Francisca Robles

University of Granada | UGR · Faculty of Science

Sex determination (SD) shows huge variation among fish and a high evolutionary rate, as illustrated by the Pleuronectiformes (flatfishes). This order is characterized by its adaptation to demersal life, compact genomes and diversity of SD mechanisms. Here, we assembled the Solea senegalensis genome, a flatfish of great commercial value, into 82 con...

The striped soldier shrimp, Plesionika edwardsii (Brandt, 1851) is a pandalid with economic value in the Mediterranean region. We have sequenced and assembled its complete mitochondrial genome, which is 15,956 bp in length and contains the same 37 genes found in most metazoan mitochondrial genomes. Its gene order and nucleotide content are similar...

Pistachio is a nut crop domesticated in the Fertile crescent and a dioecious species with ZW sex chromosomes. We sequenced the genomes of P. vera cultivar (cv.) Siirt, the female parent, and P. vera cv. Bagyolu, the male parent. Two chromosome-level reference genomes of pistachio were generated, and Z and W chromosomes were assembled. The ZW chromo...

Infectious diseases represent one of the most pressing threats to modern aquaculture at a global scale [...]

The Pleuronectiformes order, which includes several commercially-important species, has undergone extensive chromosome evolution. One of these species is Solea senegalensis, a flatfish with 2n = 42 chromosomes. In this study, a cytogenomics approach and integration with previous maps was applied to characterize the karyotype of the species. Synteny...

Sex determination (SD) mechanisms are exceptionally diverse and show high evolutionary rates in fish. Pleuronectiformes is an emblematic fish group characterized by its adaptation to demersal life and its compact genomes. Here, we present a chromosome-level genome assembly of Senegalese sole, a promising European aquaculture species. We combined lo...

Helicobacter pylori is a human pathogenic bacterium with a high genomic plasticity. Although the functional CRISPR-Cas system has not been found in its genome, CRISPR-like loci have been recently identified. In this work, 53 genomes from different geographical areas are analyzed for the search and analysis of variability of this type of structure....

Analysis by cluster of the CRISPR-like loci inserted in the VlpC gene Cluster B including 15 strains. In these strains, two deletions are observed affecting the spacer1, DR2 and spacer2. Pairwise % identity in CRISPR-like loci and complete gene: 79% and 92%, respectively.

Alignment of the sequences obtained from blastn for CRISPR-like loci detected in Shi470 and BM012A strains (E value: 10e−5, query coverage > 75%) Color indicates the degree of variation in both the Poly-E rich protein gene and its CRISPR-like loci. Dark (high values of pairwise % identity), light (low pairwise % identity). Alignment was performed w...

Phylogenetic tree constructed with the 39 CRISPR1-like detected in the SJM180 strain with a gene coding for a hypothetical protein Phylogeographic differentiation of CRISPR-like loci is not observed. Analysis was performed using MEGA7 software. The evolutionary distance scales in 0.01. Neighbor-joining method with bootstrap of 1,000 replications an...

Alignment of sequences obtained from blastn of CRISPR-like loci detected in Shi417 and Shi112 strains (E value: 10e−5, query coverage > 75%) In the figure only the region of gene including CRISPR-like locus is showed. Color indicates the degree of variation in both the gene (hypothetical protein) and its CRISPR-like loci. Dark (high values of pairw...

Analysis by cluster of the CRISPR-like loci inserted in the VlpC gene Cluster E including one strain which CRISPR-like sequence shows a deletion at the spacer1, two additional copies of DR2, and three additional copies of spacer2. Pairwise % identity in CRISPR-like loci and complete gene: 54% and 90%, respectively.

Analysis by cluster of the CRISPR-like loci inserted in the VlpC gene Cluster F including three strains. Their CRISPR-like sequences show deletion of the spacer1, and partials deletions at DR3 and spacer3. Pairwise % identity in CRISPR-like loci and complete gene: 85% and 94%, respectively.

Phylogenetic tree constructed with the 14 CRISPR-like loci detected in the gene coding for a hypothetical protein A phylogeographic differentiation of CRISPR-like loci is observed. Analysis performed using MEGA7 software. Evolutionary distance scale: 0.02 model of Jukes-Cantor. (A) Group of African and European geographical origin. (B) Amerind geog...

Blast cDNA for the VlpC gene Blast analysis with the cDNA for the VlpC gene. Analysis of the cDNA showed that this gene was expressed in 50 of the 52 strains that had this gene. This gene was not expressed only in the South Africa20 and Shi470 strains. The e-value used was 10e−5

Identification of cas domains The e-value used for the searches was 10e-5 through hmmscan. E-value: domain reliability; c-Evalue: reliability for this particular domain; acc: average probability of the aligned residuals. Measure of reliability of the alignment from 0 to 1, where 1.00 indicates that the alignment is completely reliable

Analysis by cluster of the CRISPR-like loci inserted in the VlpC gene Cluster A including 25 strains. CRISPR-like locus of these strains showed four DRs and three spacers (as reference strain) with 86% of identity. The complete sequence of VlpC gene showed an 92% of identity.

Analysis by cluster of the CRISPR-like loci inserted in the VlpC gene Cluster C including five strains. In these strains a duplication of DR2 and spacer2 is observed. Pairwise % identity in CRISPR-like loci and complete gene: 77% and 91%, respectively.

Analysis by cluster of the CRISPR-like loci inserted in the VlpC gene Cluster D including two strains. In these strains the spacers 1 and 2 are incomplete due to different deletions. Pairwise % identity in CRISPR-like loci and complete gene: 85% and 90%, respectively.

Analysis of the genomes of strains Shi470 and BM012A with Mauve and their CRISPR-like (A) Alignment of the Shi470 and BM012A genomes using Mauve software. Figures show the genome region where Poly-E rich protein gene is included. The alignment revealed that this gene was in a region close to the breaking point of an inversion that affects these str...

Phylogenetic tree constructed with the 35 CRISPR-like detected in the gene coding for a Poly-E rich protein A phylogeographic differentiation of CRISPR-like loci is observed. Analysis performed using MEGA7 software. The evolutionary distance scale : in 0.02. Neighbor-joining method with bootstrap of 1,000 replications and Jukes-Cantor model. (A) Gr...

Alignment of the sequences obtained from blastn for CRISPR1-like loci detected in SJM180 strain (E value: 10e − 5, query coverage > 75%) Color indicates the degree of variation in both the hypothetical protein gene and its CRISPR-like loci. Dark (high values of pairwise % identity), light (low pairwise % identity). Alignment was performed with Musc...

Analysis CRISPRTarget Analysis of the spacers identified by CRISPRFinder to determine their similarity with foreign genetic elements.

Alignment of the sequences obtained from blastn for CRISPR3-like loci detected in SJM180 strain (E value: 10e − 5, query coverage > 75%) Color indicates the degree of variation in both the hypothetical protein gene and its CRISPR-like loci. Dark (high values of pairwise % identity), light (low pairwise % identity). Alignment was performed with Musc...

Phylogenetic tree constructed with the 39 CRISPR3-like detected in the SJM180 strain with the gene coding for a hypothetical protein Phylogeographic differentiation of CRISPR-like loci is not observed. Analysis was performed using MEGA7 software. The evolutionary distance scales in 0.01. Neighbor-joining method with bootstrap of 1,000 replications...

Analysis by RNAFolder of the clusters of the RNA secondary structure of the different consensus DR sequences of the CRISPR-like located in H. pylori The analysis of DRs using RNAfold Server allowed us to predict the secondary structure of RNAs and record their minimum free energy (MFE). Consensus sequence was used for each cluster (described in Sup...

Table summary spacer and repeated sequences Characteristics of the repeated direct sequences (DRs) consensus and of the spacer sequences of the 22 CRISPR-like identified with CRISPRFinder

Helicobacter pylori is a human pathogenic bacterium with a high genomic plasticity. Although the functional CRISPR-Cas system has not been found in its genome, CRISPR like loci have been recently identified. In this work, 53 genomes from different geographical areas are analyzed for the search and analysis of variability of this type of structure....

Helicobacter pylori is a human pathogenic bacterium with a high genomic plasticity. Although the functional CRISPR-Cas system has not been found in its genome, CRISPR like loci have been recently identified. In this work, 53 genomes from different geographical areas are analyzed for the search and analysis of variability of this type of structure....

In the Alhambra (Granada, Spain), and in other Moorish locations, several individuals of the original variety of myrtle, the emblematic plant of their gardens, have been identified and genetically authenticated. After microsatellite analysis, we differentiated between the wild form (Myrtus communis L.) and two cultivated varieties: the one original...

Two new centromeric satellite DNAs in flatfish (Order Pleuronectiformes) have been characterized. The SacI-family from Hippoglossus hippoglossus, restricted to this species, had a monomeric size of 334 base pair (bp) and was located in most of the centromeres of its karyotype. The PvuII-family, with a monomeric size of 177 bp, was initially isolate...

This paper represents the first molecular cytogenetic characterization of the strictly dioecious pistachio tree (Pistacia vera L.). The karyotype was characterized by fluorescent in situ hybridization (FISH) with probes for 5S and 45S rDNAs, and the pistachio specific satellite DNAs PIVE-40, and PIVE-180, together with DAPI-staining. PIVE-180 has a...

Neighbor-joining tree based on PIVE-180 sequences. Numbers at each node indicate bootstrap support. Sequences from female genomic DNA start with FEM; and from male DNA with MAL. (TIF)

Southern-blot hybridization using PIVE-180 probes. Kerman (lanes 1, 3, 5, 7, and 9) and Peter (2, 4, 6, and 8) total genomic DNA cut with EcoRI (1, 2), RsaI (3, 4), HinfI (5, 6), TaqI (7, 8), and AluI (9, 10) using the monomeric PIVE-180 satellite DNA sequences as probe. (*), (**), (***) indicate monomer, dimer, and trimer, respectively. (M), (F) m...

FISH in root-tip metaphase chromosomes of P. vera (n = 15) counterstained with DAPI. 45S rDNA (A), 5S rDNA, red, and PIVE-180, green (B), and PIVE-40 (C). Bar represents 2.5 μm. (TIF)

Neighbor-joining tree based on PIVE-40 sequences. Numbers at each node indicate bootstrap support. Sequences from female genomic DNA start with FEM; and from male DNA with MAL. In red sequences that showed higher homology with non-contiguous sequences than with contiguous ones (in blue). (TIF)

The Senegalese sole (Solea senegalensis, Kaup 1858) is a flatfish species of great value for aquaculture. In this study, we develop the first linkage map in this species based on microsatellite markers characterized from genomic DNA libraries and EST databases of Senegalese sole and from other flatfish species. Three reference gynogenetic families...

In this study we have developed protocols for induced triploidy and gynogenesis of Senegalese sole (Solea senegalensis), a promising flatfish species for marine aquaculture, in order to: 1) identify the sex-determination mechanism; and 2) to improve its production by generating a) sterile fish, avoiding problems related with sexual maturation, and...

Pistacia vera L., whose edible fruit is the pistachio, is an economically important crop. It is cultivated worldwide and over 50 different varieties have been described attending to morphological and phenological characteristics. The selection of a suitable cultivar may affect the profitability of the orchards, and thus requires careful considerati...

In this work, we tested 100 potential new microsatellites (SSRs) equally derived from expressed sequence tag (EST) and enriched genomic-DNA libraries from Senegalese sole (Solea senegalensis, Kaup), a valuable cultured flatfish species. A final set of 69 new polymorphic microsatellites were validated after a population analysis, 37 of which corresp...

In this study, we identified and characterized 160 microsatellite loci from an expressed sequence tag (EST) database generated from immune-related organs of turbot (Scophthalmus maximus). A final set of 83 new polymorphic microsatellites were validated after the analysis of 40 individuals of Atlantic origin including both wild and farmed individual...

Pagurta: An interspecific hybrid of common seabream Pagrus pagrus (L., 1758) female and banded sea- bream males Pagrus auriga Valenciennes, 1843 male: phenotypic and molecular characterization Hybrids are of great interest in aquaculture. In the present study, we report for the first time an interespecific hybrid between common seabream Pagrus pagr...

When genomic DNA from the European flat oyster Ostrea edulis L. was digested by BclI enzyme, a band of about 150 bp was observed in agarose gel. After cloning and sequencing this band and analysing their molecular characteristics and genomic organization by means of Southern blot, in situ hybridisation, and polymerase chain reaction (PCR) protocols...

To clarify the species status of sturgeon from rivers of the Iberian Peninsula, eight molecular markers (4 nuclear and 4 mitochondrial) have been analysed in different specimens from historical museum samples and prehistoric samples from archaeological sites. These analyses indicate that one of these specimens (UGP captured in the Guadalquivir Rive...

Today, with all the sturgeon species almost disappearing all over the world, it is necessary to undertake their recovery under the programs for the conservation of genetic resources. The complete absence of these fish from most rivers increases the difficulties in carrying out such programs, hampering the genetic identification of specimens and the...

The meat and, above all, the caviar from sturgeons have been gastronomic emblems of delicacy from time immemorial. When sturgeons were abundant, caviar was marketed primarily from three species (Huso huso, Acipenser gueldenstaedtii and A. stellatus) mostly from the Caspian Sea. However, these are not the only species of sturgeons used traditionally...

In the course of a histopathological survey performed to discover the cause of mass mortality of the striped clam Chamelea gallina in the Balearic Islands (Spain, Mediterranean Sea), we detected a Marteilia-like parasite in 3 clams. Molecular methods were applied to identify the parasite. DNA extracted from a paraffin block was used to carry out a...

From a battery of microsatellite markers (100 loci), recently identified by our group, we have selected eight for parentage assignment in Senegal sole (Solea senegalensis). This tool is based on microsatellite loci obtained from four genomic DNA libraries and one cDNA library. Within the eight loci (six from anonymous genomic DNA sequences and two...

A highly debated problem in Acipenseridae taxonomy is whether Acipenser oxyrinchus (North American Atlantic sturgeon) and A. sturio (European Atlantic sturgeon) are true species: a detailed comparison of their karyotypes could provide relevant information. Here we describe for the first time the karyotype of A. oxyrinchus (2n = 121 +/- 3), and its...

Here, a new satellite-DNA family is isolated and characterized from wedge sole, Dicologoglossa cuneata Moreau, 1881 (Pleuronectiformes), a fish having a small genome. This satellite-DNA family of sequences was isolated by conventional cloning after digestion of genomic DNA with the DraI restriction enzyme. Repeat units are 171 bp in length with a h...

Ribosomal DNA in sturgeon is informative when analyzed at the molecular level because it bears unique characteristics that are, to a certain extent, ancestral within vertebrates. In this paper, we examine the structure and the molecular evolution of the 5S ribosomal DNA (rDNA) region in 13 sturgeon species, comparing both the 5S ribosomal RNA (rRNA...

Hybrids are of great interest in aquaculture. In the present study, we report for the first time an interespecific hybrid between common seabream Pagrus pagrus (L., 1758) females and red banded seabream Pagrus auriga (Valenciennes, 1843) males, which has been named the pagurta. This hybrid was detected in natural spawns during the period from March...

This study characterizes a repetitive DNA family of sequences in sturgeon, the PstI satellite DNA. We have found a high degree of preservation for these sequences, which are present in all 13 species analyzed, including within the genera Acipenser, Huso, and Scaphirhynchus of the family Acipenseridae. This is one of the most ancient satellite DNAs...

To date, the only native sturgeon species in Western Europe was believed to be Acipenser sturio. However, this species is currently restricted to the Gironde River (Southern France), and it poses serious difficulties for rearing in captivity and for using in recovery programme. Furthermore, it has been questioned whether A. sturio is in fact the on...

We examined the composition and evolution of a large heterochromatic region present in the genomes of certain species of the genus Muscari (Hyacinthaceae). We found that in Muscari comosum this heterochromatic region is composed mainly of a satellite DNA family, which we named MCSAT. Molecular analyses and in situ hybridization revealed that, throu...

El proceso de convergencia hacia el Espacio Europeo de Educación Superior (EEES), establece diferencias fundamentales en la concepción del proceso de enseñanza/aprendizaje dentro del sistema universitario. La docencia debe orientarse hacia el alumno como último beneficiario en la adquisición de competencias. En papel del profesorado se ve modificad...