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ARS Home » Northeast Area » Orono, Maine » National Cold Water Marine Aquaculture Center » Research » Publications at this Location » Publication #347556

Research Project: Genetic Improvement Of Marine Fish and Shellfish

Location: National Cold Water Marine Aquaculture Center

Title: The eastern oyster genome: A resource for comparative genomics in shellfish aquaculture species

item WARREN, WES - Washington University
item GUO, XIMING - Rutgers University
item Proestou, Dina
item MINX, PATRICK - Washington University
item TOMLINSON, CHAD - Washington University
item GOMEZ-CHIARRI, MARTA - University Of Rhode Island

Submitted to: Annual International Plant & Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 10/27/2017
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Oyster aquaculture is an important sector of world food production. As such, it is imperative to develop a high quality reference genome for the eastern oyster, Crassostrea virginica, to assist in the elucidation of the genomic basis of commercially important traits. All genetic, gene expression and methylation studies depend on the use of accurate assembled consensus base sequence and we predict the use of all types of variants to associate allelic state with trait variance will be expanded. Major challenges to the assembly of molluscan genomes are the high rate of polymorphism and the unique repeat architecture present in these species. To partially address these challenges, DNA from an eastern oyster produced by gynogenesis within an inbred line was used for single molecule real time sequencing of the genome (~87x coverage). All reads were assembled using FALCON to a total size of 684Mb with an N50 contig length of 1.9Mb. The predicted genome size is reported to be 578-675Mb. Total interspersed repeats were estimated to be ~36% using WindowMasker. A majority of sequences (>99%) were scaffolded into the known number of 10 chromosomes using a HiC proximity map then aligned to the eastern oyster genetic linkage map to confirm correct association. Gene annotation using the automated NCBI pipeline predicts the presence of 39,493 protein coding genes and 4,230 non-coding. This reference resource should provide a wealth of information about traits important to oyster health and development.