Two models are presented to test the hypothesis that in aphids, a particular constraint (the necessity to resist frost) could be the proximal cause for the maintenance of sex. Both models are based on temporal variability in winter survival of asexuals.They show that: i) only cyclical parthenogenesis is maintained below a threshold frequency of mild winters, because of the cold-resistance of sexually-produced eggs. ii) above a second threshold, only obligate parthenogenesis is maintained. iii) in-between, the first model predicts a mixed evolutionarily stable strategy (ESS).This would reflect well the geographic distribution of the different types of reproduction. The second model, based on the genetic control of the reproduction system in two aphid species, predicts the maintenance of polymorphism with fluctuating proportions of the two life-cycles. Males produced by obligate parthenogens play an essential role in this equilibrium (no stable polymorphism exists if this male production is set to zero). The value of the lowest possible fitness achieved by overwintering asexuals is critical.
31Faster evolution of X chromosomes has been documented in several species and results from 32 the increased efficiency of selection on recessive alleles in hemizygous males and/or from 33 increased drift due to the smaller effective population size of X chromosomes. Aphids are 34 excellent models for evaluating the importance of selection in faster-X evolution, because 35 their peculiar life-cycle and unusual inheritance of sex-chromosomes lead to equal effective 36 population sizes for X and autosomes. Because we lack a high-density genetic map for the pea 37 aphid whose complete genome has been sequenced, we assigned its entire genome to the X 38 and autosomes based on ratios of sequencing depth in males and females. Unexpectedly, we 39 found frequent scaffold misassembly, but we could unambiguously locate 13,726 genes on the 40 X and 19,263 on autosomes. We found higher non-synonymous to synonymous substitutions 41 ratios (dN/dS) for X-linked than for autosomal genes. Our analyses of substitution rates 42 together with polymorphism and expression data showed that relaxed selection is likely to 43 contribute predominantly to faster-X as a large fraction of X-linked genes are expressed at 44 low rates and thus escape selection. Yet, a minor role for positive selection is also suggested 45 by the difference between substitution rates for X and autosomes for male-biased genes (but 46 not for asexual female-biased genes) and by lower Tajima's D for X-linked than for 47 autosomal genes with highly male-biased expression patterns. This study highlights the 48 relevance of organisms displaying alternative inheritance of chromosomes to the 49 understanding of forces shaping genome evolution. 50 51 52
The composition of autumn flights of a cereal pest aphid, Rhopalosiphum padi, was studied in relation to climate. At 10 sites in France and at Rothamsted and Starcross (UK), evidence was sought for a relationship between winter temperature and the proportion of males. By calculating Goldwin's correlogram, significant correlations were detected between cold periods in the early winter and the proportions of males at the five mildest sites, suggesting an effect of temperature on the balance between holocyclic and non‐holocyclic clones. The five sites where no significant correlations were detected are generally cold in winter, and are likely to be largely dominated by holocyclic clones. The temperature in late summer/early autumn may also have an effect on the proportion of males.
DATA AVAILABILITYRaw reads and genome assemblies have been deposited in GenBank (BioProjects PRJNA329579 for Pl. viticola and PRJNA448661 for Pl. muralis). Genome assemblies, gene annotations and analysis files (e.g. orthology relationships, full tables for GO enrichment analyses, pairwise dN/dS values and branch-site tests) have been deposited in Dataverse (Pl.viticola assembly and annotation: doi.org/10.15454/4NYHD6, Pl. muralis assembly and annotation: doi.org/10.15454/Q1QJYK, analysis files: doi.org/10.15454/8NZ8X9). Links to the data and information about the grapevine downy mildew genome project can be found at ABSTRACT Downy mildews are obligate biotrophic oomycete pathogens that cause devastating plant diseases on economically important crops. Plasmopara viticola is the causal agent of grapevine downy mildew, a major disease in vineyards worldwide. We sequenced the genome of Pl. viticola with PacBio long reads and obtained a new 92.94 Mb assembly with high continuity (359 scaffolds for a N50 of 706.5 kb) due to a better resolution of repeat regions. This assembly presented a high level of gene completeness, recovering 1,592 genes encoding secreted proteins involved in plant-pathogen interactions. Pl. viticola had a two-speed genome architecture, with secreted protein-encoding genes preferentially located in gene-sparse, repeatrich regions and evolving rapidly, as indicated by pairwise dN/dS values. We also used short reads to assemble the genome of Plasmopara muralis, a closely related species infecting grape ivy (Parthenocissus tricuspidata). The lineage-specific proteins identified by comparative genomics analysis included a large proportion of RxLR cytoplasmic effectors and, more generally, genes with high dN/dS values. We identified 270 candidate genes under positive selection, including several genes encoding transporters and components of the RNA machinery potentially involved in host specialization. Finally, the Pl. viticola genome assembly generated here will allow the development of robust population genomics approaches for investigating the mechanisms involved in adaptation to biotic and abiotic selective pressures in this species.
Background Trypanosomes are protozoan parasites of vertebrates that are of medical and veterinary concern. A variety of blood-feeding invertebrates have been identified as vectors, but the role of ticks in trypanosome transmission remains unclear. Methods In this study, we undertook extensive molecular screening for the presence and genetic diversity of trypanosomes in field ticks. Results Examination of 1089 specimens belonging to 28 tick species from Europe and South America led to the identification of two new trypanosome strains. The prevalence may be as high as 4% in tick species such as the castor bean tick Ixodes ricinus, but we found no evidence of transovarial transmission. Further phylogenetic analyses based on 18S rRNA, EF1-α, hsp60 and hsp85 gene sequences revealed that different tick species, originating from different continents, often harbour phylogenetically related trypanosome strains and species. Most tick-associated trypanosomes cluster in a monophyletic clade, the Trypanosoma pestanai clade, distinct from clades of trypanosomes associated with transmission by other blood-feeding invertebrates. Conclusions These observations suggest that ticks may be specific arthropod hosts for trypanosomes of the T. pestanai clade. Phylogenetic analyses provide further evidence that ticks may transmit these trypanosomes to a diversity of mammal species (including placental and marsupial species) on most continents. Graphical Abstract
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