Genome Sequence of Photobacterium mandapamensis Strain svers.1.1, the Bioluminescent Symbiont of the Cardinal Fish Siphamia versicolor

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Photobacterium mandapamensis (Gammaproteobacteria, Vibrionaceae) is the bioluminescent symbiont of the cardinal fish Siphamia versicolor. The fish harbors a dense population of the bacterium in a ventral light organ and uses the bacterial light to attract zooplankton prey. The light organ begins to form early in larval development, through a proliferation and differentiation of intestinal epithelial cells, and it becomes colonized by P. mandapamensis after further larval development (2, 4–8, 11, 14). The specificity of the association and the ability to culture larvae of the fish (5, 8) establish a foundation for experimental analysis of how this vertebrate animal acquires, accommodates, and functions cooperatively with its bacterial symbiont. To begin gaining insight into the genetic interactions underlying the P. mandapamensis-S. versicolor association, we sequenced the genome of P. mandapamensis strain svers.1.1. This is the first genome of a symbiotic, luminous Photobacterium species to be sequenced.

The genome of svers.1.1 was sequenced using the Roche 454 GS FLX titanium platform; 310,304 single-end reads and 195,674 paired-end reads were obtained (8-kb fragments), with approximately 36-fold coverage. The sequence reads were initially assembled with GS Assembler software into 31 contigs (>500 bp).

The draft genome is 4,564,780 bp in total, with a G+C content of 40.76%. The svers.1.1 genome contains two circular chromosomes (as determined by a pulsed-field gel electrophoresis [PFGE] analysis; data not shown), as found in other Vibrionaceae (10). Identification of protein-coding sequences (CDSs) was carried out using the Microbial Genome Annotation Pipeline (MiGAP) (12) with additional information provided by Manatee (IGS Annotation Service [http://manatee.sourceforge.net]). A total of 4,026 CDSs were identified. The genome contains at least six rRNA operons and at least 74 tRNAs.

Comparisons were made to genome sequences of other Vibrionaceae to screen for P. mandapamensis genes involved in quorum-sensing regulation of bioluminescence and in symbiosis. A single, vertically inherited lux-rib operon, luxCDABEFG-ribEBHA (3, 13), was present in the svers.1.1 genome, as were homologs of the regulatory genes cyaA and crp and certain Vibrio harveyi quorum-sensing-regulatory genes, luxO, luxS, luxU, and cqsA. In contrast, homologs of other V. harveyi quorum-sensing-regulatory genes, luxR, luxL, luxM, luxN, luxP, luxQ, and cqsS, and Aliivibrio (Vibrio) fischeri quorum-sensing-regulatory genes, luxR, luxI, and ainS, were absent. Furthermore, homologs of A. fischeri genes involved in bioluminescent symbiosis with the squid Euprymna scolopes, sypG, htrB1, and rcsS (1, 9, 15), were also not present in the svers.1.1 genome. These results indicate that quorum-sensing control of luminescence, as well as other cellular functions, in P. mandapamensis differs significantly from that in other Vibrionaceae. Furthermore, bacterial genes involved in the symbiotic interactions between P. mandapamensis and the fish S. versicolor are likely to be substantially different from those involved in the A. fischeri symbiosis with the squid E. scolopes.