New SNP markers in european anchovy and albacore: useful genetic tools for stock delimitation

Peer Reviewe

Transcriptomic dataset for Sardina pilchardus: Assembly, annotation, and expression of nine tissues.

[EN]European sardine or pilchard is a planktonic small pelagic fish present from the North Sea in Europe to the coast of Senegal in the North of Africa, and across the Mediterranean sea to the Black Sea. Ecologically, sardines are an intermediary link in the trophic network, preying on plankton and being predated by larger fishes, marine mammals, and seabirds. This species is of great nutritional and economic value as a cheap but rich source of protein and fat. It is either consumed directly by humans or fed as fishmeal for aquaculture and farm animals. Despite its importance in the food basket, little is known about the molecular mechanisms involved in protein and lipid synthesis in this species. We collected nine tissues of Sardina pilchardus and reconstructed the transcriptome. In all, 198,597 transcripts were obtained, from which 68,031 are protein-coding. Quality assessment of the transcriptome was performed by back-mapping reads to the transcriptome and by searching for Single Copy Orthologs. Additionally, Gene Ontology and KEGG annotations were retrieved for most of the protein-coding genes. Finally, each library was quantified in terms of Transcripts per Million to disclose their expression patterns.We gratefully acknowledge funding from the Basque Government through a predoctoral grant (PRE_2017_2_0169) and from the Basque University System research group IT1233-19, “Applied Genomics and Bioinformatics”. We also acknowledge funding from the IFREMER institute and by FFP (France Filière Pêche) through the project CAPTAIN

A Novel Transcriptome-Derived SNPs Array for Tench (Tinca Tinca L.)

Tench (Tinca tinca L.) has great economic potential due to its high rate of fecundity and long-life span. Population genetic studies based on allozymes, microsatellites, PCR-RFLP and sequence analysis of genes and DNA fragments have revealed the presence of Eastern and Western phylogroups. However, the lack of genomic resources for this species has complicated the development of genetic markers. In this study, the tench transcriptome and genome were sequenced by high-throughput sequencing. A total of 60,414 putative SNPs were identified in the tench transcriptome using a computational pipeline. A set of 96 SNPs was selected for validation and a total of 92 SNPs was validated, resulting in the highest conversion and validation rate for a non-model species obtained to date (95.83%). The validated SNPs were used to genotype 140 individuals belonging to two tench breeds (Tabor and Hungarian), showing low (F-ST = 0.0450) but significant (<0.0001) genetic differentiation between the two tench breeds. This implies that set of validated SNPs array can be used to distinguish the tench breeds and that it might be useful for studying a range of associations between DNA sequence and traits of importance. These genomic resources created for the tench will provide insight into population genetics, conservation fish stock management, and aquaculture.This research was supported by projects CENAKVA and Reproductive and genetic approaches for fish biodiversity conservation and aquaculture (CZ02.1.01/0.0/0.0/16_025/0007370) funded by Ministry of Education, Youth and Sports of the Czech Republic, and by the Genomic Resources Research Group from the Basque University System (IT558-10) funded by the Department of Education, Universities and Research of the Basque Government. JL is supported by the pre-doctoral program Education Department of the Basque Government. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Hygroregulation, a key ability for eusocial insects: Native Western European honeybees as a case study

Sociality has brought many advantages to various hymenoptera species, including their ability of regulating physical factors in their nest (e.g., temperature). Although less studied, humidity is known to be important for egg, larval and pupal development, and also for nectar concentration. Two subspecies of Apis mellifera of the M evolutionary lineage were used as models to test the ability of a superorganism (i.e. honeybee colony) to regulate the humidity in its nest (i.e. “hygroregulation hypothesis”) in four conservation centers: two in France (A. m. mellifera) and two in Portugal (A. m. iberiensis). We investigated the ability of both subspecies to regulate the humidity in hives daily, but also during the seasons for one complete year. Our data and statistical analysis demonstrated the capacity of the bees to regulate humidity in their hive, regardless of the day, season or subspecies. Furthermore, the study showed that humidity in beehives is stable even during winter, when brood is absent, and when temperature is known to be less stable in the beehives. These results suggest that humidity is important for honeybees at every life stage, maybe because of the ‘imprint’ of the evolutionary history of this hymenopteran lineage.This work was supported in part by the research project BEEHOPE funded by the European call for projects 2013-2014 BiodivERsA / FACCEJPI from research agencies of France (ANR-14- EBID-0001), Spain (PCIN-2014-090) and Portugal (BiodivERsA /0002/2014). I. Eouzan is financed by a doctoral grant from the Ministry of National Education, Higher Education and Research (France).info:eu-repo/semantics/publishedVersio

BEEHOPE: um projeto de conservação das subespécies nativas de abelha da Europa Ocidental (linhagem M) à escala Europeia

O projeto BEEHOPE, com o título original “Honeybee conservation centres in western Europe - an innovative strategy using sustainable beekeeping to reduce honeybee decline”, foi um dos 10 aprovados na área da biodiversidade do 5º concurso transnacional (2013-2014) BiodivErsA/FACCE-JPI (http://www.biodiversa.org/766), subordinado ao tema “Promover sinergias e reduzir o compromisso entre o abastecimento de alimentos, biodiversidade e serviços dos ecossistemas”. A diversidade nativa das populações de abelha melífera (Apis mellifera) da linhagem da Europa ocidental (M) tem vindo a ser crescentemente ameaçada pela introdução massiva de colónias da linhagem da Europa oriental (C, onde se incluem as subespécies A. m. ligustica, A. m. carnica, A. m. macedónica etc.), e também por outros fatores bióticos (Varroa e vírus associados, Nosema etc.) e abióticos (pesticidas, perda e fragmentação de habitat, alterações climáticas etc.). É neste contexto que surge o projeto BEEHOPE, o qual tem por objetivo último contribuir para a conservação da diversidade genética das populações de abelha melífera da linhagem M.info:eu-repo/semantics/publishedVersio

Authoritative subspecies diagnosis tool for European honey bees based on ancestryinformative SNPs

Background With numerous endemic subspecies representing four of its five evolutionary lineages, Europe holds a large fraction of Apis mellifera genetic diversity. This diversity and the natural distribution range have been altered by anthropogenic factors. The conservation of this natural heritage relies on the availability of accurate tools for subspecies diagnosis. Based on pool-sequence data from 2145 worker bees representing 22 populations sampled across Europe, we employed two highly discriminative approaches (PCA and F-ST) to select the most informative SNPs for ancestry inference. Results Using a supervised machine learning (ML) approach and a set of 3896 genotyped individuals, we could show that the 4094 selected single nucleotide polymorphisms (SNPs) provide an accurate prediction of ancestry inference in European honey bees. The best ML model was Linear Support Vector Classifier (Linear SVC) which correctly assigned most individuals to one of the 14 subspecies or different genetic origins with a mean accuracy of 96.2% +/- 0.8 SD. A total of 3.8% of test individuals were misclassified, most probably due to limited differentiation between the subspecies caused by close geographical proximity, or human interference of genetic integrity of reference subspecies, or a combination thereof. Conclusions The diagnostic tool presented here will contribute to a sustainable conservation and support breeding activities in order to preserve the genetic heritage of European honey bees.The SmartBees project was funded by the European Commission under its FP7 KBBE programme (2013.1.3-02, SmartBees Grant Agreement number 613960) https://ec.europa.eu/research/fp7.MP was supported by a Basque Government grant (IT1233-19). The funders provided the financial support to the research, but had no role in the design of the study, analysis, interpretations of data and in writing the manuscript

New SNP markers in european anchovy and albacore: useful genetic tools for stock delimitation

Peer Reviewe

New SNP markers in european anchovy and albacore: useful genetic tools for stock delimitation

Peer Reviewe

Genetic population structure of anchovy (Engraulis encrasicolus) in North-western Europe and variability in the seasonal distribution of the stocks

A prerequisite in fisheries management is to identify biological meaningful delineations of stocks, the fundamental exploited units. The European anchovy is one such species in need to better identify stock boundaries. Indeed, despite a spawning aggregation behaviour both in the southern Bay of Biscay and southern North Sea in spring and summer, it has a seemingly continuous distribution in autumn across a broad region ranging from the Bay of Biscay to the northern North Sea including the English Channel, thus with potential mixing of the spawning units. We therefore used genetic markers (single nucleotide polymorphisms) to quantify the degree of gene flow between the currently managed fish stock of the bay of Biscay and northern areas of European anchovy’s distribution. Our results confirm the clear distinction between the Bay of Biscay and northernmost populations, with assignment of all English Channel samples to the latter. We also found a clear overall pattern of isolation by distance that resulted primarily from an increasing differentiation with geographic distance in the Northern group magnified by the lack of gene flow with the anchovies of the Bay of Biscay. The small reduction in gene diversity towards northern latitudes may indicate partial isolation of the leading-edge component of the Northern population. Quotient plots relating anchovy’s distribution to environmental covariates showed that anchovies sampled in autumn in the English Channel originate from the summer spawning aggregation in the warm, low saline and plankton rich south-eastern North Sea. This change in the seasonal distribution of the northern population mimics, but in opposite direction, the one of the Bay of Biscay where anchovy spread towards the north from the spawning habitat in the south-eastern bay. The encounter, without mixing, of the two populations west of Brittany in autumn suggests strong spawning site fidelity. Finally, we identified for the first time anchovies belonging to the estuarine ecotype in the Loire estuary. Our results therefore support current management units, yet with some uncertainties for the catches in the transition zones between the Bay of Biscay and the English Channel, and within river plumes in the vicinity of estuaries hosting the estuarine ecotype

Transcriptomic dataset for Sardina pilchardus: Assembly, annotation, and expression of nine tissues

European sardine or pilchard is a planktonic small pelagic fish present from the North Sea in Europe to the coast of Senegal in the North of Africa, and across the Mediterranean sea to the Black Sea. Ecologically, sardines are an intermediary link in the trophic network, preying on plankton and being predated by larger fishes, marine mammals, and seabirds. This species is of great nutritional and economic value as a cheap but rich source of protein and fat. It is either consumed directly by humans or fed as fishmeal for aquaculture and farm animals. Despite its importance in the food basket, little is known about the molecular mechanisms involved in protein and lipid synthesis in this species. We collected nine tissues of Sardina pilchardus and reconstructed the transcriptome. In all, 198,597 transcripts were obtained, from which 68,031 are protein-coding. Quality assessment of the transcriptome was performed by back-mapping reads to the transcriptome and by searching for Single Copy Orthologs. Additionally, Gene Ontology and KEGG annotations were retrieved for most of the protein-coding genes. Finally, each library was quantified in terms of Transcripts per Million to disclose their expression patterns