The strength and form of natural selection on transcript abundance in the wild

Gene transcription variation is known to contribute to disease susceptibility and adaptation, but we currently know very little about how contemporary natural selection shapes transcript abundance. Here, we propose a novel analytical framework to quantify the strength and form of ongoing natural selection at the transcriptome level in a wild vertebrate. We estimated selection on transcript abundance in a cohort of a wild salmonid fish (Salmo trutta) affected by an extracellular myxozoan parasite (Tetracapsuloides bryosalmonae) through mark-recapture field sampling and the integration of RNA-sequencing with classical regression-based selection analysis. We show, based on fin transcriptomes of the host, that infection by the parasite and subsequent host survival is linked to upregulation of mitotic cell cycle process. We also detect a widespread signal of disruptive selection on transcripts linked to host immune defence, host-pathogen interactions, cellular repair and maintenance. Our results provide insights into how selection can be measured at the transcriptome level to dissect the molecular mechanisms of contemporary evolution driven by climate change and emerging anthropogenic threats. We anticipate that the approach described here will enable critical information on the molecular processes and targets of natural selection to be obtained in real time

Know your enemy - Transcriptome of myxozoan Tetracapsuloides bryosalmonae reveals potential drug targets against proliferative kidney disease in salmonids

The myxozoan Tetracapsuloides bryosalmonae is a widely spread endoparasite that causes proliferative kidney disease (PKD) in salmonid fish. We developed an in silico pipeline to separate transcripts of T. bryosalmonae from the kidney tissue of its natural vertebrate host, brown trout (Salmo trutta). After stringent filtering, we constructed a partial transcriptome assembly T. bryosalmonae, comprising 3427 transcripts. Based on homology-restricted searches of the assembled parasite transcriptome and Atlantic salmon (Salmo salar) proteome, we identified four protein targets (Endoglycoceramidase, Legumain-like protease, Carbonic anhydrase 2, Pancreatic lipase-related protein 2) for the development of anti-parasitic drugs against T. bryosalmonae. Earlier work of these proteins on parasitic protists and helminths suggests that the identified anti-parasitic drug targets represent promising chemotherapeutic candidates also against T. bryosalmonae, and strengthen the view that the known inhibitors can be effective in evolutionarily distant organisms. In addition, we identified differentially expressed T. bryosalmonae genes between moderately and severely infected fish, indicating an increased abundance of T. bryosalmonae sporogonic stages in fish with low parasite load. In conclusion, this study paves the way for future genomic research in T. bryosalmonae and represents an important step towards the development of effective drugs against PKD.</p

Highly Continuous Genome Assembly of Eurasian Perch (Perca fluviatilis) Using Linked-Read Sequencing

The Eurasian perch (Perca fluviatilis) is the most common fish of the Percidae family and is widely distributed across Eurasia. Perch is a popular target for professional and recreational fisheries, and a promising freshwater aquaculture species in Europe. However, despite its high ecological, economical and societal importance, the available genomic resources for P. fluviatilis are rather limited. In this work, we report de novo assembly and annotation of the whole genome sequence of perch. The linked-read based technology with 10X Genomics Chromium chemistry and Supernova assembler produced a draft perch genome approximate to 1.0 Gbp assembly (scaffold N-50 = 6.3 Mb; the longest individual scaffold of 29.3 Mb; BUSCO completeness of 88.0%), which included 281.6 Mb of putative repeated sequences. The perch genome assembly presented here, generated from small amount of starting material (0.75 ng) and a single linked-read library, is highly continuous and considerably more complete than the currently available draft of P. fluviatilis genome. A total of 23,397 protein-coding genes were predicted, 23,171 (99%) of which were annotated functionally from either sequence homology or protein signature searches. Linked-read technology enables fast, accurate and cost-effective de novo assembly of large non-model eukaryote genomes. The highly continuous assembly of the Eurasian perch genome presented in this study will be an invaluable resource for a range of genetic, ecological, physiological, ecotoxicological, functional and comparative genomic studies in perch and other fish species of the Percidae family

The strength and form of natural selection on transcript abundance in the wild

Gene transcription variation is known to contribute to disease susceptibility and adaptation, but we currently know very little about how contemporary natural selection shapes transcript abundance. Here, we propose a novel analytical framework to quantify the strength and form of ongoing natural selection at the transcriptome level in a wild vertebrate. We estimated selection on transcript abundance in a cohort of a wild salmonid fish (Salmo trutta) affected by an extracellular myxozoan parasite (Tetracapsuloides bryosalmonae) through mark-recapture field sampling and the integration of RNA-sequencing with classical regression-based selection analysis. We show, based on fin transcriptomes of the host, that infection by the parasite and subsequent host survival is linked to upregulation of mitotic cell cycle process. We also detect a widespread signal of disruptive selection on transcripts linked to host immune defence, host-pathogen interactions, cellular repair and maintenance. Our results provide insights into how selection can be measured at the transcriptome level to dissect the molecular mechanisms of contemporary evolution driven by climate change and emerging anthropogenic threats. We anticipate that the approach described here will enable critical information on the molecular processes and targets of natural selection to be obtained in real time

Ahvena (Perca fluviatilis L.) molekulaargeneetiliste näitajate ja elukäiguomaduste analüüs

A Thesis for applying for the degree of Doctor of Philosophy in Agricultural SciencesFishes provide food and livelihood for hundreds of millions of people around the world and currently fish consumption is higher than ever before. As a consequence, the threats of over-exploitation, illegal fishing and fish trade are very high. Because biologically insensible management actions or lack of necessary regulations may lead to population collapse, better understanding of genetic population structure and fisheries-induced changes in life-history traits is essential for conservation of local fish populations. Thus, the main goals of this thesis were to generate novel genomic resources, characterize population genetic structure, and study the consequences of overfishing of Eurasian perch populations and its potential causes to various life-history traits in Estonia. The over-exploitation of Eurasian perch population had strong influence on size- and age-distribution, juvenile growth rate and age of sexual maturation in males. Development of novel low-cost genome complexity reduction protocol enabled to identify large number of single nucleotide polymorphisms and microsatellite markers. Based on observed genetic structuring between two commercially most important perch fishery locations in Estonia (Väinameri Sea region and Lake Peipus), new microsatellite markers successfully revealed the genetic origin of perch, which can be used to fight against illegal fishing and fish trade. The population genetic framework described within this thesis represents a small but important milestone towards developing biologically sound conservation and management strategies for Eurasian perch.Erinevad kalaliigid moodustavad suure osa sadade miljonite inimeste toidu- ja elatusallikast üle maailma ning selle tulemusena on paljud liigid tugevalt ülepüütud. Kalavarude kaitse ja säästliku kasutamise eelduseks on täpne teave liigi populatsioonide geneetilise muutlikkuse ja struktuuri ning kalapüügist põhjustatud elukäiguomaduste muutuste kohta. Neid aspekte arvestamata on väga keeruline kaitsemeetmeid rakendada. Sellest tulenevalt oli doktoritöö põhieesmärgiks uurida ülepüügi ja populatsiooni taastumise mõju populatsioonigeneetilistele näitajatele ja elukäiguomadustele ning välja selgitada ahvenapopulatsioonide geneetiline struktuur Eestis. Lisaeesmärgiks oli ahvena jaoks välja töötada uudseid molekulaarseid markereid (mikrosatelliidid, ühenukleotiidsed polümorfismid), mida saaks rakendada geneetilise populatsioonistruktuuri detailsemaks väljaselgitamiseks ja illegaalse püügi kahtlusega ahvenate päritolu määramiseks. Tulemustest selgus, et ülepüük mõjutas oluliselt ahvenate vanuselist struktuuri, suurust ja noorkalade kasvukiirust ning põhjustas isaste kalade varasema suguküpsuse saabumise. Uue põlvkonna sekveneerimise meetodeid kasutades oli võimalik kiirelt ja odavalt saada uut geneetilist informatsiooni, mida saab tulevikus kasutada usaldusväärseks populatsioonigeneetika näitajate hindamiseks ning illegaalse püügi kahtlusega kalade päritolu määramiseks. See võimaldab tõhusamalt võidelda illegaalse kalapüügi ja kaubandusega. Samuti saadi uut informatsiooni Eesti ahvenapopulatsioonide geneetilise struktuuri kohta nii mage- kui riimvee tingimustes. Doktoritöös kirjeldatud populatsioonigeneetiline teave ahvena kohta on oluline eeldus bioloogiliselt põhjendatud kaitsestrateegiate ning populatsioonide jätkusuutliku majandamise kavade väljatöötamiseks Eestis.The publication of this dissertation is granted by Estonian University of Life Sciences

Distribution of Non-Indigenous Crayfish Species in Estonia and Their Impacts on Noble Crayfish (<i>Astacus astacus</i> L.) Populations

Invasive non-indigenous crayfish species (NICS) are a major threat to the existence of native crayfish populations in European freshwater ecosystems. The discovery of signal crayfish Pacifastacus leniusculus, marbled crayfish Procambarus virginalis, and spiny-cheek crayfish Faxonius limosus in Estonia has increased the risk of extinction of Estonia’s only native crayfish species, the noble crayfish Astacus astacus. The aim of this study was to give an overview of the status, distribution, and impacts of P. leniusculus, F. limosus, and Procambarus virginalis on A. astacus populations and assess the effect of trapping on NICS abundance. Annual monitoring of crayfish has been carried out since 2008 as part of A. astacus conservation and the NICS eradication plan. In this study, we present data from nine sampling locations monitored from 2010 to 2022. The spread of NICS continues to increase beyond their distribution areas, and in two sampling locations P. leniusculus and A. astacus live in sympatry. Our results suggest that trapping has a limited effect on population abundance, as NICS have already caused the extinction of two A. astacus populations. However, intensive trapping should continue simultaneously with sensitive molecular techniques to monitor the spread of NICS

Data from: Genetic and life-history changes associated with fisheries-induced population collapse

Over the recent years, growing number of studies suggests that intensive size-selective fishing can cause evolutionary changes in life-history traits in the harvested population, which can have drastic negative effects on populations, ecosystems and fisheries. However, most studies to date have overlooked the potential role of immigration of fish with different phenotypes as an alternative plausible mechanism behind observed phenotypic trends. Here, we investigated the evolutionary consequences of intensive fishing simultaneously at phenotypic and molecular level in Eurasian perch (Perca fluviatilis L.) population in the Baltic Sea over a 24-year period. We detected marked changes in size- and age-distributions and increase in juvenile growth rate. We also observed reduction of age at sexual maturity in males that has frequently been considered to support the hypothesis of fisheries-induced evolution. However, combined individual-based life-history and genetic analyses indicated increased immigration of foreign individuals with different life-history patterns as an alternative mechanism behind the observed phenotypic change. This study demonstrates the value of combining genetic and phenotypic analyses and suggests that replacement or breakdown of locally adapted gene complexes may play important role in impeding the recovery of fish populations

Gen_data

The file 'Gen_data' consists of information used in population genetic analysis and includes: sampling site, sampling year, cohort and loci information

Mappe e disegni riguardanti Corfù nella Biblioteca del Museo Correr

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

SNP primer sequences

List of 12 markers that were individually validated using seven individuals by PCR and Sanger sequencing