Carmelo Ruiz-Rejón’s research while affiliated with University of Granada and other places

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Publications (29)


Figure 2. Phylogenetic tree obtained from a maximum likelihood analysis based on a Clustal Omega alignment of the miR-430 sequences found in the consensus repeat subunit of model species (a) and species of interest to fisheries and aquaculture (b), using the miR-430 sequence found in Petromyzon marinus as an outgroup. The numbers of the sequences are based on their position inside the repeat subunit, and the different variants have been classified based on their homology to the mature variants found in Danio rerio. The variants have been marked with different colours, with variant "a" in red, variant "b" in blue, and variant "c" in yellow. Numbers next to the nodes indicate the bootstrap values ranging from 0 to 1. Abbreviations: Aca = Amia calva, Aru = Acipenser ruthenus, Asp = Atractosteus spatula, Cmi = Callorhinchus milii, Dae = Danio aesculapii, Dal = Danio albolineatus, Dni = Danio nigrofasciatus, Dre = Danio rerio, Gmo = Gadus morhua, Gas = Gasterosteus aculeatus, Msa = Micropterus salmoides, Ola = Oryzias latipes, Pma = Petromyzon marinus, Ssa = Salmo salar, Str = Salmo trutta, Sse = Solea senegalensis, Tru = Takifugu rubripes, Tni = Tetraodon nigroviridis.
MiR-430 clusters in cichlids.
Cont.
miR-430 microRNA Family in Fishes: Molecular Characterization and Evolution
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July 2023

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62 Reads

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1 Citation

Animals

Claudio A. Jiménez-Ruiz

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Carmelo Ruiz-Rejón

The miR-430 microRNA family has been described in multiple fish species as one of the first microRNAs expressed by the zygote. It has been suggested that this family is implicated in maternal mRNA elimination, but may also play a role in steroidogenesis, sexual differentiation, and flatfish metamorphosis. The miR-430 sequences have been found in multiple-copy tandem clusters but evidence of their conservation outside of teleost fishes is scarce. In the present study, we have characterized the tandem repeats organization of these microRNAs in different fish species, both model and of interest in aquaculture. A phylogenetic analysis of this family has allowed us to identify that the miR-430 duplication, which took place before the Chondrostei and Neopterygii groups’ divergence, has resulted in three variants (“a”, “b”, and “c”). According to our data, variant “b” is the most closely related to the ancestral sequence. Furthermore, we have detected isolated instances of the miR-430 repeat subunit in some species, which suggests that this microRNA family may be affected by DNA rearrangements. This study provides new data about the abundance, variability, and organization of the miR-430 family in fishes.

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A chromosome-level genome assembly enables the identification of the follicule stimulating hormone receptor as the master sex determining gene in the flatfish Solea senegalensis

January 2023

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339 Reads

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21 Citations

Molecular Ecology Resources

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 SNP 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. Fshr displayed differential gene 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 non-synonymous 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.


Characterization of the complete mitochondrial genome of the striped soldier shrimp, Plesionika edwardsii (Brandt, 1851) (Crustacea: Decapoda: Pandalidae), and comparison with other species of Caridea

December 2022

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54 Reads

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1 Citation

Journal of Crustacean Biology

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 to most of the caridean mitochondrial genomes. In the comparative analysis, however, we detected in other species changes in the gene order that could be mediated by the recombination of transfer RNA genes, as well as AT skew shifts that could indicate changes in the origins of replication. All protein-coding genes of the mitochondrial genome of P. edwardsii seem to be under purifying selection, although the differences in Ka:Ks ratios suggest a disparity in the mutational constraints of some genes. This genome also presents a 1,118 bp-long non-coding sequence that encompass the control region. We have been able to find a previously described conserved sequence block in this region and assess that it forms a stem-loop structure in different species of Pandalidae, which is a shared feature with the conserved sequence blocks described in the family Alvinocarididae. We also detected microsatellites in the control region of P. edwardsii and in other species of Pandalidae and minisatellites in Lysmata vittata (Stimpson, 1860) that can account for around 20% of the additional non-coding region of this species. The phylogenetic relationships of P. edwardsii with other pandalids were assessed by two analyses: one based on the complete mitochondrial sequences and another based only on the protein-coding genes. Our study, thus, contributes to the genomic resources available for P. edwardsii and expands the current biological knowledge about the mitochondrial genomes of other caridean species.



Figure 1. Cytogenetic map of Solea senegalensis obtained with BAC probes: Yellow color indicates BACs containing microsatellites; pink color indicates BACs with genes related to sexual reproduction/differentiation; green color indicates BACs with genes related to metamorphosis; clear blue color indicates BACs containing genes related to the immune system; and dark blue color indicates BACs with genes belonging to other categories. Short arms are p and long are q (upper is p and lower is q in metacentrics). * BACs found on more than one chromosome.
Integration of the cytogenetic map of Solea senegalensis with published linkage map and physical map.
Integration of Maps Enables a Cytogenomics Analysis of the Complete Karyotype in Solea senegalensis

May 2022

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123 Reads

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7 Citations

International Journal of Molecular Sciences

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 telomeric regions on chromosomes 3, 7, 9 and 16. However, on chromosome 11, a greater abundance of DNA transposons was detected in interstitial BACs. This chromosome is syntenic with several chromosomes of the other two flatfish species, suggesting rearrangements during its evolution. A similar situation was also found on chromosome 16 (for microsatellites and low complexity sequences), but not for TEs (retroelements and DNA transposons). These differences in the distribution and abundance of repetitive elements in chromosomes that have undergone remodeling processes during the course of evolution also suggest a possible role for simple repeat sequences in rearranged regions.


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

March 2022

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143 Reads

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1 Citation

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 explore chromosome evolutionary patterns in the order. Whole genome resequencing of six males and six females enabled the identification of 41 fixed allelic variants in the follicle stimulating hormone receptor ( fshr ) gene, homozygous in females and heterozygous in males, consistent with an XX / XY chromosome system. The observed association between fshr SNPs and sex was confirmed at the species level in a broad sample, which allowed tuning up a molecular sexing tool. Fshr demonstrated differential gene expression between male and female gonads since 86 days post-fertilization, when the gonad was still an undifferentiated primordium, concomitant with the activation of other testis and ovary marker genes, such as amh and cyp19a1a genes, respectively. Interestingly, the Y-linked fshr allele, which included 24 non-synonymous variants, expressed to a higher level than the X-linked allele at all stages. We hypothesize a molecular mechanism hampering the action of the follicle stimulating hormone that would drive the undifferentiated gonad toward testis.


Long-term monitoring of B-chromosome invasion and neutralization in a population of Prospero autumnale (Asparagaceae)

May 2018

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77 Reads

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4 Citations

Evolution

B chromosomes have been reported in about 15% of eukaryotes, but long term dynamics of B chromosomes in a single natural population has rarely been analysed. Prospero autumnale plants collected in 1981 and 1983 at Cuesta de La Palma population have shown the presence of B chromosomes. We analyze here seven additional samples collected between 1987 and 2015, and show that B frequency increased significantly during the 1980's and showed minor fluctuations between 2005 and 2015. A mother‐offspring analysis of B chromosome transmission, at population level, showed significant drive on the male side (kB = 0.65) and significant drag on the female side (kB = 0.33), with average B transmission rate being very close to the Mendelian rate (0.5). No significant effects of B chromosomes were observed on a number of vigour and fertility‐related traits. Within a parasite/host framework, these results suggest that B chromosomes’ drive on the male side is the main pathway for B chromosome invasion whereas B chromosome drag on the female side might be the main manifestation of host genome resistance in this species. P. autumnale thus illuminates a novel evolutionary pathway for B chromosome neutralization by means of a decrease in B transmission through the non‐driving sex. This article is protected by copyright. All rights reserved


Table 2 Number of markers and length per LG in Senegalese sole maps 
First Haploid Genetic Map Based on Microsatellite Markers in Senegalese Sole (Solea senegalensis, Kaup 1858)

February 2015

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361 Reads

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19 Citations

Marine Biotechnology

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 were obtained by chromosome-manipulation techniques: two haploid gynogenetics, used to assign and order microsatellites to linkage groups and another diploid gynogenetic family, used for estimating marker-centromere distances. The consensus map consists of 129 microsatellites distributed in 27 linkage groups (LG), with an average density of 4.7 markers per LG and comprising 1,004 centimorgans (cM). Additionally, 15 markers remained unlinked. Through half-tetrad analysis, we were able to estimate the centromere distance for 81 markers belonging to 24 LG, representing an average of 3 markers per LG. Comparative mapping was performed between flatfish species LG and model fish species chromosomes (stickleback, Tetraodon, medaka, fugu and zebrafish). The usefulness of microsatellite markers and the genetic map as tools for comparative mapping and evolution studies is discussed.


Chromosomal manipulation in Senegalese sole (Solea senegalensis Kaup, 1858): induction of triploidy and gynogenesis

July 2014

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247 Reads

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14 Citations

Journal of Applied Genetics

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 b) all-female stocks, of higher growth rate. Triploidy was induced by means of a cold shock. Gynogenesis was induced by activating eggs with UV-irradiated sperm, and to prompt diploid gynogenesis, a cold-shock step was also used. Ploidy of putative triploid larvae and gynogenetic embryos were determined by means of karyotyping and microsatellite analysis. Haploid gynogenetic embryos showed the typical "haploid syndrome". As expected, triploid and gynogenetic groups showed lower fertilization, hatching, and survival rates than in the diploid control group. Survival rate, calculated 49 days after hatching, for haploid and diploid gynogenetic groups was similar to those observed in other fish species (0 % and 62.5 %, respectively), whereas triploids showed worse values (45 %). Sex was determined macroscopically and by histological procedures, revealing that all the diploid gynogenetic individuals were females. In conclusion, we have successfully applied chromosomal-manipulation techniques in the flatfish species Senegalese sole in order to produce triploid, haploid, and diploid gynogenetic progenies.


Table 1 Screening figures in the three families analyzed for QTL identification 
Table 3 QTL location for resistance and survival time to viral haemorrhagic septicaemia virus 
Table 5 Markers significantly associated with VHS resistance-related traits 
Table 6 Markers significantly associated with growth-related traits 
Identification of Quantitative Trait Loci Associated with Resistance to Viral Haemorrhagic Septicaemia (VHS) in Turbot (Scophthalmus maximus): A Comparison Between Bacterium, Parasite and Virus Diseases

September 2013

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174 Reads

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44 Citations

Marine Biotechnology

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 genotyped and evaluated by linear regression and maximum likelihood approaches. In addition, a comparison between QTL detected for resistance and survival time to other important bacterial and parasite diseases affecting turbot (furunculosis and scuticociliatosis) was also carried out. Finally, the relationship between QTL affecting resistance/survival time to the virus and growth-related QTL was also evaluated. Several genomic regions controlling resistance and survival time to VHS were detected. Also significant associations between the evaluated traits and genotypes at particular markers were identified, explaining up to 14 % of the phenotypic variance. Several genomic regions controlling general and specific resistance to different diseases in turbot were detected. A preliminary gene mining approach identified candidate genes related to general or specific immunity. This information will be valuable to develop marker-assisted selection programs and to discover candidate genes related to disease resistance to improve turbot production.


Citations (21)


... This was further observed in dmrt and sox genes, indicating their crucial roles in male reproductive functions, such as testicular development and spermatogenesis. In contrast, sox19b, and hsd17b showed higher expression in females, indicating their involvement, such as in steroidogenesis, ovarian development, and general female reproductive processes [19,58]. ...

Reference:

Insights into Solea senegalensis Reproduction Through Gonadal Tissue Methylation Analysis and Transcriptomic Integration
A chromosome-level genome assembly enables the identification of the follicule stimulating hormone receptor as the master sex determining gene in the flatfish Solea senegalensis

Molecular Ecology Resources

... This commercial interest has promoted the increase in genomic resources in the last decade (Robledo et al., 2017;Garcıá-Angulo et al., 2018;Cross et al., 2020;Merlo et al., 2021;Rodrıǵuez et al., 2021;de la Herrań et al., 2023), including an initial version of its genome (Guerrero-Coźar et al., 2021) and a recent improved version (de la Herrań et al., 2023). Due to the absence, until 2023, of a quality sequenced genome in this species, repetitive sequence studies on Senegalese sole had been limited to the sequence analysis of some BAC clones mapped on the chromosomes of the species Rodrıǵuez et al., 2019;Cross et al., 2020;Rodrıǵuez et al., 2021;Ramıŕez et al., 2022) and the study of TEs in the Hox gene clusters of three flatfish species, including S. senegalensis (Mendizabal-Castillero et al., 2022). ...

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

International Journal of Molecular Sciences

... Maturation of male and female gametophytes in plants implies the occurrence of several mitoses, during which B chromosome non-disjunction and gonotaxis can operate to provide post-meiotic TRD by preferential migration to the generative nucleus in the pollen grain or to the egg in the embryo sac (steps 6 and 7, respectively). Examples of male postmeiotic TRD have been reported, for instance, in Secale cereale (Hasegawa 1934), Festuca pratensis (Bösemark 1954), Aegilops speltoides (Mendelson and Zohari 1972), Hypochoeris maculata (Parker 1976), and Prospero autumnale (Lanzas et al. 2018). In rye, experimental crosses by Müntzing (1945) demonstrated that post-meiotic TRD during gametophyte maturation takes place also through the female side (step 7), thus making rye B chromosomes one of the few examples, along with the migratory locust (Pardo et al. 1994), where B chromosomes exhibit drive through both sexes. ...

Long-term monitoring of B-chromosome invasion and neutralization in a population of Prospero autumnale (Asparagaceae)
  • Citing Article
  • May 2018

Evolution

... They consider that the samples might be contaminated. In a new study, Ruiz-Rejón et al. (2000) confirmed that HindIII mitochondri-al DNA is unique to A. naccarii and A. baerii, and does not appear in A. sturio. They consider that A. sturio has followed an independent evolution to the previous species (in addition to H. huso, which is closely related to the genus Acipenser). ...

Genetic characterization of Acipenser sturio L., 1758 in relation to other sturgeon species using satellite DNA

Boletin - Instituto Espanol de Oceanografia

... Considerable effort has been made in recent years to understand the cytogenetic and genomic aspects of this species. Molina-Luzón et al. [29] developed the first haploid genetic map of Senegalese sole using gynogenetic families and 129 microsatellites, with the consensus map consisting of 27 linkage groups (LGs). Several studies have used a BAC-FISH approach to locate and map genes on the chromosomes, as well as to study aspects such as histone evolution [30], sex determination and differentiation [31][32][33], repetitive DNA families [34], and chromosomal evolution [35]. ...

First Haploid Genetic Map Based on Microsatellite Markers in Senegalese Sole (Solea senegalensis, Kaup 1858)

Marine Biotechnology

... naccarii) endemic to the North Adriatic region, in the Ticino River Park, Italy [115], and the restocking of endangered populations of dusky grouper, Epinephelus marginatus, in the Mediterranean [318], and of white seabream, Diplodus sargus, in a fishery reserve in Sicily, Italy [319]. Microsatellites have been used for the estimation of the aquaculture potential of new species such as that of the Korean kelp grouper, Epinephelus bruneus [320], yellowtail amberjack, Seriola lalandi, in Chile [321] and a flatfish Senegalese sole, Solea senegalensis [322]. ...

Chromosomal manipulation in Senegalese sole (Solea senegalensis Kaup, 1858): induction of triploidy and gynogenesis

Journal of Applied Genetics

... Moreover, the utilization of high-density genetic markers for quantitative trait locus (QTL) mapping in aquaculture species represents a pivotal strategy in unraveling trait structures and pinpointing genomic regions, underlying genes, and causal mutations that govern phenotypic variability [24]. This approach has been implemented extensively to explore QTLs associated with disease resistance in aquaculture species, such as the red sea bream (Pagrus major) [25], Pacific oyster (Crassostrea gigas) [26], black rockfish (Sebastes schlegelii) [27], and turbot (Scophthalmus maximus) [28]. ...

Identification of Quantitative Trait Loci Associated with Resistance to Viral Haemorrhagic Septicaemia (VHS) in Turbot (Scophthalmus maximus): A Comparison Between Bacterium, Parasite and Virus Diseases

Marine Biotechnology

... The capacity of L. comosa for autonomous self-pollination (also see Garrido-Ramos et al., 1998) may provide some reproductive assurance against limited cross-pollination by maintaining ovule fertilization. However, most viable seeds of this species are cross-fertilized (see Ruiz Rejón et al., 1982Rejón et al., , 1988, probably because severe inbreeding depression during seed development constrains the contribution of autonomous autogamy to seed production. Accordingly, the greater seed production by flowers on intact inflorescences in the French population indicates higher-quality pollination of these inflorescences than of clipped inflorescences, even though the numbers of pollen grains on stigmas did not differ significantly. ...

An estimate of the outcrossing rate in natural populations of Muscari comosum (Liliaceae)
  • Citing Article

... Although the chromosome numbers reported for this species are confused to some extent (2n = 8, 16?, 32?, 64?), all the populations analysed trustworthily in the Iberian Peninsula present 2n = 8. Furthermore, in certain populations there are some individuals which have a variable number of B-chromosomes (0-16 B) (RESENDE and FRANCA 1946;FERNANDES et al. 1948;GADELLA et al. 1966;VALDES 1970;FERNANDES and QUEIROS 1971;LovE and KJELLQUIST 1973;Rmz REJON 1974VALDES et al. 1978;Rmz REJON et al. 1980). ...

Existence of ADH gene duplication in the diploid level of Dipcadi serotinum (L.) Medic
  • Citing Article