scholarly journals Genome Sequencing and Transcriptome Analysis Reveal Recent Species-specific Gene Duplications in the Plastic Gilthead Sea Bream

2019 ◽  
Author(s):  
Jaume Pérez-Sánchez ◽  
Fernando Naya-Català ◽  
Beatriz Soriano ◽  
M. Carla Piazzon ◽  
Ahmed Hafez ◽  
...  
Keyword(s):  
Genome Size ◽  
Transcriptional Analysis ◽  
Gilthead Sea Bream ◽  
Sea Bream ◽  
Specific Gene ◽  
Gene Repertoire ◽  
Gene Duplications ◽  
Dna Transposons ◽  
Species Specific

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, supported by RNA-seq transcripts, identified 55,423 actively transcribed genes corresponding to 21,275 unique descriptions with more than 55% of duplicated genes. The mobilome accounts for the 75% of the full genome size and it is mostly constituted by introns (599 Mb), whereas the rest is represented by low complexity repeats, RNA retrotransposons, DNA transposons and non-coding RNAs. This mobilome also contains a large number of chimeric/composite genes (i. e. loci presenting fragments or exons mostly surrounded by LINEs and Tc1/mariner DNA transposons), whose analysis revealed an enrichment in immune-related functions and processes. Analysis of synteny and gene phylogenies uncovered a high rate of species-specific duplications, resulting from recent independent duplications rather than from genome polyploidization (2.024 duplications per gene; 0.385 excluding gene expansions). These species-specific duplications were enriched in gene families functionally related to genome transposition, immune response and sensory responses. Additionally, transcriptional analysis of liver, skeletal muscle, intestine, gills and spleen supported a high number of functionally specialized paralogs under tissue-exclusive regulation. Altogether, these findings suggest a role of recent large-scale gene duplications coupled to tissue expression diversification in the evolution of gilthead sea bream genome during its successful adaptation to a changing and pathogen-rich environment. This issue also underscores a role of evolutionary routes for rapid increase of the gene repertoire in teleost fish that are independent of polyploidization. Since gilthead sea bream has a well-recognized plasticity, the current study will advance our understanding of fish biology and how organisms of this taxon interact with the environment.

Distinct role of insulin and IGF-I and its receptors in white skeletal muscle during the compensatory growth of gilthead sea bream (Sparus aurata)

Aquaculture ◽  
2007 ◽  
Vol 267 (1-4) ◽  
pp. 188-198 ◽  
Author(s):  
Núria Montserrat ◽  
Pedro Gómez-Requeni ◽  
Giovanni Bellini ◽  
Encarnación Capilla ◽  
Jaume Pérez-Sánchez ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Compensatory Growth ◽  
Sparus Aurata ◽  
Gilthead Sea Bream ◽  
Sea Bream ◽  
Igf I ◽  
Distinct Role

scholarly journals Modulation of Gilthead Sea Bream Gut Microbiota by a Bioactive Egg White Hydrolysate: Interactions Between Bacteria and Host Lipid Metabolism

2021 ◽  
Vol 8 ◽  
Author(s):  
Fernando Naya-Català ◽  
Giulia A. Wiggers ◽  
M. Carla Piazzon ◽  
Manuel I. López-Martínez ◽  
Itziar Estensoro ◽  
...  
Keyword(s):  
Lipid Metabolism ◽  
Gut Microbiota ◽  
Sparus Aurata ◽  
Egg White ◽  
Gilthead Sea Bream ◽  
Sea Bream ◽  
Gut Health ◽  
Feed Conversion ◽  
Anterior Intestine

This study aimed to highlight the relationship between diet, animal performance and mucosal adherent gut microbiota (anterior intestine) in fish fed plant-based diets supplemented with an egg white hydrolysate (EWH) with antioxidant and anti-obesogenic activity in obese rats. The feeding trial with juveniles of gilthead sea bream (Sparus aurata) lasted 8 weeks. Fish were fed near to visual satiety with a fish meal (FM)/fish oil (FO) based diet (CTRL) or a plant-based diet with/without EWH supplementation. Specific growth rate decreased gradually from 2.16% in CTRL fish to 1.88% in EWH fish due to a reduced feed intake, and a slight impairment of feed conversion ratio. Plant-based diets feeding triggered a hyperplasic inflammation of the anterior intestine regardless of EWH supplementation. However, EWH ameliorated the goblet cell depletion, and the hepatic and intestinal lipid accumulation induced by FM/FO replacement. Illumina sequencing of gut mucosal microbiota yielded a mean of 136,252 reads per sample assigned to 2,117 OTUs at 97% identity threshold. The bacterial diversity was similar in all groups, but a significantly lower richness was found in EWH fish. At the phylum level, Proteobacteria reached the highest proportion in CTRL and EWH fish, whereas Firmicutes were decreased and Actinobacteria increased with the FM/FO replacement. The proportion of Actinobacteria was restored by dietary EWH supplementation, which also triggered a highest amount of Bacteroidetes and Spirochaetes. At a closer look, a widespread presence of Lactobacillales among groups was found. Otherwise, polysaccharide hydrolases secretors represented by Corynebacterium and Nocardioides were increased by the FM/FO replacement, whereas the mucin-degrading Streptococcus was only raised in fish fed the plant-based diet without EWH. In addition, in EWH fish, a higher abundance of Propionibacterium was related to an increased concentration of intestinal propionate. The antagonism of gut health-promoting propionate with cholesterol could explain the inferred underrepresentation of primary bile acid biosynthesis and steroid degradation pathways in the EWH fish microbiota. Altogether, these results reinforce the central role of gut microbiota in the regulation of host metabolism and lipid metabolism in particular, suggesting a role of the bioactive EWH peptides as an anti-obesity and/or satiety factor in fish.

The role of maslinic acid in the pentose phosphate pathway during growth of gilthead sea bream(Sparus Aurata)

2013 ◽  
Vol 19 (5) ◽  
pp. 709-720 ◽  
Author(s):  
Eva E. Rufino-Palomares ◽  
Fernando J. Reyes-Zurita ◽  
Leticia García-Salguero ◽  
Juan Peragón ◽  
Manuel de la Higuera ◽  
...  
Keyword(s):  
Pentose Phosphate Pathway ◽  
Sparus Aurata ◽  
Pentose Phosphate ◽  
Gilthead Sea Bream ◽  
Sea Bream ◽  
Maslinic Acid

scholarly journals Moderate and sustained exercise modulates muscle proteolytic and myogenic markers in gilthead sea bream (Sparus aurata)

2017 ◽  
Vol 312 (5) ◽  
pp. R643-R653 ◽  
Author(s):  
Emilio J. Vélez ◽  
Sheida Azizi ◽  
Esmail Lutfi ◽  
Encarnación Capilla ◽  
Alberto Moya ◽  
...  
Keyword(s):  
Gene Expression ◽  
Protein Expression ◽  
Gilthead Sea Bream ◽  
Sea Bream ◽  
Control Fish ◽  
Proliferation Marker ◽  
Continuous Growth ◽  
Gene And Protein Expression ◽  
Caudal Area

Swimming activity primarily accelerates growth in fish by increasing protein synthesis and energy efficiency. The role of muscle in this process is remarkable and especially important in teleosts, where muscle represents a high percentage of body weight and because many fish species present continuous growth. The aim of this work was to characterize the effects of 5 wk of moderate and sustained swimming in gene and protein expression of myogenic regulatory factors, proliferation markers, and proteolytic molecules in two muscle regions (anterior and caudal) of gilthead sea bream fingerlings. Western blot results showed an increase in the proliferation marker proliferating cell nuclear antigen (PCNA), proteolytic system members calpain 1 and cathepsin D, as well as vascular endothelial growth factor protein expression. Moreover, quantitative real-time PCR data showed that exercise increased the gene expression of proteases (calpains, cathepsins, and members of the ubiquitin-proteasome system in the anterior muscle region) and the gene expression of the proliferation marker PCNA and the myogenic factor MyoD in the caudal area compared with control fish. Overall, these data suggest a differential response of the two muscle regions during swimming adaptation, with tissue remodeling and new vessel formation occurring in the anterior muscle and enhanced cell proliferation and differentiation occurring in the caudal area. In summary, the present study contributes to improving the knowledge of the role of proteolytic molecules and other myogenic factors in the adaptation of muscle to moderate sustained swimming in gilthead sea bream.

scholarly journals Post-prandial Amino Acid Changes in Gilthead Sea Bream

Animals ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1889
Author(s):  
Eleni Mente ◽  
Chris G. Carter ◽  
Robin S. (Katersky) Barnes ◽  
Nikolaos Vlahos ◽  
Ioannis Nengas
Keyword(s):  
Amino Acid ◽  
White Muscle ◽  
Nutrient Utilization ◽  
Plant Protein ◽  
Gilthead Sea Bream ◽  
Sea Bream ◽  
Fishmeal Replacement ◽  
Dietary Nutrient ◽  
Species Specific ◽  
Marine Protein

Following a meal, a series of physiological changes occurs in fish as they digest, absorb and assimilate ingested nutrients. This study aims to assess post-prandial free amino acid (FAA) activity in gilthead sea bream consuming a partial marine protein (fishmeal) replacement. Sea bream were fed diets where 16 and 27% of the fishmeal protein was replaced by plant protein. The essential amino acid (EAA) composition of the white muscle, liver and gut of sea bream was strongly correlated with the EAA composition of the 16% protein replacement diet compared to the 27% protein replacement diet. The mean FAA concentration in the white muscle and liver changed at 4 to 8 h after a meal and was not different to pre-feeding (0 h) and at 24 h after feeding. It was confirmed in this study that 16% replacement of marine protein with plant protein meets the amino acid needs of sea bream. Overall, the present study contributes towards understanding post-prandial amino acid profiles during uptake, tissue assimilation and immediate metabolic processing of amino acids in sea bream consuming a partial marine protein replacement. This study suggests the need to further investigate the magnitude of the post-prandial tissue-specific amino acid activity in relation to species-specific abilities to regulate metabolism due to dietary nutrient utilization.

scholarly journals Selection following Gene Duplication Shapes Recent Genome Evolution in the Pea Aphid Acyrthosiphon pisum

2020 ◽  
Vol 37 (9) ◽  
pp. 2601-2615 ◽  
Author(s):  
Rosa Fernández ◽  
Marina Marcet-Houben ◽  
Fabrice Legeai ◽  
Gautier Richard ◽  
Stéphanie Robin ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Acyrthosiphon Pisum ◽  
High Capacity ◽  
Chromatin Accessibility ◽  
Pea Aphid ◽  
Specific Gene ◽  
Gene Duplications ◽  
Evolutionary Mechanisms ◽  
Ancestral Gene ◽  
Species Specific

Abstract Ecology of insects is as wide as their diversity, which reflects their high capacity of adaptation in most of the environments of our planet. Aphids, with over 4,000 species, have developed a series of adaptations including a high phenotypic plasticity and the ability to feed on the phloem sap of plants, which is enriched in sugars derived from photosynthesis. Recent analyses of aphid genomes have indicated a high level of shared ancestral gene duplications that might represent a basis for genetic innovation and broad adaptations. In addition, there are a large number of recent, species-specific gene duplications whose role in adaptation remains poorly understood. Here, we tested whether duplicates specific to the pea aphid Acyrthosiphon pisum are related to genomic innovation by combining comparative genomics, transcriptomics, and chromatin accessibility analyses. Consistent with large levels of neofunctionalization, we found that most of the recent pairs of gene duplicates evolved asymmetrically, showing divergent patterns of positive selection and gene expression. Genes under selection involved a plethora of biological functions, suggesting that neofunctionalization and tissue specificity, among other evolutionary mechanisms, have orchestrated the evolution of recent paralogs in the pea aphid and may have facilitated host–symbiont cooperation. Our comprehensive phylogenomics analysis allowed us to tackle the history of duplicated genes to pave the road toward understanding the role of gene duplication in ecological adaptation.

scholarly journals Specific Evolution and Gene Family Expansion of Complement 3 and Regulatory Factor H in Fish

2020 ◽  
Vol 11 ◽  
Author(s):  
Babak Najafpour ◽  
João C. R. Cardoso ◽  
Adelino V. M. Canário ◽  
Deborah M. Power
Keyword(s):  
Complement System ◽  
Sparus Aurata ◽  
Factor H ◽  
Gilthead Sea Bream ◽  
Sea Bream ◽  
Immune Gene ◽  
Gene Repertoire ◽  
Tandem Gene Duplication ◽  
Hepatic Expression ◽  
The Complement System

The complement system comprises a large family of plasma proteins that play a central role in innate and adaptive immunity. To better understand the evolution of the complement system in vertebrates and the contribution of complement to fish immunity comprehensive in silico and expression analysis of the gene repertoire was made. Particular attention was given to C3 and the evolutionary related proteins C4 and C5 and to one of the main regulatory factors of C3b, factor H (Cfh). Phylogenetic and gene linkage analysis confirmed the standing hypothesis that the ancestral c3/c4/c5 gene duplicated early. The duplication of C3 (C3.1 and C3.2) and C4 (C4.1 and C4.2) was likely a consequence of the (1R and 2R) genome tetraploidization events at the origin of the vertebrates. In fish, gene number was not conserved and multiple c3 and cfh sequence related genes were encountered, and phylogenetic analysis of each gene generated two main clusters. Duplication of c3 and cfh genes occurred across the teleosts in a species-specific manner. In common, with other immune gene families the c3 gene expansion in fish emerged through a process of tandem gene duplication. Gilthead sea bream (Sparus aurata), had nine c3 gene transcripts highly expressed in liver although as reported in other fish, extra-hepatic expression also occurs. Differences in the sequence and protein domains of the nine deduced C3 proteins in the gilthead sea bream and the presence of specific cysteine and N-glycosylation residues within each isoform was indicative of functional diversity associated with structure. The diversity of C3 and other complement proteins as well as Cfh in teleosts suggests they may have an enhanced capacity to activate complement through direct interaction of C3 isoforms with pathogenic agents.

scholarly journals Osmoregulatory role of vasotocinergic and isotocinergic systems in the gilthead sea bream (Sparus aurata L)

2018 ◽  
Vol 257 ◽  
pp. 177-183 ◽  
Author(s):  
Juan Miguel Mancera ◽  
Gonzalo Martínez-Rodríguez ◽  
Arleta Krystyna Skrzynska ◽  
Juan Antonio Martos-Sitcha
Keyword(s):  
Sparus Aurata ◽  
Gilthead Sea Bream ◽  
Sea Bream

scholarly journals Human core duplicon gene families: game changers or game players?

2019 ◽  
Vol 18 (6) ◽  
pp. 402-411 ◽  
Author(s):  
Cemalettin Bekpen ◽  
Diethard Tautz
Keyword(s):  
Positive Selection ◽  
Protein Domains ◽  
Gene Families ◽  
Specific Gene ◽  
Gene Duplications ◽  
Human Lineage ◽  
Protein Families ◽  
Cellular Pathways ◽  
Human Specific

Abstract Illuminating the role of specific gene duplications within the human lineage can provide insights into human-specific adaptations. The so-called human core duplicon gene families have received particular attention in this respect, due to special features, such as expansion along single chromosomes, newly acquired protein domains and signatures of positive selection. Here, we summarize the data available for 10 such families and include some new analyses. A picture emerges that suggests broad functions for these protein families, possibly through modification of core cellular pathways. Still, more dedicated studies are required to elucidate the function of core-duplicons gene families and how they have shaped adaptations and evolution of humans.

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