Open Access Research article

An annotated cDNA library of juvenile Euprymna scolopes with and without colonization by the symbiont Vibrio fischeri

Carlene K Chun1, Todd E Scheetz23, Maria de Fatima Bonaldo9, Bartley Brown5, Anik Clemens10, Wendy J Crookes-Goodson1, Keith Crouch4, Tad DeMartini10, Mari Eyestone4, Michael S Goodson1, Bernadette Janssens10, Jennifer L Kimbell10, Tanya A Koropatnick10, Tamara Kucaba4, Christina Smith9, Jennifer J Stewart10, Deyan Tong1, Joshua V Troll1, Sarahrose Webster4, Jane Winhall-Rice10, Cory Yap10, Thomas L Casavant235, Margaret J McFall-Ngai110 and M Bento Soares46789*

Author Affiliations

1 Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, 53706, USA

2 Department of Ophthalmology and Visual Science, University of Iowa, Iowa City, IA 52242, USA

3 Department of Biomedical Engineering, University of Iowa, Iowa City, IA 52242, USA

4 Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA

5 Department of Electrical and Computer Engineering, University of Iowa, Iowa City, IA 52242, USA

6 Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA

7 Department of Orthopaedics, University of Iowa, Iowa City, IA 52242, USA

8 Physiology and Biophysics, University of Iowa, Iowa City, IA 52242, USA

9 Children's Memorial Research Center, Northwestern University, Chicago, IL, 60614, USA

10 Pacific Biomedical Research Center, Kewalo Marine Laboratory, University of Hawaii, Honolulu, HI, 96813, USA

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BMC Genomics 2006, 7:154  doi:10.1186/1471-2164-7-154

Published: 16 June 2006

Abstract

Background

Biologists are becoming increasingly aware that the interaction of animals, including humans, with their coevolved bacterial partners is essential for health. This growing awareness has been a driving force for the development of models for the study of beneficial animal-bacterial interactions. In the squid-vibrio model, symbiotic Vibrio fischeri induce dramatic developmental changes in the light organ of host Euprymna scolopes over the first hours to days of their partnership. We report here the creation of a juvenile light-organ specific EST database.

Results

We generated eleven cDNA libraries from the light organ of E. scolopes at developmentally significant time points with and without colonization by V. fischeri. Single pass 3' sequencing efforts generated 42,564 expressed sequence tags (ESTs) of which 35,421 passed our quality criteria and were then clustered via the UIcluster program into 13,962 nonredundant sequences. The cDNA clones representing these nonredundant sequences were sequenced from the 5' end of the vector and 58% of these resulting sequences overlapped significantly with the associated 3' sequence to generate 8,067 contigs with an average sequence length of 1,065 bp. All sequences were annotated with BLASTX (E-value < -03) and Gene Ontology (GO).

Conclusion

Both the number of ESTs generated from each library and GO categorizations are reflective of the activity state of the light organ during these early stages of symbiosis. Future analyses of the sequences identified in these libraries promise to provide valuable information not only about pathways involved in colonization and early development of the squid light organ, but also about pathways conserved in response to bacterial colonization across the animal kingdom.