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.

Authoritative subspecies diagnosis tool for European honey bees based on ancestry informative 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 FST) 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.

Connectivity and population structure of albacore tuna across southeast Atlantic and southwest Indian Oceans inferred from multidisciplinary methodology.

Albacore tuna (Thunnus alalunga) is an important target of tuna fisheries in the Atlantic and Indian Oceans. The commercial catch of albacore is the highest globally among all temperate tuna species, contributing around 6% in weight to global tuna catches over the last decade. The accurate assessment and management of this heavily exploited resource requires a robust understanding of the species' biology and of the pattern of connectivity among oceanic regions, yet Indian Ocean albacore population dynamics remain poorly understood and its level of connectivity with the Atlantic Ocean population is uncertain. We analysed morphometrics and genetics of albacore (n = 1,874) in the southwest Indian (SWIO) and southeast Atlantic (SEAO) Oceans to investigate the connectivity and population structure. Furthermore, we examined the species' dispersal potential by modelling particle drift through major oceanographic features. Males appear larger than females, except in South African waters, yet the length-weight relationship only showed significant male-female difference in one region (east of Madagascar and Reunion waters). The present study produced a genetic differentiation between the southeast Atlantic and southwest Indian Oceans, supporting their demographic independence. The particle drift models suggested dispersal potential of early life stages from SWIO to SEAO and adult or sub-adult migration from SEAO to SWIO.

Genetic structure of Iranian indigenous sheep breeds: insights for conservation.

Genetic structure and genetic diversity levels of indigenous Iranian sheep breeds are not clear, despite the interest this region has in itself as an important center for domestication of livestock. Early population genetic studies have reported high levels of diversity among Iranian sheep breeds until recently, when high admixture levels and genetic homogeneity have been detected. The rapid reduction of diversity observed in Iranian breeds might be due to an increasing trend of intensive crossbreeding practices or even total replacement of native breeds by highly specialized and productive ones. From a conservative perspective, this situation is highly concerning; thus, it might be wise to consider a conservation program in Iran to preserve the original genetic diversity in native sheep breeds. In this study, a total of 1065 animals with the purest morphological features representing 24 Iranian indigenous sheep breeds were sampled, corresponding to ancestral breed diversity. These samples were genotyped for 17 microsatellite loci in order to (1) determine the native ancestral diversity of Iranian breeds, (2) define the degree of genetic relationship among studied breeds, and (3) assess conservation priorities among defined groups. Our results showed no recent loss of diversity, but high genetic diversity levels for indigenous sheep breeds in Iran. Indeed, the analysis of conservation priorities pointed out the importance of 8 breeds for maintaining Iranian sheep breeds' maximum genetic diversity. Thus, under a genetic perspective, these 8 breeds should be the ones included into conservation programs for restocking endangered areas.

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 (FST = 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.

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.

Insights on the drivers of genetic divergence in the European anchovy.

Anchovies represent the largest world's marine fish catches and the current threats on their populations impose a sustainable exploitment based on sound scientific information. In the European anchovy (Engraulis encrasicolus), the existence of several populations has been proposed but a global view is missing. Using a multidisciplinary approach, here we assessed the divergence among different ecotypes and its possible causes. SNPs have revealed two functionally distinct ecotypes overlapping in the Central Mediterranean, with one ecotype confined near the river estuaries. The same SNPs outliers also segregated two distinct populations in the near Atlantic, despite their large spatial distance. In addition, while most studies suggested that adaptation to low salinity is key to divergence, here we show that the offshore ecotype has higher environmental tolerance and an opportunistic feeding behaviour, as assessed by the study of environmental conditions, anchovy diet and trophic levels, and passive egg dispersal. These results provide insights into the anchovy evolutionary history, stressing the importance of behaviour in shaping ecotypes.

Reduced Single Nucleotide Polymorphism Panels for Assigning Atlantic Albacore and Bay of Biscay Anchovy Individuals to Their Geographic Origin: Toward Sustainable Fishery Management.

There is an increasing trend upon adding a detailed description of the origin of seafood products driven by a general interest in the implementation of sustainable fishery management plans for the conservation of marine ecosystems. North Atlantic albacore ("Bonito del Norte con Eusko Label") and Bay of Biscay anchovy ("Anchoa del Cantábrico") are two commercially important fish populations with high economical value and vulnerable to commercial fraud. This fact, together with the overexploited situation of these two populations, makes it necessary to develop a tool to identify individual origin and to detect commercial fraud. In the present study, we have developed and validated a traceability tool consisting of reduced panels of gene-associated single nucleotide polymorphisms (SNPs) suitable for assigning individuals of two species to their origin with unprecedented accuracy levels. Only 48 SNPs are necessary to assign 81.1% albacore and 93.4% anchovy individuals with 100% accuracy to their geographic origin. The total accuracy of the results demonstrates how gene-associated SNPs can revolutionize food traceability. Gene-associated SNP panels are not of mere commercial interest, but they also can result in a positive impact on sustainability of marine ecosystems through conservation of fish populations through establishing a more effective and sustainable fishery management framework and contributing to the prevention of falsified labeling.

New Nuclear SNP Markers Unravel the Genetic Structure and Effective Population Size of Albacore Tuna (Thunnus alalunga).

In the present study we have investigated the population genetic structure of albacore (Thunnus alalunga, Bonnaterre 1788) and assessed the loss of genetic diversity, likely due to overfishing, of albacore population in the North Atlantic Ocean. For this purpose, 1,331 individuals from 26 worldwide locations were analyzed by genotyping 75 novel nuclear SNPs. Our results indicated the existence of four genetically homogeneous populations delimited within the Mediterranean Sea, the Atlantic Ocean, the Indian Ocean and the Pacific Ocean. Current definition of stocks allows the sustainable management of albacore since no stock includes more than one genetic entity. In addition, short- and long-term effective population sizes were estimated for the North Atlantic Ocean albacore population, and results showed no historical decline for this population. Therefore, the genetic diversity and, consequently, the adaptive potential of this population have not been significantly affected by overfishing.

SNP discovery in European anchovy (Engraulis encrasicolus, L) by high-throughput transcriptome and genome sequencing.

Increased throughput in sequencing technologies has facilitated the acquisition of detailed genomic information in non-model species. The focus of this research was to discover and validate SNPs derived from the European anchovy (Engraulis encrasicolus) transcriptome, a species with no available reference genome, using next generation sequencing technologies. A cDNA library was constructed from four tissues of ten fish individuals corresponding to three populations of E. encrasicolus, and Roche 454 GS FLX Titanium sequencing yielded 19,367 contigs. Additionally, the European anchovy genome was sequenced for the same ten individuals using an Illumina HiSeq2000. Using a computational pipeline for combining transcriptome and genome information, a total of 18,994 SNPs met the necessary minor allele frequency and depth filters. A series of further stringent filters were applied to identify those SNPs likely to succeed in genotyping assays, and for filtering of those in potential duplicated genome regions. A novel method for detecting potential intron-exon boundaries in areas of putative SNPs has also been applied in silico to improve genotyping success. In all, 2,317 filtered putative transcriptome SNPs suitable for genotyping primer design were identified. From those, a subset of 530 were selected, with the genotyping results showing the highest reported conversion and validation rates (91.3% and 83.2%, respectively) reported to date for a non-model species. This study represents a promising strategy to discover genotypable SNPs in the exome of non-model organisms. The genomic resource generated for E. encrasicolus, both in terms of sequences and novel markers, will be informative for research into this species with applications including traceability studies, population genetic analyses and aquaculture.