" has been established to study the functional genomic basis of phenotypic variation in all salmonids including rainbow trout (https://www.faasg.org/). A trout genome sequence is now available (GenBank Accession GCA_002163495). Our team has generated a 2.17 GB genome assembly based on Illumina sequencing technology, containing 139,726 scaffolds with N50 greater than 1.7Mb. Using dense genetic maps, approximately 88% of the assembly bases-pairs were anchored and ordered within chromosomes. However, further improvements to the genome assembly and annotation will improve the accuracy and efficiency of the genomic applications such as GWAS and genomic selection in rainbow trout. The specific objectives of the proposed project are: 1) close gaps in the reference genome assembly by utilizing the long-read PacBio sequencing platform in combination with the BioNano whole genome optical map. 2) annotate the reference genome for the coding and non-coding transcript isoforms and alternative splicing, by full-length single-molecule sequencing. 3) annotate the genome for chromatin histone modifications, chromatin accessibility, by integrating data from RNA-seq, DNAse-seq, and ChIP-seq across a wide range of the rainbow trout tissues.

Approach:
We will generate 300Gb of PacBio sequence reads with N50 greater than 20Kb (approximately 100X genome coverage). A Bionano optical map, a Dovetail HiRise map of chromatin interactions and high-fidelity Illumina short reads were previously produced for the current reference genome (GCA_002163495.1). The new PacBio long-reads sequence data will be used in combination with those previously generated genome resources to generate a near-finished reference genome for rainbow trout using the assembly approach and bioinformatic tools recently described for the goat genome assembly (Bickhart et al., 2017).