Rafael Navajas-Pérez

University of Granada | UGR · Department of Genetics

Endopolyploidy is a well-documented phenomenon in the natural world, yet its biological significance remains poorly understood. A multitude of effects and consequences have been described in the literature as being attributable to this phenomenon, yet none of them have been subjected to rigorous and well-established confirmation. The measurement of...

Many population biology, ecology, and evolution experiments rely on the accuracy of the classification of individuals and the estimation of size population. The visual classification of vinegar flies, Drosophila melanogaster (Diptera: Drosophilidae), morphs is a laborious task usually performed by bench workers. Because of the size of the flies and...

Pleuronectiformes are flatfishes with high commercial value and a prominent example of successful marine adaptation through chromosomal evolution. Hence, the aim of this study was to analyze the 14 relative abundance of repetitive elements (satellite DNA and transposable elements (TE)) in the 15 genome of 10 fish species (8 flatfish) delving into t...

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 mu...

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...

Idiograms are graphical representations in which chromosomes appear ordered by their relative size, homology groups, and the presence of cytogenetic landmarks such as centromeres, secondary constrictions, and banding patterns. They have become crucial elements in cytogenetic research. Here, we describe a simple protocol for spreadsheet software to...

La Genética Mendeliana representa el primer contacto de los estudiantes con la Genética. Aunque es fundamental para entender las bases de la herencia, no recoge dos de las grandes excepciones que se producen en la naturaleza y que alteran las proporciones mendelianas: (1) las interacciones génicas, o la acción de varios genes que contribuyen a un m...

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

Los sellos son el reflejo fidedigno de la historia y la cultura de la humanidad con un potencial didáctico aún por explorar. Aquí presento una experiencia docente que usa todos los sellos postales emitidos en honor a Gregor Mendel y los pertenecientes a series postales en las que este aparece (un total de 56 piezas de 13 países). Se elaboró un cues...

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

Xenobiotic compounds are produced in high amounts by many different sources and can be degraded by different microbial species in different environments. However, they often accumulate, thus producing toxic effects in living organisms. Fungi represent the most abundant biomass in soils. Unique features of fungi include the capability to disperse hy...

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...

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...

In this chapter, we report a detailed analysis of repetitive elements in the papaya genome, including transposable elements (TEs), tandemly arrayed sequences, and high copy number genes. These repetitive sequences account for ~56 % of the papaya genome, with TEs being the most abundant at 52 %, tandem repeats at 1.3 %, and high copy number genes at...

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...

Sex determination in papaya is controlled by a recently evolved XY chromosome pair, with two slightly different Y chromosomes controlling the development of males (Y) and hermaphrodites (Yh). To study the events of early sex chromosome evolution, we sequenced the hermaphrodite-specific region of the Yh chromosome (HSY) and its X counterpart, yieldi...

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...

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...

Papaya is a major fruit crop in tropical and subtropical regions worldwide. It is trioecious with three sex forms: male, female, and hermaphrodite. Sex determination is controlled by a pair of nascent sex chromosomes with two slightly different Y chromosomes, Y for male and Yh for hermaphrodite. The sex chromosome genotypes are XY (male), XYh (herm...

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...

The origin and evolution of sexual dimorphism and the sex-determining mechanisms are major topics in Evolutionary Biology on which many studies have focused in recent decades. Among flowering plants, the origin of dioecy has resulted from quite recent events, occurring independently in about 7% of the genera. However, only a moderate number of dioe...

Sex chromosomes are thought to have evolved from an autosomal pair through the accumulation of sex-determining genes and the disruption of X-Y recombination that ultimately led to the formation of heteromorphic sex chromosomes. Early evolved plant-sex chromosomes have given rise to many studies in recent years, which have proved chromosomal rearran...

One of the most important topics in evolutionary biology concerns the origin and evolution of sex-determining systems and sex chromosomes. Certain plant species display younger sex-chromosome systems in different evolutionary stages. It is thought that the same evolutionary forces described for animals are operating in plants. However, in oppositio...

Arabica coffee (Coffea arabica L.) is a self-compatible perennial allotetraploid species (2n=4x=44), whereas Robusta coffee (C. canephora L.) is a self-incompatible perennial diploid species (2n=2x=22). C. arabica (C(a) C(a) E(a) E(a) ) is derived from a spontaneous hybridization between two closely related diploid coffee species, C. canephora (CC)...

We studied the evolution of RAE180 satellite DNA family in the North American endemic dioecious plant Rumex hastatulus. In this species, the Texas race is characterized by a single XX/XY sex chromosome system, whereas the North Carolina race has evolved a derived complex XX/XY(1)Y(2) sex chromosome system. RAE180 repeats were autosomic and poorly r...

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...

Here, we analyze the evolutionary dynamics of a satellite-DNA family in an attempt to understand the effect of factors such as location, organization, and repeat-copy number in the molecular drive process leading to the concerted-evolution pattern found in this type of repetitive sequences. The presence of RAE180 satellite-DNA in the dioecious spec...

Tandem repeats often confound large genome assemblies. A survey of tandemly arrayed repetitive sequences was carried out in whole genome sequences of the green alga Chlamydomonas reinhardtii, the moss Physcomitrella patens, the monocots rice and sorghum, and the dicots Arabidopsis thaliana, poplar, grapevine, and papaya, in order to test how these...

A satellite-DNA family (RUSI) has been isolated and characterized in Rumexinduratus Boiss and Reuter (Polygonaceae), an Iberian endemic polygamous sorrel. The RUSI repeats are 170 bp in length and approximately 68% AT-rich containing different variants of degenerate telomere motifs--(TT)(n)AN(GG)(n) -, a typical feature of subtelomeric DNA repeats...

Tesis Univ. Granada. Departamento de Genética. Leída el 15 de diciembre de 2005

Papaya (Carica papaya L.) is an important fruit crop cultivated in tropical and subtropical regions worldwide. A first draft of its genome sequence has been recently released. Together with Arabidopsis, rice, poplar, grapevine and other genomes in the pipeline, it represents a good opportunity to gain insight into the organization of plant genomes....

Papaya, a fruit crop cultivated in tropical and subtropical regions, is known for its nutritional benefits and medicinal applications. Here we report a 3x draft genome sequence of 'SunUp' papaya, the first commercial virus-resistant transgenic fruit tree to be sequenced. The papaya genome is three times the size of the Arabidopsis genome, but conta...

Sex of dioecious and gynodioecious papayas is controlled by two slightly different Y chromosomes, Y for males and Yh for hermaphrodites. All combinations of the Y and/or Yh chromosomes are lethal. We investigated the features of paired dioecious X- and Y-specific bacterial artificial chromosomes (BACs) and compared their sequences to corresponding...

Rumex papillaris Boiss, & Reut., an Iberian endemic, belongs to the section Acetosa of the genus Rumex whose main representative is R. acetosa L., a species intensively studied in relation to sex-chromosome evolution. Here, we characterize cytogenetically the chromosomal complement of R. papillaris in an effort to enhance future comparative genomic...

In Oleaceae the most outstanding biological issue is to clarify the taxonomic relationships of cultivated and wild olives. To establish the genetic relationships between the wild (Olea europaea subsp. europaea var. sylvestris (Mill.) Lehr.), the cultivated olive (Olea europaea subsp. europaea var. europaea), and other taxa of the genus Olea (Olea e...

Unlabelled: satDNA Analyzer is a program, implemented in C++, for the analysis of the patterns of variation at each nucleotide position considered independently amongst all units of a given satellite-DNA family when comparing it between a pair of species. The program classifies each site accordingly as monomorphic or polymorphic, discriminates sha...

The structural features and evolutionary state of the sex chromosomes of the XX/XY species of Rumex are unknown. Here, we report a study of the meiotic behaviour of the XY bivalent in Rumex acetosella and R. suffruticosus, a new species which we describe cytogenetically for the first time in this paper, and also that of the XY(1)Y(2) trivalent of R...

In this paper, we analyze a satellite-DNA family, the RAYSI family, which is specific of the Y chromosomes of Rumex acetosa, a dioecious plant species with a multiple sex-chromosome system in which the females are XX and the males are XY(1)Y(2). Here, we demonstrate that this satellite DNA is common to other relatives of R. acetosa, including Rumex...

Rumex acetosa is characterized by a multiple chromosome system (2n = 12 + XX for females, and 2n = 12 + XY1Y2 for males), in which sex is determined by the ratio between the number of X chromosomes and autosome sets. For a better understanding of the molecular structure and evolution of plant sex chromosomes, we have generated a sex chromosome spec...

The genus Rumex includes hermaphroditic, polygamous, gynodioecious, monoecious, and dioecious species, with the dioecious species being represented by different sex-determining mechanisms and sex-chromosome systems. Therefore, this genus represents an exceptional case study to test several hypotheses concerning the evolution of both mating systems...

One characteristic of sex chromosomes is the accumulation of a set of different types of repetitive DNA sequences in the Y chromosomes. However, little is known about how this occurs or about how the absence of recombination affects the subsequent evolutionary fate of the repetitive sequences in the Y chromosome. Here we compare the evolutionary pa...

The molecular structure of the exceptional telomeres of six plant species belonging to the order Asparagales and two species of the order Liliales was analyzed using Southern blot and fluorescence in situ hybridization. Three different situations were found, namely: i) In the two Liliales species, Tulipa australis (Liliaceae) and Merendera montana...

In a previous paper [1] we showed that Y-linked satellite-DNA sequences of Rumex (Polygonaceae) present reduced rates of evolution in relation to other autosomal satellite-DNA sequences. In the present paper, we re-analyze the same set of sequences by using the satDNA Analyzer 1.2 software, specifically developed by us for analysis of satellite DNA...