The genome sequence of Brucella pinnipedialis B2/94 sheds light on the evolutionary history of the genus Brucella

Abstract

Background: Since the discovery of the Malta fever agent, Brucella melitensis, in the 19th century, six terrestrial mammal-associated Brucella species were recognized over the next century. More recently the number of novel Brucella species has increased and among them, isolation of species B. pinnipedialis and B. ceti from marine mammals raised many questions about their origin as well as on the evolutionary history of the whole genus.

Results: We report here on the first complete genome sequence of a Brucella strain isolated from marine mammals, Brucella pinnipedialis strain B2/94. A whole gene-based phylogenetic analysis shows that five main groups of host-associated Brucella species rapidly diverged from a likely free-living ancestor close to the recently isolated B. microti. However, this tree lacks the resolution required to resolve the order of divergence of those groups. Comparative analyses focusing on a) genome segments unshared between B. microti and B. pinnipedialis, b) gene deletion/fusion events and c) positions and numbers of Brucella specific IS711 elements in the available Brucella genomes provided enough information to propose a branching order for those five groups.

Conclusions: In this study, it appears that the closest relatives of marine mammal Brucella sp. are B. ovis and Brucella sp. NVSL 07-0026 isolated from a baboon, followed by B. melitensis and B. abortus strains, and finally the group consisting of B. suis strains, including B. canis and the group consisting of the single B. neotomae species. We were not able, however, to resolve the order of divergence of the two latter groups.

Figure 1

Genus Brucella phylogenic tree based on a concatenated alignment of orthologous genes. Phylogenetic representation of species in the genus Brucella based on a concatenated alignment of orthologous genes belonging to Ochrobactrum intermedium and 39 different Brucella strains or species whose genomes are nearly complete. At each leave of the tree is summarized the presence or absence pattern of the largest sequence fragments being unshared between B. microti CCM 4915 and B. pinnipedialis B2/94 (black square: presence, gray square: partial presence, white square: absence). Because of the very different scale of divergence of the different species in consideration in this work, the figure has been split in two parts. The upper part is a bird eye view showing the more distant O. intermedium, Brucella sp. B02, B. inopinata, Brucella sp. NF2653 and Brucella sp. 83/13 while the lower part displays the host-adapted Brucella species and B. microti. All nodes have bootstrap values above 99 (on 100 replicates) except when noted in red.

Figure 2

B. pinnipedialis B2/94 specific 67 kbp genome fragment and corresponding locus in B. ovis and B. microti. Schematic representation of the genome fragments surrounding the position of the 67 kbp insert in the genome of B. pinnipedialis B2/94, reduced to a 30 kbp fragment in B. ovis ATCC 25840 and absent from B. microti CCM 4915. Black arrows represent protein coding genes and red arrows pseudogenes. Orthologous protein coding genes present in several genomes are shown linked by grey parallelograms. Coordinates along the different genomes are also indicated. Locus names are abbreviated to their suffix, except for the first locus of a line. The red stars indicate the IS711 insertion element, present in a single copy in B. microti and in two copies, at both sides of the insert in B. pinnipedialis and B. ovis. Colored rectangles indicate groups of genes that are repeated in the representation to increase legibility of the drawing.

Figure 3

IS711 positions in selected Brucella genomes. Schematic representation of the position of IS711 elements in the genome of selected Brucella including currently completely assembled Brucella (names with an asterisk) and two genomes still in partial form (B. ceti Cudo and Brucella sp. NVSL 07-0026). IS711 positions are noted by a star, some of them in smaller size to increase legibility. Orthologous IS are joined by a line. Each group of connected IS, even isolated ones, is given an identifier which allows to find the corresponding entry in Table S4 which lists the genomic positions of the IS711 elements. Chromosomes (or contigs) are depicted as rectangles. The chromosomes of B. melitensis 16 M are reversed with respect to the original genomic coordinates.