The Anaplasma ovis genome reveals a high proportion of pseudogenes

Abstract

Background: The genus Anaplasma is made up of organisms characterized by small genomes that are undergoing reductive evolution. Anaplasma ovis, one of the seven recognized species in this genus, is an understudied pathogen of sheep and other ruminants. This tick-borne agent is thought to induce only mild clinical disease; however, small deficits may add to larger economic impacts due to the wide geographic distribution of this pathogen.

Results: In this report we present the first complete genome sequence for A. ovis and compare the genome features with other closely related species. The 1,214,674 bp A. ovis genome encodes 933 protein coding sequences, the split operon arrangement for ribosomal RNA genes, and more pseudogenes than previously recognized for other Anaplasma species. The metabolic potential is similar to other Anaplasma species. Anaplasma ovis has a small repertoire of surface proteins and transporters. Several novel genes are identified.

Conclusions: Analyses of these important features and significant gene families/genes with potential to be vaccine candidates are presented in a comparative context. The availability of this genome will significantly facilitate research for this pathogen.

Keywords: Comparative genomics; Diagnostic assay; Genome sequence; Rickettsial pathogen; Vaccine development.

Fig. 1

Circular map of the Anaplasma ovis genome. The outermost ring shows the genome size in 100 kb increments. Moving inwards, the light blue marks indicate the coding sequences on the forward and reverse strands, the black marks indicate pseudogenes, the next ring contains the noncoding RNAs with tRNAs in green, rRNAs in red and other ncRNAs in orange. The innermost ring shows the GC skew, with olive green being positive and purple being negative. Image made in DNAplotter

Fig. 2

Phylogenetic tree based on 16S sequences. Accession numbers are given for 16S sequences from A. platys and A. bovis. Other 16S sequences were taken from whole genomes with accession numbers as follows: A. centrale: CP001759; A. ovis Haibei: CP015994; A. marginale: CP00030; A. phagocytophilum: CP000235. Rickettsia felis (CP000053) was used as an out group. The evolutionary history was inferred using the Neighbor-Joining method [61]. The optimal tree with the sum of branch length = 0.23834825 is shown. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches [62]. The evolutionary distances were computed using the Kimura 2-parameter method [63] and are in the units of the number of base substitutions per site. Evolutionary analyses were conducted in MEGA7 [64]. This tree is representative of the Maximum Likelihood tree

Fig. 3

Omp13 alignment showing potential start sites. The first 80 codons of the A. ovis Omp13 sequence are shown on the top line (Omp13 AOV_04835), and the corresponding A. marginale sequence (St. Maries strain) in the middle and the A. centrale (Israel strain) sequence on the bottom line. The asterisk shows the position of the stop codon in the A. ovis sequence. The arrows show potential start sites downstream from the stop codon. In the A. centrale sequence, the arrow shows the annotated start codon (GTG), however the sequence upstream from this start is open and contains an in frame methionine start codon. The amino-terminal sequence is not conserved. The methionine at the right most arrow is conserved in all three species, and could be the appropriate start codon for this protein

Fig. 4

Whole Genome Alignment of Anaplasma species. Whole genome alignments were done using Artemis Comparison Tool. Panel a shows the comparison of A. centrale (CP001759) and A. marginale (CP000030) with A. ovis Haibei (CP015994). The A. centrale genome was flipped for the alignment. Panel b shows the alignment of A. ovis Haibei and A. marginale with the Idaho pseudochromosome (PKOE00000000). Red indicates regions of identity in the same orientation while blue indicates regions of identity with the opposite orientation