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ARS Home » Southeast Area » Stuttgart, Arkansas » Harry K. Dupree Stuttgart National Aquaculture Research Cntr » Research » Publications at this Location » Publication #356178

Research Project: Developing Nutritional, Genetic, and Management Strategies to Enhance Warmwater Finfish Production

Location: Harry K. Dupree Stuttgart National Aquaculture Research Cntr

Title: The striped bass Morone saxatilis genome sequence assembly

item ANDERSON, LINNEA - North Carolina State University
item BALTZEGAR, DAVID - North Carolina State University
item Fuller, Adam
item Abernathy, Jason
item READING, BENJAMIN - North Carolina State University

Submitted to: Aquaculture America Conference
Publication Type: Abstract Only
Publication Acceptance Date: 2/21/2019
Publication Date: 3/11/2019
Citation: Anderson, L.K., Baltzegar, D.A., Fuller, S.A., Abernathy, J.W., Reading, B.J. 2019. The striped bass Morone saxatilis genome sequence assembly. Aquaculture 2019, March 7-11, 2019, New Orleans, Louisana. p. 50.

Interpretive Summary:

Technical Abstract: The striped bass (Morone saxatilis) is a perciform fish of recreational and commercial importance. We report the striped bass genome assembly, which was completed using a combinatorial approach of Illumina and Pacific Biosciences sequencing and Chicago® and Dovetail™ Hi-C + HiRise™ scaffolding (Table 1). A total of 38 Gb of Illumina short-read sequence was generated using both single read and paired-end runs of varying lengths, comprising over 21 lanes on an Illumina GAIIx platform. Over 573 million short-reads were produced, with 106 million reads generated as paired-end sequence (average length of all reads was 67.8 bp). These short-reads were used to generate a CLC Genomics Workbench (version 5.5) de novo assembly having greater than 66x coverage of the striped bass genome. The Illumina short-read assembly was then scaffolded using Chicago® and Dovetail™ Hi-C + HiRise™ technology. The final assembly was then refined by an additional 1.6 Gb of Pacific Biosciences sequence (2.8x coverage) using PBJelly in a cost-effective whole genome shotgun approach. Compared to the initial 569 Mb Illumina short-read assembly, the final 598 Mb striped bass genome assembly reduced assembly scaffold number by 75-fold and increased scaffold N50 by 1284-fold. Analysis of Benchmarking Universal Single-Copy Orthologs (BUSCO) indicates that 90.1% of these gene are present in the final assembly and the low number of assembly scaffolds (629), of which 21 contain most of the genome sequence (L90 = 21 scaffolds) is consistent with a haploid chromosome number of 24 for striped bass. Ab-initio and evidence-based gene predictions performed using the MAKER Annotation Pipeline identified 27,485 coding genes for striped bass and these data are hosted at Striped bass and other fish genomes provide powerful resources for selective breeding of sustainable aquaculture species, as well as enhance studies of fish biology and evolution.