Manuel A Garrido-Ramos

Manuel A Garrido-Ramos
University of Granada | UGR · Department of Genetics

PhD

About

88
Publications
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2,713
Citations
Citations since 2016
17 Research Items
1061 Citations
2016201720182019202020212022050100150200
2016201720182019202020212022050100150200
2016201720182019202020212022050100150200
2016201720182019202020212022050100150200

Publications

Publications (88)
Article
Full-text available
Background The full catalog of satellite DNA (satDNA) within a same genome constitutes the satellitome. The Library Hypothesis predicts that satDNA in relative species reflects that in their common ancestor, but the evolutionary mechanisms and pathways of satDNA evolution have never been analyzed for full satellitomes. We compare here the satellito...
Preprint
Full-text available
Background The full catalogue of satellite DNA (satDNA) within a same genome constitutes the satellitome. The Library Hypothesis predicts that satDNA in relative species reflects that in their common ancestor, but the evolutionary mechanisms and pathways of satDNA evolution have never been analyzed for full satellitomes. We compare here the satelli...
Article
Full-text available
Vandenboschia speciosa is an endangered tetraploid fern species with a large genome (10.5 Gb). Its geographical distribution is characterized by disjoined tertiary flora refuges, with relict populations that survived past climate crises. Here we analyze the transposable elements (TEs) and found that they comprise about 76% of the V. speciosa genome...
Article
Full-text available
Doubly uniparental inheritance (DUI) of mitochondrial DNA (mtDNA) in bivalve mollusks is one of the most notable departures from the paradigm of strict maternal inheritance of mtDNA among metazoans. Recently, work on the Mediterranean mussel Mytilus galloprovincialis suggested that a nucleotide motif in the control region of this species, known as...
Article
Full-text available
We sequenced the sporophyte transcriptome of Killarney fern (Vandenboschia speciosa (Willd.) G. Kunkel). In addition to being a rare endangered Macaronesian-European endemism, this species has a huge genome (10.52 Gb) as well as particular biological features and extreme ecological requirements. These characteristics, together with the systematic p...
Article
The twenty-first century began with a certain indifference to the research of satellite DNA (satDNA). Neither genome sequencing projects were able to accurately encompass the study of satDNA nor classic methodologies were able to go further in undertaking a better comprehensive study of the whole set of satDNA sequences of a genome. Nonetheless, kn...
Chapter
Mitochondrial DNA (mtDNA) is typically passed on to progeny only by the female parent. The phenomenon of “doubly uniparental inheritance” (DUI) of mtDNA in many bivalve species is a fascinating exception to the paradigm of strict maternal inheritance of mtDNA. In this review, we survey the current state of knowledge of DUI and discuss several activ...
Article
Full-text available
Background and aims: Vandenboschia speciosa is a highly vulnerable fern species, with a large genome (10.5 Gb). Haploid gametophytes and diploid sporophytes are perennial, can reproduce vegetatively, and certain populations are composed only of independent gametophytes. These features make this fern a good model: (1) for high-throughput analysis o...
Article
Full-text available
We provide here the first full chloroplast genome sequence, i.e., the plastome, for a species belonging to the fern order Hymenophyllales. The phylogenetic position of this order within leptosporangiate ferns, together with the general scarcity of information about fern plastomes, places this research as a valuable study on the analysis of the dive...
Article
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...
Article
Full-text available
We report and discuss the results of a quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis of the expression patterns of seven three amino acid loop extension (TALE) homeobox genes (four KNOTTED-like homeobox (KNOX) and three BEL1-like homeobox (BELL) genes) identified after next generation sequencing (NGS) and assembly...
Article
Full-text available
Satellite DNA represents one of the most fascinating parts of the repetitive fraction of the eukaryotic genome. Since the discovery of highly repetitive tandem DNA in the 1960s, a lot of literature has extensively covered various topics related to the structure, organization, function, and evolution of such sequences. Today, with the advent of geno...
Article
We report and discuss the results of a quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis of the expression patterns of six MADS-box genes (VsMB2 to VsMB7 genes) identified after Next Generation Sequencing (NGS) and assembly of two transcriptomes, those of the sporophyte and the gametophyte, of the endangered fern speci...
Article
For decades, satellite DNAs have been the hidden part of genomes. Initially considered as junk DNA, there is currently an increasing appreciation of the functional significance of satellite DNA repeats and of their sequences. Satellite DNA families accumulate in the heterochromatin in different parts of the eukaryotic chromosomes, mainly in pericen...
Article
Full-text available
In a previous work, we characterized the HinfI satellite DNA family in the subtribe Centaureinae (Cardueae) demonstrating that a "library" of eight HinfI subfamilies would exist in the common ancestor of all Centaureinae, which were differentially amplified in different lineages. Now, we extend our study by analyzing a total of 219 additional repea...
Article
Full-text available
Background and Aims Subtribe Centaureinae appears to be an excellent model group in which to analyse satellite DNA and assess the influence that the biology and/or the evolution of different lineages have had on the evolution of this class of repetitive DNA. Phylogenetic analyses of Centaureinae support two main phases of radiation, leading to two...
Article
Eukaryotic genomes are composed of both unique and repetitive DNA sequences. These latter form families of different classes that may be organized in tandem or may be dispersed within genomes with a moderate to high degree of repetitiveness. The repetitive DNA fraction may represent a high proportion of a particular genome due to correlation betwee...
Book
The experimental data that have been generated using new molecular techniques associated with the completion of genome projects have changed our perception of the structural features, functional implications and evolutionary dynamics of repetitive DNA sequences. This volume of Genome Dynamics provides a valuable update on recent developments in res...
Article
Full-text available
SarkOne is a genus-specific satellite-DNA family, isolated from the genomes of the species of the genus Sarcocapnos. This satellite DNA is composed of repeats with a consensus length of 855 bp and a mean G+C content of 52.5%. We have sequenced a total of 189 SarkOne monomeric repeats belonging to a total of seven species of the genus Sarcocapnos. T...
Article
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...
Article
Full-text available
We have examined the mitochondrial DNA (mtDNA) content of several somatic tissues from male and female individuals of the blue mussel, Mytilus edulis. As expected from the mode of doubly uniparental inheritance (DUI) of mtDNA that is characteristic of this genus, the dominant type of mtDNA in male gonads was the male-transmitted M type. In contrast...
Article
Pagurta: An interspecific hybrid of common seabream Pagrus pagrus (L., 1758) female and banded sea- bream males Pagrus auriga Valenciennes, 1843 male: phenotypic and molecular characterization Hybrids are of great interest in aquaculture. In the present study, we report for the first time an interespecific hybrid between common seabream Pagrus pagr...
Article
Full-text available
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...
Article
Full-text available
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...
Chapter
Today, with all the sturgeon species almost disappearing all over the world, it is necessary to undertake their recovery under the programs for the conservation of genetic resources. The complete absence of these fish from most rivers increases the difficulties in carrying out such programs, hampering the genetic identification of specimens and the...
Chapter
The meat and, above all, the caviar from sturgeons have been gastronomic emblems of delicacy from time immemorial. When sturgeons were abundant, caviar was marketed primarily from three species (Huso huso, Acipenser gueldenstaedtii and A. stellatus) mostly from the Caspian Sea. However, these are not the only species of sturgeons used traditionally...
Article
Full-text available
In the course of a histopathological survey performed to discover the cause of mass mortality of the striped clam Chamelea gallina in the Balearic Islands (Spain, Mediterranean Sea), we detected a Marteilia-like parasite in 3 clams. Molecular methods were applied to identify the parasite. DNA extracted from a paraffin block was used to carry out a...
Article
Marteilia refringens is a protozoan parasite recognized as a significant pathogen of the European flat oyster Ostrea edulis. It is believed to have a complex life-cycle involving several hosts. In this study, we applied molecular approaches to identify this parasite in samples of the razor clam Solen marginatus from the south west coast of Spain. W...
Article
A large euchromatic supernumerary segment (ss) occurs at a high frequency in a natural population of Scilla autumnalis from the west of the Iberian Peninsula. Mother-offspring analyses have shown random pollination of all bulbs lacking the extra segment but non-random pollination of some bulbs carrying it. With a single exception, ss transmission a...
Article
From a battery of microsatellite markers (100 loci), recently identified by our group, we have selected eight for parentage assignment in Senegal sole (Solea senegalensis). This tool is based on microsatellite loci obtained from four genomic DNA libraries and one cDNA library. Within the eight loci (six from anonymous genomic DNA sequences and two...
Article
Full-text available
A highly debated problem in Acipenseridae taxonomy is whether Acipenser oxyrinchus (North American Atlantic sturgeon) and A. sturio (European Atlantic sturgeon) are true species: a detailed comparison of their karyotypes could provide relevant information. Here we describe for the first time the karyotype of A. oxyrinchus (2n = 121 +/- 3), and its...
Article
Full-text available
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...
Article
Full-text available
Here, a new satellite-DNA family is isolated and characterized from wedge sole, Dicologoglossa cuneata Moreau, 1881 (Pleuronectiformes), a fish having a small genome. This satellite-DNA family of sequences was isolated by conventional cloning after digestion of genomic DNA with the DraI restriction enzyme. Repeat units are 171 bp in length with a h...
Article
Within the genus Centaurea (subtribe Centaureinae, tribe Cardueae, Compositae) hybridizations and reticulate-evolution phenomena have widely been recognized. This is especially true in the taxa included in the subgroup Acrolophus from the western Mediterranean area, in which recurrent hybridizations of parapatric ("microallopatric") lineages within...
Article
Full-text available
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...
Article
Full-text available
Currently, three species of Muscari subg. Botryanthus are recognized in the Iberian Peninsula: two diploids (2n = 18), M. atlanticum and M. cazorlanum, and one morphologically variable species with three different ploidy levels, M. neglectum (2n = 36, 45, 54). We have made a comparative study of numerous Iberian populations to clarify the taxonomy...
Article
Full-text available
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...
Article
Full-text available
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...
Article
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...
Article
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
Ribosomal DNA in sturgeon is informative when analyzed at the molecular level because it bears unique characteristics that are, to a certain extent, ancestral within vertebrates. In this paper, we examine the structure and the molecular evolution of the 5S ribosomal DNA (rDNA) region in 13 sturgeon species, comparing both the 5S ribosomal RNA (rRNA...
Article
Full-text available
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...
Article
Full-text available
Hybrids are of great interest in aquaculture. In the present study, we report for the first time an interespecific hybrid between common seabream Pagrus pagrus (L., 1758) females and red banded seabream Pagrus auriga (Valenciennes, 1843) males, which has been named the pagurta. This hybrid was detected in natural spawns during the period from March...
Article
Full-text available
Marteilia refringens is a paramyxean parasite which infects the flat oyster Ostrea edulis and mussels (Mytilus galloprovincialis), where it has been attributed to a separate species, Marteilia maurini, by several authors. Doubts persist though as to the existence or not of two species of Marteilia in Europe. We have devised a molecular method for t...
Article
We have analysed a centromeric satellite DNA family that is conserved in several commercial and non-commercial oyster species (Ostrea edulis, O. stentina, Crassostrea angulata, C. gigas, C. gasar, C. ariakensis, C. virginica and C. sikamea). This satellite DNA family is composed of AT-rich repeat sequences of 166+/-2 bp and presents a 9-bp motif si...
Article
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...
Article
Full-text available
To date, the only native sturgeon species in Western Europe was believed to be Acipenser sturio. However, this species is currently restricted to the Gironde River (Southern France), and it poses serious difficulties for rearing in captivity and for using in recovery programme. Furthermore, it has been questioned whether A. sturio is in fact the on...
Article
To evaluate the genetic contribution to myocardial infarction in a homogeneous Caucasian population (a Mediterranean Spanish population) with very low frequency of coronary heart disease (CHD). We analyzed a total of 210 subjects, younger than 55 years, considered to be a low-risk population (104 cases of myocardial infarction and 106 control), and...
Article
The phylogenetic relationships within the taxonomically controversial Sparidae family of fish are inferred using two satellite-DNA families as phylogenetic markers. The cross-hybridization, strength and restriction patterns of hybridizing the monomer units of these two satellite-DNA families to the DNAs of ten sparid species, served as an index of...
Article
Full-text available
The cultivation of oyster presents some problems related with the identification and differentiation of species as Ostrea edulis (European flat oyster) with respect to Ostrea stentina (Provence oyster) or Crassostrea angulata (portuguese oyster). Crossostrea gigas (Pacific oyster). We have characterized a satellite DNA family and used it as a molec...
Article
Full-text available
 To solve problems concerning the status of the taxa described in the genus Sarcocapnos, we have conducted a study using morphological, pollen morphology (light microscopy), cytogenetic and molecular techniques. Focusing on the last technique, we have sequenced ITS-1 and ITS-2 of nuclear rDNA. The species differ basically according to 5 morphologic...
Article
Full-text available
In this study, the phylogenetic relationships and which the taxonomic status of the species belonging to the Sparidae family (Pisces: Perciformes) are analysed and revised. This study includes species of this family that are distributed by the North-eastern Atlantic and Mediterranean coasts, is based on the analysis of two satellite DNA families. W...
Article
In this study, the phylogenetic relationships and which the taxonomic status of the species belonging to the Sparidae family (Pisces: Perciformes) are analysed and revised. This study includes species of this family that are distributed by the North-eastern Atlantic and Mediterranean coasts, is based on the analysis of two satellite DNA families. W...
Article
Full-text available
We examined the composition and evolution of a large heterochromatic region present in the genomes of certain species of the genus Muscari (Hyacinthaceae). We found that in Muscari comosum this heterochromatic region is composed mainly of a satellite DNA family, which we named MCSAT. Molecular analyses and in situ hybridization revealed that, throu...
Article
Full-text available
The Hind III satellite DNA family, isolated from the Acipenser naccarii genome, was used as a probe for fluorescent in-situ hybridization (FISH) on the karyotype of seven sturgeon species, six belonging to the genus Acipenser and one to Huso. All species except one (A. sturio) exhibit from 8 to 80 chromosome hybridization signals, mainly localized...