Striped Bass Genome Project
The striped bass (Morone saxatilis) is a perciform fish of recreational and commercial importance in North America. We employed a hybrid assembly approach to produce the striped bass genome using 38,000,000,000 base pairs of Illumina short-read sequence (66-fold genome coverage) and an additional 1,600,000,000 base pairs of Pacific Biosciences single molecule, real-time long-read sequence (2.8-fold genome coverage). The 585,100,000 base pair (585.1 Mbp) genome assembly contains 35,010 scaffolds. Ab-initio and evidence-based gene predictions were performed using the MAKER Annotation Pipeline, identifying 27,485 protein coding genes.
This project entitled Implementing Genome Resources for Temperate Basses (Genus Morone) was funded by the National Research Support Project 8 (NRSP-8, United States Department of Agriculture National Institute of Food and Agriculture) program. Through the release of the striped bass genome assembly, we endeavor to foster ongoing and future research efforts into the selective breeding of striped bass and other moronid species, as well as a greater interest into the diversity, evolutionary history, and biology of teleost fishes. A key objective of the project was to establish bioinformatic annotation and curation resources needed to make the striped bass genome available to the public research in a user-friendly (JBrowse) format. Additional funding and resources for this project was provided by North Carolina SeaGrant and the North Carolina State University College of Agriculture and Life Sciences.
Upcoming Manuscript
Reading*, B.J., Baltzegar*, D.A., Dashiell, C., Chapman, R.W., Schilling, J., Williams, V.N., Ring, B.D., Hopper, M., McGinty, A.S., Borski, R.J., McCoy, S., Hiramatsu, N., Matsubara, T., Schaff, J.E., Opperman, C.H., and Sullivan, C.V. The striped bass (Morone saxatilis) genome sequence reveals a complex evolutionary history for teleost vitellogenins. *These authors contributed equally to this manuscript. (Manuscript in preparation).
Additional Information
For additional information about the striped bass genome, hybrid striped bass aquaculture, or genetic improvement for the hybrid striped bass industry contact Dr. Benjamin Reading.
Additional Genomics Resources for Striped Bass
Ovary Transcriptome
The Striped Bass ovary transcriptome high-throuput sequencing project generated 144,302 short read cDNA sequences derived from ovarian mRNA representing all oocyte growth and maturation stages, including atretic oocytes and ovulated eggs. These sequences were clustered with CAP3, which resulted in 11,208 contigs. This data repository represents the blast annotations against the GO database and can be accessed here.
Reading, B.J., Chapman, R.W., Schaff, J.E., Scholl, E.H., Opperman, C.H., and Sullivan, C.V. 2012. An ovary transcriptome for all maturational stages of the striped bass (Morone saxatilis), a highly advanced perciform fish. BMC Research Notes 5:111 (doi: 10.1186/1756-0500-5-111).