The striped bass Morone saxatilis genome sequence assembly

Authors: ANDERSON, LINNEA - North Carolina State University; BALTZEGAR, DAVID - North Carolina State University; Fuller, Adam; Abernathy, Jason; 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 https://appliedecology.cals.ncsu.edu/striped-bass-genome-project/. 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.