Carlos Fernández

Carlos Fernández
University of Santiago de Compostela | USC · Department of Genetics

PhD in Biology

About

82
Publications
12,150
Reads
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1,657
Citations
Citations since 2017
33 Research Items
712 Citations
2017201820192020202120222023020406080100120140
2017201820192020202120222023020406080100120140
2017201820192020202120222023020406080100120140
2017201820192020202120222023020406080100120140
Introduction
I am interested in different topics about functional genomics of turbot (Scophthalmus maximus) and my research focuses on molecular marker design; data base analysis and functional annotation of sequences; microarray design and statistical analysis. Also, I am interested in the analyses of the differences in morphological quantitative traits and the population genetic differentiation of three spine stickleback (Gasterosteus aculeatus).
Additional affiliations
December 2002 - present
University of Santiago de Compostela
Position
  • Researcher
Education
November 1994 - June 2004

Publications

Publications (82)
Preprint
Full-text available
The edible cockle ( Cerastoderma edule ) is a widely cultivated bivalve with relevant ecological value roles and high value for shellfisheries in different European regions. The emergence of new threats, such as the parasite Marteilia cochillia , has impaired the production and ecosystem of shellfish beds where the parasite was detected. Knowledge...
Article
Full-text available
Abstract Knowledge on correlations between environmental factors and genome divergence between populations of marine species is crucial for sustainable management of fisheries and wild populations. The edible cockle (Cerastoderma edule) is a marine bivalve distributed along the Northeast Atlantic coast of Europe and is an important resource from bo...
Article
The vomeronasal organ (VNO) is a chemosensory organ specialized in pheromone detection that shows a broad morphofunctional and genomic diversity among mammals. However, its expression patterns have only been well-characterized in mice. Here, we provide the first comprehensive RNA sequencing study of the rabbit VNO across gender and sexual maturatio...
Preprint
Full-text available
Knowledge on how environmental factors shape the genome of marine species is crucial for sustainable management of fisheries and wild populations. The edible cockle (Cerastoderma edule) is a marine bivalve distributed along the Northeast Atlantic coast of Europe and is an important resource from both commercial and ecological perspectives. We perfo...
Article
Full-text available
Tasas de crecimiento en dos poblaciones naturales de Gasterosteus aculeatus en el noroeste de España: relación con otros parámetros vitales Se analizaron las tasas de crecimiento de dos poblaciones naturales de Galicia (noroeste de España) del pez espinoso Gasterosteus aculeatus, cuyo ciclo biológico es estrictamente anual. Para ello, se utilizó un...
Article
Full-text available
The European flat oyster (Ostrea edulis) is a highly appreciated mollusk with an important aquaculture production throughout the 20th century, in addition to playing an important role on coastal ecosystems. Overexploitation of natural beds, habitat degradation, introduction of non‐native species and epidemic outbreaks have severely affected this im...
Article
Full-text available
Selective breeding for improving host responses to infectious pathogens is a promising option for disease control. In fact, disease resilience, the ability of a host to survive or cope with infectious challenge, has become a highly desirable breeding goal. However, resilience is a complex trait composed of two different host defence mechanisms, nam...
Article
• Application of genomics tools for conservation purposes (i.e. conservation genomics) allows looking deep into the genetic structure and adaptations of populations and species in order to define management units, trace exploited stocks, and identification of species. • In this work, a double‐digestion restriction‐site‐associated DNA sequencing (dd...
Article
Full-text available
Unraveling adaptive genetic variation represents, in addition to the estimate of population demographic parameters, a cornerstone for the management of aquatic natural living resources, which in turn, represent the raw material for breeding programs. The turbot (Scophthalmus maximus) is a marine flatfish of high commercial value living on the Europ...
Data
Fluorescent in situ hybridisation (FISH) of Characidium gomesi mitotic plates with female-specific RAD locus probes.
Article
A combination of a RADseq method (ddRAD) with long read high throughput sequencing (Roche 454) was tuned up in order to identify and validate a set of SNPs useful for gene diversity analysis in two important South American commercial tuna (Thunnus albacares and Scomberomorus brasiliensis). A total of 11 and 21 individuals of T. albacares and S. bra...
Article
Fish species exhibit substantial variation in the degree of genetic differentiation between sex chromosome pairs, and therefore offer the opportunity to study the full range of sex chromosome evolution. We used restriction-site associated DNA sequencing (RAD-seq) to study the sex chromosomes of Characidium gomesi, a species with conspicuous heterom...
Article
Full-text available
Genetic isolation and drift may imperil peripheral populations of wide-ranging species more than central ones. Therefore, information about species genetic variability and population structure is invaluable for conservation managers. The Iberian populations of three-spined stickleback lie at the southwestern periphery of the European distribution o...
Data
Basic descriptors of the 18 polymorphic microsatellite loci selected to assess the genetic diversity and differentiation of G. aculeatus. k, number of alleles; AR, allelic richness overall populations (based on sample size of 16 diploid individuals); HO, observed heterozygosity; HE, expected heterozygosity. Significance of FIS was obtained after 1,...
Data
Details about the samples used in the present study. (PDF)
Data
95% statistical parsimony network obtained for 172 mitochondrial haplotypes (755 bp) of G. aculeatus. Our cytb data were aligned and collapsed with the homologous fragments reported in Europe by prior literature [17, 20, 24, 49–54]. The basal haplotype/s were inferred using the homologous fragment of a Japanese specimen of G. aculeatus (Accession n...
Data
Geographic distances (km) between sampling localities. Above diagonal: straight line distances. Below diagonal: shortest pairwise water distances among sampling sites using Google Earth. Note that samples from S14 (Valencia) were geographically coded as located at river Orlina (42°23’6.09”N, 3°1’59.29”E), the source of individuals for the transloca...
Data
Geographic and frequency distribution of the 48 mitochondrial haplotypes (cytochrome b (cytb) and control region (cr)) of G. aculeatus (rows) obtained by the present study. (DOCX)
Data
Proportional contribution to allelic and mitochondrial diversity of each of the 15 extant sites using data from nuclear microsatellites and haplotype sequences (cytb+cr), respectively. (PDF)
Data
Identification of the most likely number of G. aculeatus populations by the analysis of microsatellite data with STRUCTURE 2.3.4. Up: estimated log probability of data for the different number of inferred clusters (K); bars correspond to standard deviation, after 20 independent runs. Down: rate of change in the log probability of data between succe...
Data
Proportion of null alleles in loci initially used to genotype the 17 sites where G. aculeatus was sampled for the present study. Loci stn3, stn12 and stn174 excluded from this calculation due to presence of intermediate (1 bp difference) alleles. (DOCX)
Data
Original code, frequency and geographic origin of the 172 mitochondrial haplotypes (cytb) of G. aculeatus used in the present work. (XLSX)
Article
Full-text available
Free radicals are extremely reactive and produce damage and modify cell functions. Furthermore, superoxide dismutase and catalase are believed to play a key role in the enzymatic defence of the cells. Indeed, some authors have argued that reduced free-radical damage could explain increased longevity. Margaritifera margaritifera is one of the longes...
Article
Flatfish have a high market acceptance thus representing a profitable aquaculture production. The main farmed species is the turbot (Scophthalmus maximus) followed by Japanese flounder (Paralichthys olivaceous) and tongue sole (Cynoglossus semilaevis), but other species like Atlantic halibut (Hippoglossus hippoglossus), Senegalese sole (Solea seneg...
Article
Full-text available
The turbot is a flatfish (Pleuronectiformes) with increasing commercial value, which has prompted active genomic research aimed at more efficient selection. Here we present the sequence and annotation of the turbot genome, which represents a milestone for both boosting breeding programmes and ascertaining the origin and diversification of flatfish....
Article
Full-text available
Growth traits represent a main goal in aquaculture breeding programs and may be related to adaptive variation in wild fisheries. Integrating quantitative trait loci (QTL) mapping and next generation sequencing can greatly help to identify variation in candidate genes, which can result in marker-assisted selection and better genetic structure inform...
Article
Full-text available
Variability at 20 microsatellite loci was examined to assess the population genetic structure, gene flow, and effective population size (N e) in three populations of three-spined stickleback (Gasterosteus aculeatus) from the upper basin of the Miño River in Galicia, NW Spain, where this species is threatened. The three populations showed similar le...
Article
The turbot (Scophthalmusmaximus) is a species of great relevance to European aquaculture and hence might benefit from enhanced genomic resources. The aim of this study was to integrate all previous turbot mapping resources to obtain a dense consensus genetic map. A total of 514 single nucleotide polymorphisms (SNP) and microsatellite markers from r...
Article
Full-text available
One of the main objectives of genetic breeding programs in turbot industry is to reduce disease-related mortality. In the present study, a genome scan to detect quantitative trait loci (QTL) affecting resistance and survival to viral haemorrhagic septicaemia (VHS) was carried out. Three full-sib families with approximately 90 individuals each were...
Article
Full-text available
Background Genomic resources for plant and animal species that are under exploitation primarily for human consumption are increasingly important, among other things, for understanding physiological processes and for establishing adequate genetic selection programs. Current available techniques for high-throughput sequencing have been implemented in...
Article
Full-text available
Background: Genomic resources for plant and animal species that are under exploitation primarily for human consumption are increasingly important, among other things, for understanding physiological processes and for establishing adequate genetic selection programs. Current available techniques for high-throughput sequencing have been implemented i...
Article
Full-text available
The turbot (Scophthalmus maximus) is a commercially valuable flatfish and one of the most promising aquaculture species in Europe. Two transcriptome 454-pyrosequencing runs were used in order to detect Single Nucleotide Polymorphisms (SNPs) in genes related to immune response and gonad differentiation. A total of 866 true SNPs were detected in 140...
Article
Full-text available
The turbot (Scophthalmus maximus) is a relevant species in European aquaculture. The small turbot genome provides a source for genomics strategies to use in order to understand the genetic basis of productive traits, particularly those related to sex, growth and pathogen resistance. Genetic maps represent essential genomic screening tools allowing...
Data
Full-text available
Table S3. Number of markers and map length for each linkage group (LG) of turbot.
Data
Figure S2. Consensus, female and male genetic maps of turbot.
Data
Figure S4. Oxford grid showing syntenies between the turbot linkage map and the zebrafish genome.
Data
Full-text available
Figure S1. Correspondence between the nine family maps used to construct the turbot consensus map.
Data
Figure S3. Comparative mapping between the turbot map and the five model teleost genomes.
Data
Table S5. Putative syntenic markers (60) between the turbot genetic map and four model Acanthopterygii genomes.
Data
Table S4. Putative syntenic markers (210) between the turbot genetic map and the stickleback genome.
Article
Disease resistance-related traits have received increasing importance in aquaculture breeding programs worldwide. Currently, genomic information offers new possibilities in breeding to address the improvement of this kind of traits. The turbot is one of the most promising European aquaculture species, and Philasterides dicentrarchi is a scuticocili...
Article
Full-text available
Morphological and DNA sequence data has been used to propose hypotheses of relationships within the Characiformes with minimal comparative discussion of causes underpinning the major intraordinal diversification patterns. We explore potential primary morphological factors controlling the early diversification process in some Neotropical characiform...
Article
Full-text available
We evaluated the expression profiles of turbot in spleen, liver, and head kidney across five temporal points of the Philasterides dicentrarchi infection process using an 8x15K Agilent oligo-microarray. The microarray included 2,176 different fivefold replicated gene probes designed from a turbot 3' sequenced EST database. We were able to identify 2...
Article
Full-text available
We evaluated the expression profiles of turbot in the spleen, liver, and head kidney across five temporal points of the Aeromonas salmonicida infection process using an 8 × 15 K Agilent oligo-microarray. The microarray included 2,176 different fivefold replicated gene probes designed from a turbot 3' sequenced EST database. We were able to identify...
Article
An expressed sequence tag (EST) turbot database from immune tissues was tracked to identify and validate single nucleotide polymorphism (SNP) markers suitable for map construction and population analysis in turbot (Scophthalmus maximus). By means of a stringent bioinformatic tracking strategy, 341 contigs containing true SNPs were identified among...
Article
An expressed sequence tag database from immune tissues was used to design the first high-density turbot (Scophthalmus maximus) oligo-microarray with the aim of identifying candidate genes for tolerance to pathogens. Specific oligonucleotides (60 mers) were successfully designed for 2,716 out of 3,482 unique sequences of the database. An Agilent cus...
Article
Full-text available
Sex determination in fish is a labile character in evolutionary terms. The sex-determining (SD) master gene can differ even between closely related fish species. This group is an interesting model for studying the evolution of the SD region and the gonadal differentiation pathway. The turbot (Scophthalmus maximus) is a flatfish of great commercial...
Article
Full-text available
Free radicals are extremely reactive and produce damage and modify cell functions. Furthermore, superoxide dismutase and catalase are believed to play a key role in the enzymatic defence of the cells. Indeed, some authors have argued that reduced free-radical damage could explain increased longevity. Margaritifera margaritifera is one of the longes...
Article
The detection of microsatellite sequences within expressed sequence tags (ESTs) connects potential markers with specific genes, generating type I markers. We have developed and mapped by linkage analysis a set of EST-derived microsatellites in the turbot, Scophthalmus maximus. One hundred and ninety-one microsatellites were identified from 9256 tur...
Article
Full-text available
The turbot (Scophthalmus maximus; Scophthalmidae; Pleuronectiformes) is a flatfish species of great relevance for marine aquaculture in Europe. In contrast to other cultured flatfish, very few genomic resources are available in this species. Aeromonas salmonicida and Philasterides dicentrarchi are two pathogens that affect turbot culture causing se...
Data
Comparison of gene expression profiles regulated in response to turbot pathogens. The total number and distribution among libraries (Aeromonas, Philasterides, control) of sequences from contigs with 6 or more sequences is presented. The homology with public databases (e-value), the function and the probability of departure from the null hypothesis...
Data
Comparison of ESTs grouped according to GO terms among the three turbot cDNA libraries. contigs of annotated genes are shown grouped according to GO term categories (Molecular function; Biological process; Cellular component) and split into the three turbot libraries from which sequences were obtained. The expression pattern of each gene at each li...
Article
Seventy nine microsatellite markers selected across all linkage groups (LG) from a previous turbot genetic map were studied in a diploid meiogynogenetic family for centromere mapping using half-tetrad analysis. Significant deviations from Mendelian segregation were observed at 25% loci analyzed. The clustering of distorted loci at specific LGs, sug...
Article
Full-text available
A consensus microsatellite-based linkage map of the turbot (Scophthalmus maximus) was constructed from two unrelated families. The mapping panel was derived from a gynogenetic family of 96 haploid embryos and a biparental diploid family of 85 full-sib progeny with known linkage phase. A total of 242 microsatellites were mapped in 26 linkage groups,...
Article
Full-text available
1. The European freshwater pearl mussel, Margaritifera margaritifera (Bivalvia: Unionoida), is one of the most threatened mussels. The Iberian populations of this species are considered peripheral because their distinct characters such as growth rate and longevity, and require development of effective conservation strategies. 2. We assessed populat...
Conference Paper
Full-text available
A total of 11.616 cDNAs partially sequenced from three different cDNA libraries of turbot (Scophthalmus maximus) after infection with Aeromonas salmonicida and Philasterides dicentrarchi and from healthy fish, were analyzed. Clustering and assembly of 9.978 high-quality sequences revealed 3.482 different putative transcripts. Blast searches showed...
Article
Full-text available
A genetic analysis of freshwater pearl mussel Margaritifera margaritifera populations from NW Spain, a peripheral area of its European distribution, was carried out using microsatellite markers. These populations were formerly reported as genetically differentiated on the basis of growth and longevity studies. Ten loci previously characterized in p...