Complete Genome Sequence of the Fruiting Myxobacterium Corallococcus coralloides DSM 2259

Abstract

Corallococcus coralloides, like most other myxobacteria, undergoes a developmental program culminating in the formation of fruiting bodies. C. coralloides fruiting bodies are morphologically distinct from those of other fruiting myxobacteria for which full-length genome sequences are available. The genome sequence of the 10.0-Mb C. coralloides genome is presented herein.

GENOME ANNOUNCEMENT

In response to starvation, most myxobacteria initiate a developmental program that culminates in the formation of multicellular, spore-filled fruiting bodies (8). Fruiting body morphology is species specific, i.e., genetically determined, and highly variable (2, 12). While the fruiting bodies of the model organism Myxococcus xanthus are relatively simple morphologically, resembling haystacks, numerous myxobacterial species construct fruiting bodies that exhibit a high degree of morphological complexity, including stalks, sporangioles, and appendages. To date, we understand little about the genetic mechanisms underlying this morphological complexity and diversity.

Among bacteria, fruiting body formation is restricted to myxobacteria (12), suggesting that the last common ancestor of the myxobacteria already harbored the genetic program for fruiting body formation. Surprisingly, recent comparative genomic analyses indicate that the genetic programs for fruiting body formation are likely not highly conserved in different myxobacteria (5). To provide a framework for understanding the evolution of the genetic program(s) for fruiting body formation and morphology, we sequenced and annotated the genome of Corallococcus coralloides DSM 2259, a member of the suborder Cystobacterineae. C. coralloides forms fruiting bodies with coral-shaped appendages that extend up and away from the central fruiting body structure (2).

C. coralloides DSM 2259 was obtained from the DSMZ (Deutsche Sammlung von Mikrooganismen und Zellkulturen GmbH), and fruiting body formation was verified. Sequence data were generated using the 454 XLR Titanium platform (42-fold coverage). A total of 981,135 filtered reads were assembled into a single scaffold using combined Newbler (10) and Celera (11) assembly results. Sanger-based sequencing was performed to verify the assembly and to close gaps. Genome annotation was generated by manually curating the combined results of MAGPIE (3), RAST (1), PRODIGAL (6), and BASys (14) annotation predictions.

The complete genome sequence of the C. coralloides DSM 2259 chromosome contains 10,080,619 bp, with a GC content of 69.9%. A total of 8,033 protein-coding genes (CDSs) were identified, with an average length of 1,148 bp. Fifty-nine tRNA genes and three rRNA operons were identified. In total, the predicted genes account for approximately 91.7% of the genome sequence length. Functional assignments, obtained using database comparisons, were determined for 58% of the CDSs. These findings are similar to those determined for other genome sequences of fruiting myxobacteria, i.e., Sorangium cellulosum (13), Haliangium ochraceum (7), M. xanthus (4), Myxococcus fulvus (9), and Stigmatella aurantiaca (5), with genome sizes of 13.0 Mb, 9.4 Mb, 9.1 Mb, 9.0 Mb, and 10.3 Mb, respectively. Further, global synteny is apparent between the four Cystobacterineae genomes of C. coralloides, M. xanthus, S. aurantiaca, and M. fulvus, and C. coralloides shares the inversion described for M. fulvus (9).

The C. coralloides genome sequence will allow us to analyze with greater resolution the evolution of the genetic programs leading to fruiting body formation and may provide new insights regarding genetic determinants of fruiting body morphology.

Nucleotide sequence accession number.

The genome sequence was deposited in GenBank under accession number CP003389.