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Crassostrea virginica sequence assembly C_virginica-3.0 release notes: 
 We have sequenced the genome of the Eastern oyster using DNA from a gynogenetic oyster of an inbred line produced at the Haskin Shellfish Research Laboratory, Rutgers University, known as sample ... RU13XGHG1-28 from either a single tissue or pooled extracts from two tissues (mantle, adductor muscle). Sequences were generated on the Pacific Biosciences RSII instrument (P6/C4 chemistry) to approx. 74x genome coverage based on a genome size estimate of 675 Mb. All reads were assembled with the FALCON algorithm then error corrected using the Quiver and Pilon algorithms. Scaffolds were generated with the SSPACE-LongRead software. We determined the initial draft assembly contained a high number of single copy gene counts suggesting assembly of heterozygous loci. To ensure proper gene annotation we attempted to generate a mostly haploid representation of the draft assembly using transcript mapping to the draft assembly. All contigs were retained in the C_virginica-3.0 assembly that had single best hits to transcripts.
 Of the 685 Mb genome (C_virginica-3.0), the total assembly N50 contig and scaffold lengths are 1.97Mb (n=668) and 75.94Mb (n=10), respectively.
 For questions regarding this C_virginica-3.0 assembly please contact Dr. Marta Gomez-Chiarri, Department of Fisheries, Animal and Veterinary Science, University of Rhode Island, 169 CBLS, Kingston, RI 02881, USA or Dr. Wes Warren, McDonnell Genome Institute at Washington University School of Medicine, St. Louis.

 Credits:
 Funding - USDA 20158701622942-Sequencing of the genome of the eastern oyster, Crassostrea virginica to PI - Marta Gomez-Chiarri
 DNA source and isolation - Ximing Guo, Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, 6959 Miller Avenue, Port Norris, NJ 08349, USA; Dina Proestou, USDA Agricultural Research Service, National Cold Water Marine Aquaculture Center, 469 CBLS, Kingston, RI 02881, USA
 Sequencing - McDonnell Genome Institute at Washington University School of Medicine, St. Louis.
 Assembly, Assembly/Map Integration - LaDeana Hillier, Chad Tomlinson, Pat Minx, Wesley Warren, McDonnell Genome Institute at Washington University School of Medicine, St. Louis.
 Assembly submission - Pat Minx, LaDeana Hillier, McDonnell Genome Institute at Washington University School of Medicine, St. Louis.
 Linkage mapping - Yan He and Ximing Guo, Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, 6959 Miller Avenue, Port Norris, NJ 08349, USA.
 RNAseq data - Dina Proestou, USDA Agricultural Research Service, National Cold Water Marine Aquaculture Center, 469 CBLS, Kingston, RI 02881, USA; Marta Gomez-Chiarri and Tejashree Modak, Department of Fisheries, Animal and Veterinary Science, University of Rhode Island, 169 CBLS, Kingston, RI 02881, USA.

 Data use:
 The Crassostrea virginica sequence is made freely available to the community by McDonnell Genome Institute at Washington University School of Medicine, with the following understanding:
 1. The data may be freely downloaded, used in analyses, and repackaged in databases. 2. Users are free to use the data in scientific papers analyzing these data if the providers of this data are properly cited.

 Assembly statistics: SCAFFOLDS
 COUNT 10 
 LENGTH 684723884 
 AVG 68472388 
 N50 75944018
 LARGEST 104168038 
 (ID: LG9_Scaffold_1, BASES_ONLY_LENGTH: 104159038)
 Scaffolds > 1M: 10 ( 684723884 bp )
 Scaffolds 250K--1M: 0 ( 0 bp )
 Scaffolds 100K--250K: 0 ( 0 bp )
 Scaffolds 10K--100K: 0 ( 0 bp )
 Scaffolds 5K--10K: 0 ( 0 bp )
 Scaffolds 2K--5K: 0 ( 0 bp )
 Scaffolds 0--2K: 0 ( 0 bp )
 CONTIGS
 COUNT 668 
 LENGTH 684658084 
 AVG 1024937 
 N50 1971208
 LARGEST 9802061 
 Contigs > 1M: 238 ( 522420151 bp )
 Contigs 250K--1M: 243 ( 145713162 bp )
 Contigs 100K--250K: 72 ( 12359820 bp )
 Contigs 10K--100K: 94 ( 4065194 bp )
 Contigs 5K--10K: 11 ( 71898 bp )
 Contigs 2K--5K: 7 ( 23884 bp )
 Contigs 0--2K: 3 ( 3975 bp )  more

Global statistics