Masculinization of the X Chromosome in the Pea Aphid

International audienceEvolutionary theory predicts that sexually antagonistic mutations accumulate differentially on the X chromosome and autosomes in species with an XY sex-determination system, with effects (masculinization or feminization of the X) depending on the dominance of mutations. Organisms with alternative modes of inheritance of sex chromosomes offer interesting opportunities for studying sexual conflicts and their resolution, because expectations for the preferred genomic location of sexually antagonistic alleles may differ from standard systems. Aphids display an XX/X0 system and combine an unusual inheritance of the X chromosome with the alternation of sexual and asexual reproduction. In this study, we first investigated theoretically the accumulation of sexually antagonistic mutations on the aphid X chromosome. Our results show that i) the X is always more favourable to the spread of male-beneficial alleles than autosomes, and should thus be enriched in sexually antagonistic alleles beneficial for males, ii) sexually antagonistic mutations beneficial for asexual females accumulate preferentially on autosomes, iii) in contrast to predictions for standard systems, these qualitative results are not affected by the dominance of mutations. Under the assumption that sex-biased gene expression evolves to solve conflicts raised by the spread of sexually antagonistic alleles, one expects that male-biased genes should be enriched on the X while asexual female-biased genes should be enriched on autosomes. Using gene expression data (RNA-Seq) in males, sexual females and asexual females of the pea aphid, we confirm these theoretical predictions. Although other mechanisms than the resolution of sexual antagonism may lead to sex-biased gene expression, we argue that they could hardly explain the observed difference between X and autosomes. On top of reporting a strong masculinization of the aphid X chromosome, our study highlights the relevance of organisms displaying an alternative mode of sex chromosome inheritance to understanding the forces shaping chromosome evolution

Differential gene expression according to race and host plant in the pea aphid

Host-race formation in phytophagous insects is thought to provide the opportunity for local adaptation and subsequent ecological speciation. Studying gene expression differences among host-races may help to identify phenotypes under (or resulting from) divergent selection and their genetic, molecular and physiological bases. The pea aphid (Acyrthosiphon pisum) comprises host-races specialising on numerous plants in the Fabaceae, and provides a unique system for examining the early stages of diversification along a gradient of genetic and associated adaptive divergence. In this study, we examine transcriptome-wide gene expression both in response to environment and across pea aphid races selected to cover the range of genetic divergence reported in this species complex. We identify changes in expression in response to host-plant, indicating the importance of gene expression in aphid-plant interactions. Races can be distinguished on the basis of gene expression, and higher numbers of differentially expressed genes are apparent between more divergent races; these expression differences between host-races may result from genetic drift and reproductive isolation, and possibly divergent selection. Expression differences related to plant adaptation include a sub-set of chemosensory and salivary genes. Genes showing expression changes in response to host plant do not make up a large portion of between-race expression differences, providing confirmation of previous studies’ findings that genes involved in expression differences between diverging populations or species are not necessarily those showing initial plasticity in the face of environmental change

Fast Evolution and Lineage-Specific Gene Family Expansions of Aphid Salivary Effectors Driven by Interactions with Host-Plants

Effector proteins play crucial roles in plant-parasite interactions by suppressing plant defenses and hijacking plant physiological responses to facilitate parasite invasion and propagation. Although effector proteins have been characterized in many microbial plant pathogens, their nature and role in adaptation to host plants are largely unknown in insect herbivores. Aphids rely on salivary effector proteins injected into the host plants to promote phloem sap uptake. Therefore, gaining insight into the repertoire and evolution of aphid effectors is key to unveiling the mechanisms responsible for aphid virulence and host plant specialization. With this aim in mind, we assembled catalogues of putative effectors in the legume specialist aphid, Acyrthosiphon pisum, using transcriptomics and proteomics approaches. We identified 3,603 candidate effector genes predicted to be expressed in A. pisum salivary glands (SGs), and 740 of which displayed up-regulated expression in SGs in comparison to the alimentary tract. A search for orthologs in 17 arthropod genomes revealed that SG-up-regulated effector candidates of A. pisum are enriched in aphid-specific genes and tend to evolve faster compared with the whole gene set. We also found that a large fraction of proteins detected in the A. pisum saliva belonged to three gene families, of which certain members show evidence consistent with positive selection. Overall, this comprehensive analysis suggests that the large repertoire of effector candidates in A. pisum constitutes a source of novelties promoting plant adaptation to legumes

Les principaux types de polymorphisme

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Microsatellites, répétitions de séquences simples : SSR

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Utilisation des polymorphismes : QTL, GWAS et scans génomiques

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Contribution of Epigenetic Mechanisms in the Regulation of Environmentally-Induced Polyphenism in Insects

International audienceMany insect species display a remarkable ability to produce discrete phenotypes in response to changes in environmental conditions. Such phenotypic plasticity is referred to as polyphenism. Seasonal, dispersal and caste polyphenisms correspond to the most-studied examples that are environmentally-induced in insects. Cues that induce such dramatic phenotypic changes are very diverse, ranging from seasonal cues, habitat quality changes or differential larval nutrition. Once these signals are perceived, they are transduced by the neuroendocrine system towards their target tissues where gene expression reprogramming underlying phenotypic changes occur. Epigenetic mechanisms are key regulators that allow for genome expression plasticity associated with such developmental switches. These mechanisms include DNA methylation, chromatin remodelling and histone post-transcriptional modifications (PTMs) as well as non-coding RNAs and have been studied to various extents in insect polyphenism. Differential patterns of DNA methylation between phenotypes are usually correlated with changes in gene expression and alternative splicing events, especially in the cases of dispersal and caste polyphenism. Combinatorial patterns of histone PTMs provide phenotype-specific epigenomic landscape associated with the expression of specific transcriptional programs, as revealed during caste determination in honeybees and ants. Alternative phenotypes are also usually associated with specific non-coding RNA profiles. This review will provide a summary of the current knowledge of the epigenetic changes associated with polyphenism in insects and highlights the potential for these mechanisms to be key regulators of developmental transitions triggered by environmental cues

How does the landscape affect patch occupancy in metapopulation models? Comparing Euclidean vs landscape-based inter-patch distance

Dispersal barriers and corridors between habitat patches can strongly affect colonization processes, and therefore patch occupation probability. However, most metapopulation dynamic models assume that heterogeneity in the landscape between patches can be neglected, basing dispersal on the Euclidean (shortest) distance between patches. For heterogeneous landscapes inter-patch distance should take into account the resistance of landscape features to movement, as with the least-cost algorithms implemented in Geographic Information Systems (GIS). In this study, we explore how patch occupancy is sensitive to Euclidean versus a landscape-based distance (least-cost algorithm). We illustrate our method with two metapopulations of the Yellow-bellied Toad (Bombina variegata) in the Rhone plain, Switzerland. The approach allows us to identify which patches are the most sensitive to the inter-patch landscape; i.e., from a conservation point of view, those patches where improving connectivity (e.g., by building vegetated corridors, removing barriers to dispersal) might be a valuable management scenario

The grape phylloxera genome sequencing project

In the framework of the International Aphid Genomics Consortium (IAGC) and the i5K initative, the Phylloxera Genomics Initiative proposes the sequencing of the grape phylloxera (Daktulosphaira vitifoliae Fitch) genome through an integrated approach. Currently, DNA sequencing and pre-assembly of an Australian lineage have been obtained by performing a single lane of HiSeq2000 sequencing. This resulted in a low coverage of the genome and a low N50 for scaffolds (903 bp). In the meantime, a genome sequence of a French lineage (Bordeaux) is currently processed. In addition to genomic sequences, we generated a large scale collection of transcript sequences by performing high throughput transcriptomes for both gall and leaf feeding individuals. The annotation of this transcriptome has already identified 17,372 proteins among which 12,617 were predicted to be complete. The phylloxera genome revealed a markedly higher AT content compared to the pea aphid (which has already an AT-rich genome). Knowledge of the genome of the phylloxera will improve our understanding of many of the specific biological features of this invasive pest. The present project will also provide essential comparisons between aphid (in the broad sense) genomes and an extraordinary resource for understanding major features of aphid evolution, such as the rapid radiation after host shifting from gymnosperms to angiosperms

Accelerated evolution of sex chromosomes in aphids, an X0 system.

International audienceSex chromosomes play a role in many important biological processes, including sex determination, genomic conflicts, imprinting and speciation. In particular, they exhibit several unusual properties such as inheritance pattern, hemizygosity and reduced recombination, which influence their response to evolutionary factors (e.g. drift, selection, demography). Here, we examine the evolutionary forces driving X chromosome evolution in aphids, an XO system where females are homozygous (XX) and males hemizygous (X0) at sex chromosomes. We show by simulations that the unusual mode of transmission of the X chromosome in aphids coupled to cyclical parthenogenesis results in similar effective population sizes and predicted levels of genetic diversity for X chromosomes and autosomes under neutral evolution. These results contrast with expectations from standard XX/XY or XX/X0 systems (where the effective population size of the X is 3/4 of that of autosomes) and have deep consequences for aphid X chromosome evolution. We then localized 52 microsatellites markers on the X and 351 on autosomes. We genotyped 167 individuals with 356 of these loci and found similar levels of allelic richness on the X and on the autosomes, as predicted by our simulations. In contrast, we detected higher dN and dN/dS ratio for X-linked genes compared to autosomal genes, a pattern compatible with either positive or relaxed selection. Given that both types of chromosomes have similar effective population sizes and that the single copy of the X chromosome of male aphids exposes its recessive genes to selection, some degree of positive selection seems to best explain the higher rates of evolution of X-linked genes. Overall, this study highlights the particular relevance of aphids to study the evolutionary factors driving sex chromosomes and genome evolution