Francisca Robles - Academia.edu (original) (raw)

Papers by Francisca Robles

Research paper thumbnail of Integration of Maps Enables a Cytogenomics Analysis of the Complete Karyotype in Solea senegalensis

International Journal of Molecular Sciences

The Pleuronectiformes order, which includes several commercially-important species, has undergone... more 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 analysis of S. senegalensis was carried out using two flatfish as a reference: Cynoglossus semilaevis and Scophthalmus maximus. Most S. senegalensis chromosomes (or chromosome arms for metacentrics and submetacentrics) showed a one-to-one macrosyntenic pattern with the other two species. In addition, we studied how repetitive sequences could have played a role in the evolution of S. senegalensis bi-armed (3, and 5–9) and acrocentric (11, 12 and 16) chromosomes, which showed the highest rearrangements compared with the reference species. A higher abundance of TEs (Transposable Elements) and other repeated elements was observed adjacent to ...

Research paper thumbnail of Ajuste genético basado en series de tiempo de modelos de leslie

Un conjunto de relaciones establecidas explícita y/o implícitamente entre un alumno o un grupo de... more Un conjunto de relaciones establecidas explícita y/o implícitamente entre un alumno o un grupo de alumnos, en cierto medio y un sistema educativo con la finalidad de lograr que estos alumnos se apropien de un saber constituido o en vías de construcción"

Research paper thumbnail of A chromosome-level genome assembly enables the identification of the follicle stimulating hormone receptor as the master sex determining gene in Solea senegalensis

Sex determination (SD) mechanisms are exceptionally diverse and show high evolutionary rates in f... more 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 long- and short-read sequencing and a highly dense genetic map to obtain a contiguous assembly of 613 Mb (N50 = 29.0 Mb, 99% of the assembly in the n = 21 chromosomes of its karyotype). The correspondence between this new assembly and the Senegalese sole chromosomes was established by fluorescence in situ hybridization with BAC probes. Orthology within Pleuronectiformes was assessed by using the chromosome-level genomes of six important commercial flatfishes covering a broad phylogenetic spectrum of the order. A total of 7936 single-gene orthologues, shared by the six species, were used to identify syntenies in Pleuronectiformes and to explo...

Research paper thumbnail of A chromosome‐level genome assembly enables the identification of the follicule stimulating hormone receptor as the master sex‐determining gene in the flatfish <i>Solea senegalensis</i>

Molecular Ecology Resources, Jan 15, 2023

Sex determination (SD) shows huge variation among fish and a high evolutionary rate, as illustrat... more 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 contigs (614 Mb) combining long‐ and short‐read sequencing, which were next scaffolded using a highly dense genetic map (28,838 markers, 21 linkage groups), representing 98.9% of the assembly. Further, we established the correspondence between the assembly and the 21 chromosomes by using BAC‐FISH. Whole genome resequencing of six males and six females enabled the identification of 41 single nucleotide polymorphism variants in the follicle stimulating hormone receptor (fshr) consistent with an XX/XY SD system. The observed sex association was validated in a broader independent sample, providing a novel molecular sexing tool. The fshr gene displayed differential expression between male and female gonads from 86 days post‐fertilization, when the gonad is still an undifferentiated primordium, concomitant with the activation of amh and cyp19a1a, testis and ovary marker genes, respectively, in males and females. The Y‐linked fshr allele, which included 24 nonsynonymous variants and showed a highly divergent 3D protein structure, was overexpressed in males compared to the X‐linked allele at all stages of gonadal differentiation. We hypothesize a mechanism hampering the action of the follicle stimulating hormone driving the undifferentiated gonad toward testis.

Research paper thumbnail of Identification of Sturgeon Caviar Using DNA Markers

Springer eBooks, 2009

The meat and, above all, the caviar from sturgeons have been gastronomic emblems of delicacy from... more 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) ...

Research paper thumbnail of The Molecular Cytogenetic Characterization of Pistachio (Pistacia vera L.) Suggests the Arrest of Recombination in the Largest Heteropycnotic Pair HC1

PLOS ONE, Dec 3, 2015

This paper represents the first molecular cytogenetic characterization of the strictly dioecious ... more 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 monomeric unit of 176-178 bp and high sequence homology between family members; PIVE-40 has a 43 bp consensus monomeric unit, and is most likely arranged in higher order repeats (HORs) of two units. The P. vera genome is highly heterochromatic, and prominent DAPI positive blocks are detected in most chromosomes. Despite the difficulty in classifying chromosomes according to morphology, 10 out of 15 pairs (2n = 30) could be distinguished by their unique banding patterns using a combination of FISH probes. Significantly, the largest pair, designated HC1, is strongly heteropycnotic, shows differential condensation, and has massive enrichment in PIVE-40 repeats. There are two types of HC1 chromosomes (type-I and type-II) with differing PIVE-40 hybridization signal. Only type-I/II heterozygotes and type-I homozygotes individuals were found. We speculate that the differentiation between the two HC1 chromosomes is due to suppression of homologous recombination at meiosis, reinforced by the presence of PIVE-40 HORs and differences in PIVE-40 abundance. This would be compatible with a ZW sex-determination system in the pistachio tree.

Research paper thumbnail of Evolution of ancient satellite DNAs in sturgeon genomes

Gene, Aug 1, 2004

This study characterizes a repetitive DNA family of sequences in sturgeon, the PstI satellite DNA... more 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 found to date, because it has been estimated to be more than 100 million years old. Alternatively, to the current view that most satellite DNAs are species-specific or preserved in a few closely related species, the PstI family and other previously characterized sturgeon satellite DNA, the HindIII, represent the most fascinating exceptions to the rapid sequence change usually undergone by satellite DNAs. Here, we compare the evolutionary pattern of these two satellite DNA families, PstI and HindIII, which differ markedly in length, sequence, and nucleotide composition. We have found that, in contrast to the situation in most other living beings, a high degree of preservation, a slow sequence change rate and slowed concerted evolution, appears to be a general rule for sturgeon satellite DNAs. The possible causes for all these features are discussed in the light of the evolutionary specifics found within these ancient organisms.

Research paper thumbnail of Report on the 6th Genomics in Aquaculture (GIA) Symposium Held in Granada, Spain, 4–6 May 2022

Aquaculture Journal, May 16, 2022

This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY

Research paper thumbnail of The Forgotten Myrtle of the Alhambra Gardens of Granada: Restoring and Authenticating World Heritage

Journal of Agricultural Science and Technology, Dec 1, 2016

In the Alhambra (Granada, Spain), and in other Moorish locations, several individuals of the orig... more 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 to the Alhambra, the Moorish myrtle (subsp. baetica), and the variety introduced in more modern times (subsp. tarentina). The genetic and morphological differences between these two varieties confirm the taxonomic distinctness of the subsp. baetica. With very few individuals known, this Moorish myrtle is on the verge of extinction. The genetic identification offers the opportunity to restore a key element of this 14th-century garden and enhance the authenticity of a World Heritage site.

Research paper thumbnail of Pagurta: an interspecific hybried of common seabream Pagrus pagrus L., 1758) female and banded seabream males Pagrus auriga Valenciennes, 1843 male: phenotypic and molecular characterization

Research paper thumbnail of Exploitation of a turbot ( Scophthalmus maximus L.) immune‐related expressed sequence tag (EST) database for microsatellite screening and validation

Molecular Ecology Resources, Mar 3, 2012

In this study, we identified and characterized 160 microsatellite loci from an expressed sequence... more 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 individuals. The allele number and the expected heterozygosity ranged from 2 to 18 and from 0.021 to 0.951, respectively. Evidences of null alleles at moderate-high frequencies were detected at six loci using population data. None of the analysed loci showed deviations from Mendelian segregation after the analysis of five full-sib families including approximately 92 individuals ⁄ family. The markers are used to consolidate the turbot genetic map, and because they are mostly EST-derived, they will be very useful for comparative genomic studies within flatfishes and with model fish species. Using an in silico approach, we detected significant homologies of microsatellite sequences with the EST databases of the flatfish species with highest genomic resources (Senegalese sole, Atlantic halibut, bastard halibut) in 31% of these turbot markers. The conservation of these microsatellites within Pleuronectiformes will pave the way for anchoring genetic maps of different species and identifying genomic regions related to productive traits.

Research paper thumbnail of Analysis of Mitochondrial and Nuclear DNA Markers in Old Museum Sturgeons Yield Insights About the Species Existing in Western Europe: A. sturio, A. naccarii and A. oxyrinchus

Springer eBooks, 2009

Today, with all the sturgeon species almost disappearing all over the world, it is necessary to u... more 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 their correct species assignment. However, with the development of new and reliable molecular genetic techniques, many studies such as this are yielding insights concerning the sturgeon species that inhabited European rivers in the past. In the last few years, our group has developed forensic techniques to isolate DNA from ancient sturgeon specimens preserved in museums. These DNA samples have been the subject of various analyses conducted on several nuclear and mitochondrial DNA markers. The combined use of both types of markers has provided accurate genetic identification of these specimens and has overcome the problem of misinterpretation caused by hybridization and introgression. Here, we show that, in addition to Acipenser sturio (the only species previously believed to inhabit the rivers of Western Europe), two other species, Acipenser naccarii and Acipenser oxyrinchus lived in these rivers. Thus, we have found evidence for the presence of A. naccarii in the Guadalquivir river in the Iberian Peninsula and in some rivers in Italy from the Tyrrhenian/Ligurian side, as well as for the presence of A. oxyrinchus in the Ebro river in Spain. Our studies clarify the distribution of sturgeon species in the Western Mediterranean and open new perspectives for recovery plans.

Research paper thumbnail of Characterization of the complete mitochondrial genome of the striped soldier shrimp, <i>Plesionika edwardsii</i> (Brandt, 1851) (Crustacea: Decapoda: Pandalidae), and comparison with other species of Caridea

Journal of Crustacean Biology, Dec 1, 2022

they are genetically similar enough to be considered sister species, they are indeed two distinct... more they are genetically similar enough to be considered sister species, they are indeed two distinct species.

Research paper thumbnail of Table_S1

Comparative analysis of turbot microsatellites with Senegalese sole (Solea senegalensis), bastard... more Comparative analysis of turbot microsatellites with Senegalese sole (Solea senegalensis), bastard halibut (Paralichthys olivaceus) and Atlantic halibut (Hippoglossus hippoglossus)

Research paper thumbnail of DOI 10.1007/s004120000115 ORIGINAL ARTICLE

A heterochromatic satellite DNA is highly amplified in a single chromosome of Muscari (Hyacinthac... more A heterochromatic satellite DNA is highly amplified in a single chromosome of Muscari (Hyacinthaceae)

Research paper thumbnail of Validation and comparison of microsatellite markers derived from Senegalese sole (Solea senegalensis, Kaup) genomic and expressed sequence tags libraries

Molecular Ecology Resources, 2012

In this work, we tested 100 potential new microsatellites (SSRs) equally derived from expressed s... more 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 corresponded to the first EST library constructed for Senegalese sole (EST-SSR). Although differences were not significant, EST sequences provided a higher proportion of quality markers (74%) than anonymous ones (64%). Most of the rejected anonymous SSRs (17 loci) were discarded because they did not generate PCR products; only one was monomorphic. On the contrary, all EST-SSRs gave PCR products, although monomorphism was more frequent (26%). Altogether, the number of alleles per locus was fairly similar in both SSR types, ranging from 2 to 19. The observed and expected heterozygosities varied from 0.105 to 1 and from 0.108 to 0.937, respectively. The main difference between the two sets was the percentage of annotated loci, being higher in EST-SSRs, as expected. Within the EST-SSRs, 46% of them showed flanking regions that significantly matched with EST sequences from other three flatfish species; however, the microsatellite itself was present only on half of these cases. These two new SSR sets constitute a suitable tool for fingerprinting, gene flow, genetic diversity, genome mapping studies and molecular-assisted breeding in this species.

Research paper thumbnail of Genetic Identification of Western Mediterranean Sturgeons and its Implication for Conservation

Conservation Genetics, Aug 1, 2004

To date, the only native sturgeon species in Western Europe was believed to be Acipenser sturio. ... more 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 only species within the rivers of Western Europe, as A. naccarii, a species previously considered endemic of the Adriatic region, has been reported from the Iberian Peninsula in recent years. Here, we have used forensic techniques to obtain DNA from several museum specimens of sturgeons caught in the Spanish Guadalquivir River and in other European rivers. We analysed DNA sequences from these specimens for five genetic markers (three nuclear and two mitochondrial regions), which were subsequently compared with sequences obtained from A. sturio and A. naccarii. Our study demonstrates that A. naccarii coexists with A. sturio, from the Adriatic Sea to the Iberian Peninsula, a finding that could be taken into account in future sturgeon recovery programmes in Western Europe.

Research paper thumbnail of olecular characterization of the interspecific hybrid Pistacia vigros

A new Pistacia variety, VIGROS, has been characterized here using nuclear and chloroplastidial DN... more A new Pistacia variety, VIGROS, has been characterized here using nuclear and chloroplastidial DNA sequences, which are suitable tools for genetic improvement and cultivar identification. The nuclear DNA sequences (ribosomal ITS1, 5.8S, ITS2) determined that VIGROS is an interspecific hybrid between Pistacia vera L. and Pistacia atlantica Desf. The chloroplastidial DNA sequences (trnC-D, trnL-F regions) demonstrated that VIGROS bears a haplotype 100% coincident with that of P. vera, which would then be

Research paper thumbnail of Determining the specific status of the Iberian sturgeons by means genetic analyses of old specimens

Advances in Bioscience and Biotechnology, 2010

To clarify the species status of sturgeon from rivers of the Iberian Peninsula, eight molecular m... more 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 River in the 19th century) is A. sturio, based on all the eight molecular markers, four of them used from the first time in this study. In previous analyses based on 5 genetic markers, our group assigned two specimens captured in this river in the 1970-80s (EBD8173 and EBD8401) to the species A. naccarii, suggesting the presence of this species in the Iberian Peninsula. In this work, this conclusion is drawn after successfully obtaining a mitochondrial marker in a very old scute from a prehistoric site (Acinipo, about 1500 BC, from the Guadalquivir River basin). On the other hand, in the specimen EBD8174 captured in the Guadalquivir in 1975, we have obtained two new mitochondrial markers confirming that it can be considered A. sturio for all the mitochondrial markers, but nuclear ones identify it as A. naccarii. Finally, two very old samples (Nerja E-VI and Nerja N/62-63) were not successfully characterized by any molecular markers. Some aspects and consequences of our results are discussed, such as the origin of the "mosaic" specimen EBD8174 and, above all, the native status of A. naccarii in historic and prehistoric times in the southern Iberian Peninsula.

Research paper thumbnail of Determinig the Specific Status of the Iberian Sturgeons by Means Genetic Analyses of Old Specimens

To clarify the species status of sturgeon from rivers of the Iberian Peninsula, eight molecular m... more 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 River in the 19th century) is A. sturio, based on all the eight molecular markers, four of them used from the first time in this study. In previous analyses based on 5 genetic markers, our group assigned two specimens captured in this river in the 1970-80s (EBD8173 and EBD8401) to the species A. naccarii, suggesting the presence of this species in the Iberian Peninsula. In this work, this conclusion is drawn after successfully obtaining a mitochondrial marker in a very old scute from a prehistoric site (Acinipo, about 1500 BC, from the Guadalquivir River basin). On the other hand, in the specimen EBD8174 captured in the Guadalquivir in 1975, w...

Research paper thumbnail of Integration of Maps Enables a Cytogenomics Analysis of the Complete Karyotype in Solea senegalensis

International Journal of Molecular Sciences

The Pleuronectiformes order, which includes several commercially-important species, has undergone... more 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 analysis of S. senegalensis was carried out using two flatfish as a reference: Cynoglossus semilaevis and Scophthalmus maximus. Most S. senegalensis chromosomes (or chromosome arms for metacentrics and submetacentrics) showed a one-to-one macrosyntenic pattern with the other two species. In addition, we studied how repetitive sequences could have played a role in the evolution of S. senegalensis bi-armed (3, and 5–9) and acrocentric (11, 12 and 16) chromosomes, which showed the highest rearrangements compared with the reference species. A higher abundance of TEs (Transposable Elements) and other repeated elements was observed adjacent to ...

Research paper thumbnail of Ajuste genético basado en series de tiempo de modelos de leslie

Un conjunto de relaciones establecidas explícita y/o implícitamente entre un alumno o un grupo de... more Un conjunto de relaciones establecidas explícita y/o implícitamente entre un alumno o un grupo de alumnos, en cierto medio y un sistema educativo con la finalidad de lograr que estos alumnos se apropien de un saber constituido o en vías de construcción"

Research paper thumbnail of A chromosome-level genome assembly enables the identification of the follicle stimulating hormone receptor as the master sex determining gene in Solea senegalensis

Sex determination (SD) mechanisms are exceptionally diverse and show high evolutionary rates in f... more 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 long- and short-read sequencing and a highly dense genetic map to obtain a contiguous assembly of 613 Mb (N50 = 29.0 Mb, 99% of the assembly in the n = 21 chromosomes of its karyotype). The correspondence between this new assembly and the Senegalese sole chromosomes was established by fluorescence in situ hybridization with BAC probes. Orthology within Pleuronectiformes was assessed by using the chromosome-level genomes of six important commercial flatfishes covering a broad phylogenetic spectrum of the order. A total of 7936 single-gene orthologues, shared by the six species, were used to identify syntenies in Pleuronectiformes and to explo...

Research paper thumbnail of A chromosome‐level genome assembly enables the identification of the follicule stimulating hormone receptor as the master sex‐determining gene in the flatfish <i>Solea senegalensis</i>

Molecular Ecology Resources, Jan 15, 2023

Sex determination (SD) shows huge variation among fish and a high evolutionary rate, as illustrat... more 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 contigs (614 Mb) combining long‐ and short‐read sequencing, which were next scaffolded using a highly dense genetic map (28,838 markers, 21 linkage groups), representing 98.9% of the assembly. Further, we established the correspondence between the assembly and the 21 chromosomes by using BAC‐FISH. Whole genome resequencing of six males and six females enabled the identification of 41 single nucleotide polymorphism variants in the follicle stimulating hormone receptor (fshr) consistent with an XX/XY SD system. The observed sex association was validated in a broader independent sample, providing a novel molecular sexing tool. The fshr gene displayed differential expression between male and female gonads from 86 days post‐fertilization, when the gonad is still an undifferentiated primordium, concomitant with the activation of amh and cyp19a1a, testis and ovary marker genes, respectively, in males and females. The Y‐linked fshr allele, which included 24 nonsynonymous variants and showed a highly divergent 3D protein structure, was overexpressed in males compared to the X‐linked allele at all stages of gonadal differentiation. We hypothesize a mechanism hampering the action of the follicle stimulating hormone driving the undifferentiated gonad toward testis.

Research paper thumbnail of Identification of Sturgeon Caviar Using DNA Markers

Springer eBooks, 2009

The meat and, above all, the caviar from sturgeons have been gastronomic emblems of delicacy from... more 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) ...

Research paper thumbnail of The Molecular Cytogenetic Characterization of Pistachio (Pistacia vera L.) Suggests the Arrest of Recombination in the Largest Heteropycnotic Pair HC1

PLOS ONE, Dec 3, 2015

This paper represents the first molecular cytogenetic characterization of the strictly dioecious ... more 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 monomeric unit of 176-178 bp and high sequence homology between family members; PIVE-40 has a 43 bp consensus monomeric unit, and is most likely arranged in higher order repeats (HORs) of two units. The P. vera genome is highly heterochromatic, and prominent DAPI positive blocks are detected in most chromosomes. Despite the difficulty in classifying chromosomes according to morphology, 10 out of 15 pairs (2n = 30) could be distinguished by their unique banding patterns using a combination of FISH probes. Significantly, the largest pair, designated HC1, is strongly heteropycnotic, shows differential condensation, and has massive enrichment in PIVE-40 repeats. There are two types of HC1 chromosomes (type-I and type-II) with differing PIVE-40 hybridization signal. Only type-I/II heterozygotes and type-I homozygotes individuals were found. We speculate that the differentiation between the two HC1 chromosomes is due to suppression of homologous recombination at meiosis, reinforced by the presence of PIVE-40 HORs and differences in PIVE-40 abundance. This would be compatible with a ZW sex-determination system in the pistachio tree.

Research paper thumbnail of Evolution of ancient satellite DNAs in sturgeon genomes

Gene, Aug 1, 2004

This study characterizes a repetitive DNA family of sequences in sturgeon, the PstI satellite DNA... more 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 found to date, because it has been estimated to be more than 100 million years old. Alternatively, to the current view that most satellite DNAs are species-specific or preserved in a few closely related species, the PstI family and other previously characterized sturgeon satellite DNA, the HindIII, represent the most fascinating exceptions to the rapid sequence change usually undergone by satellite DNAs. Here, we compare the evolutionary pattern of these two satellite DNA families, PstI and HindIII, which differ markedly in length, sequence, and nucleotide composition. We have found that, in contrast to the situation in most other living beings, a high degree of preservation, a slow sequence change rate and slowed concerted evolution, appears to be a general rule for sturgeon satellite DNAs. The possible causes for all these features are discussed in the light of the evolutionary specifics found within these ancient organisms.

Research paper thumbnail of Report on the 6th Genomics in Aquaculture (GIA) Symposium Held in Granada, Spain, 4–6 May 2022

Aquaculture Journal, May 16, 2022

This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY

Research paper thumbnail of The Forgotten Myrtle of the Alhambra Gardens of Granada: Restoring and Authenticating World Heritage

Journal of Agricultural Science and Technology, Dec 1, 2016

In the Alhambra (Granada, Spain), and in other Moorish locations, several individuals of the orig... more 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 to the Alhambra, the Moorish myrtle (subsp. baetica), and the variety introduced in more modern times (subsp. tarentina). The genetic and morphological differences between these two varieties confirm the taxonomic distinctness of the subsp. baetica. With very few individuals known, this Moorish myrtle is on the verge of extinction. The genetic identification offers the opportunity to restore a key element of this 14th-century garden and enhance the authenticity of a World Heritage site.

Research paper thumbnail of Pagurta: an interspecific hybried of common seabream Pagrus pagrus L., 1758) female and banded seabream males Pagrus auriga Valenciennes, 1843 male: phenotypic and molecular characterization

Research paper thumbnail of Exploitation of a turbot ( Scophthalmus maximus L.) immune‐related expressed sequence tag (EST) database for microsatellite screening and validation

Molecular Ecology Resources, Mar 3, 2012

In this study, we identified and characterized 160 microsatellite loci from an expressed sequence... more 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 individuals. The allele number and the expected heterozygosity ranged from 2 to 18 and from 0.021 to 0.951, respectively. Evidences of null alleles at moderate-high frequencies were detected at six loci using population data. None of the analysed loci showed deviations from Mendelian segregation after the analysis of five full-sib families including approximately 92 individuals ⁄ family. The markers are used to consolidate the turbot genetic map, and because they are mostly EST-derived, they will be very useful for comparative genomic studies within flatfishes and with model fish species. Using an in silico approach, we detected significant homologies of microsatellite sequences with the EST databases of the flatfish species with highest genomic resources (Senegalese sole, Atlantic halibut, bastard halibut) in 31% of these turbot markers. The conservation of these microsatellites within Pleuronectiformes will pave the way for anchoring genetic maps of different species and identifying genomic regions related to productive traits.

Research paper thumbnail of Analysis of Mitochondrial and Nuclear DNA Markers in Old Museum Sturgeons Yield Insights About the Species Existing in Western Europe: A. sturio, A. naccarii and A. oxyrinchus

Springer eBooks, 2009

Today, with all the sturgeon species almost disappearing all over the world, it is necessary to u... more 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 their correct species assignment. However, with the development of new and reliable molecular genetic techniques, many studies such as this are yielding insights concerning the sturgeon species that inhabited European rivers in the past. In the last few years, our group has developed forensic techniques to isolate DNA from ancient sturgeon specimens preserved in museums. These DNA samples have been the subject of various analyses conducted on several nuclear and mitochondrial DNA markers. The combined use of both types of markers has provided accurate genetic identification of these specimens and has overcome the problem of misinterpretation caused by hybridization and introgression. Here, we show that, in addition to Acipenser sturio (the only species previously believed to inhabit the rivers of Western Europe), two other species, Acipenser naccarii and Acipenser oxyrinchus lived in these rivers. Thus, we have found evidence for the presence of A. naccarii in the Guadalquivir river in the Iberian Peninsula and in some rivers in Italy from the Tyrrhenian/Ligurian side, as well as for the presence of A. oxyrinchus in the Ebro river in Spain. Our studies clarify the distribution of sturgeon species in the Western Mediterranean and open new perspectives for recovery plans.

Research paper thumbnail of Characterization of the complete mitochondrial genome of the striped soldier shrimp, <i>Plesionika edwardsii</i> (Brandt, 1851) (Crustacea: Decapoda: Pandalidae), and comparison with other species of Caridea

Journal of Crustacean Biology, Dec 1, 2022

they are genetically similar enough to be considered sister species, they are indeed two distinct... more they are genetically similar enough to be considered sister species, they are indeed two distinct species.

Research paper thumbnail of Table_S1

Comparative analysis of turbot microsatellites with Senegalese sole (Solea senegalensis), bastard... more Comparative analysis of turbot microsatellites with Senegalese sole (Solea senegalensis), bastard halibut (Paralichthys olivaceus) and Atlantic halibut (Hippoglossus hippoglossus)

Research paper thumbnail of DOI 10.1007/s004120000115 ORIGINAL ARTICLE

A heterochromatic satellite DNA is highly amplified in a single chromosome of Muscari (Hyacinthac... more A heterochromatic satellite DNA is highly amplified in a single chromosome of Muscari (Hyacinthaceae)

Research paper thumbnail of Validation and comparison of microsatellite markers derived from Senegalese sole (Solea senegalensis, Kaup) genomic and expressed sequence tags libraries

Molecular Ecology Resources, 2012

In this work, we tested 100 potential new microsatellites (SSRs) equally derived from expressed s... more 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 corresponded to the first EST library constructed for Senegalese sole (EST-SSR). Although differences were not significant, EST sequences provided a higher proportion of quality markers (74%) than anonymous ones (64%). Most of the rejected anonymous SSRs (17 loci) were discarded because they did not generate PCR products; only one was monomorphic. On the contrary, all EST-SSRs gave PCR products, although monomorphism was more frequent (26%). Altogether, the number of alleles per locus was fairly similar in both SSR types, ranging from 2 to 19. The observed and expected heterozygosities varied from 0.105 to 1 and from 0.108 to 0.937, respectively. The main difference between the two sets was the percentage of annotated loci, being higher in EST-SSRs, as expected. Within the EST-SSRs, 46% of them showed flanking regions that significantly matched with EST sequences from other three flatfish species; however, the microsatellite itself was present only on half of these cases. These two new SSR sets constitute a suitable tool for fingerprinting, gene flow, genetic diversity, genome mapping studies and molecular-assisted breeding in this species.

Research paper thumbnail of Genetic Identification of Western Mediterranean Sturgeons and its Implication for Conservation

Conservation Genetics, Aug 1, 2004

To date, the only native sturgeon species in Western Europe was believed to be Acipenser sturio. ... more 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 only species within the rivers of Western Europe, as A. naccarii, a species previously considered endemic of the Adriatic region, has been reported from the Iberian Peninsula in recent years. Here, we have used forensic techniques to obtain DNA from several museum specimens of sturgeons caught in the Spanish Guadalquivir River and in other European rivers. We analysed DNA sequences from these specimens for five genetic markers (three nuclear and two mitochondrial regions), which were subsequently compared with sequences obtained from A. sturio and A. naccarii. Our study demonstrates that A. naccarii coexists with A. sturio, from the Adriatic Sea to the Iberian Peninsula, a finding that could be taken into account in future sturgeon recovery programmes in Western Europe.

Research paper thumbnail of olecular characterization of the interspecific hybrid Pistacia vigros

A new Pistacia variety, VIGROS, has been characterized here using nuclear and chloroplastidial DN... more A new Pistacia variety, VIGROS, has been characterized here using nuclear and chloroplastidial DNA sequences, which are suitable tools for genetic improvement and cultivar identification. The nuclear DNA sequences (ribosomal ITS1, 5.8S, ITS2) determined that VIGROS is an interspecific hybrid between Pistacia vera L. and Pistacia atlantica Desf. The chloroplastidial DNA sequences (trnC-D, trnL-F regions) demonstrated that VIGROS bears a haplotype 100% coincident with that of P. vera, which would then be

Research paper thumbnail of Determining the specific status of the Iberian sturgeons by means genetic analyses of old specimens

Advances in Bioscience and Biotechnology, 2010

To clarify the species status of sturgeon from rivers of the Iberian Peninsula, eight molecular m... more 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 River in the 19th century) is A. sturio, based on all the eight molecular markers, four of them used from the first time in this study. In previous analyses based on 5 genetic markers, our group assigned two specimens captured in this river in the 1970-80s (EBD8173 and EBD8401) to the species A. naccarii, suggesting the presence of this species in the Iberian Peninsula. In this work, this conclusion is drawn after successfully obtaining a mitochondrial marker in a very old scute from a prehistoric site (Acinipo, about 1500 BC, from the Guadalquivir River basin). On the other hand, in the specimen EBD8174 captured in the Guadalquivir in 1975, we have obtained two new mitochondrial markers confirming that it can be considered A. sturio for all the mitochondrial markers, but nuclear ones identify it as A. naccarii. Finally, two very old samples (Nerja E-VI and Nerja N/62-63) were not successfully characterized by any molecular markers. Some aspects and consequences of our results are discussed, such as the origin of the "mosaic" specimen EBD8174 and, above all, the native status of A. naccarii in historic and prehistoric times in the southern Iberian Peninsula.

Research paper thumbnail of Determinig the Specific Status of the Iberian Sturgeons by Means Genetic Analyses of Old Specimens

To clarify the species status of sturgeon from rivers of the Iberian Peninsula, eight molecular m... more 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 River in the 19th century) is A. sturio, based on all the eight molecular markers, four of them used from the first time in this study. In previous analyses based on 5 genetic markers, our group assigned two specimens captured in this river in the 1970-80s (EBD8173 and EBD8401) to the species A. naccarii, suggesting the presence of this species in the Iberian Peninsula. In this work, this conclusion is drawn after successfully obtaining a mitochondrial marker in a very old scute from a prehistoric site (Acinipo, about 1500 BC, from the Guadalquivir River basin). On the other hand, in the specimen EBD8174 captured in the Guadalquivir in 1975, w...