Genome Sequence of Reyranella massiliensis, a Bacterium Associated with Amoebae

Abstract

Reyranella massiliensis is an Alphaproteobacterium member of the class Rhodospirillaceae, growing in amoebae. We sequenced the genome of type strain 521^T. It is composed of a 5,792,218-bp chromosome and encodes 5,675 protein-coding genes and 53 RNA genes, including 3 rRNA genes.

GENOME ANNOUNCEMENT

Reyranella massiliensis was first isolated from a freshwater sample, from the river Le Reyran (France), using a coculture procedure with Acanthamoeba polyphaga amoeba. This is a Gram-negative bacillus, classified within the alphaproteobacteria in the class Rhodospirillaceae. It is so far the only member of the genus member of the genus Reyranella, and three isolates were isolated, all from freshwater (6). The 521^T type strain was isolated from the river Le Reyran. The second and the third strains, 3B26 and S184, were isolated from cooling-tower water samples in Paris (France) and Le Pontet (France), respectively. All three strains grew well on buffered charcoal yeast extract (BCYE) and on Columbia sheep blood agar. The strains represent Gram-negative, Gimenez-positive, nonmotile, and microaerophilic bacilli. The closest genus related to Reyranella sp. with regard to the complete sequencing of the 16S rRNA gene is Rhodospirillum photometricum, with 92% similarity.

The genome was pyrosequenced using a 454 GS FLX Titanium platform (Roche, Branford, CT) (5) and assembled using Newbler software v2.5.3 (Roche). A total of 508,384 reads were obtained using paired-end sequencing. The draft genome of Reyranella massiliensis 521^T consists of a single scaffold of 42 contigs containing 5,771,094 bp with a G+C content of 64.9% and an estimated size (including gaps) of 5,792,218 bp. Potential coding sequences (CDSs) were predicted using Prodigal software (3) with default parameters, whereas the predicted ORFs were excluded if they were spanning a sequencing-gap region. Assignment of protein functions was performed by searching the GenBank, Clusters of Orthologous Groups (COGs), and Pfam databases using BLASTP (1, 8, 10). Of the 5,675 CDSs that were identified, representing a coding capacity of 5,346,330 bp (92.3% of the complete genome), 5,728 were protein-coding genes, including 5,494 assigned to the COGs (9) database. Using SignalP v4.0 (7), we identified 12 signal peptide cleavage sites. Using BLASTN and tRNAscan-SE (8), the genome was shown to encode 53 RNA genes, including 3 rRNA genes in a single operon and 50 tRNA genes.

Using the RAST server (2), by comparison with the closely fully annotated genome which is currently available in GenBank, Rhodospirillum rubrum ATCC 11170^T (4.4 Mb; accession number CP000230), Reyranella massiliensis exhibits 1,729 common genes. Genes involved in encoding some functioning parts (“motility and chemotaxis” and “photosynthesis”) are present only in R. rubrum, while those involved in other functioning parts (“sulfur metabolism” or “metabolism of aromatic compounds”) are mostly found in R. massiliensis (+66.67% and +65%, respectively).

Nucleotide sequence accession numbers.

The R. massiliensis genome, consisting of 40 contigs arranged in one scaffold, was deposited in GenBank under accession numbers CAKO01000001 to CAKO01000042.