Draft genome assembly of the freshwater apex predator wels catfish (Silurus glanis) using linked-read sequencing

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 completeness = 84.2%), which included 313.3 Mb of putative repeated sequences. In total, 21,316 protein-coding genes were predicted, of which 96% were annotated functionally from either sequence homology or protein signature searches. The highly continuous genome assembly will be an invaluable resource for aquaculture genomics, genetics, conservation, and breeding research of S. glanis

Euroopa säga (Silurus clanis) paljundamine ja kasvatamine vee korduvkasutusega süsteemis

Säga on Kesk- ja Ida-Euroopas kasvatatud peamiselt ekstensiivmeetodil koos karpkalalastega juba enam kui 100 aastat (Linhart jt. 2002). Säga kogutoodang Euroopas ja Aasias oli 2001. aastal 645 tonni ja 2020. aastaks oli see suurenenud 2403 tonnini (FAO, 2022). Samas ulatus säga sugulasliigi, Amuuri säga toodangumaht 2020. aastal Aasias 351 468 tonnini (FAO, 2022). Suurimad sägatootjad Euroopas on Ukraina, Ungari, Bulgaaria, Saksamaa ja Poola ning Aasias Usbekistan, Kasahstan ja Türgi (FAO, 2022). Enamasti kasvatatakse säga tiikides või korduva veekasutusega viljelussüsteemides (RAS). RAS süsteemis kasvatamisel võib säga saavutada 1,5 kg kehamassi juba 7-8 kuuga (Linhart jt. 2002). Liha on valge, luudeta, madala rasvasisaldusega (6-8%) ning seda on kerge kulinaarselt töödelda. Enamasti kalad suitsutatakse või fileeritakse. Säga hind Euroopa restoranides on umbes sama, mis haugil ja kohal (Linhart jt. 2002). Säga on üks suurima kasvukiirusega röövkalasid Euroopas ja tänu oma kiirele kasvule ja suurepärastele tarbimisomadustele (maitsev väheste luudega liha, kõrge lihasaagis, puuduvad soomused) ka perspektiivne uus vesiviljelusliik Eestis. Tänu soojalembusele võiks säga olla eriti sobiv just RAS-is kasvatamiseks. Eesti kalakasvatajatel on olemas mõningane kogemus naabermaadest sisse toodud noorkalade turustamissuuruseni kasvatamise osas, kuid puuduvad kogemused, teadmised ja oskused säga kunstliku paljundamise ja mitmete kasvatamistehnoloogia oluliste aspektide (sobivaim sööt ja söötmisrežiim, kasvukiirus sõltuvalt temperatuurist, optimaalne-maksimaalne asustustihedus, sobiv-piisav vee hapnikusisaldus ja muud veekvaliteedi näitajad) osas. Käesoleva käsiraamatu eesmärgiks on anda ülevaade säga paljundamisest ja kasvatamisest korduva veekasutusega viljelussüsteemis, toetudes nii kirjanduse andmetele kui Eesti Maaülikooli vesiviljeluse õppetooli teadlaste kogemustele, mis omandati Euroopa Merendus- ja Kalandusfondi rakenduskava 2014-2020 meetme 2.1 „Vesiviljeluse innovatsioonitoetus“ projekti „Säga (Silurus glanis) kui perspektiivse uue vesiviljelusliigi kunstliku paljundamise ja kasvatamise tehnoloogiate väljaarendamine ning parimate omadustega liinide väljaselgitamine“ (01.07.2017-31.12.2022) raames. Projektis osalesid EMÜ vesiviljeluse õppetooli töötajad Riho Gross (projekti juht), Härmo Hiiemäe, Heiki Jaanuska, Priit Päkk, Oksana Burimski, Lilian Pukk, Siim Kahar ja Taigor Veevo

Discovery and application of insertion-deletion (INDEL) polymorphisms for QTL mapping of early life-history traits in Atlantic salmon

<p>Abstract</p> <p>Background</p> <p>For decades, linkage mapping has been one of the most powerful and widely used approaches for elucidating the genetic architecture of phenotypic traits of medical, agricultural and evolutionary importance. However, successful mapping of Mendelian and quantitative phenotypic traits depends critically on the availability of fast and preferably high-throughput genotyping platforms. Several array-based single nucleotide polymorphism (SNP) genotyping platforms have been developed for genetic model organisms during recent years but most of these methods become prohibitively expensive for screening large numbers of individuals. Therefore, inexpensive, simple and flexible genotyping solutions that enable rapid screening of intermediate numbers of loci (~75-300) in hundreds to thousands of individuals are still needed for QTL mapping applications in a broad range of organisms.</p> <p>Results</p> <p>Here we describe the discovery of and application of insertion-deletion (INDEL) polymorphisms for cost-efficient medium throughput genotyping that enables analysis of >75 loci in a single automated sequencer electrophoresis column with standard laboratory equipment. Genotyping of INDELs requires low start-up costs, includes few standard sample handling steps and is applicable to a broad range of species for which expressed sequence tag (EST) collections are available. As a proof of principle, we generated a partial INDEL linkage map in Atlantic salmon (<it>Salmo salar</it>) and rapidly identified a number of quantitative trait loci (QTLs) affecting early life-history traits that are expected to have important fitness consequences in the natural environment.</p> <p>Conclusions</p> <p>The INDEL genotyping enabled fast coarse-mapping of chromosomal regions containing QTL, thus providing an efficient means for characterization of genetic architecture in multiple crosses and large pedigrees. This enables not only the discovery of larger number of QTLs with relatively smaller phenotypic effect but also provides a cost-effective means for evaluation of the frequency of segregating QTLs in outbred populations which is important for further understanding how genetic variation underlying phenotypic traits is maintained in the wild.</p

Outlier Loci Detect Intraspecific Biodiversity amongst Spring and Autumn Spawning Herring across Local Scales

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 communitie

Wild Estonian and Russian sea trout (Salmo trutta) in Finnish coastal sea trout catches : results of genetic mixed-stock analysis

Peer reviewe

Meritaimen- ja lohikantojen tila ja elvyttäminen kolmessa itäisen Suomenlahden jokivesistössä

Sout-East Finland - Russia ENPI CBC 2007-2012 Contact person: Nina PeuhkuriWe investigated by electrofishing the state of sea trout population and also the fish assemblage as a whole in two Finnish–Russian cross-border river systems, Mustajoki/Tchornaja/Soskuanjoki/Malinovka and Hounijoki/Buslovka/Rakkolanjoki/Seleznevka, draining into the Gulf of Finland. Based on the fish assemblage, we assessed the ecological status of the rivers. In the third of our target river systems, Gladyshevka/Rotshinka in the Karelian Isthmus, our interest was particularly focused on the Atlantic salmon population. In Mustajoki/Tchornaja/Soskuanjoki/Malinovka, trout dominated in density the upper reaches and small tributaries, their densities decreasing towards the river mouth. Restoration of rapids led to increased trout densities, but benign weather conditions may partly explain the trend. The trout population in this river system was found to be genetically unique and diverse. In Hounijoki/Buslovka/Rakkolanjoki/Seleznevka, only a few trout were found − from the Russian side. The absence of trout, especially from the upper reaches, is due to migration obstacles but also probably to poorer water quality compared to Mustajoki/Tchornaja/Soskuanjoki/Malinovka. This was also reflected in the poorer ecological status. In Gladyshevka/Rotshinka, both salmon and trout were caught from the River Gladyshevka, but neither of these from the River Rotshinka. The densities of salmon in the River Gladyshevka partly reflect the releases of hatchery fish. We established a broodstock of the Mustajoki/Tchornaja/Soskuanjoki/Malinovka trout to enhance restoration of this native sea trout population still found on both the Finnish and Russian sides of the cross-border riversdraining into the Gulf of Finland. We also transferred wild-caught trout to the River Soskuanjoki on the Finnish side and upper reaches of the River Malinovka on the Russian side to promote the existence of the population in the whole river system in the wild. Later observations of trout from the Finnish side suggested that trout accepted the area. We also analysed in which proportions trout from different native or hatchery populations around the Gulf of Finland are represented in the Finnish coastal sea trout catch. Genetic analyses indicated that at least 75% of the catch originated from Finnish hatchery releases, and at least 20% of the catch consisted of wild trout, mostly from Estonia. Trout from the cross-border rivers represented only about 1% of the total catch. Scale analysis of a sample of captured trout indicated that individuals were caught young and often undersized. The salmon releases into the River Gladyshevka started over a decade ago were continued during the project. Salmon were also released into the River Rakkolanjoki. A sample of released salmon was additionally tagged with T-bar anchor tags prior to release to gain information on their migration based on tag recoveries. Seven tags have so far been recovered.; Selvitimme sähkökoekalastuksin meritaimenkantojen tilaa sekä kalastoa kahdessa Suomen ja Venäjän rajajokivesistössä, Mustajoki/Tchornaja/Soskuanjoki/Malinovka ja Hounijoki/Buslovka/Rakkolanjoki/Seleznevka, jotka laskevat Viipurinlahteen itäisellä Suomenlahdella. Arvioimme kalastoon perustuen jokivesistöjen ekologisen tilan. Kolmas hankkeen kohdevesistö, jossa mielenkiintomme kohteena oli erityisesti merilohi, oli Karjalan kannaksella sijaitseva Gladyshevka/Rotshinka, joka on tärkeä merilohen palauttamiskohde itäisellä Suomenlahdella Venäjän puolella. Taimenen poikastiheydet ylittivät Mustajoki/Tchornaja/Soskuanjoki/Malinovka -jokivesistössä muiden kalalajien tiheydet erityisesti latvavesissä sekä sivu-uomissa. Taimentiheydet laskivat jokisuulle mentäessä. Taimenen poikastiheydet kasvoivat tutkimuksen aikana kunnostetuilla koskilla. Osittain kasvu voi selittyä taimenen lisääntymiselle ja poikasille suotuisilla sääolosuhteilla. Mustajoki/Tchornaja/Soskuanjoki/Malinovka -jokivesistön taimenkanta osoittautui perinnöllisesti ainutlaatuiseksi ja monimuotoiseksi. Hounijoki/Buslovka/Rakkolanjoki/Seleznevka -jokivesistöstä löytyi vai jokunen taimen Venäjän puolelta. Taimenen puuttuminen erityisesti jokivesistön yläosista selittyy nousuesteillä, mutta osittain myös veden Mustajoki/Tchornaja/Soskuanjoki/Malinovka -jokivesistöä heikommalla laadulla. Tätä heijasti myös havaittu huonompi ekologinen tila. Gladyshevka/Rotshinka -jokivesistöstä saatiin sekä lohta että taimenta Gladyshevka-joesta, mutta Rotshinka-joesta ei lajeista kumpaakaan. Glahyshevka-joessa havaitut lohitiheydet selittyvät osittain jokeen tehdyillä lohi-istutuksilla. Mustajoki/Tchornaja/Soskuanjoki/Malinovka -jokivesistön taimenesta perustettiin viljelyyn emokalasto tämän ainoan Suomen ja Venäjän puolelta Viipurinlahteen laskevista rajajoista tavatun alkuperäisen meritaimenkannan säilyttämiseksi ja suojelemiseksi. Villejä taimenia siirrettiin myös Soskuanjokeen ja Malinovka-joen yläosiin taimenkannan olemassaolon turvaamiseksi koko jokivesistön alueella. Soskuanjoesta myöhemmin tehtyjen havaintojen perusteella taimenet hyväksyivät siirtoalueen. Selvitimme myös, miten luonnontaimenkannat ja laitoskannat ovat edustettuina Suomen rannikon taimensaaliissa. Geneettiset analyysit osoittivat, että vähintään 75 % saaliista on peräisin laitoskannoista. Ainakin viidennes saaliista oli peräisin luonnonkannoista, enimmäkseen Viron puolelta. Rajajokiemme taimenten todettiin muodostavan taimenen kokonaissaaliista vain n. 1 %. Suomuanalyysit osoittivat taimenten jäävän saaliiksi nuorina ja usein alamittaisina. Yli vuosikymmen sitten aloitettua istutuksin toteutettua merilohen elvytysprojektia Gladyshevka-joella jatkettiin tässä hankkeessa. Merilohta istutettiin myös Rakkolanjokeen. Istukkaita myös merkittiin t-ankkurimerkein ennen vapautusta vaellustietojen kartuttamiseksi. Palautustiedot on saatu tähän mennessä seitsemästä merkistä.This project is co­funded by the European Union, the Russian Federation and the Republic of Finlan

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

Draft Genome Assembly of the Freshwater Apex Predator Wels Catfish (Silurus glanis) Using Linked-Read Sequencing

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 completeness = 84.2%), which included 313.3 Mb of putative repeated sequences. In total, 21,316 protein-coding genes were predicted, of which 96% were annotated functionally from either sequence homology or protein signature searches. The highly continuous genome assembly will be an invaluable resource for aquaculture genomics, genetics, conservation, and breeding research of S. glanis.</p

Spatial and intra-host distribution of myxozoan parasite Tetracapsuloides bryosalmonae among Baltic sea trout (Salmo trutta)

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

Whole-genome sequencing illuminates multifaceted targets of selection to humic substances in Eurasian perch

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 single nucleotide polymorphisms, of which >10,000 were identified as potential candidates under selection (associated with >3000 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 the multifaceted nature of humic adaptation and provides the foundation for further investigation of causal mutations underlying phenotypic traits of ecological and evolutionary importance