Discovering the means to control the increasing dissemination of pathogenic vibrios driven by recent climate change is challenged by the limited knowledge of the mechanisms in charge of Vibrio spp. persistence and spread in the time of global warming. To learn about physiological and gene expression patterns associated with the long-term persistence of V. harveyi at elevated temperatures, we studied adaptation of this marine bacterium in seawater microcosms at 30 °C which closely mimicked the upper limit of sea surface temperatures around the globe. We found that nearly 90% of cells lost their culturability and became partly damaged after two weeks, thus suggesting a negative impact of the combined action of elevated temperature and shortage of carbon on V. harveyi survival. Moreover, further gene expression analysis revealed that major adaptive mechanisms were poorly coordinated and apparently could not sustain cell fitness. On the other hand, elevated temperature and starvation promoted expression of many virulence genes, thus potentially reinforcing the pathogenicity of this organism. These findings suggest that the increase in disease outbreaks caused by V. harveyi under rising sea surface temperatures may not reflect higher cell fitness, but rather an increase in virulence enabling V. harveyi to escape from adverse environments to nutrient rich, host-pathogen associations. ; This work was supported by the Spanish Ministry of Economy and Competitiveness grant CGL2015-70929-R, Ikerbasque (Basque Foundation for Science) and pre-doctoral grants PRE-2013-1-901 (I.M.) from the Basque Government and PIF15/101 (E.O.) from the University of the Basque Country. A.E.-C. is funded by ISCIII of the MINECO (Ref: PT17/0009/0019) and cofinanced by FEDER.
Campylobacter jejuni is a foodborne pathogen causing bacterial gastroenteritis, with the highest incidence reported in Europe. The prevalence of antibiotic resistance in C. jejuni, as well as in many other bacterial pathogens, has increased over the last few years. In this report, we describe the presence of a plasmid in a multi-drug-resistant C. jejuni strain isolated from a gastroenteritis patient. Mating experiments demonstrated the transference of this genetic element (pCjH01) among C. jejuni by plasmid conjugation. The pCjH01 plasmid was sequenced and assembled, revealing high similarity (97% identity) with pTet, a described tetracycline resistance encoding plasmid. pCjH01 (47.7 kb) is a mosaic plasmid composed of a pTet backbone that has acquired two discrete DNA regions. Remarkably, one of the acquired sequences carried an undescribed variant of the aadE-sat4-aphA-3 gene cluster, providing resistance to at least kanamycin and gentamycin. Aside from the antibiotic resistance genes, the cluster also carries genes coding for putative regulators, such as a sigma factor of the RNA polymerase and an antisigma factor. Homology searches suggest that Campylobacter exchanges genetic material with distant G-positive bacterial genera. ; This research was funded by the Spanish Ministry of Economy and Competitiveness [grant AGL2013-45339R], the Spanish Ministry of Science, Innovation and Universities (MCIU), State Bureau of Investigation (AIE), the European Regional Development Fund (FEDER) [grant PGC2018-096958-B-I00], and the Catalonian government [grant 2017SGR499]. PG was the recipient of an ADR fellowship of the University of Barcelona
The evolution of winged insects revolutionized terrestrial ecosystems and led to the largest animal radiation on Earth. However, we still have an incomplete picture of the genomic changes that underlay this diversification. Mayflies, as one of the sister groups of all other winged insects, are key to understanding this radiation. Here, we describe the genome of the mayfly Cloeon dipterum and its gene expression throughout its aquatic and aerial life cycle and specific organs. We discover an expansion of odorant-binding-protein genes, some expressed specifically in breathing gills of aquatic nymphs, suggesting a novel sensory role for this organ. In contrast, flying adults use an enlarged opsin set in a sexually dimorphic manner, with some expressed only in males. Finally, we identify a set of wing-associated genes deeply conserved in the pterygote insects and find transcriptomic similarities between gills and wings, suggesting a common genetic program. Globally, this comprehensive genomic and transcriptomic study uncovers the genetic basis of key evolutionary adaptations in mayflies and winged insects. ; This project was mainly funded by the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement 657732 to I.A., Grant BFU2015-66040-P to F.Ca., institutional Grant MDM-2016-0687 (MINECO, Spain). Additional funding was provided by the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (ERC-StG-LS2-637591 to M.I.), the Spanish Ministerio de Ciencia (BFU2017-89201-P to M.I., RYC-2016-20089 and PGC2018-099392-A-I00 to I.M.)
Background Olive tree (Olea europaea L. subsp. europaea, Oleaceae) has been the most emblematic perennial crop for Mediterranean countries since its domestication around 6000 years ago in the Levant. Two taxonomic varieties are currently recognized: cultivated (var. europaea) and wild (var. sylvestris) trees. However, it remains unclear whether olive cultivars derive from a single initial domestication event followed by secondary diversification, or whether cultivated lineages are the result of more than a single, independent primary domestication event. To shed light into the recent evolution and domestication of the olive tree, here we analyze a group of newly sequenced and available genomes using a phylogenomics and population genomics framework. Results We improved the assembly and annotation of the reference genome, newly sequenced the genomes of twelve individuals: ten var. europaea, one var. sylvestris, and one outgroup taxon (subsp. cuspidata)—and assembled a dataset comprising whole genome data from 46 var. europaea and 10 var. sylvestris. Phylogenomic and population structure analyses support a continuous process of olive tree domestication, involving a major domestication event, followed by recurrent independent genetic admixture events with wild populations across the Mediterranean Basin. Cultivated olives exhibit only slightly lower levels of genetic diversity than wild forms, which can be partially explained by the occurrence of a mild population bottleneck 3000–14,000 years ago during the primary domestication period, followed by recurrent introgression from wild populations. Genes associated with stress response and developmental processes were positively selected in cultivars, but we did not find evidence that genes involved in fruit size or oil content were under positive selection. This suggests that complex selective processes other than directional selection of a few genes are in place. Conclusions Altogether, our results suggest that a primary domestication area in the eastern Mediterranean basin was followed by numerous secondary events across most countries of southern Europe and northern Africa, often involving genetic admixture with genetically rich wild populations, particularly from the western Mediterranean Basin. ; This research has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement No 724173; RETVOLUTION)". IJ was supported in part by a grant from the Peruvian Ministry of Education: "Beca Presidente de la República" (2013-III). ; Postprint (published version)
Background: Olive tree (Olea europaea L. subsp. europaea, Oleaceae) has been the most emblematic perennial crop for Mediterranean countries since its domestication around 6000 years ago in the Levant. Two taxonomic varieties are currently recognized: cultivated (var. europaea) and wild (var. sylvestris) trees. However, it remains unclear whether olive cultivars derive from a single initial domestication event followed by secondary diversification, or whether cultivated lineages are the result of more than a single, independent primary domestication event. To shed light into the recent evolution and domestication of the olive tree, here we analyze a group of newly sequenced and available genomes using a phylogenomics and population genomics framework. Results: We improved the assembly and annotation of the reference genome, newly sequenced the genomes of twelve individuals: ten var. europaea, one var. sylvestris, and one outgroup taxon (subsp. cuspidata)-and assembled a dataset comprising whole genome data from 46 var. europaea and 10 var. sylvestris. Phylogenomic and population structure analyses support a continuous process of olive tree domestication, involving a major domestication event, followed by recurrent independent genetic admixture events with wild populations across the Mediterranean Basin. Cultivated olives exhibit only slightly lower levels of genetic diversity than wild forms, which can be partially explained by the occurrence of a mild population bottleneck 3000-14,000 years ago during the primary domestication period, followed by recurrent introgression from wild populations. Genes associated with stress response and developmental processes were positively selected in cultivars, but we did not find evidence that genes involved in fruit size or oil content were under positive selection. This suggests that complex selective processes other than directional selection of a few genes are in place. Conclusions: Altogether, our results suggest that a primary domestication area in the eastern Mediterranean basin was followed by numerous secondary events across most countries of southern Europe and northern Africa, often involving genetic admixture with genetically rich wild populations, particularly from the western Mediterranean Basin. ; This research has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement No 724173; RETVOLUTION)". IJ was supported in part by a grant from the Peruvian Ministry of Education: "Beca Presidente de la República" (2013-III).
Background: The Mediterranean mussel Mytilus galloprovincialis is an ecologically and economically relevant edible marine bivalve, highly invasive and resilient to biotic and abiotic stressors causing recurrent massive mortalities in other bivalves. Although these traits have been recently linked with the maintenance of a high genetic variation within natural populations, the factors underlying the evolutionary success of this species remain unclear. Results: Here, after the assembly of a 1.28-Gb reference genome and the resequencing of 14 individuals from two independent populations, we reveal a complex pan-genomic architecture in M. galloprovincialis, with a core set of 45,000 genes plus a strikingly high number of dispensable genes (20,000) subject to presence-absence variation, which may be entirely missing in several individuals. We show that dispensable genes are associated with hemizygous genomic regions affected by structural variants, which overall account for nearly 580 Mb of DNA sequence not included in the reference genome assembly. As such, this is the first study to report the widespread occurrence of gene presence-absence variation at a whole-genome scale in the animal kingdom. Conclusions: Dispensable genes usually belong to young and recently expanded gene families enriched in survival functions, which might be the key to explain the resilience and invasiveness of this species. This unique pan-genome architecture is characterized by dispensable genes in accessory genomic regions that exceed by orders of magnitude those observed in other metazoans, including humans, and closely mirror the open pan-genomes found in prokaryotes and in a few non-metazoan eukaryotes. ; This work was conducted with the support of the projects AGL2011-14507-E, AGL2015-65705-R, RTI2018-095997-B-I00 (Ministerio de Ciencia, Innovación y Universidades, Spain) and INCITE 10PXIB402096PR, IN607B 2016/12 (Consellería de Economía, Emprego e Industria - GAIN, Xunta de Galicia). Antonio Figueras, Beatriz Novoa, Rebeca Moreira, Alberto Pallavicini, Marco Gerdol, Paola Venier, and Umberto Rosani are supported by the European Union's Horizon 2020 research and innovation programme under grant agreement no. 678589. David Posada is supported by the European Research Council, the Spanish Ministry of Economy and Competitiveness, and Xunta de Galicia. We acknowledge the support of the Spanish Ministry of Science and Innovation to the EMBL partnership, the Centro de Excelencia Severo Ochoa, the CERCA Programme/Generalitat de Catalunya, the Spanish Ministry of Science and Innovation through the Instituto de Salud Carlos III, the Generalitat de Catalunya through Departament de Salut and Departament d'Empresa i Coneixement, and the Co-financing by the Spanish Ministry of Science and Innovation with funds from the European Regional Development Fund (ERDF) corresponding to the 2014-2020 Smart Growth Operating Program
12 pages, 5 figures, 6 tables, supplemental material https://doi.org/10.25387/g3.12640691 ; The octocoral, Paramuricea clavata, is a habitat-forming anthozoan with a key ecological role in rocky benthic and biodiversity-rich communities in the Mediterranean and Eastern Atlantic. Shallow populations of P. clavata in the North-Western Mediterranean are severely affected by warming-induced mass mortality events (MMEs). These MMEs have differentially impacted individuals and populations of P. clavata (i.e., varied levels of tissue necrosis and mortality rates) over thousands of kilometers of coastal areas. The eco-evolutionary processes, including genetic factors, contributing to these differential responses remain to be characterized. Here, we sequenced a P. clavata individual with short and long read technologies, producing 169.98 Gb of Illumina paired-end and 3.55 Gb of Oxford Nanopore Technologies (ONT) reads. We obtained a de novo genome assembly accounting for 607 Mb in 64,145 scaffolds. The contig and scaffold N50s are 19.15 Kb and 23.92 Kb, respectively. Despite of the low contiguity of the assembly, its gene completeness is relatively high, including 75.8% complete and 9.4% fragmented genes out of the 978 metazoan genes contained in the metazoa_odb9 database. A total of 62,652 protein-coding genes have been annotated. This assembly is one of the few octocoral genomes currently available. This is undoubtedly a valuable resource for characterizing the genetic bases of the differential responses to thermal stress and for the identification of thermo-resistant individuals and populations. Overall, having the genome of P. clavata will facilitate studies of various aspects of its evolutionary ecology and elaboration of effective conservation plans such as active restoration to overcome the threats of global change ; We acknowledge the funding support of the European Union's Horizon 2020 research and innovation program under grant agreement No 689518 (MERCES) and the Strategic Funding UID/Multi/04423/2013 through national funds provided by FCT – Foundation for Science and Technology and European Regional Development Fund (ERDF), in the framework of the programme PT2020. JBL is funded by an assistant researcher contract framework of the RD Unit - UID/Multi/04423/2019 - Interdisciplinary Centre of Marine and Environmental Research – financed by the European Regional Development Fund (ERDF) through COMPETE2020 - Operational Program for Competitiveness and Internationalisation (POCI) and national funds through FCT/MCTES (PIDDAC). AA was partially supported by the FCT project PTDC/CTA-AMB/31774/2017 (POCI-01-0145-FEDER/031774/2017). DGG was supported by an FPU grant (FPU15/05457) from the Spanish Ministry of Education. We acknowledge support of the Spanish Ministry of Science and Innovation to the EMBL partnership, the Centro de Excelencia Severo Ochoa, the CERCA Programme / Generalitat de Catalunya, the Spanish Ministry of Science and Innovation through the Instituto de Salud Carlos III, the Generalitat de Catalunya through Departament de Salut and Departament d'Empresa i Coneixement, and the Co-financing by the Spanish Ministry of Science and Innovation with funds from the European Regional Development Fund (ERDF) corresponding to the 2014-2020 Smart Growth Operating Program. JBL and JG planned and granted the funding to start the project ; Peer reviewed
Large-scale gene duplication, including whole-genome duplication (WGD), is a very common phenomenon in eukaryotic genomes. Bursts of gene duplications are considered a major source of evolutionary innovation and have been associated with the increase in biological complexity and adaptive radiations of species (Zhang 2003). In particular, large-scale gene duplications, generally associated with WGDs, have been reported for many eukaryotic lineages including plants (Van de Peer et al. 2017), fungi (Marcet-Houben and Gabaldón 2015), and animals (Taylor et al. 2001). Although large-scale duplication seems less pervasive in animals than in plants, a growing number of studies report such events in animals. Among other lineages, putative WGDs have been described at the base of vertebrates (Ohno 1970; Dehal and Boore 2005; Putnam et al. 2008), and in several lineages of fish (Christoffels et al. 2004; Glasauer and Neuhauss 2014), amphibians (Mable et al. 2011; Session et al. 2016), and arthropods (Jacobson et al. 2013; Kenny et al. 2016; Schwager et al. 2017; Li et al. 2018). Aphids belong to the infraorder Aphidomorpha that includes three families: Aphididae, Adelgidae, and Phylloxeridae (Favret 2013; Nováková et al. 2013; Blackman and Eastop 2000). Aphids and related (Aphidomorpha) species (Becker-Migdisova and Aizenberg 1962) are hemipteran insects that feed on plant sap (Tjallingii 1995). This specialized diet, rich in carbohydrates but poor in nitrogen compounds, has resulted in several adaptations including the establishment of tight relationships with bacterial endosymbionts (Scarborough et al. 2005; Moya et al. 2008; von Dohlen et al. 2017). There are more than 5,000 described aphid species, of which, about 450 have been collected from crop plants, and 100 are considered of significant economic importance (Van Emden and Harrington 2017). Genomes of several aphid species of agricultural interest have been sequenced, including Acyrthosiphon pisum, Myzus persicae, Diuraphis noxia, Aphis glycines, and Sipha flava (International Aphid Genomics Consortium 2010; Nicholson et al. 2015; Mathers et al. 2017; Wenger et al. 2017). However, except for S. flava (subfamily Chaitophorinae), the sequenced aphids belong to a single subfamily, Aphidinae, limiting our understanding of the genomic diversity in this group of insects. Remarkably, most genome analyses in these species have revealed an important number of paralogous sequences and expanded gene families, including amino acid transporters, odorant and gustatory receptor genes, miRNA-specific dicer-1, ago1 genes, and pasha, among others (Smadja et al. 2009; Huerta-Cepas et al. 2010; Jaubert-Possamai et al. 2010; Duncan et al. 2016; Mathers et al. 2017). However, the close relatedness of the sequenced species provides little resolution to the phylogenetic placement of the duplication events, particularly the ancestral ones. Recent studies have focused on assessing patterns of sequence and expression divergence among recently duplicated genes in A. pisum (Fernández et al. 2019) or M. persicae (Mathers et al. 2017). They have also inspected the distribution of old and young A. pisum paralogs along chromosomes, by categorizing the age of genes that are best-reciprocal hits of each other based on the amount of synonymous substitutions (Li et al. 2019). However, we still lack a proper understanding of when the ancestral duplications occurred, and whether they can be linked to phenotypic innovations shared by aphids or related species. To better assess the origin of the paralogous genes of aphids we sequenced the genome of Cinara cedri (Lachninae subfamily, tribe Eulachnini), the first representative genome from an early-branching lineage of the Aphididae family. Cinara species (and most Lachninae) are particular among aphids as they feed on conifers (gymnosperms), whereas all the other genome-sequenced aphids feed on angiosperms. Another clear difference between the Lachninae and the rest of aphids is that two co-obligate endosymbionts (Buchnera aphidicola, Serratia symbiotica) are present in this group, whereas only B. aphidicola is obligate for the rest of aphids (Latorre and Manzano-Marín 2017). We used a phylogeny-based approach (Huerta-Cepas and Gabaldón 2011) to provide the relative timing of aphid duplications in a phylogenetic framework that includes 21 other fully sequenced genomes and two transcriptomes. Our results provide compelling evidence for an ancestral wave of gene duplications, whose origin predates the diversification of all sequenced aphids, adelgids, and phyloxerids, but are subsequent to their divergence from the Coccoidea lineage, ∼106–227 Ma. ; This research was funded by European Regional Development Fund (ERDF) and Ministerio de Economía y Competitividad (Spain) (Grant Nos. PGC2018-099344-B-100 and BFU2015-67107). T.G. group also acknowledges support from the Catalan Research Agency (AGAUR) SGR857, and grants from the European Union's Horizon 2020 research and innovation program under the grant agreements ERC-2016-724173 and MSC-747607. T.G. also receives support from an INB (Grant No. PT17/0009/0023—ISCIII-SGEFI/ERDF). The authors want to thank Sophia Derdak for her help in the genome polishing step. ; Peer Reviewed ; Postprint (published version)
Aphids (Aphidoidea) are a diverse group of hemipteran insects that feed on plant phloem sap. A common finding in studies of aphid genomes is the presence of a large number of duplicated genes. However, when these duplications occurred remains unclear, partly due to the high relatedness of sequenced species. To better understand the origin of aphid duplications we sequenced and assembled the genome of Cinara cedri, an early branching lineage (Lachninae) of the Aphididae family. We performed a phylogenomic comparison of this genome with 20 other sequenced genomes, including the available genomes of five other aphids, along with the transcriptomes of two species belonging to Adelgidae (a closely related clade to the aphids) and Coccoidea. We found that gene duplication has been pervasive throughout the evolution of aphids, including many parallel waves of recent, species-specific duplications. Most notably, we identified a consistent set of very ancestral duplications, originating from a large-scale gene duplication predating the diversification of Aphidomorpha (comprising aphids, phylloxerids, and adelgids). Genes duplicated in this ancestral wave are enriched in functions related to traits shared by Aphidomorpha, such as association with endosymbionts, and adaptation to plant defenses and phloem-sap-based diet. The ancestral nature of this duplication wave (106–227 Ma) and the lack of sufficiently conserved synteny make it difficult to conclude whether it originated from a whole-genome duplication event or, alternatively, from a burst of large-scale segmental duplications. Genome sequencing of other aphid species belonging to different Aphidomorpha and related lineages may clarify these findings. ; This research was funded by European Regional Development Fund (ERDF) and Ministerio de Economía y Competitividad (Spain) (Grant Nos. PGC2018-099344-B-100 and BFU2015-67107). T.G. group also acknowledges support from the Catalan Research Agency (AGAUR) SGR857, and grants from the European Union's Horizon 2020 research and innovation program under the grant agreements ERC-2016-724173 and MSC-747607. T.G. also receives support from an INB (Grant No. PT17/0009/0023—ISCIII-SGEFI/ERDF). ; Peer reviewed
The turbot is a flatfish (Pleuronectiformes) with increasing commercial value, which has prompted active genomic research aimed at more efficient selection. Here we present the sequence and annotation of the turbot genome, which represents a milestone for both boosting breeding programmes and ascertaining the origin and diversification of flatfish. We compare the turbot genome with model fish genomes to investigate teleost chromosome evolution. We observe a conserved macrosyntenic pattern within Percomorpha and identify large syntenic blocks within the turbot genome related to the teleost genome duplication. We identify gene family expansions and positive selection of genes associated with vision and metabolism of membrane lipids, which suggests adaptation to demersal lifestyle and to cold temperatures, respectively. Our data indicate a quick evolution and diversification of flatfish to adapt to benthic life and provide clues for understanding their controversial origin. Moreover, we investigate the genomic architecture of growth, sex determination and disease resistance, key traits for understanding local adaptation and boosting turbot production, by mapping candidate genes and previously reported quantitative trait loci. The genomic architecture of these productive traits has allowed the identification of candidate genes and enriched pathways that may represent useful information for future marker-assisted selection in turbot. ; This work was funded by the Spanish Government: projects Consolider Ingenio: Aquagenomics (CSD2007-00002) and Metagenoma de la Península Ibérica (CSD2007-00005), Ministerio de Economía y Competitividad and European Regional Development Funds (AGL2012-35904), and Ministerio de Economía y Competitividad (AGL2014-51773 and AGL2014-57065-R); and Local Government Xunta de Galicia (GRC2014/010). P.P. and D.R. gratefully acknowledge the Spanish Ministerio de Educación for their FPU fellowships (AP2010-2408, AP2012-0254). Funding to pay the Open Access publication charges for this article was provided by the Ministerio de Economía y Competitividad (AGL2014-51773) and Xunta de Galicia (GRC2014/010).
Aphids (Aphidoidea) are a diverse group of hemipteran insects that feed on plant phloem sap. A common finding in studies of aphid genomes is the presence of a large number of duplicated genes. However, when these duplications occurred remains unclear, partly due to the high relatedness of sequenced species. To better understand the origin of aphid duplications we sequenced and assembled the genome of Cinara cedri, an early branching lineage (Lachninae) of the Aphididae family. We performed a phylogenomic comparison of this genome with 20 other sequenced genomes, including the available genomes of five other aphids, along with the transcriptomes of two species belonging to Adelgidae (a closely related clade to the aphids) and Coccoidea. We found that gene duplication has been pervasive throughout the evolution of aphids, including many parallel waves of recent, species-specific duplications. Most notably, we identified a consistent set of very ancestral duplications, originating from a large-scale gene duplication predating the diversification of Aphidomorpha (comprising aphids, phylloxerids, and adelgids). Genes duplicated in this ancestral wave are enriched in functions related to traits shared by Aphidomorpha, such as association with endosymbionts, and adaptation to plant defenses and phloem-sap-based diet. The ancestral nature of this duplication wave (106-227 Ma) and the lack of sufficiently conserved synteny make it difficult to conclude whether it originated from a whole-genome duplication event or, alternatively, from a burst of large-scale segmental duplications. Genome sequencing of other aphid species belonging to different Aphidomorpha and related lineages may clarify these findings. ; This research was funded by European Regional Development Fund (ERDF) and Ministerio de Economía y Competitividad (Spain) (Grant Nos. PGC2018-099344-B-100 and BFU2015-67107). T.G. group also acknowledges support from the Catalan Research Agency (AGAUR) SGR857, and grants from the European Union's Horizon 2020 research and innovation program under the grant agreements ERC-2016-724173 and MSC-747607. T.G. also receives support from an INB (Grant No. PT17/0009/0023—ISCIII-SGEFI/ERDF). The genome, annotation and sequencing reads have been deposited at the European Nucleotide Archive (ENA) under the project accession PRJEB33415
The turbot is a flatfish (Pleuronectiformes) with increasing commercial value, which has prompted active genomic research aimed at more efficient selection. Here we present the sequence and annotation of the turbot genome, which represents a milestone for both boosting breeding programmes and ascertaining the origin and diversification of flatfish. We compare the turbot genome with model fish genomes to investigate teleost chromosome evolution. We observe a conserved macrosyntenic pattern within Percomorpha and identify large syntenic blocks within the turbot genome related to the teleost genome duplication. We identify gene family expansions and positive selection of genes associated with vision and metabolism of membrane lipids, which suggests adaptation to demersal lifestyle and to cold temperatures, respectively. Our data indicate a quick evolution and diversification of flatfish to adapt to benthic life and provide clues for understanding their controversial origin. Moreover, we investigate the genomic architecture of growth, sex determination and disease resistance, key traits for understanding local adaptation and boosting turbot production, by mapping candidate genes and previously reported quantitative trait loci. The genomic architecture of these productive traits has allowed the identification of candidate genes and enriched pathways that may represent useful information for future marker-assisted selection in turbot ; This work was funded by the Spanish Government: projects Consolider Ingenio: Aquagenomics (CSD2007-00002) and Metagenoma de la Península Ibérica (CSD2007-00005), Ministerio de Economía y Competitividad and European Regional Development Funds (AGL2012-35904), and Ministerio de Economía y Competitividad (AGL2014-51773 and AGL2014-57065-R); and Local Government Xunta de Galicia (GRC2014/010). P.P. and D.R. gratefully acknowledge the Spanish Ministerio de Educación for their FPU fellowships (AP2010-2408, AP2012-0254) ; SI
