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Malignant pleural mesothelioma (MPM) is an aggressive cancer with rising incidence and challenging clinical management. Through a large series of whole-genome sequencing data, integrated with transcriptomic and epigenomic data using multiomics factor analysis, we demonstrate that the current World Health Organization classification only accounts for up to 10% of interpatient molecular differences. Instead, the MESOMICS project paves the way for a morphomolecular classification of MPM based on four dimensions: ploidy, tumor cell morphology, adaptive immune response and CpG island methylator profile. We show that these four dimensions are complementary, capture major interpatient molecular differences and are delimited by extreme phenotypes that—in the case of the interdependent tumor cell morphology and adapted immune response—reflect tumor specialization. These findings unearth the interplay between MPM functional biology and its genomic history, and provide insights into the variations observed in the clinical behavior of patients with MPM.

Orestias ascotanensis (Cyprinodontidae) is a teleost pupfish endemic to springs feeding into the Ascotan saltpan in the Chilean Altiplano (3,700 m.a.s.l.) and represents an opportunity to study adaptations to high-altitude aquatic environments. We have de novo assembled the genome of O. ascotanensis at high coverage. Comparative analysis of the O. ascotanensis genome showed an overall process of contraction, including loss of genes related to G-protein signaling, chemotaxis and signal transduction, while there was expansion of gene families associated with microtubule-based movement and protein ubiquitination. We identified 818 genes under positive selection, many of which are involved in DNA repair. Additionally, we identified novel and conserved microRNAs expressed in O. ascotanensis and its closely-related species, Orestias gloriae. Our analysis suggests that positive selection and expansion of genes that preserve genome stability are a potential adaptive mechanism to cope with the increased solar UV radiation to which high-altitude animals are exposed to.

BackgroundMalignant Pleural Mesothelioma (MPM) is a rare understudied cancer associated with exposure to asbestos. So far, MPM patients have benefited marginally from the genomics medicine revolution due to the limited size or breadth of existing molecular studies. In the context of the MESOMICS project, we have performed the most comprehensive molecular characterization of MPM to date, with the underlying dataset made of the largest whole genome sequencing series yet reported, together with transcriptome sequencing and methylation arrays for 120 MPM patients.ResultsWe first provide comprehensive quality controls for all samples, of both raw and processed data. Due to the difficulty in collecting specimens from such rare tumors, a part of the cohort does not include matched normal material. We provide a detailed analysis of data processing of these tumor-only samples, showing that all somatic alteration calls match very stringent criteria of precision and recall. Finally, integrating our data with previously published multi-omic MPM datasets (n=374 in total), we provide an extensive molecular phenotype map of MPM based on the multi-task theory. The generated map can be interactively explored and interrogated on the UCSC TumorMap portal (https://tumormap.ucsc.edu/?bookmark=746c4bc0e8bc4eb5f280cdd8lc7dcc783955faf2e2b493d0d205b7dle92b98c4).ConclusionsThis new high quality MPM multi-omics dataset, together with the state-of-art bioinformatics and interactive visualization tools we provide, will support the development of precision medicine in MPM that is particularly challenging to implement in rare cancers due to limited molecular studies.

Reconstruction of genome-based metabolic model is a useful approach for the assessment of metabolic pathways, genes and proteins involved in the environmental fitness capabilities or pathogenic potential as well as for biotechnological processes development. Pseudomonas sp. LFM046 was selected as a good polyhydroxyalkanoates (PHA) producer from carbohydrates and plant oils. Its complete genome sequence and metabolic model were obtained. Analysis revealed that the gnd gene, encoding 6-phosphogluconate dehydrogenase, is absent in Pseudomonas sp. LFM046 genome. In order to improve the knowledge about LFM046 metabolism, the coenzyme specificities of different enzymes was evaluated. Furthermore, the heterologous expression of gnd genes from Pseudomonas putida KT2440 (NAD+ dependent) and Escherichia coli MG1655 (NADP+ dependent) in LFM046 was carried out and provoke a delay on cell growth and a reduction in PHA yield, respectively. The results indicate that the adjustment in cyclic Entner-Doudoroff pathway may be an interesting strategy for it and other bacteria to simultaneously meet divergent cell needs during cultivation phases of growth and PHA production.

Mycoplasma hyopneumoniae is the most costly pathogen for swine production. Although several studies have focused on the host-bacterium association, little is known about the changes in gene expression of swine cells upon infection. To improve our understanding of this interaction, we infected swine epithelial NPTr cells with M. hyopneumoniae strain J to identify differentially expressed mRNAs and miRNAs. The levels of 1,268 genes and 170 miRNAs were significantly modified post-infection. Up-regulated mRNAs were enriched in genes related to redox homeostasis and antioxidant defense, known to be regulated by the transcription factor NRF2 in related species. Down-regulated mRNAs were enriched in genes associated with cytoskeleton and ciliary functions. Bioinformatic analyses suggested a correlation between changes in miRNA and mRNA levels, since we detected down-regulation of miRNAs predicted to target antioxidant genes and up-regulation of miRNAs targeting ciliary and cytoskeleton genes. Interestingly, most down-regulated miRNAs were detected in exosome-like vesicles suggesting that M. hyopneumoniae infection induced a modification of the composition of NPTr-released vesicles. Taken together, our data indicate that M. hyopneumoniae elicits an antioxidant response induced by NRF2 in infected cells. In addition, we propose that ciliostasis caused by this pathogen is partially explained by the down-regulation of ciliary genes.

SummaryMalignant Pleural Mesothelioma (MPM) is an aggressive cancer with rising incidence and challenging clinical management. Using the largest series of whole-genome sequencing data integrated with transcriptomic and epigenomic data using multi-omic factor analysis, we demonstrate that MPM heterogeneity arises from four sources of variation: tumor cell morphology, ploidy, adaptive immune response, and CpG island methylator phenotype. Previous genomic studies focused on describing only the tumor cell morphology factor, although we robustly find the three other sources in all publicly available cohorts. We prove how these sources of variation explain the biological functions performed by the cancer cells, and how genomic events shape MPM molecular profiles. We show how these new sources of variation help understand the heterogeneity of the clinical behavior of MPM and drug responses measured in cell lines. These findings unearth the interplay between MPM functional biology and its genomic history, and ultimately, inform classification, prognostication and treatment.Graphical abstract

Using Illumina HiSeq ™ 2000 sequencing platform (100 bp double-end reads), we performed transcriptome analysis of flower (F), green (G) and pink (P) fruit stages of red raspberry. Transcriptome was obtained by the de-novo assembly of 298 Million high-quality reads through Trinity assembler, out of the 41,650 high quality transcripts, 18,171 coding sequences were successfully characterized using databases such as UniProtKB, NCBI Non-Redundant, KEGG, Gene Ontology, and InterPro-Scan. A total of 2409 transcripts were further identified as differentially expressed genes (DEGs) between the three libraries generated, and 253 DEGs were found between different fruit stages. Singular enrichment analysis of gene ontology (GO) detected an important group of DEGs over-expressed during fruit development; and associated with ethylene, auxin conjugation, abscisic acid response, brassinosteroids biosynthesis and signaling, and cell-wall disassembly processes. Our transcriptome data provides valuable insights on genes involved in the ripening process of Rubus fruit, as a representative of non-model fruit species, and may help in developing these cultivars with improved fruit quality characteristics in the years to come.

Whole human genome sequencing initiatives help us understand population history and the basis of genetic diseases. Current data mostly focuses on Old World populations, and the information of the genomic structure of Native Americans, especially those from the Southern Cone is scant. Here we present annotation and variant discovery from high-quality complete genome sequences of a cohort of 11 Mapuche-Huilliche individuals (HUI) from Southern Chile. We found approximately 3.1 × 106 single nucleotide variants (SNVs) per individual and identified 403,383 (6.9%) of novel SNVs events. Analyses of large-scale genomic events detected 680 copy number variants (CNVs) and 4,514 structural variants (SVs), including 398 and 1,910 novel events, respectively. Global ancestry composition of HUI genomes revealed that the cohort represents a sample from a marginally admixed population from the Southern Cone, whose main genetic component derives from Native American ancestors. Additionally, we found that HUI genomes contain variants in genes associated with 5 of the 6 leading causes of noncommunicable diseases in Chile, which may have an impact on the risk of prevalent diseases in Chilean and Amerindian populations. Our data represents a useful resource that can contribute to population-based studies and for the design of early diagnostics or prevention tools for Native and admixed Latin American populations.

BackgroundThe rice weevil Sitophilus oryzae is one of the most important agricultural pests, causing extensive damage to cereal in fields and to stored grains. S. oryzae has an intracellular symbiotic relationship (endosymbiosis) with the Gram-negative bacterium Sodalis pierantonius and is a valuable model to decipher host-symbiont molecular interactions.ResultsWe sequenced the Sitophilus oryzae genome using a combination of short and long reads to produce the best assembly for a Curculionidae species to date. We show that S. oryzae has undergone successive bursts of transposable element (TE) amplification, representing 72% of the genome. In addition, we show that many TE families are transcriptionally active, and changes in their expression are associated with insect endosymbiotic state. S. oryzae has undergone a high gene expansion rate, when compared to other beetles. Reconstruction of host-symbiont metabolic networks revealed that, despite its recent association with cereal weevils (30 Kyear), S. pierantonius relies on the host for several amino acids and nucleotides to survive and to produce vitamins and essential amino-acids required for insect development and cuticle biosynthesis.ConclusionsHere we present the genome of an agricultural pest beetle, which may act as a foundation for pest control. In addition, S. oryzae may be a useful model for endosymbiosis, and studying TE evolution and regulation, along with the impact of TEs on eukaryotic genomes.

International audience; Selective breeding and genetic improvement have left detectable signatures on the genomes of domestic species. The elucidation of such signatures is fundamental for detecting genomic regions of biological relevance to domestication and improving management practices. In aquaculture, domestication was carried out independently in different locations worldwide, which provides opportunities to study the parallel effects of domestication on the genome of individuals that have been selected for similar traits. In this study, we aimed to detect potential genomic signatures of domestication in two independent pairs of wild/domesticated Atlantic salmon populations of Canadian and Scottish origins, respectively. Putative genomic regions under divergent selection were investigated using a 200K SNP array by combining three different statistical methods based either on allele frequencies (LFMM, Bayescan) or haplotype differentiation (Rsb). We identified 337 and 270 SNPs potentially under divergent selection in wild and hatchery populations of Canadian and Scottish origins, respectively. We observed little overlap between results obtained from different statistical methods, highlighting the need to test complementary approaches for detecting a broad range of genomic footprints of selection. The vast majority of the outliers detected were population-specific but we found four candidate genes that were shared between the populations. We propose that these candidate genes may play a role in the parallel process of domestication. Overall, our results suggest that genetic drift may have override the effect of artificial selection and/or point toward a different genetic basis underlying the expression of similar traits in different domesticated strains. Finally, it is likely that domestication may predominantly target polygenic traits (e.g., growth) such that its genomic impact might be more difficult to detect with methods assuming selective sweeps.

The anuran Rhinella spinulosa is distributed along the Andes Range at altitudes that undergo wide daily and seasonal variation in temperature. One of the populations inhabits geothermal streams, a stable environment that influences life history traits such as the timing of metamorphosis. To investigate whether this population has undergone local adaptation to this unique habitat, we carried out transcriptome analyses in animals from two localities in two developmental stages (prometamorphic and metamorphic) and exposed them to two temperatures (20 and 25 °C). RNA-Seq, de novo assembly and annotation defined a transcriptome revealing 194,469 high quality SNPs, with 1,507 genes under positive selection. Comparisons among the experimental conditions yielded 1,593 differentially expressed genes. A bioinformatics search for candidates revealed a total of 70 genes that are highly likely to be implicated in the adaptive response of the population living in a stable environment, compared to those living in an environment with variable temperatures. Most importantly, the population inhabiting the geothermal environment showed decreased transcriptional plasticity and reduced genetic variation compared to its counterpart from the non-stable environment. This analysis will help to advance the understanding of the molecular mechanisms that account for the local adaptation to geothermal streams in anurans.

The sea louse (Caligus rogercresseyi) is an external parasite and considered one of the most important health problems in the salmon farming industry. Resistance to conventional chemical treatments has been demonstrated. Sufficient additive genetic variation has been determined to include selection for resistance to this parasite in Atlantic salmon breeding programs. The aim of this study was to perform a Genome Wide Association Study in order to dissect the genetic factors involved in the resistance to C. rogercresseyi, one of the most important species of sea lice in the Chilean salmon farming. 2628 Atlantic salmon smolts, which had been experimentally infested with C. rogercresseyi, were genotyped using a 50K SNP array. Genome Wide Association Analysis was conducted using a polygenic model. A heritability of 0.12 for resistance to this louse species was estimated using genomic information. This result was consistent with estimates from previous studies which used pedigree records in the same population. Only one SNP, located on chromosome 21, was significant at a local level, explaining 0.5% of the phenotypic variance and 4% of the genomic heritability for sea lice resistance. This SNP is located in an intronic region of a predicted gene which codes for Collagen alpha-1. Our results suggest that resistance to C. rogercresseyi can be considered a polygenic trait, controlled by many variants of relatively small effect. Thus the incorporation of genomic information through genomic selection could be the most appropriate approach for breeding purposes. Statement of relevance Caligus resistance has a polygenic genetic architecture.

Background Current South American populations trace their origins mainly to three continental ancestries, i.e. European, Amerindian and African. Individual variation in relative proportions of each of these ancestries may be confounded with socio-economic factors due to population stratification. Therefore, ancestry is a potential confounder variable that should be considered in epidemiologic studies and in public health plans. However, there are few studies that have assessed the ancestry of the current admixed Chilean population. This is partly due to the high cost of genome-scale technologies commonly used to estimate ancestry. In this study we have designed a small panel of SNPs to accurately assess ancestry in the largest sampling to date of the Chilean mestizo population (n = 3349) from eight cities. Our panel is also able to distinguish between the two main Amerindian components of Chileans: Aymara from the north and Mapuche from the south. Results A panel of 150 ancestry-informative markers (AIMs) of SNP type was selected to maximize ancestry informativeness and genome coverage. Of these, 147 were successfully genotyped by KASPar assays in 2843 samples, with an average missing rate of 0.012, and a 0.95 concordance with microarray data. The ancestries estimated with the panel of AIMs had relative high correlations (0.88 for European, 0.91 for Amerindian, 0.70 for Aymara, and 0.68 for Mapuche components) with those obtained with AXIOM LAT1 array. The country’s average ancestry was 0.53 ± 0.14 European, 0.04 ± 0.04 African, and 0.42 ± 0.14 Amerindian, disaggregated into 0.18 ± 0.15 Aymara and 0.25 ± 0.13 Mapuche. However, Mapuche ancestry was highest in the south (40.03%) and Aymara in the north (35.61%) as expected from the historical location of these ethnic groups. We make our results available through an online app and demonstrate how it can be used to adjust for ancestry when testing association between incidence of a disease and nongenetic risk factors. Conclusions We have conducted the most extensive sampling, across many different cities, of current Chilean population. Ancestry varied significantly by latitude and human development. The panel of AIMs is available to the community for estimating ancestry at low cost in Chileans and other populations with similar ancestry.

Generating accurate genome assemblies of large, repeat-rich human genomes has proved difficult using only long, error-prone reads, and most human genomes assembled from long reads add accurate short reads to polish the consensus sequence. Here we report an algorithm for hybrid assembly, WENGAN, that provides very high quality at low computational cost. We demonstrate de novo assembly of four human genomes using a combination of sequencing data generated on ONT PromethION, PacBio Sequel, Illumina and MGI technology. WENGAN implements efficient algorithms to improve assembly contiguity as well as consensus quality. The resulting genome assemblies have high contiguity (contig NG50: 17.24–80.64 Mb), few assembly errors (contig NGA50: 11.8–59.59 Mb), good consensus quality (QV: 27.84–42.88) and high gene completeness (BUSCO complete: 94.6–95.2%), while consuming low computational resources (CPU hours: 187–1,200). In particular, the WENGAN assembly of the haploid CHM13 sample achieved a contig NG50 of 80.64 Mb (NGA50: 59.59 Mb), which surpasses the contiguity of the current human reference genome (GRCh38 contig NG50: 57.88 Mb)., The genome assembler WENGAN produces high-quality human genome sequences at low computational cost.

This work presents the molecular foundation of a consortium of five efficient bacteria strains isolated from copper mines currently used in state of the art industrial-scale biotechnology. The strains Acidithiobacillus thiooxidans Licanantay, Acidiphilium multivorum Yenapatur, Leptospirillum ferriphilum Pañiwe, Acidithiobacillus ferrooxidans Wenelen and Sulfobacillus thermosulfidooxidans Cutipay were selected for genome sequencing based on metal tolerance, oxidation activity and bioleaching of copper efficiency. An integrated model of metabolic pathways representing the bioleaching capability of this consortium was generated. Results revealed that greater efficiency in copper recovery may be explained by the higher functional potential of L. ferriphilum Pañiwe and At. thiooxidans Licanantay to oxidize iron and reduced inorganic sulfur compounds. The consortium had a greater capacity to resist copper, arsenic and chloride ion compared to previously described biomining strains. Specialization and particular components in these bacteria provided the consortium a greater ability to bioleach copper sulfide ores.

BackgroundWhole human genome sequencing initiatives provide a compendium of genetic variants that help us understand population history and the basis of genetic diseases. Current data mostly focuses on Old World populations and information on the genomic structure of Native Americans, especially those from the Southern Cone is scant.ResultsHere we present a high-quality complete genome sequence of 11 Mapuche-Huilliche individuals (HUI) from Southern Chile (85% genomic and 98% exonic coverage at > 30X), with 96–97% high confidence calls. We found approximately 3.1×106 single nucleotide variants (SNVs) per individual and identified 403,383 (6.9%) of novel SNVs that are not included in current sequencing databases. Analyses of large-scale genomic events detected 680 copy number variants (CNVs) and 4,514 structural variants (SVs), including 398 and 1,910 novel events, respectively. Global ancestry composition of HUI genomes revealed that the cohort represents a marginally admixed population from the Southern Cone, whose genetic component is derived from early Native American ancestors. In addition, we found that HUI genomes display highly divergent and novel variants with potential functional impact that converge in ontological categories essential in cell metabolic processes.ConclusionsMapuche-Huilliche genomes contain a unique set of small– and large-scale genomic variants in functionally linked genes, which may contribute to susceptibility for the development of common complex diseases or traits in admixed Latinos and Native American populations. Our data represents an ancestral reference panel for population-based studies in Native and admixed Latin American populations.

International audience; Background: Long-read sequencing technologies are the ultimate solution for genome repeats, allowing near reference-level reconstructions of large genomes. However, long-read de novo assembly pipelines are computationally intense and require a considerable amount of coverage, thereby hindering their broad application to the assembly of large genomes. Alternatively, hybrid assembly methods that combine short-and long-read sequencing technologies can reduce the time and cost required to produce de novo assemblies of large genomes. Results: Here, we propose a new method, called Fast-SG, that uses a new ultrafast alignment-free algorithm specifically designed for constructing a scaffolding graph using lightweight data structures. Fast-SG can construct the graph from either short or long reads. This allows the reuse of efficient algorithms designed for short-read data and permits the definition of novel modular hybrid assembly pipelines. Using comprehensive standard datasets and benchmarks, we show how Fast-SG outperforms the state-of-the-art short-read aligners when building the scaffolding graph and can be used to extract linking information from either raw or error-corrected long reads. We also show how a hybrid assembly approach using Fast-SG with shallow long-read coverage (5X) and moderate computational resources can produce long-range and accurate reconstructions of the genomes of Arabidopsis thaliana (Ler-0) and human (NA12878). Conclusions: Fast-SG opens a door to achieve accurate hybrid long-range reconstructions of large genomes with low effort, high portability, and low cost.

Rap1 signaling is important for migration, differentiation, axonal growth, and during neuronal polarity. Rap1 can be activated by external stimuli, which in turn regulates specific guanine nucleotide exchange factors such as C3G, among others. Cdk5 functions are also important to neuronal migration and differentiation. Since we found that pharmacological inhibition of Cdk5 by using roscovitine reduced Rap1 protein levels in COS-7 cells and also C3G contains three putative phosphorylation sites for Cdk5, we examined whether the Cdk5-dependent phosphorylation of C3G could affect Rap1 expression and activity. We co-transfected C3G and tet-OFF system for p35 over-expression, an activator of Cdk5 activity into COS-7 cells, and then we evaluated phosphorylation in serine residues in C3G by immunoprecipitation and Western blot. We found that p35 over-expression increased C3G-serine-phosphorylation while inhibition of p35 expression by tetracycline or inhibition of Cdk5 activity with roscovitine decreased it. Interestingly, we found that MG-132, a proteasome inhibitor, rescue Rap1 protein levels in the presence of roscovitine. Besides, C3G-serine-phosphorylation and Rap1 protein levels were reduced in brain from Cdk5(-/-) as compared with the Cdk5(+/+) brain. Finally, we found that p35 over-expression increased Rap1 activity while inhibition of p35 expression by tetracycline or roscovitine decreased Rap1 activity. These results suggest that Cdk5-mediated serine-phosphorylation of C3G may control Rap1 stability and activity, and this may potentially impact various neuronal functions such as migration, differentiation, and polarity.

Background Nannochloropsis salina (= Eustigmatophyceae) is a marine microalga which has become a biotechnological target because of its high capacity to produce polyunsaturated fatty acids and triacylglycerols. It has been used as a source of biofuel, pigments and food supplements, like Omega 3. Only some Nannochloropsis species have been sequenced, but none of them benefit from a genome-scale metabolic model (GSMM), able to predict its metabolic capabilities. Results We present iNS934, the first GSMM for N. salina, including 2345 reactions, 934 genes and an exhaustive description of lipid and nitrogen metabolism. iNS934 has a 90% of accuracy when making simple growth/no-growth predictions and has a 15% error rate in predicting growth rates in different experimental conditions. Moreover, iNS934 allowed us to propose 82 different knockout strategies for strain optimization of triacylglycerols. Conclusions iNS934 provides a powerful tool for metabolic improvement, allowing predictions and simulations of N. salina metabolism under different media and genetic conditions. It also provides a systemic view of N. salina metabolism, potentially guiding research and providing context to -omics data. Electronic supplementary material The online version of this article (doi:10.1186/s12918-017-0441-1) contains supplementary material, which is available to authorized users.

Acidithiobacillus ferrooxidans is a chemolithoautotrophic acidophilic bacterium that obtains its energy from the oxidation of ferrous iron, elemental sulfur, or reduced sulfur minerals. This capability makes it of great industrial importance due to its applications in biomining. During the industrial processes, A. ferrooxidans survives to stressing circumstances in its environment, such as an extremely acidic pH and high concentration of transition metals. In order to gain insight into the organization of A. ferrooxidans regulatory networks and to provide a framework for further studies in bacterial growth under extreme conditions, we applied a genome-wide annotation procedure to identify 87 A. ferrooxidans transcription factors. We classified them into 19 families that were conserved among diverse prokaryotic phyla. Our annotation procedure revealed that A. ferrooxidans genome contains several members of the ArsR and MerR families, which are involved in metal resistance and detoxification. Analysis of their sequences revealed known and potentially new mechanism to coordinate gene-expression in response to metal availability. A. ferrooxidans inhabit some of the most metal-rich environments known, thus transcription factors identified here seem to be good candidates for functional studies in order to determine their physiological roles and to place them into A. ferrooxidans transcriptional regulatory networks.

A broad portfolio of phenotypic diversity in natural organisms can buffer against exploitation and increase species persistence in disturbed ecosystems. The study of genomic variation that accounts for ecological and evolutionary adaptation can represent a powerful approach to extend understanding of phenotypic variation in nature. Here we present a chromosome-level reference genome assembly for Chinook salmon ( Oncorhynchus tshawytscha ; 2.36 Gb) that enabled association mapping of life-history variation and phenotypic traits for this species. Whole-genome re-sequencing of populations with distinct life-history traits provided evidence that divergent selection was extensive throughout the genome within and among phylogenetic lineages, indicating that a broad portfolio of phenotypic diversity exists in this species that is related to local adaptation and life-history variation. Association mapping with millions of genome-wide SNPs revealed that a genomic region of major effect on chromosome 28 was associated with phenotypes for premature and mature arrival to spawning grounds and was consistent across three distinct phylogenetic lineages. Our results demonstrate how genomic resources can enlighten the genetic basis of known phenotypes in exploited species and assist in clarifying phenotypic variation that may be difficult to observe in naturally occurring organisms.

The 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-quality genome assembly for Atlantic salmon (Salmo salar), and show that large genomic reorganizations, coinciding with bursts of transposon-mediated repeat expansions, were crucial for the post-Ss4R rediploidization process. Comparisons of duplicate gene expression patterns across a wide range of tissues with orthologous genes from a pre-Ss4R outgroup unexpectedly demonstrate far more instances of neofunctionalization than subfunctionalization. Surprisingly, we find that genes that were retained as duplicates after the teleost-specific whole-genome duplication 320 million years ago were not more likely to be retained after the Ss4R, and that the duplicate retention was not influenced to a great extent by the nature of the predicted protein interactions of the gene products. Finally, we demonstrate that the Atlantic salmon assembly can serve as a reference sequence for the study of other salmonids for a range of purposes. Supplementary information The online version of this article (doi:10.1038/nature17164) contains supplementary material, which is available to authorized users., The genome sequence is presented for the Atlantic salmon (Salmo salar), providing information about a rediploidization following a salmonid-specific whole-genome duplication event that resulted in an autotetraploidization. Supplementary information The online version of this article (doi:10.1038/nature17164) contains supplementary material, which is available to authorized users., A window on salmonid genome evolution William Davidson and colleagues report sequencing and assembly of the Atlantic salmon genome, which they demonstrate as a useful reference to also improve the genome assembly of other salmanoids. Their analyses provide insights into duplicate retention patterns across two rounds of whole-genome duplication that have occurred in this lineage. Supplementary information The online version of this article (doi:10.1038/nature17164) contains supplementary material, which is available to authorized users.

Background Berry size is considered as one of the main selection criteria in table grape breeding programs. However, this is a quantitative and polygenic trait, and its genetic determination is still poorly understood. Considering its economic importance, it is relevant to determine its genetic architecture and elucidate the mechanisms involved in its expression. To approach this issue, an RNA-Seq experiment based on Illumina platform was performed (14 libraries), including seedless segregants with contrasting phenotypes for berry weight at fruit setting (FST) and 6–8 mm berries (B68) phenological stages. Results A group of 526 differentially expressed (DE) genes were identified, by comparing seedless segregants with contrasting phenotypes for berry weight: 101 genes from the FST stage and 463 from the B68 stage. Also, we integrated differential expression, principal components analysis (PCA), correlations and network co-expression analyses to characterize the transcriptome profiling observed in segregants with contrasting phenotypes for berry weight. After this, 68 DE genes were selected as candidate genes, and seven candidate genes were validated by real time-PCR, confirming their expression profiles. Conclusions We have carried out the first transcriptome analysis focused on table grape seedless segregants with contrasting phenotypes for berry weight. Our findings contributed to the understanding of the mechanisms involved in berry weight determination. Also, this comparative transcriptome profiling revealed candidate genes for berry weight which could be evaluated as selection tools in table grape breeding programs. Electronic supplementary material The online version of this article (doi:10.1186/s12870-016-0789-1) contains supplementary material, which is available to authorized users.

Background Pisciricketssia salmonis is the causal agent of Salmon Rickettsial Syndrome (SRS), which affects salmon species and causes severe economic losses. Selective breeding for disease resistance represents one approach for controlling SRS in farmed Atlantic salmon. Knowledge concerning the architecture of the resistance trait is needed before deciding on the most appropriate approach to enhance artificial selection for P. salmonis resistance in Atlantic salmon. The purpose of the study was to dissect the genetic variation in the resistance to this pathogen in Atlantic salmon. Methods 2,601 Atlantic salmon smolts were experimentally challenged against P. salmonis by means of intra-peritoneal injection. These smolts were the progeny of 40 sires and 118 dams from a Chilean breeding population. Mortalities were recorded daily and the experiment ended at day 40 post-inoculation. Fish were genotyped using a 50K Affymetrix® Axiom® myDesignTM Single Nucleotide Polymorphism (SNP) Genotyping Array. A Genome Wide Association Analysis was performed on data from the challenged fish. Linear regression and logistic regression models were tested. Results Genome Wide Association Analysis indicated that resistance to P. salmonis is a moderately polygenic trait. There were five SNPs in chromosomes Ssa01 and Ssa17 significantly associated with the traits analysed. The proportion of the phenotypic variance explained by each marker is small, ranging from 0.007 to 0.045. Candidate genes including interleukin receptors and fucosyltransferase have been found to be physically linked with these genetic markers and may play an important role in the differential immune response against this pathogen. Conclusions Due to the small amount of variance explained by each significant marker we conclude that genetic resistance to this pathogen can be more efficiently improved with the implementation of genetic evaluations incorporating genotype information from a dense SNP array. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2038-7) contains supplementary material, which is available to authorized users.

International audience; The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the portal are independently administered and funded by their host organizations. The BioMart data federation technology provides a unified interface to all the available data. The latest version of the portal comes with many new databases that have been created by our ever-growing community. It also comes with better support and extensibility for data analysis and visualization tools. A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one million requests per day. Building on this level of service and the wealth of information that has become available, the BioMart Community Portal has introduced a new, more scalable and cheaper alternative to the large data stores maintained by specialized organizations.

Acidithiobacillus thiooxidans is a sulfur oxidizing acidophilic bacterium found in many sulfur-rich environments. It is particularly interesting due to its role in bioleaching of sulphide minerals. In this work, we report the genome sequence of At. thiooxidans Licanantay, the first strain from a copper mine to be sequenced and currently used in bioleaching industrial processes. Through comparative genomic analysis with two other At. thiooxidans non-metal mining strains (ATCC 19377 and A01) we determined that these strains share a large core genome of 2109 coding sequences and a high average nucleotide identity over 98%. Nevertheless, the presence of 841 strain-specific genes (absent in other At. thiooxidans strains) suggests a particular adaptation of Licanantay to its specific biomining environment. Among this group, we highlight genes encoding for proteins involved in heavy metal tolerance, mineral cell attachment and cysteine biosynthesis. Several of these genes were located near genetic motility genes (e.g. transposases and integrases) in genomic regions of over 10 kbp absent in the other strains, suggesting the presence of genomic islands in the Licanantay genome probably produced by horizontal gene transfer in mining environments.

Background Grapevine (Vitis vinifera L.) is the most important Mediterranean fruit crop, used to produce both wine and spirits as well as table grape and raisins. Wine and table grape cultivars represent two divergent germplasm pools with different origins and domestication history, as well as differential characteristics for berry size, cluster architecture and berry chemical profile, among others. ‘Sultanina’ plays a pivotal role in modern table grape breeding providing the main source of seedlessness. This cultivar is also one of the most planted for fresh consumption and raisins production. Given its importance, we sequenced it and implemented a novel strategy for the de novo assembly of its highly heterozygous genome. Results Our approach produced a draft genome of 466 Mb, recovering 82% of the genes present in the grapevine reference genome; in addition, we identified 240 novel genes. A large number of structural variants and SNPs were identified. Among them, 45 (21 SNPs and 24 INDELs) were experimentally confirmed in ‘Sultanina’ and six SNPs in other 23 table grape varieties. Transposable elements corresponded to ca. 80% of the repetitive sequences involved in structural variants and more than 2,000 genes were affected in their structure by these variants. Some of these genes are likely involved in embryo development, suggesting that they may contribute to seedlessness, a key trait for table grapes. Conclusions This work produced the first structural variants and SNPs catalog for grapevine, constituting a novel and very powerful tool for genomic studies in this key fruit crop, particularly useful to support marker assisted breeding in table grapes.

The genome of potato, a major global food crop, was recently sequenced. The work presented here details the integration of the potato reference genome (DM) with a new sequence-tagged site marker-based linkage map and other physical and genetic maps of potato and the closely related species tomato. Primary anchoring of the DM genome assembly was accomplished by the use of a diploid segregating population, which was genotyped with several types of molecular genetic markers to construct a new similar to 936 cM linkage map comprising 2469 marker loci. In silico anchoring approaches used genetic and physical maps from the diploid potato genotype RH89-039-16 (RH) and tomato. This combined approach has allowed 951 superscaffolds to be ordered into pseudomolecules corresponding to the 12 potato chromosomes. These pseudomolecules represent 674 Mb (similar to 93%) of the 723 Mb genome assembly and 37,482 (similar to 96%) of the 39,031 predicted genes. The superscaffold order and orientation within the pseudomolecules are closely collinear with independently constructed high density linkage maps. Comparisons between marker distribution and physical location reveal regions of greater and lesser recombination, as well as regions exhibiting significant segregation distortion. The work presented here has led to a greatly improved ordering of the potato reference genome superscaffolds into chromosomal pseudomolecules. Potato Genome Sequencing grant, UK; Scottish Government Rural and Environmental Science and Analytical Services Division (RESAS); Department for Environment, Food and Rural Affairs (DEFRA)Department for Environment, Food & Rural Affairs (DEFRA); Agriculture and Horticulture Development Board (AHDB)-Potato Council; Biotechnology and Biological Sciences Research Council (BBSRC)Biotechnology and Biological Sciences Research Council (BBSRC) [BB/F012640]; New Zealand Institute for Crop & Food Research Ltd Strategic Science Initiative; New Zealand Institute for Plant & Food Research Ltd Capability Fund, New Zealand; NMEA (Netherlands Ministry of Economic Affairs); CBSG (Centre for BioSystems Genomics); STW (Netherlands Technology Foundation), The Netherlands [07796]; Teagasc Core Funding; DAFF-Research Stimulus Fund, Ireland; International Potato Center (CIP-CGIAR)/CRP RTB, Peru; CONICYTComision Nacional de Investigacion Cientifica y Tecnologica (CONICYT) [Fondap 1509007, PBCT-PSD-03]; CONICYT (Basal CMM); CIRIC INRIA; INIA-Ministry of Agriculture of Chile, Chile; FEMCIDI OEA [PE/09/02 MINCyT-CONCyTEC]; Instituto Nacional de Tecnologia Agropecuaria (INTA-Core Funds); Ministerio de Ciencia y Tecnologia (MINCyT), Argentina; Proyecto FEMCIDI-OEA [SEDI/AE-305 /09]; Proyecto Bilateral Argentina, Per; FINCyT [099-FINCyT-EQUIP-2009) / (076-FINCyT-PIN-2008)]; Prestamo BID [1663/OC-PE]; Instituto Nacional de Innovacion Agraria, Ministry of Agriculture of Peru; Peruvian Ministry of Agriculture, Technical Secretariat of coordination; CGIAR; Consejo Nacional de Ciencia, Tecnologia e Innovacion Tecnologica, Peru (CONCYTEC); Special Multilateral Fund of the Inter-American Council for Integral Development (FEMCIDI-Peru); Biotechnology and Biological Sciences Research CouncilBiotechnology and Biological Sciences Research Council (BBSRC) [BB/F012640/1] We thank Andrzej Kilian (Diversity Arrays Technology, Australia) for DArT genotyping of the DMDD mapping population. We acknowledge Peter E. Hedley and Clare Booth (The James Hutton Institute, UK) for help with SNP genotyping. We thank S. B. Divito (Instituto Nacional de Tecnologia Agropecuaria, Balcarce, Argentina) for technical assistance. We are also grateful to Luke Ramsay and Peter E. Hedley (The James Hutton Institute, UK) for comments on the manuscript. AFLP and WGP are (registered) trademarks owned by KeyGene N.V. We acknowledge the funding made available by the Potato Genome Sequencing grant, UK [Scottish Government Rural and Environmental Science and Analytical Services Division (RESAS), Department for Environment, Food and Rural Affairs (DEFRA), Agriculture and Horticulture Development Board (AHDB)-Potato Council, Biotechnology and Biological Sciences Research Council (BBSRC, Grant BB/F012640)]; New Zealand Institute for Crop & Food Research Ltd Strategic Science Initiative and the New Zealand Institute for Plant & Food Research Ltd Capability Fund, New Zealand; NMEA (Netherlands Ministry of Economic Affairs), CBSG (Centre for BioSystems Genomics), STW (Netherlands Technology Foundation grant 07796), The Netherlands; Teagasc Core Funding, DAFF-Research Stimulus Fund, Ireland; International Potato Center (CIP-CGIAR)/CRP RTB, Peru; CONICYT (Fondap 1509007, Basal CMM, PBCT-PSD-03), CIRIC INRIA, INIA-Ministry of Agriculture of Chile, Chile; FEMCIDI OEA, PE/09/02 MINCyT-CONCyTEC, 2010-2011, Instituto Nacional de Tecnologia Agropecuaria (INTA-Core Funds) and Ministerio de Ciencia y Tecnologia (MINCyT), Argentina; Proyecto FEMCIDI-OEA SEDI/AE-305 /09 (2008-2012), Proyecto Bilateral Argentina, Per; FINCyT (099-FINCyT-EQUIP-2009) / (076-FINCyT-PIN-2008), Prestamo BID no. 1663/OC-PE, Instituto Nacional de Innovacion Agraria, Ministry of Agriculture of Peru, Peruvian Ministry of Agriculture, Technical Secretariat of coordination with the CGIAR, Consejo Nacional de Ciencia, Tecnologia e Innovacion Tecnologica, Peru (CONCYTEC), Special Multilateral Fund of the Inter-American Council for Integral Development (FEMCIDI-Peru).

Background Data normalization is a key step in gene expression analysis by qPCR. Endogenous control genes are used to estimate variations and experimental errors occurring during sample preparation and expression measurements. However, the transcription level of the most commonly used reference genes can vary considerably in samples obtained from different individuals, tissues, developmental stages and under variable physiological conditions, resulting in a misinterpretation of the performance of the target gene(s). This issue has been scarcely approached in woody species such as grapevine. Results A statistical criterion was applied to select a sub-set of 19 candidate reference genes from a total of 242 non-differentially expressed (NDE) genes derived from a RNA-Seq experiment comprising ca. 500 million reads obtained from 14 table-grape genotypes sampled at four phenological stages. From the 19 candidate reference genes, VvAIG1 (AvrRpt2-induced gene) and VvTCPB (T-complex 1 beta-like protein) were found to be the most stable ones after comparing the complete set of genotypes and phenological stages studied. This result was further validated by qPCR and geNorm analyses. Conclusions Based on the evidence presented in this work, we propose to use the grapevine genes VvAIG1 or VvTCPB or both as a reference tool to normalize RNA expression in qPCR assays or other quantitative method intended to measure gene expression in berries and other tissues of this fruit crop, sampled at different developmental stages and physiological conditions.

Cyclin-dependent kinase 5 (Cdk5) is a proline-directed serine/threonine kinase predominantly active in the nervous system where it regulates several processes such as neuronal migration, cytoskeletal dynamics, axonal guidance, and neurotransmission. We constructed a position specific scoring matrix (PSSM) based on a dataset of sites shown to be phosphorylated both in vivo and in vitro by Cdk5. This dataset was curated manually through an exhaustive search of published experimental data. We then used this PSSM to perform a search in the mouse proteome through Scansite, a web-based tool for matching sequence patterns in large databases. Considering a stringent cut-off score of 0.5, we identified 354 new putative sites present in 291 proteins. In order to assess the robustness of our results, ten random subsets (of 80 sites each) of the original dataset were used to construct new PSSMs, which were then used as input for a new Scansite search, leading to the recovery of 81% of the 354 sites by at least 5 PSSMs. In order to reduce the number of false positives in our sequence-based approach, we evaluated which of these predicted sites were phosphorylated in vivo as determined by multiple phosphoproteomics studies carried out through mass spectrometry and available in the PhosphoSitePlus database. This step resulted in a very promising list of 132 putative phosphorylation sites for Cdk5, of which, 51 are specifically phosphorylated in brain tissue, and some are involved in functions regulated by Cdk5 such as axonal growth, synaptic plasticity and neurotransmission. Other phosphorylation sites in our list suggest that Cdk5 might regulate processes through mechanisms not previously recognized such as the control of mRNA splicing.

SalmonDB is a new multiorganism database containing EST sequences from Salmo salar, Oncorhynchus mykiss and the whole genome sequence of Danio rerio, Gasterosteus aculeatus, Tetraodon nigroviridis, Oryzias latipes and Takifugu rubripes, built with core components from GMOD project, GOPArc system and the BioMart project. The information provided by this resource includes Gene Ontology terms, metabolic pathways, SNP prediction, CDS prediction, orthologs prediction, several precalculated BLAST searches and domains. It also provides a BLAST server for matching user-provided sequences to any of the databases and an advanced query tool (BioMart) that allows easy browsing of EST databases with user-defined criteria. These tools make SalmonDB database a valuable resource for researchers searching for transcripts and genomic information regarding S. salar and other salmonid species. The database is expected to grow in the near feature, particularly with the S. salar genome sequencing project. Database URL: http://genomicasalmones.dim.uchile.cl/