Whole genome sequencing and annotation of the fish pathogen Edwardsiella ictaluri
NRI competitive grant no:2004-35600-14180
The disease caused by Edwardsiella ictaluri, enteric septicemia of catfish (ESC), is the most economically important disease of farm-raised channel catfish, which is the largest aquaculture industry in the United States. Genetic systems and challenge models are well established for E. ictaluri, but current investigations on how E. ictaluri causes disease are slowed by the need to clone and sequence individual genes. The purpose of this study is to obtain a finished, complete sequence of the Edwardsiella ictaluri genome using a collaborative effort between investigators that will provide sequencing expertise and investigators that will provide the biological expertise for this particular pathogen. Whole-genome sequencing of E. ictaluri will accelerate research on the pathogenesis of ESC, possibly allowing the development of an effective treatment or preventive method.
The overall objective of this research project is to obtain a complete sequence of the genome from the channel catfish pathogen Edwardsiella ictaluri. Secondary objectives of this proposal are to 1) educate and train personnel at Mississippi State University and Louisiana State University in genome sequencing techniques and annotation through hands-on participation, and 2) disseminate knowledge from this project to the aquatic animal health research community and formulate plans and collaborative teams for future functional genomics research based on the E. ictaluri genome sequence.
Three plasmid libraries were constructed and used to complete shotgun sequencing to approximately 8-fold coverage. A small insert library was constructed in pSMART (Lucigen, Middleton, WI) (1-2kb average insert size), medium insert libraries were constructed in pBK-CMV (3-5kb average insert sizes), and a large insert library (ca. 40kb) was also constructed in pCC1FOS (Epicenter, Madison,WI). The E. ictaluri sequence data was released in September 2004 and is being provided as assembled contigs on the Laboratory for Genomics and Bioinformatics website (http://micro-gen.ouhsc.edu/e_ictal/e_ictal_home.htm). Three-fold coverage of the genome was reached on October 8, 2004, and 8X coverage was achieved on January 31, 2005. To assist in closure, 19X coverage of 454 sequencing was conducted (70,616,471 bp with an average read length of 99 bp). The genome was annotated with the TIGR Annotation Engine, identifying a total of 3945 ORFs.
Functional predictions for the ORFs indicate that the physiology of E. ictaluri is similar in many respects to other members of the Enterobacteriaceae, including Escherichia coli O157:H7, Salmonella enterica, Yersinia pestis, and Erwinia carotovora. However, E. ictaluri does have some unique features; for example, its genome contains a higher number of genes involved in DNA recombination, replication, and repair; protein stabilization; and two-component regulatory systems. This may indicate that E. ictaluri is adapted to survival in more stressful or diverse environments than the other Enterobacteriaceae species we compared it to. Interestingly, the genome had 203 transposable elements, which is considerably higher than the other four species. This is surprising because E. ictaluri only has one serovar and is generally considered to be phenotypically homogenous. By contrast, E. coli and S. enterica are each composed of more than 100 serovars and are relatively diverse species, yet E. ictaluri has more transposable elements than both species combined. Another surprising finding was that E. ictaluri has fewer genes classified as unknown function or hypothetical than E. coli O157:H7.
Project director: Mark Lawrence
Project co-directors: David Dyer, Ronald Thune, and Allison Gillaspy
Project personnel: Michele Williams, Christie Landry, Michelle Banes
Publications:
Williams, M. L., D. W. Dyer, A. F. Gillaspy, R. L. Thune, C. A. Landry, G. C. Waldbieser, S. C. Schuster, and M. L. Lawrence. 2006. The Edwardsiella ictaluri genome sequencing project. International Symposium on Aquatic Animal Health, San Francisco, California |
