A resource for sustainable management:<i>De novo</i> assembly and annotation of the liver transcriptome of the Atlantic chub mackerel, <i>Scomber colias</i>

Mackerels represent a valuable fishery worldwide. Their ample geographic distribution and capture levels make them an insightful model to address stock management strategies in the context of global changes. Yet, and despite recent impressive genome and transcriptome sequencing efforts from teleost species, available resources from the Scombridae family are comparatively scarce. Here, we generated the first high-quality de novo assembly of the liver transcriptome of the Atlantic chub mackerel (Scomber colias). Through the use of RNA-Seq Illumina technology, 111,124,228 clean reads were obtained for the liver transcriptome. De novo assembly resulted in 93,731 transcripts with an N50 of 1462 bp. This dataset provides an important insight into the context of fisheries management. Keywords: RNA-Seq, Scombridae, Stock management, Atlantic chub mackerel, Live

Molecular evolution and the role of oxidative stress in the expansion and functional diversification of cytosolic glutathione transferases

<p>Abstract</p> <p>Background</p> <p>Cytosolic glutathione transferases (cGST) are a large group of ubiquitous enzymes involved in detoxification and are well known for their undesired side effects during chemotherapy. In this work we have performed thorough phylogenetic analyses to understand the various aspects of the evolution and functional diversification of cGSTs. Furthermore, we assessed plausible correlations between gene duplication and substrate specificity of gene paralogs in humans and selected species, notably in mammalian enzymes and their natural substrates.</p> <p>Results</p> <p>We present a molecular phylogeny of cytosolic GSTs that shows that several classes of cGSTs are more ubiquitous and thus have an older ancestry than previously thought. Furthermore, we found that positive selection is implicated in the diversification of cGSTs. The number of duplicate genes per class is generally higher for groups of enzymes that metabolize products of oxidative damage.</p> <p>Conclusions</p> <p>1) Protection against oxidative stress seems to be the major driver of positive selection in mammalian cGSTs, explaining the overall expansion pattern of this subfamily;</p> <p>2) Given the functional redundancy of GSTs that metabolize xenobiotic chemicals, we would expect the loss of gene duplicates, but by contrast we observed a gene expansion of this family, which likely has been favored by: i) the diversification of endogenous substrates; ii) differential tissue expression; and iii) increased specificity for a particular molecule;</p> <p>3) The increased availability of sequence data from diversified taxa is likely to continue to improve our understanding of the early origin of the different cGST classes.</p

DivA:detection of non-homologous and very divergent regions in protein sequence alignments

BACKGROUND: Sequence alignments are used to find evidence of homology but sometimes contain regions that are difficult to align which can interfere with the quality of the subsequent analyses. Although it is possible to remove problematic regions manually, this is non-practical in large genome scale studies, and the results suffer from irreproducibility arising from subjectivity. Some automated alignment trimming methods have been developed to remove problematic regions in alignments but these mostly act by removing complete columns or complete sequences from the MSA, discarding a lot of informative sites. FINDINGS: Here we present a tool that identifies Divergent windows in protein sequence Alignments (DivA). DivA makes no assumptions on evolutionary models, and it is ideal for detecting incorrectly annotated segments within individual gene sequences. DivA works with a sliding-window approach to estimate four divergence-based parameters and their outlier values. It then classifies a window of a sequence of an alignment as very divergent (potentially non-homologous) if it presents a combination of outlier values for the four parameters it calculates. The windows classified as very divergent can optionally be masked in the alignment. CONCLUSIONS: DivA automatically identifies very divergent and incorrectly annotated genic regions in MSAs avoiding the subjective and time-consuming problem of manual annotation. The output is clear to interpret and allows the user to take more informed decisions for reducing the amount of sequence discarded but still finding the potentially erroneous and non-homologous regions. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1756-0500-7-806) contains supplementary material, which is available to authorized users

The adaptive evolution of the mammalian mitochondrial genome

<p>Abstract</p> <p>Background</p> <p>The mitochondria produce up to 95% of a eukaryotic cell's energy through oxidative phosphorylation. The proteins involved in this vital process are under high functional constraints. However, metabolic requirements vary across species, potentially modifying selective pressures. We evaluate the adaptive evolution of 12 protein-coding mitochondrial genes in 41 placental mammalian species by assessing amino acid sequence variation and exploring the functional implications of observed variation in secondary and tertiary protein structures.</p> <p>Results</p> <p>Wide variation in the properties of amino acids were observed at functionally important regions of cytochrome <it>b </it>in species with more-specialized metabolic requirements (such as adaptation to low energy diet <it>or </it>large body size, such as in elephant, dugong, sloth, and pangolin, and adaptation to unusual oxygen requirements, for example diving in cetaceans, flying in bats, and living at high altitudes in alpacas). Signatures of adaptive variation in the NADH dehydrogenase complex were restricted to the loop regions of the transmembrane units which likely function as protons pumps. Evidence of adaptive variation in the cytochrome <it>c </it>oxidase complex was observed mostly at the interface between the mitochondrial and nuclear-encoded subunits, perhaps evidence of co-evolution. The ATP8 subunit, which has an important role in the assembly of F₀, exhibited the highest signal of adaptive variation. ATP6, which has an essential role in rotor performance, showed a high adaptive variation in predicted loop areas.</p> <p>Conclusion</p> <p>Our study provides insight into the adaptive evolution of the mtDNA genome in mammals and its implications for the molecular mechanism of oxidative phosphorylation. We present a framework for future experimental characterization of the impact of specific mutations in the function, physiology, and interactions of the mtDNA encoded proteins involved in oxidative phosphorylation.</p

Consequences of breed formation on patterns of genomic diversity and differentiation: the case of highly diverse peripheral Iberian cattle

Iberian primitive breeds exhibit a remarkable phenotypic diversity over a very limited geographical space. While genomic data are accumulating for most commercial cattle, it is still lacking for these primitive breeds. Whole genome data is key to understand the consequences of historic breed formation and the putative role of earlier admixture events in the observed diversity patterns.info:eu-repo/semantics/publishedVersio

Patterns of Positive Selection in Six Mammalian Genomes

Genome-wide scans for positively selected genes (PSGs) in mammals have provided insight into the dynamics of genome evolution, the genetic basis of differences between species, and the functions of individual genes. However, previous scans have been limited in power and accuracy owing to small numbers of available genomes. Here we present the most comprehensive examination of mammalian PSGs to date, using the six high-coverage genome assemblies now available for eutherian mammals. The increased phylogenetic depth of this dataset results in substantially improved statistical power, and permits several new lineage- and clade-specific tests to be applied. Of ∼16,500 human genes with high-confidence orthologs in at least two other species, 400 genes showed significant evidence of positive selection (FDR<0.05), according to a standard likelihood ratio test. An additional 144 genes showed evidence of positive selection on particular lineages or clades. As in previous studies, the identified PSGs were enriched for roles in defense/immunity, chemosensory perception, and reproduction, but enrichments were also evident for more specific functions, such as complement-mediated immunity and taste perception. Several pathways were strongly enriched for PSGs, suggesting possible co-evolution of interacting genes. A novel Bayesian analysis of the possible “selection histories” of each gene indicated that most PSGs have switched multiple times between positive selection and nonselection, suggesting that positive selection is often episodic. A detailed analysis of Affymetrix exon array data indicated that PSGs are expressed at significantly lower levels, and in a more tissue-specific manner, than non-PSGs. Genes that are specifically expressed in the spleen, testes, liver, and breast are significantly enriched for PSGs, but no evidence was found for an enrichment for PSGs among brain-specific genes. This study provides additional evidence for widespread positive selection in mammalian evolution and new genome-wide insights into the functional implications of positive selection.</p

Adaptive venom evolution and toxicity in octopods is driven by extensive novel gene formation, expansion, and loss

Background: Cephalopods represent a rich system for investigating the genetic basis underlying organismal novelties. This diverse group of specialized predators has evolved many adaptations including proteinaceous venom. Of particular interest is the blue-ringed octopus genus (Hapalochlaena), which are the only octopods known to store large quantities of the potent neurotoxin, tetrodotoxin, within their tissues and venom gland. Findings: To reveal genomic correlates of organismal novelties, we conducted a comparative study of 3 octopod genomes, including the Southern blue-ringed octopus (Hapalochlaena maculosa). We present the genome of this species and reveal highly dynamic evolutionary patterns at both non-coding and coding organizational levels. Gene family expansions previously reported in Octopus bimaculoides (e.g., zinc finger and cadherins, both associated with neural functions), as well as formation of novel gene families, dominate the genomic landscape in all octopods. Examination of tissue-specific genes in the posterior salivary gland revealed that expression was dominated by serine proteases in non–tetrodotoxin-bearing octopods, while this family was a minor component in H. maculosa. Moreover, voltage-gated sodium channels in H. maculosa contain a resistance mutation found in pufferfish and garter snakes, which is exclusive to the genus. Analysis of the posterior salivary gland microbiome revealed a diverse array of bacterial species, including genera that can produce tetrodotoxin, suggestive of a possible production source. Conclusions: We present the first tetrodotoxin-bearing octopod genome H. maculosa, which displays lineage-specific adaptations to tetrodotoxin acquisition. This genome, along with other recently published cephalopod genomes, represents a valuable resource from which future work could advance our understanding of the evolution of genomic novelty in this family