The 22,000-year-old cave painting of an Atlantic salmon (Salmo salar) near the Vézère River in France is a reminder of our fascination with, and dependence on, Atlantic salmon throughout human history. Atlantic salmon belongs to the salmonid lineage which comprises 11 genera, with at least 70 species that exhibit a wide range of ecological adaptations and use a variety of marine and freshwater life history strategies 1 . Salmonids hold important positions as socially iconic species and economic resources within aquaculture, wild fisheries and recreational sport fisheries. Moreover, they serve as key indicator species of the health of North Atlantic and Pacific coastal and river ecosystems.All teleosts share at least three rounds of whole-genome duplication (WGD), 1R and 2R before the divergence of lamprey from the jawed vertebrates 2 , and a third teleost-specific WGD (Ts3R) at the base of the teleosts ~320 million years ago (Mya) [3][4][5] . Very little is known about the mechanisms of genomic and chromosomal reorganization after WGD in vertebrates because the 1R, 2R and Ts3R occurred so long ago that few clear signatures of post-WGD reorganization events remain. In contrast, a fourth WGD (the Ss4R salmonid-specific autotetraploidization event) occurred in the common ancestor of salmonids ~80 Mya after their divergence from Esociformes ~125 Mya 6-8 (Fig. 1), and the continued presence of multivalent pairing at meiosis and evidence of tetrasomic inheritance in salmonid species suggests that diploidy is not yet fully re-established 6,9,10 . Salmonids thus appear to provide an unprecedented opportunity for studying vertebrate genome evolution after an autotetraploid WGD 11,12 over a time period that is long enough to reveal long-term evolutionary patterns, but short enough to give a high-resolution picture of the process. In addition, they provide an excellent setting for contextualizing genome evolution with a dramatic post-WGD species radiation and intricate adaptations to a whole range of life history regimes.Here we present a high-quality reference genome assembly of the Atlantic salmon, and use it to describe major patterns characterizing the post-Ss4R salmonid genome evolution over the past 80 million years (Myr). Our results challenge the recent claim that rediploidization in salmonids has been a gradual process unlinked to significant genome rearrangements 13 . They also challenge current views about the relative importance of sub-and neofunctionalization in vertebrate genomes (reviewed in ref. 14), and the importance of dosage balance as a gene duplicate retention mechanism 15 . Genome characterizationThe Atlantic salmon reference genome assembly (GenBank: GCA_000233375.4) adds up to 2.97 gigabases (Gb) with aThe whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about the evolutionary fate of a duplicated vertebrate genome in 70 extant lineages. Here we present a high...

Exposing natural selection driving phenotypic and genotypic adaptive differentiation is an extraordinary challenge. Given that an organism's life stages are exposed to the same environmental variations, we reasoned that fitness components, such as the lag, rate, and efficiency of growth, directly reflecting performance in these life stages, should often be selected in concert. We therefore conjectured that correlations between fitness components over natural isolates, in a particular environmental context, would constitute a robust signal of recent selection. Critically, this test for selection requires fitness components to be determined by different genetic loci. To explore our conjecture, we exhaustively evaluated the lag, rate, and efficiency of asexual population growth of natural isolates of the model yeast Saccharomyces cerevisiae in a large variety of nitrogen-limited environments. Overall, fitness components were well correlated under nitrogen restriction. Yeast isolates were further crossed in all pairwise combinations and coinheritance of each fitness component and genetic markers were traced. Trait variations tended to map to quantitative trait loci (QTL) that were private to a single fitness component. We further traced QTLs down to single-nucleotide resolution and uncovered loss-of-function mutations in RIM15, PUT4, DAL1, and DAL4 as the genetic basis for nitrogen source use variations. Effects of SNPs were unique for a single fitness component, strongly arguing against pleiotropy between lag, rate, and efficiency of reproduction under nitrogen restriction. The strong correlations between life stage performances that cannot be explained by pleiotropy compellingly support adaptive differentiation of yeast nitrogen source use and suggest a generic approach for detecting selection.

BackgroundSalmonids are ray-finned fishes which constitute 11 genera and at least 70 species including Atlantic salmon, whitefishes, graylings, rainbow trout, and char. The common ancestor of all Salmonidae experienced a whole genome duplication (WGD) ~80 million years ago, resulting in an autotetraploid genome. Genomic rediplodization is still going on in salmonid species, providing an unique system for studying evolutionary consequences of whole genome duplication. In recent years, high quality genome sequences of Atlantic salmon and Rainbow trout has been established, due to their scientific and commercial values. In this paper we introduce SalmoBase (http://www.salmobase.org/), a tool for making molecular resources for salmonids public available in a framework of visualizations and analytic tools.ResultsSalmoBase has been developed as a part of the ELIXIR.NO project. Currently, SalmoBase contains molecular resources for Atlantic salmon and Rainbow trout. Data can be accessed through BLAST, Genome Browser (GBrowse), Genetic Variation Browser (GVBrowse) and Gene Expression Browser (GEBrowse).ConclusionsTo the best of our knowledge, SalmoBase is the first database which integrates salmonids data and allow users to study salmonids in an integrated framework. The database and its tools (e.g., comparative genomics tools, synteny browsers) will be expanded as additional public resources describing other Salmonidae genomes become available.

A major rationale for the advocacy of epigenetically mediated adaptive responses is that they facilitate faster adaptation to environmental challenges. This motivated us to develop a theoretical–experimental framework for disclosing the presence of such adaptation‐speeding mechanisms in an experimental evolution setting circumventing the need for pursuing costly mutation–accumulation experiments. To this end, we exposed clonal populations of budding yeast to a whole range of stressors. By growth phenotyping, we found that almost complete adaptation to arsenic emerged after a few mitotic cell divisions without involving any phenotypic plasticity. Causative mutations were identified by deep sequencing of the arsenic‐adapted populations and reconstructed for validation. Mutation effects on growth phenotypes, and the associated mutational target sizes were quantified and embedded in data‐driven individual‐based evolutionary population models. We found that the experimentally observed homogeneity of adaptation speed and heterogeneity of molecular solutions could only be accounted for if the mutation rate had been near estimates of the basal mutation rate. The ultrafast adaptation could be fully explained by extensive positive pleiotropy such that all beneficial mutations dramatically enhanced multiple fitness components in concert. As our approach can be exploited across a range of model organisms exposed to a variety of environmental challenges, it may be used for determining the importance of epigenetic adaptation‐speeding mechanisms in general.

The Norwegian e-Infrastructure for Life Sciences (NeLS) has been developed by ELIXIR Norway to provide its users with a system enabling data storage, sharing, and analysis in a project-oriented fashion. The system is available through easy-to-use web interfaces, including the Galaxy workbench for data analysis and workflow execution. Users confident with a command-line interface and programming may also access it through Secure Shell (SSH) and application programming interfaces (APIs).  NeLS has been in production since 2015, with training and support provided by the help desk of ELIXIR Norway. Through collaboration with NorSeq, the national consortium for high-throughput sequencing, an integrated service is offered so that sequencing data generated in a research project is provided to the involved researchers through NeLS. Sensitive data, such as individual genomic sequencing data, are handled using the TSD (Services for Sensitive Data) platform provided by Sigma2 and the University of Oslo. NeLS integrates national e-infrastructure storage and computing resources, and is also integrated with the SEEK platform in order to store large data files produced by experiments described in SEEK.   In this article, we outline the architecture of NeLS and discuss possible directions for further development.

Meadow fescue (Festuca pratensis Huds.) is one of the most important forage grasses in temperate regions. It is a diploid (2n = 14) outbreeding species that belongs to the genus Festuca. Together with Lolium perenne, they are the most important genera of forage grasses. Meadow fescue has very high quality of yield with good winter survival and persistency. However, extensive genomic resources for meadow fescue have not become available so far. To address this lack of comprehensive publicly available datasets, we have developed functionally annotated draft genome sequences of two meadow fescue genotypes, ‘HF7/2’ and ‘B14/16’, and constructed the platform ForageGrassBase, available at http://foragegrass.org/, for data visualization, download and querying. This is the first open-access platform that provides extensive genomic resources related to this forage grass species. The current database provides the most up-to-date draft genome sequence along with structural and functional annotations for genes that can be accessed using Genome Browser (GBrowse), along with comparative genomic alignments to Arabidopsis, L. perenne, barley, rice, Brachypodium and maize genomes. We have integrated homologous search tool BLAST also for the users to analyze their data. Combined, GBrowse, BLAST and downloadable data gives a user-friendly access to meadow fescue genomic resources. To our knowledge, ForageGrassBase is the first genome database dedicated to forage grasses. The current forage grass database provides valuable resources for a range of research fields related to meadow fescue and other forage crop species, as well as for plant research communities in general. The genome database can be accessed at http://foragegrass.org.

BackgroundMeadow fescue (Festuca pratensis Huds.) is one of the most important forage grasses in temperate regions. F. pratensis is a diploid (2n =14) outbreeding species that belongs to the genus Festuca. Together with Lolium, they are the most important genera of forage grasses in temperate regions. F. pratensis has good winter survival, with high quality dry matter yields and persistency, and is suitable both for frequent-cutting conservation regimes and for grazing. It is a significant component of species-rich permanent pastures in the temperate regions, ensuring high forage yield under harsh climatic conditions where other productive forage grass species are unable to grow. However, genomic resources for F. Pratensis is not available so far.ResultsThe draft genome sequences of two F. pratensis genotypes “HF7/2” and “B14/16” are reported in this study. Here, using the draft genome, functional annotation datasets of two F. pratensis cultivars, we have constructed the F. pratensis genome database http://foragegrass.org/, the first open-access platform to provide comprehensive genomic resources related to this forage grass species. The current version of this database provides the most up-to-date draft genome sequence along with structural and functional annotations for genes using Genome Browser (GBrowse). In addition, we have integrated comparative genomic tracks for F. pratensis genomes by mapping F.pratensis genome to the barley, rice, Brachypodium and maize genomes. We have integrated homologus search tool BLAST also for the users to analyze their data. Combined, GBrowse, BLAST and downloadble data gives an user friendly access to F. pratensis genomic resouces. All data in the database were manually curated.ConclusionTo our knowledge, ForageGrassBase is the first genome database dedicated to forage grasses. It provides valuable resources for a range of research fields related to F. pratensis and other forage crop species, as well as for plant research communities in general. The genome database can be accessed at http://foragegrass.org. In the near future, we will expand the ForageGrassBase by adding genomic tools for other forage grass species, as soon as their genomes become available.

No abstract