Riho Gross
Estonian University of Life Sciences, Department of Aquaculture, Faculty Member
Proliferative kidney disease caused by the myxozoan parasite Tetracapsuloides bryosalmonae has been actively studied in juvenile salmonids for decades. However, very little is known about parasite prevalence and its geographical and... more
Proliferative kidney disease caused by the myxozoan parasite Tetracapsuloides bryosalmonae has been actively studied in juvenile salmonids for decades. However, very little is known about parasite prevalence and its geographical and intra‐host distribution at older life stages. We screened T. bryosalmonae among adult sea trout (Salmo trutta) (n = 295) collected along the Estonian Baltic Sea coastline together with juvenile trout from 33 coastal rivers (n = 1752) to assess spatial infection patterns of the adult and juvenile fish. The parasite was detected among 38.6% of adult sea trout with the prevalence increasing from west to east, and south to north, along the coastline. A similar pattern was observed in juvenile trout. Infected sea trout were also older than uninfected fish and the parasite was detected in sea trout up to the age of 6 years. Analysis of intra‐host distribution of the parasite and strontium to calcium ratios from the otoliths revealed that (re)infection through freshwater migration may occur among adult sea trout. The results of this study indicate that T. bryosalmonae can persist in a brackish water environment for several years and that returning sea trout spawners most likely contribute to the parasite life cycle by transmitting infective spores.
Research Interests: Zoology, Biology, Fish Diseases, Fisheries Sciences, Fishery, and 5 moreTrout, Juvenile, Veterinary Sciences, Salmo, and Myxozoa
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Abstract 48 novel tetranucleotide microsatellite loci were developed for the noble crayfish ( Astacus astacus ) using Illumina MiSeq next generation sequencing technology. It was demonstrated that 25 loci were polymorphic and 19 loci... more
Abstract 48 novel tetranucleotide microsatellite loci were developed for the noble crayfish ( Astacus astacus ) using Illumina MiSeq next generation sequencing technology. It was demonstrated that 25 loci were polymorphic and 19 loci could be co-amplified in a single multiplex polymerase chain reaction (PCR) assay and genotyped as a single panel on Applied Biosystems 3500 Genetic Analyser. The 19-plex assay was tested on 232 individuals of A. astacus originating from seven wild populations in Czech Republic and in Estonia. The multiplex assay designed in this study can be successfully applied in studies requiring high genetic resolution, such as population structuring, relatedness analysis, and stock identification. 21 loci were also successfully cross-amplified in the narrow-clawed crayfish ( Astacus leptodactylus ) from which 14 were polymorphic. In addition, 13 loci (both monomorphic and polymorphic) possessed species-specific allele size range in A. astacus and A. leptodactylus and can be applied for detecting possible hybrids between these sister species. Statement of relevance The novel 19-plex microsatellite assay can be applied for genetic management of captive stocks of the noble crayfish (selection of strains, planning of matings, avoiding of inbreeding) and in studies requiring high genetic resolution, such as parentage assessment, relatedness analysis or strain identification.
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Many salmonid fish populations are threatened by genetic homogenization, primarily due to introgressive hybridization with hatchery‐reared conspecifics. By applying genomewide analysis using two molecular marker types (1986 SNPs and 17... more
Many salmonid fish populations are threatened by genetic homogenization, primarily due to introgressive hybridization with hatchery‐reared conspecifics. By applying genomewide analysis using two molecular marker types (1986 SNPs and 17 microsatellites), we assessed the genetic impacts of inadvertent gene flow via straying from hatchery releases on wild populations of Atlantic salmon in the Gulf of Finland, Baltic Sea, over 16 years (1996–2012). Both microsatellites and SNPs revealed congruent population genetic structuring, indicating that introgression changed the genetic make‐up of wild populations by increasing genetic diversity and reducing genetic divergence. However, the degree of genetic introgression varied among studied populations, being higher in the eastern part and lower in the western part of Estonia, which most likely reflects the history of past stocking activities. Using kernel smoothing and permutation testing, we detected considerable heterogeneity in introgression patterns across the genome, with a large number of regions exhibiting nonrandom introgression widely dispersed across the genome. We also observed substantial variation in nonrandom introgression patterns within populations, as the majority of genomic regions showing elevated or reduced introgression were not consistently detected among temporal samples. This suggests that recombination, selection and stochastic processes may contribute to complex nonrandom introgression patterns. Our results suggest that (i) some genomic regions in Atlantic salmon are more vulnerable to introgressive hybridization, while others show greater resistance to unidirectional gene flow; and (ii) the hybridization of previously separated populations leads to complex and dynamic nonrandom introgression patterns that most likely have functional consequences for indigenous populations.
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Research Interests: Conservation Genetics, Gene Flow, Biology, Ecology, Genetic Diversity, and 14 moreBiological Sciences, Environmental Sciences, Population, Genetic Structure, Stocking, Genetic Differentiation, Genetic Divergence, Conservation Unit, Large Scale, Grayling, Genetic distance, Conservation strategies, Maximum Likelihood Method, and microsatellite loci
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Individual genotypes for six herring samples from the Gulf of Rig
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qPCR quantification cycle as inferred by the online tool 'Real-time PCR Miner' http://miner.ewindup.info/ given per plate and well, including amplification efficiencies and efficiency-corrected quantification cycl
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Sanger sequencing alignments are in BioEdit (*.bio) and Fasta format (*.fas)
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PythonCodes.zip - custom Python scripts used in the study
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This file is a tab-delimited text file containing all the relevant data needed to reproduce the analyses presented in Bruneaux 2016. The first line is a header containing column names. Each row corresponds to one fish individual. Each... more
This file is a tab-delimited text file containing all the relevant data needed to reproduce the analyses presented in Bruneaux 2016. The first line is a header containing column names. Each row corresponds to one fish individual. Each column corresponds to one variable, with data collected either during field work or during post-processing of the samples in the lab (see the ReadMe file for details about the variables)
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Background Determining the physiological effects of parasites and characterizing genes involved in host responses to infections are essential to improving our understanding of host-parasite interactions and their ecological and... more
Background Determining the physiological effects of parasites and characterizing genes involved in host responses to infections are essential to improving our understanding of host-parasite interactions and their ecological and evolutionary consequences. This task, however, is complicated by high diversity and complex life histories of many parasite species. The use of transcriptomics in the context of wild-caught specimens can help ameliorate this by providing both qualitative and quantitative information on gene expression patterns in response to parasites in specific host organs and tissues. Here, we evaluated the physiological impact of the widespread parasite, the pike tapeworm (Triaenophorus nodulosus),on its second intermediate host, the Eurasian perch (Perca fluviatilis). Methods We used an RNAseq approach to analyse gene expression in the liver, the target organ of T. nodulosus plerocercoids, and spleen which is one of the main immune organs in teleost fishes. We compared p...
STR genotyping error file used in parental reconstruction analysis using the program Colon
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STR genotypes for Salmo trutta individuals from River Mustoj
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STR genotypes for Salmo trutta individuals from River Altj
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Health after pathogen contact varies among individuals because of differences in pathogen load (which is limited by resistance) and disease severity in response to pathogen load (which is limited by tolerance). To understand... more
Health after pathogen contact varies among individuals because of differences in pathogen load (which is limited by resistance) and disease severity in response to pathogen load (which is limited by tolerance). To understand pathogen-induced host evolution, it is critical to know not only the relative contributions of nongenetic and genetic variation to resistance and tolerance but also how they change environmentally. We quantified nongenetic and genetic variation in parasite load and the associated temperature-dependent disease among trout siblings from two rivers. We detected a genetic variance for parasite load 6.6 times as large in the colder river. By contrast, genetic variance for disease traits tended to be larger in the warmer river, where the disease was manifested more severely. The relationships between disease severity and pathogen load (tolerance) exhibited plateaus at low pathogen load and stronger steepening slopes at high pathogen load in the warmer river. Our study demonstrates the environmental influence on disease severity, nongenetic and genetic variance for health-damage-limiting host abilities, and the shape of tolerance curves. Environmental variability is predicted to govern the presence and intensity of selection, change the relative contributions of nongenetic and genetic variance, and therefore hamper evolution toward more resistant and tolerant hosts
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List of 12 markers that were individually validated using seven individuals by PCR and Sanger sequencing
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Massively parallel sequencing a small proportion of the whole genome at high coverage enables answering a wide range of questions from molecular evolution and evolutionary biology to animal and plant breeding and forensics. In this study,... more
Massively parallel sequencing a small proportion of the whole genome at high coverage enables answering a wide range of questions from molecular evolution and evolutionary biology to animal and plant breeding and forensics. In this study, we describe the development of restriction-site associated DNA (RAD) sequencing approach for Ion Torrent PGM platform. Our protocol results in extreme genome complexity reduction using two rare-cutting restriction enzymes and strict size selection of the library allowing sequencing of a relatively small number of genomic fragments with high sequencing depth. We applied this approach to a common freshwater fish species, the Eurasian perch (Perca fluviatilis L.), and generated over 2.2 MB of novel sequence data consisting of ~17 000 contigs, identified 1259 single nucleotide polymorphisms (SNPs). We also estimated genetic differentiation between the DNA pools from freshwater (Lake Peipus) and brackish water (the Baltic Sea) populations and identified SNPs with the strongest signal of differentiation that could be used for robust individual assignment in the future. This work represents an important step towards developing genomic resources and genetic tools for the Eurasian perch. We expect that our ddRAD sequencing protocol for semiconductor sequencing technology will be useful alternative for currently available RAD protocols
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(INDEL) polymorphisms for QTL mapping of early
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Abstract 48 novel tetranucleotide microsatellite loci were developed for the noble crayfish ( Astacus astacus ) using Illumina MiSeq next generation sequencing technology. It was demonstrated that 25 loci were polymorphic and 19 loci... more
Abstract 48 novel tetranucleotide microsatellite loci were developed for the noble crayfish ( Astacus astacus ) using Illumina MiSeq next generation sequencing technology. It was demonstrated that 25 loci were polymorphic and 19 loci could be co-amplified in a single multiplex polymerase chain reaction (PCR) assay and genotyped as a single panel on Applied Biosystems 3500 Genetic Analyser. The 19-plex assay was tested on 232 individuals of A. astacus originating from seven wild populations in Czech Republic and in Estonia. The multiplex assay designed in this study can be successfully applied in studies requiring high genetic resolution, such as population structuring, relatedness analysis, and stock identification. 21 loci were also successfully cross-amplified in the narrow-clawed crayfish ( Astacus leptodactylus ) from which 14 were polymorphic. In addition, 13 loci (both monomorphic and polymorphic) possessed species-specific allele size range in A. astacus and A. leptodactylus and can be applied for detecting possible hybrids between these sister species. Statement of relevance The novel 19-plex microsatellite assay can be applied for genetic management of captive stocks of the noble crayfish (selection of strains, planning of matings, avoiding of inbreeding) and in studies requiring high genetic resolution, such as parentage assessment, relatedness analysis or strain identification.
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Kalakasvatus on üks osa kiiresti arenevast majandusharust – akvakultuurist e vesiviljelusest. Võrreldes loomakasvatusega on see väga uus ja mitmekesine valdkond. Rääkimata sellest, et vesiviljelus hõlmab ka veetaimede kasvatamist,... more
Kalakasvatus on üks osa kiiresti arenevast majandusharust – akvakultuurist e vesiviljelusest. Võrreldes loomakasvatusega on see väga uus ja mitmekesine valdkond. Rääkimata sellest, et vesiviljelus hõlmab ka veetaimede kasvatamist, erinevad lülijalgsete hulka kuuluvad vähid ja limuste hulka kuuluvad austrid kaladest, kes on selgroogsed, palju rohkem kui traditsioonilised loomakasvatuse objektid imetajad ja linnud. Kuigi Eestis kasvatatakse ka vähki, on kalad meie vesiviljeluses nii valdavad ja traditsioonilised, et edaspidi kasutame sõna kalakasvatus Eesti tähenduses vesiviljeluse sünonüümina. Kalakasvatus on viimase paarikümne aastaga läbi teinud uskumatult kiire arengu. Lõhe tootmine Norras ja Tšiilis, huntahvena (sea bass) ja kuld-merikogre (sea bream) tootmine Vahemeremaadel, kammelja (turbot) tootmine Hispaanias on lühikese aja jooksul mitmekordistunud. Taolist toodangu tõusu pole täheldatud üheski traditsioonilises loomakasvatuse valdkonnas. Soome kalakasvandused toodavad praeg...
Herring, Clupea harengus, is one of the ecologically and commercially most important species in European northern seas, where two distinct ecotypes have been described based on spawning time; spring and autumn. To date, it is unknown if... more
Herring, Clupea harengus, is one of the ecologically and commercially most important species in European northern seas, where two distinct ecotypes have been described based on spawning time; spring and autumn. To date, it is unknown if these spring and autumn spawning herring constitute genetically distinct units. We assessed levels of genetic divergence between spring and autumn spawning herring in the Baltic Sea using two types of DNA markers, microsatellites and Single Nucleotide Polymorphisms, and compared the results with data for autumn spawning North Sea herring. Temporally replicated analyses reveal clear genetic differences between ecotypes and hence support reproductive isolation. Loci showing non-neutral behaviour, so-called outlier loci, show convergence between autumn spawning herring from demographically disjoint populations, potentially reflecting selective processes associated with autumn spawning ecotypes. The abundance and exploitation of the two ecotypes have varied strongly over space and time in the Baltic Sea, where autumn spawners have faced strong depression for decades. The results therefore have practical implications by highlighting the need for specific management of these co-occurring ecotypes to meet requirements for sustainable exploitation and ensure optimal livelihood for coastal communities
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Õpikud2013. aastal valminud Eesti vesiviljeluse sektori arengustrateegia aastateks 2014–2020 sisuline osa keskendub muuhulgas sektori tegevuse analüüsile, tulevikuvisioonidele ja eesmärkide väljatoomisele. Koostatud dokumendis leitakse,... more
Õpikud2013. aastal valminud Eesti vesiviljeluse sektori arengustrateegia aastateks 2014–2020 sisuline osa keskendub muuhulgas sektori tegevuse analüüsile, tulevikuvisioonidele ja eesmärkide väljatoomisele. Koostatud dokumendis leitakse, et Eesti vesiviljeluse turgu, eeskätt vikerforelli müüki, mõjutab olulisel määral konkurents Põhjamaade lõhe ja vikerforelli impordi näol. Osa imporditavast kalast läheb suurema lisandväärtusega eksporti, osa jääb Eesti turule. Samuti tõdetakse, et Eesti vesiviljeluse toodete eksport on olnud suhteliselt tagasihoidlik. Peamiseks ekspordi artikliks on olnud angerjas, mida on müüdud Hollandi töötlejale. Väikestes kogustes on eksporditud ka tuurlasi ja jõevähki. Eesti tingimustes tuleks fookus seada eeskätt nende toodete arendamisele ja juurutamisele, mis otseselt ei konkureeri Põhjamaadest, peamiselt Norrast imporditava toorkalaga. Võimalusteks on näiteks mahetooted, kõrgema lisandväärtusega kalatooted, teatud tingimustel üleminek vikerforelli kasvatuselt teistele liikidele, uued liigid jne. Ekspordi kasvu peamise võimalusena nähaksegi strateegias just Eesti viljelustingimustega sobivate ja kõrge välisnõudlusega liikide nagu näiteks angerjas, jõevähk, tuurlased, siig ja täiesti uute perspektiivsete liikide viljelemist ning seda toetavat arendustööd. Strateegia töötubades osalenute hinnangul ei ole ühte, teistest selgelt eristuva potentsiaaliga liiki. Rahvusvahelise konkurentsivõime poolest hinnati enim jõevähki ja siiga, turu atraktiivsuse poolest angerjat ja tuura. Kokkuvõttena tõdeti, et otsingud perspektiivsete liikide osas on jätkumas. Võimalik, et nendeks kujunevad hoopiski seni kasvatuses vähe levinud kalad nagu näiteks ahven ja koha. Eelnenust tulenevalt tahavad raamatu „Kalakasvatus. Perspektiivsed liigid“ autorid anda omapoolse panuse strateegias välja toodud probleemide lahendamisse. Raamatu koostamisel on teinud koostööd TÜ Kalanduse teabekeskuse, EMÜ Veterinaarmeditsiini ja loomakasvatuse instituudi ning EMÜ Põllumajandus- ja keskkonnainstituudi teadlased ja õppejõud. Käesolev raamat on suunatud EMÜ vesiviljeluse ja kalanduse, rakendushüdrobioloogia ja loomaarstiõppe üliõpilastele aga samuti TTÜ EestiMereakadeemia ja Järvamaa Kutsehariduskeskuse õppureile. Autorid loodavad samuti, et raamat leiab sooja vastuvõtu alustavate või uutele väljakutsetele avatud, aga ka kogenud kalakasvatajate seas. Autorid tänavad koostöö ja avatuse eest Toomas Armulikku ja Silver Sirpi ning panuse eest kujundamisse Marje Aidi ja asjakohaste kommentaaride eest Ene Saadret. Autorite nimel Priit Päkk ja Tiit Paaver Tartus 2015 aasta vastlakuu
The wels catfish (Silurus glanis) is one of the largest freshwater fish species in the world. This top predator plays a key role in ecosystem stability, and represents an iconic trophy-fish for recreational fishermen. S. glanis is also a... more
The wels catfish (Silurus glanis) is one of the largest freshwater fish species in the world. This top predator plays a key role in ecosystem stability, and represents an iconic trophy-fish for recreational fishermen. S. glanis is also a highly valued species for its high-quality boneless flesh, and has been cultivated for over 100 years in Eastern and Central Europe. The interest in rearing S. glanis continues to grow; the aquaculture production of this species has almost doubled during the last decade. However, despite its high ecological, cultural and economic importance, the available genomic resources for S. glanis are very limited. To fulfill this gap we report a de novo assembly and annotation of the whole genome sequence of a female S. glanis. The linked-read based technology with 10X Genomics Chromium chemistry and Supernova assembler produced a highly continuous draft genome of S. glanis: ∼0.8Gb assembly (scaffold N50 = 3.2 Mb; longest individual scaffold = 13.9 Mb; BUSCO ...
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Extreme environments are inhospitable to the majority of species, but some organisms are able to survive in such hostile conditions due to evolutionary adaptations. For example, modern bony fishes have colonized various aquatic... more
Extreme environments are inhospitable to the majority of species, but some organisms are able to survive in such hostile conditions due to evolutionary adaptations. For example, modern bony fishes have colonized various aquatic environments, including perpetually dark, hypoxic, hypersaline and toxic habitats. Eurasian perch (Perca fluviatilis) is among the few fish species of northern latitudes that is able to live in very acidic humic lakes. Such lakes represent almost "nocturnal" environments; they contain high levels of dissolved organic matter, which in addition to creating a challenging visual environment, also affects a large number of other habitat parameters and biotic interactions. To reveal the genomic targets of humic-associated selection, we performed whole-genome sequencing of perch originating from 16 humic and 16 clear-water lakes in northern Europe. We identified over 800,000 SNPs, of which >10,000 were identified as potential candidates under selection (associated with >3,000 genes) using multiple outlier approaches. Our findings suggest that adaptation to the humic environment may involve hundreds of regions scattered across the genome. Putative signals of adaptation were detected in genes and gene families with diverse functions, including organism development and ion transportation. The observed excess of variants under selection in regulatory regions highlights the importance of adaptive evolution via regulatory elements, rather than via protein sequence modification. Our study demonstrates the power of whole-genome analysis to illuminate multifaceted nature of humic adaptation and provides the foundation for further investigation of causal mutations underlying phenotypic traits of ecological and evolutionary importance.
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Additional file 2: Table S1. Sampling location, year, number of samples for RNA-seq NGS, number of samples for parasite screening. Table S2. Samples, location, Illumina reads statistics and the main parasite OTUs as revealed by Kraken and... more
Additional file 2: Table S1. Sampling location, year, number of samples for RNA-seq NGS, number of samples for parasite screening. Table S2. Samples, location, Illumina reads statistics and the main parasite OTUs as revealed by Kraken and RDP. Table S3. RNA-seq mapping statistics. Table S4. List of 265 differentially expressed genes in perch identified by RNA-seq (Padj < 0.05), sorted by log2 fold change. Table S5. List of gene ontology (GO) terms with significant (FDR ≤ 0.05) enrichment among the differentially expressed genes. Table S6. Absorbance ratios, specific ultraviolet absorbance and specific colour absorbance for studied lakes.
Additional file 3: Text S1. Expanded methods description.
Phenotype data on parasite free Salmo trutta individuals from three Estonian rivers
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Phenotype and sampling information for Salmo trutta individuals from rivers Altja and Mustoja
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Individual genotype data assessed at 17 microsatellite loc
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The file 'Gen_data' consists of information used in population genetic analysis and includes: sampling site, sampling year, cohort and loci information
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Extreme environments are inhospitable to the majority of species, but some organisms are able to survive in such hostile conditions due to evolutionary adaptations. For example, modern bony fishes have colonized various aquatic... more
Extreme environments are inhospitable to the majority of species, but some organisms are able to survive in such hostile conditions due to evolutionary adaptations. For example, modern bony fishes have colonized various aquatic environments, including perpetually dark, hypoxic, hypersaline and toxic habitats. Eurasian perch (Perca fluviatilis) is among the few fish species of northern latitudes that is able to live in extremely acidic humic lakes. Such lakes represent almost “nocturnal” environments; they contain high levels of dissolved organic matter, which in addition to creating a challenging visual environment, also affects a large number of other habitat parameters and biotic interactions. To reveal the genomic targets of humic-associated selection, we performed whole-genome sequencing of perch originating from 16 humic and 16 clear-water lakes in northern Europe. We identified over 800,000 SNPs, of which >10,000 were identified as potential candidates under selection (asso...