Plant glacial refugia in Europe

Izmjene glacijala i interglacijala u razdoblju Kvartara utjecale su na geografsku rasprostranjenost vrsta u Europi danas. Vrste koje su bile bolje prilagođene na umjerenu klimu bile su ograničene na područja refugija u vrijeme glacijala dok su vrste koje su bile prilagođene na hladnu klimu bile ograničene na područja refugija u interglacijalima. Poseban utjecaj na geografski raspon vrsta imao je posljednji glacijalni maksimum. Glacijalni refugiji nalazili su se na jugu Europe (Apeninskom poluotoku, Pirinejskom poluotoku i Balkanu). Postojanje kriptičnih refugija za vrste umjerene klime koji su se nalazili sjevernije još uvijek je predmet mnogih znanstvenih rasprava. U ovom radu pokazana je mogućnost postojanja takvih refugija na primjeru obične bukve (Fagus sylvatica) i divlje jabuke (Malus sylvestris). Također, cilj ovog rada bio je dati uvid u kompleksne procese koji su se događali u refugijima tijekom posljednjeg glacijanog maksimuma i procese kolonizacije koji su uslijedili nakon njega. Naglašena je uloga glacijalnih refugija kao žarišta genske raznolikosti Europe te potreba za zaštitom tih područja. Potrebna su daljnja, detaljnija paleobotanička i genetička istraživanja kako bi se dobio detaljniji uvid u prošlost biljnih i drugih vrsta na Europskom kontinentu. Razumijevanje prošlosti glacijalnih refugija omogućit će bolja predviđanja utjecaja trenutnih klimatskih promjena na živi svijet.Changes between glacial and interglacial periods in Quaternary have influenced the geographical species distribution in Europe. Temperate-adapted species were confined to refugial areas during glacial periods while cold-adapted species were confined to refugial areas during the interglacial. Last glacial maximum had a significant influence on the today’s species distribution. Glacial refugia were located in the Iberian, Italian and Balkan Peninsula. The existence of cryptic, more northern glacial refugia for temperate species is still questioned by many scientists. In this paper, the possibility of existence for such refugia is demonstrated on examples of European beech (Fagus sylvatica) and wild apple (Malus sylvestris). The aim of this review was to give insights on the complex processes that happened in the glacial refugia during last glacial maximum and postglacial colonization. The role of glacial refugia as “hotspots” of genetic diversity in Europe and the need for their protection has been emphasized. Further paleobotanical and genetic research is needed to get a more precise insight in plant and other species’ history on European continent. Better understanding of the history of glacial refugia could give better predictions on influence of current climatic change on today’s species

Plant glacial refugia in Europe

Izmjene glacijala i interglacijala u razdoblju Kvartara utjecale su na geografsku rasprostranjenost vrsta u Europi danas. Vrste koje su bile bolje prilagođene na umjerenu klimu bile su ograničene na područja refugija u vrijeme glacijala dok su vrste koje su bile prilagođene na hladnu klimu bile ograničene na područja refugija u interglacijalima. Poseban utjecaj na geografski raspon vrsta imao je posljednji glacijalni maksimum. Glacijalni refugiji nalazili su se na jugu Europe (Apeninskom poluotoku, Pirinejskom poluotoku i Balkanu). Postojanje kriptičnih refugija za vrste umjerene klime koji su se nalazili sjevernije još uvijek je predmet mnogih znanstvenih rasprava. U ovom radu pokazana je mogućnost postojanja takvih refugija na primjeru obične bukve (Fagus sylvatica) i divlje jabuke (Malus sylvestris). Također, cilj ovog rada bio je dati uvid u kompleksne procese koji su se događali u refugijima tijekom posljednjeg glacijanog maksimuma i procese kolonizacije koji su uslijedili nakon njega. Naglašena je uloga glacijalnih refugija kao žarišta genske raznolikosti Europe te potreba za zaštitom tih područja. Potrebna su daljnja, detaljnija paleobotanička i genetička istraživanja kako bi se dobio detaljniji uvid u prošlost biljnih i drugih vrsta na Europskom kontinentu. Razumijevanje prošlosti glacijalnih refugija omogućit će bolja predviđanja utjecaja trenutnih klimatskih promjena na živi svijet.Changes between glacial and interglacial periods in Quaternary have influenced the geographical species distribution in Europe. Temperate-adapted species were confined to refugial areas during glacial periods while cold-adapted species were confined to refugial areas during the interglacial. Last glacial maximum had a significant influence on the today’s species distribution. Glacial refugia were located in the Iberian, Italian and Balkan Peninsula. The existence of cryptic, more northern glacial refugia for temperate species is still questioned by many scientists. In this paper, the possibility of existence for such refugia is demonstrated on examples of European beech (Fagus sylvatica) and wild apple (Malus sylvestris). The aim of this review was to give insights on the complex processes that happened in the glacial refugia during last glacial maximum and postglacial colonization. The role of glacial refugia as “hotspots” of genetic diversity in Europe and the need for their protection has been emphasized. Further paleobotanical and genetic research is needed to get a more precise insight in plant and other species’ history on European continent. Better understanding of the history of glacial refugia could give better predictions on influence of current climatic change on today’s species

Plant glacial refugia in Europe

Izmjene glacijala i interglacijala u razdoblju Kvartara utjecale su na geografsku rasprostranjenost vrsta u Europi danas. Vrste koje su bile bolje prilagođene na umjerenu klimu bile su ograničene na područja refugija u vrijeme glacijala dok su vrste koje su bile prilagođene na hladnu klimu bile ograničene na područja refugija u interglacijalima. Poseban utjecaj na geografski raspon vrsta imao je posljednji glacijalni maksimum. Glacijalni refugiji nalazili su se na jugu Europe (Apeninskom poluotoku, Pirinejskom poluotoku i Balkanu). Postojanje kriptičnih refugija za vrste umjerene klime koji su se nalazili sjevernije još uvijek je predmet mnogih znanstvenih rasprava. U ovom radu pokazana je mogućnost postojanja takvih refugija na primjeru obične bukve (Fagus sylvatica) i divlje jabuke (Malus sylvestris). Također, cilj ovog rada bio je dati uvid u kompleksne procese koji su se događali u refugijima tijekom posljednjeg glacijanog maksimuma i procese kolonizacije koji su uslijedili nakon njega. Naglašena je uloga glacijalnih refugija kao žarišta genske raznolikosti Europe te potreba za zaštitom tih područja. Potrebna su daljnja, detaljnija paleobotanička i genetička istraživanja kako bi se dobio detaljniji uvid u prošlost biljnih i drugih vrsta na Europskom kontinentu. Razumijevanje prošlosti glacijalnih refugija omogućit će bolja predviđanja utjecaja trenutnih klimatskih promjena na živi svijet.Changes between glacial and interglacial periods in Quaternary have influenced the geographical species distribution in Europe. Temperate-adapted species were confined to refugial areas during glacial periods while cold-adapted species were confined to refugial areas during the interglacial. Last glacial maximum had a significant influence on the today’s species distribution. Glacial refugia were located in the Iberian, Italian and Balkan Peninsula. The existence of cryptic, more northern glacial refugia for temperate species is still questioned by many scientists. In this paper, the possibility of existence for such refugia is demonstrated on examples of European beech (Fagus sylvatica) and wild apple (Malus sylvestris). The aim of this review was to give insights on the complex processes that happened in the glacial refugia during last glacial maximum and postglacial colonization. The role of glacial refugia as “hotspots” of genetic diversity in Europe and the need for their protection has been emphasized. Further paleobotanical and genetic research is needed to get a more precise insight in plant and other species’ history on European continent. Better understanding of the history of glacial refugia could give better predictions on influence of current climatic change on today’s species

De novo assembly of Procambarus virginalis Lyko, 2017 transcriptome and gene expression in response to the pathogen Aphanomyces astaci Shikora, 1906

Jedna on najveći prijetnji za populacije nativnih europskih slatkovodnih rakova je patogen Aphanomyces astaci Shikora, 1906 iz razreda Oomycetes, koji uzrokuje bolest račju kugu letalnu za nativne vrste slatkovodnih rakova. Mramorni rak, Procambarus virginalis Lyko, 2017 invazivna je vrsta i poznati prenositelj račje kuge. U ovom istraživanju proučen je imunosni odgovor 30 jedinki mramornog raka na infekciju s A. astaci. Korištena su dva soja patogena; PsI- visoko virulentan i As- nisko virulentan. Uzorkovanje hepatopankreasa rakova iz pokusa provedeno je tri i 21 dan nakon izlaganja patogenu te je provedena izolacija RNA. Iz fragmenata RNA, dobivenih sekvenciranjem, sastavljan je de novo transkriptom visoke kvalitete kojeg čini 60,004 gena. Za 41.9% transkripata je pronađena anotacija. Analiza diferencijalne ekspresije otkrila je 102 diferencijalno eksprimirana gena. Većina diferencijalno eksprimiranih gena bila je među uzorcima jedinki uzorkovanih 21 dana nakon infekcije. Među diferencijalno eksprimiranim genima bili su prisutni poznati efektori urođene imunosti rakova: serpin, lektini tipa-C i crustini. Novootkriveni su i geni s potencijalnom ulogom u urođenoj imunosti rakova. Oni predstavljaju predmet za buduća istraživanja urođene imunosti rakovaOne of the biggest threats for freshwater crayfish populations is the pathogen Aphanomyces astaci Shikora, 1906 from the class Oomycetes that causes a disease lethal for native crayfish species, crayfish plague. The marbled crayfish, Procambarus virginalis Lyko, 2017 is an invasive crayfish species, known to be resistant to the crayfish plague disease. In this study the immune response to an A. astaci infection of 30 marbled crayfish exposed to two strains of A. astaci (PsI- high virulence and As- low virulence) was investigated. Hepatopancreas samples were taken at two time points, three days and 21 days post challenge. From the RNA sequencing reads, high-quality de novo transcriptomes of marbled crayfish were assembled containing 60,004 genes. Annotation was available for 41.9% of the transcripts. Differential gene expression analysis revealed in total 102 differentially expressed genes. More differentially expressed genes were observed among the samples from the second time point. Among the differentially expressed genes several known effectors of the crayfish innate immunity were detected. Previously unreported genes with potential role in crayfish innate immunity were also identified. They represent targets for future studies on crayfish innate immunity

De novo assembly of Procambarus virginalis Lyko, 2017 transcriptome and gene expression in response to the pathogen Aphanomyces astaci Shikora, 1906

Jedna on najveći prijetnji za populacije nativnih europskih slatkovodnih rakova je patogen Aphanomyces astaci Shikora, 1906 iz razreda Oomycetes, koji uzrokuje bolest račju kugu letalnu za nativne vrste slatkovodnih rakova. Mramorni rak, Procambarus virginalis Lyko, 2017 invazivna je vrsta i poznati prenositelj račje kuge. U ovom istraživanju proučen je imunosni odgovor 30 jedinki mramornog raka na infekciju s A. astaci. Korištena su dva soja patogena; PsI- visoko virulentan i As- nisko virulentan. Uzorkovanje hepatopankreasa rakova iz pokusa provedeno je tri i 21 dan nakon izlaganja patogenu te je provedena izolacija RNA. Iz fragmenata RNA, dobivenih sekvenciranjem, sastavljan je de novo transkriptom visoke kvalitete kojeg čini 60,004 gena. Za 41.9% transkripata je pronađena anotacija. Analiza diferencijalne ekspresije otkrila je 102 diferencijalno eksprimirana gena. Većina diferencijalno eksprimiranih gena bila je među uzorcima jedinki uzorkovanih 21 dana nakon infekcije. Među diferencijalno eksprimiranim genima bili su prisutni poznati efektori urođene imunosti rakova: serpin, lektini tipa-C i crustini. Novootkriveni su i geni s potencijalnom ulogom u urođenoj imunosti rakova. Oni predstavljaju predmet za buduća istraživanja urođene imunosti rakovaOne of the biggest threats for freshwater crayfish populations is the pathogen Aphanomyces astaci Shikora, 1906 from the class Oomycetes that causes a disease lethal for native crayfish species, crayfish plague. The marbled crayfish, Procambarus virginalis Lyko, 2017 is an invasive crayfish species, known to be resistant to the crayfish plague disease. In this study the immune response to an A. astaci infection of 30 marbled crayfish exposed to two strains of A. astaci (PsI- high virulence and As- low virulence) was investigated. Hepatopancreas samples were taken at two time points, three days and 21 days post challenge. From the RNA sequencing reads, high-quality de novo transcriptomes of marbled crayfish were assembled containing 60,004 genes. Annotation was available for 41.9% of the transcripts. Differential gene expression analysis revealed in total 102 differentially expressed genes. More differentially expressed genes were observed among the samples from the second time point. Among the differentially expressed genes several known effectors of the crayfish innate immunity were detected. Previously unreported genes with potential role in crayfish innate immunity were also identified. They represent targets for future studies on crayfish innate immunity

De novo assembly of Procambarus virginalis Lyko, 2017 transcriptome and gene expression in response to the pathogen Aphanomyces astaci Shikora, 1906

Jedna on najveći prijetnji za populacije nativnih europskih slatkovodnih rakova je patogen Aphanomyces astaci Shikora, 1906 iz razreda Oomycetes, koji uzrokuje bolest račju kugu letalnu za nativne vrste slatkovodnih rakova. Mramorni rak, Procambarus virginalis Lyko, 2017 invazivna je vrsta i poznati prenositelj račje kuge. U ovom istraživanju proučen je imunosni odgovor 30 jedinki mramornog raka na infekciju s A. astaci. Korištena su dva soja patogena; PsI- visoko virulentan i As- nisko virulentan. Uzorkovanje hepatopankreasa rakova iz pokusa provedeno je tri i 21 dan nakon izlaganja patogenu te je provedena izolacija RNA. Iz fragmenata RNA, dobivenih sekvenciranjem, sastavljan je de novo transkriptom visoke kvalitete kojeg čini 60,004 gena. Za 41.9% transkripata je pronađena anotacija. Analiza diferencijalne ekspresije otkrila je 102 diferencijalno eksprimirana gena. Većina diferencijalno eksprimiranih gena bila je među uzorcima jedinki uzorkovanih 21 dana nakon infekcije. Među diferencijalno eksprimiranim genima bili su prisutni poznati efektori urođene imunosti rakova: serpin, lektini tipa-C i crustini. Novootkriveni su i geni s potencijalnom ulogom u urođenoj imunosti rakova. Oni predstavljaju predmet za buduća istraživanja urođene imunosti rakovaOne of the biggest threats for freshwater crayfish populations is the pathogen Aphanomyces astaci Shikora, 1906 from the class Oomycetes that causes a disease lethal for native crayfish species, crayfish plague. The marbled crayfish, Procambarus virginalis Lyko, 2017 is an invasive crayfish species, known to be resistant to the crayfish plague disease. In this study the immune response to an A. astaci infection of 30 marbled crayfish exposed to two strains of A. astaci (PsI- high virulence and As- low virulence) was investigated. Hepatopancreas samples were taken at two time points, three days and 21 days post challenge. From the RNA sequencing reads, high-quality de novo transcriptomes of marbled crayfish were assembled containing 60,004 genes. Annotation was available for 41.9% of the transcripts. Differential gene expression analysis revealed in total 102 differentially expressed genes. More differentially expressed genes were observed among the samples from the second time point. Among the differentially expressed genes several known effectors of the crayfish innate immunity were detected. Previously unreported genes with potential role in crayfish innate immunity were also identified. They represent targets for future studies on crayfish innate immunity

Abundance and Diversification of Repetitive Elements in Decapoda Genomes

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

Recurring infection by crayfish plague pathogen only marginally affects survival and growth of marbled crayfish

Invasive alien crayfish threaten the diversity of freshwater ecosystems and native crayfish fauna. In Europe, this is largely due to transmission of the crayfish plague to susceptible native crayfish. Many invasive species tolerate crayfish plague, but the infection still has the potential to reduce the fitness of a tolerant host due to energy trade-offs between immune response maintenance and life-history traits, such as growth and reproduction. In combination with other unfavourable conditions, such a response could alter further invasion success of an otherwise successful crayfish invader. We examined whether repeated infection with one of the most virulent haplogroups of crayfish plague agent (Aphanomyces astaci) affects growth or survival of the juvenile marbled crayfish (Procambarus virginalis). Juveniles were exposed to i) two levels of pathogen concentrations, and ii) two different feeding regimes under the higher pathogen concentration. In all performed trials, repeated infection reduced growth rates, while the combination of recurring infection and food limitation significantly increased mortality. The average energy cost of the immune response was estimated at 12.07 J/day for individuals weighing 0.3 grams. Since infections were frequent and pathogen concentrations high, results suggest that marbled crayfish is resistant to A. astaci pathogen and its survival is only affected by adding the stress of food limitation. The survival of almost half of the individuals exposed to high pathogen loads and extreme food limitation indicates that chronic infection by crayfish plague is unlikely to be an important factor impeding invasion success of the marbled crayfish, even under harsh conditions. Our results add to the growing body of evidence that marbled crayfish has potential to become one of the most successful freshwater invaders