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53. Comparative transcriptome analysis of noble crayfish and marbled crayfish immune response to Aphanomyces astaci challenges

Author

Boštjančić, Ljudevit Luka, primary, Francesconi, Caterina, additional, Rutz, Christelle, additional, Hoffbeck, Lucien, additional, Poidevin, Laetitia, additional, Kress, Arnaud, additional, Jussila, Japo, additional, Makkonen, Jenny, additional, Feldmeyer, Barbara, additional, Bálint, Miklós, additional, Lecompte, Odile, additional, and Theissinger, Kathrin, additional

Published
2021
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54. De novo assembly and annotation of the marbled and noble crayfish hepatopancreas transcriptomes

Author

Boštjančić, Ljudevit Luka, Francesconi, Caterina, Rutz, Christelle, Hoffbeck, Lucien, Poidevin, Laetitia, Kress, Arnaud, Japo Jussila, Makonnen, Jenny, Feldmeyer, Barbara, Bálint, Miklós, Lecompte, Odile, Theissinger, Kathrin, Laboratoire des sciences de l'ingénieur, de l'informatique et de l'imagerie (ICube), Institut National des Sciences Appliquées - Strasbourg (INSA Strasbourg), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-École Nationale du Génie de l'Eau et de l'Environnement de Strasbourg (ENGEES)-Réseau nanophotonique et optique, Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Matériaux et nanosciences d'Alsace (FMNGE), Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), École Nationale du Génie de l'Eau et de l'Environnement de Strasbourg (ENGEES)-Université de Strasbourg (UNISTRA)-Institut National des Sciences Appliquées - Strasbourg (INSA Strasbourg), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Les Hôpitaux Universitaires de Strasbourg (HUS)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et Nanosciences Grand-Est (MNGE), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, and Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI]
Published
2021

55. Editorial: Conservation of European Freshwater Crayfish

Author

Theissinger, Kathrin, Edsman, L, Maguire, I., Dieguez-Uribeondo, Javier, Jussila, Japo, Theissinger, Kathrin, Edsman, L, Maguire, I., Dieguez-Uribeondo, Javier, and Jussila, Japo

Abstract

Freshwater ecosystem functioning is often thought to be dominated by fish, determining the community structure via top-down control and ecosystem engineering. However, freshwater crayfish can have an even stronger effect on food web and ecosystem functioning, operating as keystone species in a water body (Longshaw and Stebbing, 2016). As environmental engineers, crayfish have a significant impact on the biodiversity within their habitat (Souty-Grosset et al., 2006). Yet over the past 150 years freshwater crayfish in Europe have faced a novel challenge in the form of a lethal disease caused by the oomycete Aphanomyces astaci Schikora 1906, introduced by alien crayfish species of North American origin. Today, the European native crayfish population trends are in decline nearing extinction in several cases (Souty-Grosset et al., 2006; Jussila et al., 2014). The introduction of different A. astaci strains in Europe and the repeated introductions of their North American host species are a classic example of a man-made ecological disaster (Jussila et al.), stemming from the naive belief that the manipulation of an ecosystem would be straightforward. The alien crayfish species, which were supposed to replace the eradicated native stocks, not only transfer the deadly disease but in many parts of Europe also outcompete their native crayfish counterparts, because they are more aggressive giving them additional advantage regarding habitat competition in addition to higher fecundity (Alonso and Martínez, 2006). Introductions of new alien crayfish stocks and thus new A. astaci strains will inevitably lead to the total eradication of the remaining native European crayfish stocks. In this Research Topic we collected scientific work on crayfish conservation from multiple scales, ranging from molecular to species and ecosystem levels, to address the consequences of invasive crayfish and host-parasite interactions on European freshwater biodiversity and ecosystem functioning, aiding

Published
2021

56. Money Kills Native Ecosystems: European Crayfish as an Example

Author

Jussila, Japo, Edsman, Lennart, Maguire, Ivana, Dieguez-Uribeondo, Javier, Theissinger, Kathrin, Jussila, Japo, Edsman, Lennart, Maguire, Ivana, Dieguez-Uribeondo, Javier, and Theissinger, Kathrin

Abstract

Native European crayfish conservation was triggered by invasion of crayfish plague disease agent, Aphanomyces astaci, starting 1860s in Northern Italy. Resulting crayfish plague epidemics quickly spread over Continental Europe, then to Finland, Sweden and finally, after running amok around Europe, A. astaci was discovered also in Iberian Peninsula, Norway, Ireland, and United Kingdom in 1970s and 1980s. By that time significant proportion of native crayfish stocks had been lost, and while crayfish plague epidemics were still recorded, also industrialization and waterways construction were causing damage to remaining native crayfish stocks. While alien crayfish introductions, at least Faxonius limosus, already gave rise to first wave of crayfish plague epidemics in late 19th century, later in 1960s it was decided that introductions of alien Pacifastacus leniusculus should be initiated to replace native European crayfish populations. Decisions were based on presumed advantages for fishery, suitable habitat requirements and supposed immunity against A. astaci. Furthermore, conservation of native European crayfish species was sidelined and focus shifted toward alien crayfish stocking routine and consumption. Alien crayfish species introductions resulted in repeated waves of crayfish plague epidemics among remaining native crayfish stocks. It was soon discovered that alien crayfish of North American origin were, as suspected, permanent reservoirs for A. astaci, that some of those alien species were losing their resistance against selected strains of A. astaci and struggled in European aquatic ecosystems. In this article, we introduce numerous motives behind grand mistake of introducing alien crayfish species to Europe and then promoting their stocks instead of focusing on conservation of native crayfish species. We outline how false economical, biological and ecologic assumptions were used to justify a hasty introduction of alien crayfish, which has further devastated na

Published
2021

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

Author

Dobrović, Ana, Geček, Sunčana, Klanjšček, Tin, Haberle, Ines, Dragičević, Paula, Pavić, Dora, Petelinec, Ana, Boštjančić, Ljudevit Luka, Bonassin, Lena, Theissinger, Kathrin, and Hudina, Sandra

Subjects
CRAYFISH, LIFE history theory, HAPLOGROUPS, INTRODUCED species, PATHOGENIC microorganisms, INFECTION
Abstract

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. [ABSTRACT FROM AUTHOR]

Published
2022
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60. Erratum : Using DNA metabarcoding for assessing chironomid diversity and community change in mosquito controlled temporary wet-lands (Metabarcoding and Metagenomics 2 (e21060) DOI: 10.3897/mbmg.2.21060)

Author

Theissinger, Kathrin, Kästel, Anna, Elbrecht, Vasco, Makkonen, Jenny, Michiels, Susanne, Schmidt, Susanne I., Allgeier, Stefanie, Leese, Florian, and Brühl, Carsten A.

Subjects
Biologie
Abstract

Explanation regarding the background leading to this corrigendum The main reasons for this corrigendum were discrepancies between the detected number of chironomids in a report from 2014 and the MBMG article, published in 2018. In the MBMG article from 2018, overall more chironomids were reported that were not detected in the report from 2014. The reasons for this are outlined below. In general, the abundance data used in this study were part of a project conducted in 2013, which investigated the influence of mosquito control with Bti on the food web. This study was approved and financed by the town Neustadt an der Weinstrasse (Germany). The township requested a project report, which was due in March 2014. By this time, the data were not finally evaluated. In particular, a taxonomic training course for determining Chironomidae subfamilies was attended later in the year 2014 by some of the project participants. After this training, we found out that many chironomids of the subfamily Orthocladiinae were wrongly determined as Cecidomyiidae. This had direct impacts on the results and created differences in comparison to the report that was published 2014. All detected differences between the report and this manuscript are listed below in Table SI1. In this context of clarification, we came across some additional mistakes in the Microsoft Access database query of the abundance data, where a filter was missing for excluding traps that dried out during summer. In addition, the project in 2013 was conducted over a longer period, namely 18 weeks after initial Bti application (WAA). In the MBMG article, we only used the data until WAA13, because after this week, too many traps dried out, with only some data points for aquatic insects remaining. However, in the originally-published MBMG article, we falsely included emergence data of all individuals until WAA18, including terrestrial taxa from traps that dried out. This mistake has now been corrected, which led to a reduction in the number of detected taxa and individuals, including chironomids and mosquitoes (see article in “tracked changes” below). For full transparency, a new Suppl. material 3 with all abundance data has now been added to the corrected version of our article. Due to the strong within-site heterogeneity and the resulting highly variable numbers of chironomids detected per trap within each site, we reduced our overall statement of a clearly negative Bti effect on the chironomid community and discuss the need for more true replicates to overcome the problem of a highly-patchy chironomid distribution within a water body. We have restructured the start of the abstract and introduction to emphasise the importance of chironomids in bioassessments (by moving sections of the text up). The authors apologize for any inconveniences resulting from these changes and want to explicitly thank the editorial staff for the very thorough review of our study and support in correcting the mistakes. Finally, we would like to point out that the mistake only affected the overall abundance data, but the metabarcoding part of the study was not concerned and has not been changed. Korrektur zu 10.3897/mbmg.2.21060

Published
2020

62. Corrigendum: Using DNA metabarcoding for assessing chironomid diversity and community change in mosquito controlled temporary wetlands. MBMG 2: e21060. https://doi.org/10.3897/mbmg.2.21060

Author

Theissinger, Kathrin, primary, Kästel, Anna, additional, Elbrecht, Vasco, additional, Makkonen, Jenny, additional, Michiels, Susanne, additional, Schmidt, Susanne I., additional, Allgeier, Stefanie, additional, Leese, Florian, additional, and Brühl, Carsten A., additional

Published
2020
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66. Phylogeography, genetic stocks, and conservation implications for an Australian endemic marine turtle

Author

FitzSimmons, Nancy N., primary, Pittard, Stewart D., additional, McIntyre, Nathan, additional, Jensen, Michael P., additional, Guinea, Mick, additional, Hamann, Mark, additional, Kennett, Rod, additional, Leis, Brett, additional, Limpus, Colin J., additional, Limpus, Duncan J., additional, McCann, Megan J., additional, MacDonald, Anna J., additional, McFarlane, Glenn, additional, Parmenter, C. John, additional, Pendoley, Kellie, additional, Prince, Robert T., additional, Scheltinga, Leigh, additional, Theissinger, Kathrin, additional, Tucker, Anton D., additional, Waayers, David, additional, Whiting, Andrea, additional, and Whiting, Scott, additional

Published
2020
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67. Multifaceted implications of the competition between native and invasive crayfish: a glimmer of hope for the native’s long-term survival

Author

Pacioglu, Octavian, primary, Theissinger, Kathrin, additional, Alexa, Andreea, additional, Samoilă, Corina, additional, Sîrbu, Ovidiu-Ioan, additional, Schrimpf, Anne, additional, Zubrod, Jochen P., additional, Schulz, Ralf, additional, Pîrvu, Mălina, additional, Lele, Sandra-Florina, additional, Jones, John I., additional, and Pârvulescu, Lucian, additional

Published
2019
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72. MtDNA allows the sensitive detection and haplotyping of the crayfish plague disease agentAphanomyces astacishowing clues about its origin and migration

Author

Makkonen, Jenny, primary, Jussila, Japo, additional, Panteleit, Jörn, additional, Keller, Nina Sophie, additional, Schrimpf, Anne, additional, Theissinger, Kathrin, additional, Kortet, Raine, additional, Martín-Torrijos, Laura, additional, Sandoval-Sierra, Jose Vladimir, additional, Diéguez-Uribeondo, Javier, additional, and Kokko, Harri, additional

Published
2018
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73. Supplementary material 2 from: Theissinger K, Kästel A, Elbrecht V, Makkonen J, Michiels S, Schmidt S, Allgeier S, Leese F, Brühl C (2018) Using DNA metabarcoding for assessing chironomid diversity and community change in mosquito controlled temporary wetlands. Metabarcoding and Metagenomics 2: e21060. https://doi.org/10.3897/mbmg.2.21060

Author

Theissinger, Kathrin, primary, Kästel, Anna, additional, Elbrecht, Vasco, additional, Makkonen, Jenny, additional, Michiels, Susanne, additional, Schmidt, Susanne, additional, Allgeier, Stefanie, additional, Leese, Florian, additional, and Brühl, Carsten, additional

Published
2018
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74. Supplementary material 1 from: Theissinger K, Kästel A, Elbrecht V, Makkonen J, Michiels S, Schmidt S, Allgeier S, Leese F, Brühl C (2018) Using DNA metabarcoding for assessing chironomid diversity and community change in mosquito controlled temporary wetlands. Metabarcoding and Metagenomics 2: e21060. https://doi.org/10.3897/mbmg.2.21060

Author

Theissinger, Kathrin, primary, Kästel, Anna, additional, Elbrecht, Vasco, additional, Makkonen, Jenny, additional, Michiels, Susanne, additional, Schmidt, Susanne, additional, Allgeier, Stefanie, additional, Leese, Florian, additional, and Brühl, Carsten, additional

Published
2018
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76. Supplementary material 3 from: Theissinger K, Kästel A, Elbrecht V, Makkonen J, Michiels S, Schmidt S, Allgeier S, Leese F, Brühl C (2018) Using DNA metabarcoding for assessing chironomid diversity and community change in mosquito controlled temporary wetlands. Metabarcoding and Metagenomics 2: e21060. https://doi.org/10.3897/mbmg.2.21060

Author

Theissinger, Kathrin, primary, Kästel, Anna, additional, Elbrecht, Vasco, additional, Makkonen, Jenny, additional, Michiels, Susanne, additional, Schmidt, Susanne, additional, Allgeier, Stefanie, additional, Leese, Florian, additional, and Brühl, Carsten, additional

Published
2018
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77. Supplementary material 4 from: Theissinger K, Kästel A, Elbrecht V, Makkonen J, Michiels S, Schmidt S, Allgeier S, Leese F, Brühl C (2018) Using DNA metabarcoding for assessing chironomid diversity and community change in mosquito controlled temporary wetlands. Metabarcoding and Metagenomics 2: e21060. https://doi.org/10.3897/mbmg.2.21060

Author

Theissinger, Kathrin, primary, Kästel, Anna, additional, Elbrecht, Vasco, additional, Makkonen, Jenny, additional, Michiels, Susanne, additional, Schmidt, Susanne, additional, Allgeier, Stefanie, additional, Leese, Florian, additional, and Brühl, Carsten, additional

Published
2018
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78. Supplementary material 1 from: Theissinger K, Kästel A, Elbrecht V, Makkonen J, Michiels S, Schmidt S, Allgeier S, Leese F, Brühl C (2017) Using DNA metabarcoding for assessing chironomid diversity and community change in mosquito controlled temporary wetlands. Metabarcoding and Metagenomics 1: e21060. https://doi.org/10.3897/mbmg.1.21060

Author

Theissinger, Kathrin, primary, Kästel, Anna, additional, Elbrecht, Vasco, additional, Makkonen, Jenny, additional, Michiels, Susanne, additional, Schmidt, Susanne, additional, Allgeier, Stefanie, additional, Leese, Florian, additional, and Brühl, Carsten, additional

Published
2017
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79. Supplementary material 4 from: Theissinger K, Kästel A, Elbrecht V, Makkonen J, Michiels S, Schmidt S, Allgeier S, Leese F, Brühl C (2017) Using DNA metabarcoding for assessing chironomid diversity and community change in mosquito controlled temporary wetlands. Metabarcoding and Metagenomics 1: e21060. https://doi.org/10.3897/mbmg.1.21060

Author

Theissinger, Kathrin, primary, Kästel, Anna, additional, Elbrecht, Vasco, additional, Makkonen, Jenny, additional, Michiels, Susanne, additional, Schmidt, Susanne, additional, Allgeier, Stefanie, additional, Leese, Florian, additional, and Brühl, Carsten, additional

Published
2017
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80. Supplementary material 3 from: Theissinger K, Kästel A, Elbrecht V, Makkonen J, Michiels S, Schmidt S, Allgeier S, Leese F, Brühl C (2017) Using DNA metabarcoding for assessing chironomid diversity and community change in mosquito controlled temporary wetlands. Metabarcoding and Metagenomics 1: e21060. https://doi.org/10.3897/mbmg.1.21060

Author

Theissinger, Kathrin, primary, Kästel, Anna, additional, Elbrecht, Vasco, additional, Makkonen, Jenny, additional, Michiels, Susanne, additional, Schmidt, Susanne, additional, Allgeier, Stefanie, additional, Leese, Florian, additional, and Brühl, Carsten, additional

Published
2017
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82. Supplementary material 2 from: Theissinger K, Kästel A, Elbrecht V, Makkonen J, Michiels S, Schmidt S, Allgeier S, Leese F, Brühl C (2017) Using DNA metabarcoding for assessing chironomid diversity and community change in mosquito controlled temporary wetlands. Metabarcoding and Metagenomics 1: e21060. https://doi.org/10.3897/mbmg.1.21060

Author

Theissinger, Kathrin, primary, Kästel, Anna, additional, Elbrecht, Vasco, additional, Makkonen, Jenny, additional, Michiels, Susanne, additional, Schmidt, Susanne, additional, Allgeier, Stefanie, additional, Leese, Florian, additional, and Brühl, Carsten, additional

Published
2017
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86. First large-scale genetic analysis of the vulnerable noble crayfish Astacus astacus in Europe

Author

Schrimpf, Anne, Theissinger, Kathrin, Dahlem, Jennifer, Pârvulescu, Lucian, Maguire, Ivana, Schulz, Holger, Schulz, Ralf, and Füreder, Leopold

Subjects
phylogeography, haplotype diversity, microsatellite analysis, human translocation, glacial refugia
Abstract

Global changes, human impact and climatic cycles had a severe impact on the distribution and diversity of the vulnerable European noble crayfish Astacus astacus. The main aim of this study was to resolve the natural genetic structure of European noble crayfish populations and to estimate to what degree human translocations dissolved the natural genetic make-up. We sampled 500 individuals from 120 populations across Europe. We sequenced a 350 base pair (bp) fragment of the mitochondrial cytochrome oxidase subunit I (COI) and a 500 bp fragment of 16s rRNA (16S). Furthermore, for 24 populations a microsatellite analysis was performed based on six polymorphic loci. Twenty-two COI-haplotypes and sixteen 16S-haplotypes were identified, with each one common haplotype found across the whole study area. The high number of private haplotypes suggested two separate glacial refugia on the western and central Balkan. In contrast, very low haplotype diversities in central Europe were detected, which could result from human translocations and/or founder effects due to postglacial re-colonization. Microsatellites exhibited strong genetic differentiation between central and eastern Europe as well as between the central and western Balkan, but little among central European populations. Despite human translocations a differentiation of noble crayfish populations in all major catchment areas was detectable. Our data thus support the establishment of distinct evolutionary significant units to protect the present-day genetic diversity of A. astacus in Europe.

Published
2012

87. MtDNA allows the sensitive detection and haplotyping of the crayfish plague disease agent Aphanomyces astaci showing clues about its origin and migration.

Author

Makkonen, Jenny, Jussila, Japo, Panteleit, Jörn, Keller, Nina Sophie, Schrimpf, Anne, Theissinger, Kathrin, Kortet, Raine, Martín-Torrijos, Laura, Sandoval-Sierra, Jose Vladimir, Diéguez-Uribeondo, Javier, and Kokko, Harri

Subjects
CRAYFISH, PROCAMBARUS clarkii, MITOCHONDRIAL DNA, PLAGUE, EPIDEMICS
Abstract

The oomycete Aphanomyces astaci , the causative agent of crayfish plague, is listed as one of the 100 worst invasive species in the world, destroying the native crayfish populations throughout Eurasia. The aim of this study was to examine the potential of selected mitochondrial (mt) genes to track the diversity of the crayfish plague pathogen A. astaci. Two sets of primers were developed to amplify the mtDNA of ribosomal rnnS and rnnL subunits. We confirmed two main lineages, with four different haplogroups and five haplotypes among 27 studied A. astaci strains. The haplogroups detected were (1) the A-haplogroup with the a-haplotype strains originating from Orconectes sp., Pacifastacus leniusculus and Astacus astacus ; (2) the B-haplogroup with the b-haplotype strains originating from the P. leniusculus ; (3) the D-haplogroup with the d1 and d2-haplotypes strains originating from Procambarus clarkii ; and (4) the E-haplogroup with the e-haplotype strains originating from the Orconectes limosus. The described markers are stable and reliable and the results are easily repeatable in different laboratories. The present method has high applicability as it allows the detection and characterization of the A. astaci haplotype in acute disease outbreaks in the wild, directly from the infected crayfish tissue samples. [ABSTRACT FROM AUTHOR]

Published
2018
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96. Phylogeography of noble crayfish ( Astacus astacus) reveals multiple refugia.

Author

Schrimpf, Anne, Theissinger, Kathrin, Dahlem, Jenifer, Maguire, Ivana, Pârvulescu, Lucian, Schulz, Holger K., and Schulz, Ralf

Subjects
*CHROMOSOMAL translocation, *ASTACUS astacus, *CRAYFISH, *CYTOCHROME oxidase, *WATERSHEDS, *HAPLOTYPES
Abstract

Reconstructing the phylogeographic history of a species can aid in defining areas of conservation priority. For freshwater species, historical river structure plays a significant role in explaining genetic differentiation and population structure. However, human-induced translocations can erase the natural genetic structure, especially for species of commercial interest such as the noble crayfish ( Astacus astacus)., Our aim was to reconstruct the current genetic structure of the endangered noble crayfish in central Europe to identify refugial areas that are hotspots of genetic diversity. We analysed a fragment of the mitochondrial cytochrome oxidase subunit I, and the 16 S r RNA from 540 noble crayfish specimens from 156 sampling sites distributed around five European sea basins. Additionally, we conducted a microsatellite analysis of 289 individuals from 22 sites., Both mitochondrial and nuclear markers revealed genetically relatively homogenous populations in central Europe that had been influenced by anthropogenic translocations. However, some areas (Eider catchment in northern Germany and Rhineland-Palatinate in south-western Germany) show a distinct genetic structure with endemic haplotypes and private alleles indicating (i) that these areas were refugia for A. astacus in central Europe and (ii) that these populations have not been subject to anthropogenic translocations. Further, we found the highest genetic diversity in the Black Sea basin and particularly high differentiation between populations from the western Balkans and the remaining Black Sea populations. The split between Western Balkan and the remaining European populations is estimated to have occurred approximately 700 k years before present, whereas remaining differentiations occurred within the last 450 k years. Using migration modelling, we detected that the North Sea basin and the Baltic Sea basin were colonised independently via different colonisation paths from the eastern Black Sea basin, while the western Balkans did not contribute to this colonisation., Our results suggest the existence of at least two refugial areas in south-eastern Europe. To conserve maximum genetic diversity, conservation priorities for noble crayfish should focus on the south-eastern European genetic hotspots and on populations in central Europe that hold an autochthonous genetic structure (e.g. Langsee in the Eider catchment area). We further propose that each river catchment should form a separate management unit to reduce anthropogenic genetic homogenisation. [ABSTRACT FROM AUTHOR]

Published
2014
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97. Isolation and characterization of 10 highly polymorphic di- and trinucleotide microsatellite markers in the mayfly Ameletus inopinatus (Ephemeroptera: Siphlonuridae).

Author

THEISSINGER, KATHRIN, FELDHEIM, KEVIN A., TAUBMANN, JULIA, SEITZ, ALFRED, and PAULS, STEFFEN U.

Subjects
*MAYFLIES, *MICROSATELLITE repeats, *GENETIC polymorphisms, *HARDY-Weinberg formula, *INSECT populations, *GENETICS
Abstract

We describe the isolation of ten polymorphic microsatellite loci from the mayfly Ameletus inopinatus. Loci had di- or trinucleotide repeat motifs and were highly variable with three to 17 alleles (mean = 7.15). Observed heterozygosity ranged from 0.143 to 0.905. One locus (Ami_202) showed significant deviation from Hardy–Weinberg equilibrium in one population, but no evidence for null alleles. One locus (Ami_73) was significantly linked with three other loci. The remaining nine loci should prove highly informative for population genetic studies. [ABSTRACT FROM AUTHOR]

Published
2008
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98. The era of reference genomes in conservation genomics

Author

Giulio Formenti, Kathrin Theissinger, Carlos Fernandes, Iliana Bista, Aureliano Bombarely, Christoph Bleidorn, Claudio Ciofi, Angelica Crottini, José A. Godoy, Jacob Höglund, Joanna Malukiewicz, Alice Mouton, Rebekah A. Oomen, Sadye Paez, Per J. Palsbøll, Christophe Pampoulie, María J. Ruiz-López, Hannes Svardal, Constantina Theofanopoulou, Jan de Vries, Ann-Marie Waldvogel, Guojie Zhang, Camila J. Mazzoni, Erich D. Jarvis, Miklós Bálint, Fedor Čiampor, Jacob Hoglund, Per Palsbøll, María José Ruiz-López, Goujie Zhang, Erich Jarvis, Sargis A. Aghayan, Tyler S. Alioto, Isabel Almudi, Nadir Alvarez, Paulo C. Alves, Isabel R. Amorim, Agostinho Antunes, Paula Arribas, Petr Baldrian, Paul R. Berg, Giorgio Bertorelle, Astrid Böhne, Andrea Bonisoli-Alquati, Ljudevit L. Boštjančić, Bastien Boussau, Catherine M. Breton, Elena Buzan, Paula F. Campos, Carlos Carreras, L. FIlipe Castro, Luis J. Chueca, Elena Conti, Robert Cook-Deegan, Daniel Croll, Mónica V. Cunha, Frédéric Delsuc, Alice B. Dennis, Dimitar Dimitrov, Rui Faria, Adrien Favre, Olivier D. Fedrigo, Rosa Fernández, Gentile Francesco Ficetola, Jean-François Flot, Toni Gabaldón, Dolores R. Galea Agius, Guido R. Gallo, Alice M. Giani, M. Thomas P. Gilbert, Tine Grebenc, Katerina Guschanski, Romain Guyot, Bernhard Hausdorf, Oliver Hawlitschek, Peter D. Heintzman, Berthold Heinze, Michael Hiller, Martin Husemann, Alessio Iannucci, Iker Irisarri, Kjetill S. Jakobsen, Sissel Jentoft, Peter Klinga, Agnieszka Kloch, Claudius F. Kratochwil, Henrik Kusche, Kara K.S. Layton, Jennifer A. Leonard, Emmanuelle Lerat, Gianni Liti, Tereza Manousaki, Tomas Marques-Bonet, Pável Matos-Maraví, Michael Matschiner, Florian Maumus, Ann M. Mc Cartney, Shai Meiri, José Melo-Ferreira, Ximo Mengual, Michael T. Monaghan, Matteo Montagna, Robert W. Mysłajek, Marco T. Neiber, Violaine Nicolas, Marta Novo, Petar Ozretić, Ferran Palero, Lucian Pârvulescu, Marta Pascual, Octávio S. Paulo, Martina Pavlek, Cinta Pegueroles, Loïc Pellissier, Graziano Pesole, Craig R. Primmer, Ana Riesgo, Lukas Rüber, Diego Rubolini, Daniele Salvi, Ole Seehausen, Matthias Seidel, Simona Secomandi, Bruno Studer, Spyros Theodoridis, Marco Thines, Lara Urban, Anti Vasemägi, Adriana Vella, Noel Vella, Sonja C. Vernes, Cristiano Vernesi, David R. Vieites, Robert M. Waterhouse, Christopher W. Wheat, Gert Wörheide, Yannick Wurm, Gabrielle Zammit, Repositório da Universidade de Lisboa, Formenti, Giulio, Theissinger, Kathrin, Fernandes, Carlo, Bista, Iliana, Bombarely, Aureliano, Bleidorn, Christoph, Ciofi, Claudio, Crottini, Angelica, Godoy, José A., Höglund, Jacob, Malukiewicz, Joanna, Mouton, Alice, Oomen, Rebekah A., Paez, Sadye, Palsbøll, Per J., Pampoulie, Christophe, Ruiz-López, María J., Svardal, Hanne, Theofanopoulou, Constantina, de Vries, Jan, Waldvogel, Ann-Marie, Zhang, Guojie, Mazzoni, Camila J., Jarvis, Erich D., Bálint, Mikló, Čiampor, Fedor, Hoglund, Jacob, Palsbøll, Per, José Ruiz-López, María, Zhang, Goujie, Jarvis, Erich, Aghayan, Sargis A., Alioto, Tyler S., Almudi, Isabel, Alvarez, Nadir, Alves, Paulo C., R Amorim, Isabel, Antunes, Agostinho, Arribas, Paula, Baldrian, Petr, R Berg, Paul, Bertorelle, Giorgio, Böhne, Astrid, Bonisoli-Alquati, Andrea, L Boštjančić, Ljudevit, Boussau, Bastien, M Breton, Catherine, Buzan, Elena, F Campos, Paula, Carreras, Carlo, FIlipe Castro, L., Chueca, Luis J., Conti, Elena, Cook-Deegan, Robert, Croll, Daniel, V Cunha, Mónica, Delsuc, Frédéric, Dennis, Alice B., Dimitrov, Dimitar, Faria, Rui, Favre, Adrien, Fedrigo, Olivier D., Fernández, Rosa, Francesco Ficetola, Gentile, Flot, Jean-Françoi, Gabaldón, Toni, Galea Agius, Dolores R., Gallo, Guido R., Giani, Alice M., Thomas P Gilbert, M., Grebenc, Tine, Guschanski, Katerina, Guyot, Romain, Hausdorf, Bernhard, Hawlitschek, Oliver, D Heintzman, Peter, Heinze, Berthold, Hiller, Michael, Husemann, Martin, Iannucci, Alessio, Irisarri, Iker, S Jakobsen, Kjetill, Jentoft, Sissel, Klinga, Peter, Kloch, Agnieszka, F Kratochwil, Claudiu, Kusche, Henrik, KS Layton, Kara, A Leonard, Jennifer, Lerat, Emmanuelle, Liti, Gianni, Manousaki, Tereza, Marques-Bonet, Toma, Matos-Maraví, Pável, Matschiner, Michael, Maumus, Florian, Mc Cartney, Ann M., Meiri, Shai, Melo-Ferreira, José, Mengual, Ximo, Monaghan, Michael T., Montagna, Matteo, Robertwmysłajek, T Neiber, Marco, Nicolas, Violaine, Novo, Marta, Ozretić, Petar, Palero, Ferran, Pârvulescu, Lucian, Pascual, Marta, Paulo, Octávio S., Pavlek, Martina, Pegueroles, Cinta, Pellissier, Loc, Pesole, Graziano, R Primmer, Craig, Riesgo, Ana, Rüber, Luka, Rubolini, Diego, Salvi, Daniele, Seehausen, Ole, Seidel, Matthia, Secomandi, Simona, Studer, Bruno, Theodoridis, Spyro, Thines, Marco, Urban, Lara, Vasemägi, Anti, Vella, Adriana, Vella, Noel, C Vernes, Sonja, Vernesi, Cristiano, R Vieites, David, M Waterhouse, Robert, W Wheat, Christopher, Wörheide, Gert, Wurm, Yannick, Zammit., and Gabrielle, Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Eléments transposables, évolution, populations, Département génétique, interactions et évolution des génomes [LBBE] (GINSENG), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Barcelona Supercomputing Center, European Reference Genome Atlas (ERGA) Consortium, University of St Andrews. School of Biology, University of St Andrews. St Andrews Bioinformatics Unit, Palsbøll lab, Marine Biology, University of Zurich, and Bálint, Miklós

Subjects
QH301 Biology, 580 Plants (Botany), Genetics -- Research, Evolutionsbiologi, biodiversity conservation, conservation genetics, ERGA, European Reference Genome Atlas, Conservation genetics, Biodiversity conservation, Animal genome mapping, udc:630*1, Genome, GE, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDE.BE.BIOD]Environmental Sciences/Biodiversity and Ecology/domain_sde.be.biod, Biodiversity [MeSH], Genomics [MeSH], Ecology, Evolution, Behavior and Systematics, Genome [MeSH], 3rd-DAS, Genomics, Biodiversity, referenčni genomi, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDE.BE.BEC]Environmental Sciences/Biodiversity and Ecology/domain_sde.be.bec, Chemistry, 10121 Department of Systematic and Evolutionary Botany, genomika, GE Environmental Sciences, Informàtica::Aplicacions de la informàtica::Bioinformàtica [Àrees temàtiques de la UPC], biodiverziteta, Settore BIO/18 - GENETICA, education, QH426 Genetics, QH301, VDP::Matematikk og Naturvitenskap: 400::Basale biofag: 470, [SDE.BE.EVO]Environmental Sciences/Biodiversity and Ecology/domain_sde.be.evo, Genetics, genomi, 10211 Zurich-Basel Plant Science Center, Genomes, Genetik, Biology, QH426, Evolutionary Biology, Ambientale, Ecología, Genética, 1105 Ecology, Evolution, Behavior and Systematics, Wildlife conservation, 570 Life sciences, biology, Human medicine, Animal genetics, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Genètica
Abstract

Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics, and are expected to revolutionize conservation genomics., Trends in Ecology & Evolution, 37 (3), ISSN:0169-5347, ISSN:1872-8383

Published
2022

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

Author

Boštjančić, Ljudevit Luka, Theissinger, Kathrin, and Maguire, Ivana

Subjects
račja kuga, PRIRODNE ZNANOSTI. Biologija, marbled crayfish, maramorni rak, RNA sequencing, NATURAL SCIENCES. Biology, RNA sekvenciranje, crayfish plague, innate immunity, urođena imunost
Abstract

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 rakova One 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.

Published
2021

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