Genome Sequencing and Transcriptome Analysis Reveal Recent Species-specific Gene Duplications in the Plastic Gilthead Sea Bream
AbstractGilthead sea bream is an economically important fish species that is remarkably well-adapted to farming and changing environments. Understanding the genomic basis of this plasticity will serve to orientate domestication and selective breeding towards more robust and efficient fish. To address this goal, a draft genome assembly was reconstructed combining short- and long-read high-throughput sequencing with genetic linkage maps. The assembled unmasked genome spans 1.24 Gb of an expected 1.59 Gb genome size with 932 scaffolds (∼732 Mb) anchored to 24 chromosomes that are available as a karyotype browser at www.nutrigroup-iats.org/seabreambrowser. Homology-based functional annotation, …
Acting locally - affecting globally: RNA sequencing of gilthead sea bream with a mild Sparicotyle chrysophrii infection reveals effects on apoptosis, immune and hypoxia related genes
[Background] Monogenean flatworms are the main fish ectoparasites inflicting serious economic losses in aquaculture. The polyopisthocotylean Sparicotyle chrysophrii parasitizes the gills of gilthead sea bream (GSB, Sparus aurata) causing anaemia, lamellae fusion and sloughing of epithelial cells, with the consequent hypoxia, emaciation, lethargy and mortality. Currently no preventive or curative measures against this disease exist and therefore information on the host-parasite interaction is crucial to find mitigation solutions for sparicotylosis. The knowledge about gene regulation in monogenean-host models mostly comes from freshwater monopysthocotyleans and almost nothing is known about …
Additional file 4: of Acting locally - affecting globally: RNA sequencing of gilthead sea bream with a mild Sparicotyle chrysophrii infection reveals effects on apoptosis, immune and hypoxia related genes
Exploratory analysis of the samples prior to differential expression study. The FPKM density distributions showed three samples with anomalies (red arrows and red in the legend) that were not included in downstream analyses: gill infected parasitized 1 (A), gill infected non-parasitized 5 (B) and spleen infected 2 (D). All liver samples (C) showed uniform distributions and were included in the analyses. (PDF 292 kb)
Effect of virgin low density polyethylene microplastic ingestion on intestinal histopathology and microbiota of gilthead sea bream
© 2021 The Authors.
Additional file 3: of Acting locally - affecting globally: RNA sequencing of gilthead sea bream with a mild Sparicotyle chrysophrii infection reveals effects on apoptosis, immune and hypoxia related genes
Pathway classification of DE genes. Bar plots representing the percentage of proteins involved in each broad Reactome pathway. The column labelled Reactome was added as a reference to show the percentage of genes in each category in the database. The other columns represent the percentage of differentially expressed (DE) genes in each category when considering all DE genes in all the tissues of the current experiment (Total) or per tissue, when compared to the control uninfected group. Gill samples are separated in parasitized (P) and non-parasitized (NP) gill sections. (PDF 343 kb)
Client Applications and Server-Side Docker for Management of RNASeq and/or VariantSeq Workflows and Pipelines of the GPRO Suite
The GPRO suite is an in-progress bioinformatic project for -omics data analysis. As part of the continued growth of this project, we introduce a client- and server-side solution for comparative transcriptomics and analysis of variants. The client-side consists of two Java applications called “RNASeq” and “VariantSeq” to manage pipelines and workflows based on the most common command line interface tools for RNA-seq and Variant-seq analysis, respectively. As such, “RNASeq” and “VariantSeq” are coupled with a Linux server infrastructure (named GPRO Server-Side) that hosts all dependencies of each application (scripts, databases, and command line interface software). Implementation of the Serv…
Additional file 1: of Acting locally - affecting globally: RNA sequencing of gilthead sea bream with a mild Sparicotyle chrysophrii infection reveals effects on apoptosis, immune and hypoxia related genes
A) PCR-array results: Mean and SEM of the fold changes of the 45 selected genes in Sparicotyle infected fish (n = 10) calculated relative to the control uninfected group (n = 10) in parasitized gill portions (with parasite presence), non-parasitized gill portions (no parasite present) and spleen. Student’s t test or Mann-Whitney-Wilcoxon test when normality conditions were not met were used to calculate p values comparing expression levels of control and infected animals per gene. Dark red and green indicate significantly up- or down-regulated genes, respectively, with p
Genome Sequencing and Transcriptome Analysis Reveal Recent Species-Specific Gene Duplications in the Plastic Gilthead Sea Bream (Sparus aurata)
Gilthead sea bream is an economically important fish species that is remarkably well-adapted to farming and changing environments. Understanding the genomic basis of this plasticity will serve to orientate domestication and selective breeding toward more robust and efficient fish. To address this goal, a draft genome assembly was reconstructed combining short- and long-read high-throughput sequencing with genetic linkage maps. The assembled unmasked genome spans 1.24 Gb of an expected 1.59 Gb genome size with 932 scaffolds (~732 Mb) anchored to 24 chromosomes that are available as a karyotype browser at www.nutrigroup-iats.org/seabreamdb. Homology-based functional annotation, supported by R…
Additional file 2: of Acting locally - affecting globally: RNA sequencing of gilthead sea bream with a mild Sparicotyle chrysophrii infection reveals effects on apoptosis, immune and hypoxia related genes
Gene ontology (GO) enrichment analysis based on the number of DE genes per tissue (FDR cutoff 0.05). The Tabs entitled “TISSUE EnrichGO” contain the detailed lists of the enriched GO total, up- and down-regulated sorted by ontology (Biological process (BP), Cellular compartment (CC) and Molecular function (MF)). (XLSX 49 kb)