Genome sequencing of the fish pathogen Flavobacterium columnare

NRI competitive grant no: 2006-35600-16571

Flavobacterium columnare is a bacterial pathogen that affects commercial aquaculture, the ornamental fish industry, and wild fish populations in both the U.S. and worldwide. In particular, it is the second most prevalent disease of farm-raised channel catfish, which is the largest aquaculture industry in the U.S. In spite of the magnitude of this disease problem, very little is known about how F. columnare causes disease, and an effective preventive method is still not available. The overall objective of this research project is to obtain a complete sequence of the F. columnare genome, which will enable new research methods to identify disease-causing genes and will accelerate vaccine development research. The F. columnare genome also has biological significance because it is a member of the Bacteroidetes, which is a group of bacteria that has few sequenced genomes but contains some of the most abundant bacterial species in mammalian intestines and in aquatic environments.

To obtain a complete sequence of the F. columnare genome, we are using a collaborative effort between investigators that provide expertise in genome sequencing and the biology of this particular pathogen. Small and medium insert libraries (3-6 kb, 6-10 kb, and 10-12 kb average insert size) were constructed at Mississippi State University using F. columnare strain ATCC 49512. End sequencing was conducted to 8-fold coverage at The Laboratory for Genomics and Bioinformatics at the University of Oklahoma Health Sciences Center. Sequences were assembled using Phred/Phrap. The current assembly contains 36 contigs >2 Kb in length and the genome size is 3.13 Mb. The finishing stages of the sequencing are being conducted at Mississippi State University. Automated annotation will utilize the TIGR Annotation Engine.

This research will enable functional genomics research and accelerate hypothesis-driven research on this pathogen that affects multiple fish species.

Project director: Mark Lawrence
Project co-director: David Dyer, Allison Gillaspy, Attila Karsi
Project personnel: Nicole Benton, Pradeep Dumpala, Erin Corb

Publications:

Karsi, A., and M. L. Lawrence.  2006.  Construction of genomic libraries from Flavobacterium columnare using Lucigen’s BigEasy Linear Cloning System.  eLucidations 6:1-3.

Lawrence, M. L., D. W. Dyer, A. F. Gillaspy, A. Karsi, and N. Benton.  2007.  The Flavobacterium columnare genome sequencing project.  Flavobacterium 2007 Workshop, Shepherdstown, West Virginia.