Background: For over a century, scientists have studied host-pathogen interactions between the crayfish plague disease agent Aphanomyces astaci and freshwater crayfish. It has been hypothesised that North American crayfish hosts are disease-resistant due to the long-lasting coevolution with the pathogen. Similarly, the increasing number of latent infections reported in the historically sensitive European crayfish hosts seems to indicate that similar coevolutionary processes are occurring between European crayfish and A. astaci. Our current understanding of these host-pathogen interactions is largely focused on the innate immunity processes in the crayfish haemolymph and cuticle, but the molecular basis of the observed disease-resistance and susceptibility remain unclear. To understand how coevolution is shaping the host’s molecular response to the pathogen, susceptible native European noble crayfish and invasive disease-resistant marbled crayfish were challenged with two A. astaci strains of different origin: a haplogroup A strain (introduced to Europe at least 50 years ago, low virulence) and a haplogroup B strain (signal crayfish in lake Tahoe, USA, high virulence). Here, we compare the gene expression profiles of the hepatopancreas, an integrated organ of crayfish immunity and metabolism. Results: We characterised several novel innate immune-related gene groups in both crayfish species. Across all challenge groups, we detected 412 differentially expressed genes (DEGs) in the noble crayfish, and 257 DEGs in the marbled crayfish. In the noble crayfish, a clear immune response was detected to the haplogroup B strain, but not to the haplogroup A strain. In contrast, in the marbled crayfish we detected an immune response to the haplogroup A strain, but not to the haplogroup B strain. Conclusions: We highlight the hepatopancreas as an important hub for the synthesis of immune molecules in the response to A. astaci. A clear distinction between the innate immune response in the marbled crayfish and the noble crayfish is the capability of the marbled crayfish to mobilise a higher variety of innate immune response effectors. With this study we outline that the type and strength of the host immune response to the pathogen is strongly influenced by the coevolutionary history of the crayfish with specific A. astaci strains.

For 150 years the crayfish plague disease agentAphanomyces astacihas been the cause of mass mortalities among native European crayfish populations. However, recently several studies have highlighted the great variability ofA. astacivirulence and crayfish resistance toward the disease. The main aim of this study was to compare the response of two crayfish species, the European native noble crayfish (Astacus astacus) and the invasive alien marbled crayfish (Procambarus virginalis), to anA. astacichallenge with a highly virulent strain from haplogroup B and a lowly virulent strain from haplogroup A. In a controlled infection experiment we showed a high resistance of marbled crayfish against anA. astaciinfection, with zoospores from the highly virulent haplogroup B strain being able to infect the crayfish, but unable to cause signs of disease. Furthermore, we demonstrated a reduced virulence in theA. astacistrain belonging to haplogroup A, as shown by the light symptoms and the lack of mortality in the generally susceptible noble crayfish. Interestingly, in both marbled crayfish and noble crayfish challenged with this strain, we observed a significant decrease of the detected amount of pathogen’s DNA during the experiment, suggesting that thisA. astacihaplogroup A strain has a decreased ability of penetrating into the cuticle of the crayfish. Our results provide additional evidence of how drastically strains belonging toA. astacihaplogroup B and haplogroup A differ in their virulence. This study confirmed the adaptation of one specificA. astacihaplogroup A strain to their novel European hosts, supposedly due to reduced virulence. This feature might be the consequence ofA. astaci’s reduced ability to penetrate into the crayfish. Finally, we experimentally showed that marbled crayfish are remarkably resistant against the crayfish plague disease and could potentially be latently infected, acting as carriers of highly virulentA. astacistrains.

Repetitive elements are a major component of DNA sequences due to their ability to propagate through the genome. Characterization of Metazoan repetitive profiles is improving; however, current pipelines fail to identify a significant proportion of divergent repeats in non-model organisms. The Decapoda order, for which repeat content analyses are largely lacking, is characterized by extremely variable genome sizes that suggest an important presence of repetitive elements. Here, we developed a new standardized pipeline to annotate repetitive elements in non-model organisms, which we applied to twenty Decapoda and six other Crustacea genomes. Using this new tool, we identified 10% more repetitive elements than standard pipelines. Repetitive elements were more abundant in Decapoda species than in other Crustacea, with a very large number of highly repeated satellite DNA families. Moreover, we demonstrated a high correlation between assembly size and transposable elements and different repeat dynamics between Dendrobranchiata and Reptantia. The patterns of repetitive elements largely reflect the phylogenetic relationships of Decapoda and the distinct evolutionary trajectories within Crustacea. In summary, our results highlight the impact of repetitive elements on genome evolution in Decapoda and the value of our novel annotation pipeline, which will provide a baseline for future comparative analyses.

The crayfish plague disease agent, Aphanomyces astaci, has coevolved with the native European crayfish since its arrival to mainland Europe in the 1860s. There are indications that some of the A. astaci strains are of reduced virulence, while the resistance against A. astaci infection varies among native European crayfish stocks. In Lake Venesjärvi, Finland, a potential case of latent crayfish plague infection was observed in the early 2000s. We have isolated an oomycete from live Astacus astacus originating from Lake Venesjärvi and identified it as A. a staci of haplogroup A by specific qPCR, nuclear ITS and mitochondrial LSU and SSU sequencies, and named the isolate as UEF_VEN5/14. The A. astaci was isolated from a potentially latently infected A. astacus, subsequently identified, genotyped and proven to be of reduced virulence in a separate infection challenge experiment under laboratory conditions. These findings add to speculations of rather rapid coevolution of A. astaci and European native crayfish and support the reports on latent crayfish plague infections among wild native European crayfish.

The invasive spiny-cheek crayfish (Faxonius limosus) has been able to colonize many European waterbodies since its first introduction into Europe, threatening the indigenous crayfish fauna. The remarkable reproductive plasticity of this species has been suggested as an important factor contributing to the alarming invasiveness of this species. In this study, we compared the reproductive strategies of an invasive (F. limosus) and a sympatric indigenous crayfish (Pontastacus leptodactylus). We questioned if the reproductive abilities, namely parthenogenesis and multiple paternity, may contribute to an ongoing invasion process in the Lower Danube. Using microsatellites, we genotyped the mothers and their offspring from 11 clutches of F. limosus and 18 clutches of P. leptodactylus. While no parthenogenesis has been found in F. limosus populations, multiple paternity has been detected for the first time in both species, with comparable incidence. The results of the study indicate that multiple paternity does not play a dominant role in the successful colonization of F. limosus in the Danube. However, the presented results have to be regarded as a pilot study, with a limited number of samples and loci investigated. Given the relevance of mating system knowledge for management measures, future studies with larger sample number could provide valuable contributions to ongoing conservation actions.

Objectives: Crayfish plague disease, caused by the oomycete pathogen Aphanomyces astaci represents one of the greatest risks for the biodiversity of the freshwater crayfish. This data article covers the de novo transcriptome assembly and annotation data of the noble crayfish and the marbled crayfish challenged with Ap. astaci. Following the controlled infection experiment (Francesconi et al. in Front Ecol Evol, 2021, https://doi.org/10.3389/fevo.2021.647037), we conducted a differential gene expression analysis described in (Boštjančić et al. in BMC Genom, 2022, https://doi.org/10.1186/s12864-022-08571-z) Data description: In total, 25 noble crayfish and 30 marbled crayfish were selected. Hepatopancreas tissue was isolated, followed by RNA sequencing using the Illumina NovaSeq 6000 platform. Raw data was checked for quality with FastQC, adapter and quality trimming were conducted using Trimmomatic followed by de novo assembly with Trinity. Assembly quality was assessed with BUSCO, at 93.30% and 93.98% completeness for the noble crayfish and the marbled crayfish, respectively. Transcripts were annotated using the Dammit! pipeline and assigned to KEGG pathways. Respective transcriptome and raw datasets may be reused as the reference transcriptome assemblies for future expression studies.