Anaplasma capra in sheep and goats on Corsica Island, France: A European lineage within A. capra clade II?

Anaplasmosis is a tick-transmitted disease due to several species of the genus Anaplasma. In 2019, we demonstrated the presence of Anaplasma capra in two deer species at a zoological park in mainland France. As we suspected its presence in Corsica, we surveyed 11 geographically distant sheep or goat farms. Using molecular tools such as nested PCR targeting 16S ribosomal RNA (rRNA), citrate synthase (gltA) and heat-shock protein (groEL) genes, we detected the presence of A. capra on 5/11 farms, in 26/108 blood samples (24%), in sheep as well as in goats. Genotyping and phylogenetic analysis of A. capra revealed that isolates from Corsica island grouped closely with A. capra isolates reported in red deer and swamp deer from a zoological reserve in mainland France, as well as in roe deer from Spain, in a separate and well supported clade within A. capra clade II. This third report of the tick-borne bacterium A. capra in Europe suggests a potentially larger presence of this pathogen on the European continent, on domestic, native as well as wild ruminants, a broad host range already described in Asian countries for this species.

Comparison of gene repertoires and patterns of evolutionary rates in eight aphid species that differ by reproductive mode.

In theory, the loss of sexual reproduction is expected to result in the accumulation of deleterious mutations. In aphids, two main types of life cycle, cyclic and obligate parthenogenesis, represent respectively "sexual" and "asexual" reproductive modes. We used the complete pea aphid genome and previously published expressed sequence tags (ESTs) from two other aphid species. In addition, we obtained 100,000 new ESTs from five more species. The final set comprised four sexual and four asexual aphid species and served to test the influence of the reproductive mode on the evolutionary rates of genes. We reconstructed coding sequences from ESTs and annotated these genes, discovering a novel peptide gene family that appears to be among the most highly expressed transcripts from several aphid species. From 203 genes found to be 1:1 orthologs among the eight species considered, we established a species tree that partly conflicted with taxonomy (for Myzus ascalonicus). We then used this topology to evaluate the dynamics of evolutionary rates and mutation accumulation in the four sexual and four asexual taxa. No significant increase of the nonsynonymous to synonymous ratio or of nonsynonymous mutation numbers was found in any of the four branches for asexual taxa. We however found a significant increase of the synonymous rate in the branch leading to the asexual species Rhopalosiphum maidis, which could be due to a change in the mutation rate or to an increased number of generations implied by its change of life cycle.

Juvenile hormone titre and related gene expression during the change of reproductive modes in the pea aphid.

Most aphids show reproductive polyphenism, i.e. they alternate their reproductive modes from parthenogenesis to sexual reproduction in response to short photoperiods. Although juvenile hormone (JH) has been considered a likely candidate for regulating the transition from asexual to sexual reproduction after photoperiod sensing, there are few studies investigating the direct relationship between JH titres and the reproductive-mode change. In addition, the sequencing of the pea aphid genome has allowed identification of the genes involved in the JH pathway, which in turn allows us to examine their expression levels in relation to the reproductive-mode change. Using liquid chromatography-mass spectrometry in the pea aphid, JHIII titre was shown to be lower in aphids producing sexual morphs under short-day conditions than in aphids producing parthenogenetic morphs under long-day conditions. The expression levels of genes upstream and downstream of JH action were quantified by real-time quantitative reverse-transcription-PCR across the reproductive-mode change. The expression level of JH esterase, which is responsible for JH degradation, was significantly higher in aphids reared under short-day conditions. This suggests that the upregulation of the JH degradation pathway may be responsible for the lower JHIII titre in aphids exposed to short-days, leading to the production of sexual morphs.

Comparative analysis of the Acyrthosiphon pisum genome and expressed sequence tag-based gene sets from other aphid species.

To study gene repertoires and their evolution within aphids, we compared the complete genome sequence of Acyrthosiphon pisum (reference gene set) and expressed sequence tag (EST) data from three other species: Myzus persicae, Aphis gossypii and Toxoptera citricida. We assembled ESTs, predicted coding sequences, and identified potential pairs of orthologues (reciprocical best hits) with A. pisum. Pairwise comparisons show that a fraction of the genes evolve fast (high ratio of non-synonymous to synonymous rates), including many genes shared by aphids but with no hit in Uniprot. A detailed phylogenetic study for four fast-evolving genes (C002, JHAMT, Apo and GH) shows that rate accelerations are often associated with duplication events. We also compare compositional patterns between the two tribes of aphids, Aphidini and Macrosiphini.

AphidBase: a centralized bioinformatic resource for annotation of the pea aphid genome.

AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System designed to organize and distribute genomic data and annotations for a large international community was constructed using open source software tools from the Generic Model Organism Database (GMOD). The system includes Apollo and GBrowse utilities as well as a wiki, blast search capabilities and a full text search engine. AphidBase strongly supported community cooperation and coordination in the curation of gene models during community annotation of the pea aphid genome. AphidBase can be accessed at http://www.aphidbase.com.

Tempo and mode of early gene loss in endosymbiotic bacteria from insects.

BACKGROUND: Understanding evolutionary processes that drive genome reduction requires determining the tempo (rate) and the mode (size and types of deletions) of gene losses. In this study, we analysed five endosymbiotic genome sequences of the gamma-proteobacteria (three different Buchnera aphidicola strains, Wigglesworthia glossinidia, Blochmannia floridanus) to test if gene loss could be driven by the selective importance of genes. We used a parsimony method to reconstruct a minimal ancestral genome of insect endosymbionts and quantified gene loss along the branches of the phylogenetic tree. To evaluate the selective or functional importance of genes, we used a parameter that measures the level of adaptive codon bias in E. coli (i.e. codon adaptive index, or CAI), and also estimates of evolutionary rates (Ka) between pairs of orthologs either in free-living bacteria or in pairs of symbionts. RESULTS: Our results demonstrate that genes lost in the early stages of symbiosis were on average less selectively constrained than genes conserved in any of the extant symbiotic strains studied. These results also extend to more recent events of gene losses (i.e. among Buchnera strains) that still tend to concentrate on genes with low adaptive bias in E. coli and high evolutionary rates both in free-living and in symbiotic lineages. In addition, we analyzed the physical organization of gene losses for early steps of symbiosis acquisition under the hypothesis of a common origin of different symbioses. In contrast with previous findings we show that gene losses mostly occurred through loss of rather small blocks and mostly in syntenic regions between at least one of the symbionts and present-day E. coli. CONCLUSION: At both ancient and recent stages of symbiosis evolution, gene loss was at least partially influenced by selection, highly conserved genes being retained more readily than lowly conserved genes: although losses might result from drift due to the bottlenecking of endosymbiontic populations, we demonstrated that purifying selection also acted by retaining genes of greater selective importance.

Genetic architecture of sexual and asexual populations of the aphid Rhopalosiphum padi based on allozyme and microsatellite markers.

Cyclical parthenogens, including aphids, are attractive models for comparing the genetic outcomes of sexual and asexual reproduction, which determine their respective evolutionary advantages. In this study, we examined how reproductive mode shapes genetic structure of sexual (cyclically parthenogenetic) and asexual (obligately parthenogenetic) populations of the aphid Rhopalosiphum padi by comparing microsatellite and allozyme data sets. Allozymes showed little polymorphism, confirming earlier studies with these markers. In contrast, microsatellite loci were highly polymorphic and showed patterns very discordant from allozyme loci. In particular, microsatellites revealed strong heterozygote excess in asexual populations, whereas allozymes showed heterozygote deficits. Various hypotheses are explored that could account for the conflicting results of these two types of genetic markers. A strong differentiation between reproductive modes was found with both types of markers. Microsatellites indicated that sexual populations have high allelic polymorphism and heterozygote deficits (possibly because of population subdivision, inbreeding or selection). Little geographical differentiation was found among sexual populations confirming the large dispersal ability of this aphid. In contrast, asexual populations showed less allelic polymorphism but high heterozygosity at most loci. Two alternative hypotheses are proposed to explain this heterozygosity excess: allele sequence divergence during long-term asexuality or hybrid origin of asexual lineages. Clonal diversity of asexual lineages of R. padi was substantial suggesting that they could have frozen genetic diversity from the pool of sexual lineages. Several widespread asexual genotypes were found to persist through time, as already seen in other aphid species, a feature seemingly consistent with the general-purpose genotype hypothesis.

Multiple routes to asexuality in an aphid species.

Cyclical parthenogens, including aphids, are important models for studying the evolution of sex. However, little is known about transitions to asexuality in aphids, although the mode of origin of asexual lineages has important consequences for their level of genetic diversity, ecological adaptability and the outcome of competition with their sexual relatives. Thus, we surveyed nuclear, mitochondrial and biological data obtained on cyclical and obligate parthenogens of the bird cherry-oat aphid, Rhopalosiphum padi (L), to investigate the frequency of transitions from sexuality to permanent asexuality. Many instances of asexual lineages retaining the ability to produce males are known in aphids, so particular attention was paid to the existence of occasional matings between females from sexual lineages and males produced by asexual lineages, which have the potential to produce new asexual lineages. Phylogenetic inference based on microsatellite and mitochondrial data indicates at least three independent origins of asexuality in R. padi, yielding the strongest evidence to date for multiple origins of asexuality in an aphid. Moreover, several lines of evidence demonstrate that transitions to asexuality result from two mechanisms: a complete spontaneous loss of sex and repeated gene flow from essentially asexual lineages into sexual ones.

Coexistence between cyclical parthenogens, obligate parthenogens, and intermediates in a fluctuating environment

We evaluate the cost of sex in cyclical parthenogens coexisting with obligate parthenogens that produce a few sexuals, a situation found in numerous species. In aphids and cladocera, sex is generally the only way to produce a resistant form; this gives a potential ecological advantage to sex. We focus on the selective factor constituted by variations of the environment, that may be alternatively advantageous to cyclical parthenogens (cold winters in aphids, drought in daphnia) or to obligate parthenogens. Our calculations show that the production of a few sexuals by lineages that are essentially obligate parthenogens has a critical effect on the balance between the different life-cycles, especially when this production is limited to males. This male production by intermediates confers additional fitness to obligate parthenogenesis genes and then sharply increases the cost of sex. Copyright 1998 Academic Press