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Publications (166)
Predicted secondary structures of the putative novel miRNA. A total of 38 putative novel miRNA were detected in the six libraries. The mature miRNA sequences are shown in green color.
Pathway annotation of the miRNA targets. The miRNA targets were included in 130 KEGG pathways.
Gene ontology terms of biological function and molecular processes of miRNA targets. Members of 22 conserved miRNA families were involved in diverse biological functions and processes.
The most abundant gene ontology terms from the biological function ontology. Eight ontology terms were found with significant abundance (p <0.05).
The current developments in life sciences face a big challenge, with the need of dealing with huge amounts of data and the increasing demand of computational resources, both in hardware and in software, pushing the limits of the available state-of-the-art at an affordable price. This paper introduces a computer cluster whose building blocks are the...
The elements of the periodic table are made of populations of isotopes (atoms with the same number of protons, but different number of neutrons). Interestingly, such isotopes may be differentially distributed in the nature. On some instances, such selective fractionation is carried out inside the living organisms, due to their peculiar physiologies...
The elements of the periodic table are made of populations of isotopes (atoms with the same number of protons, but different number of neutrons). Interestingly, such isotopes may be differentially distributed in the nature. On some instances, such selective fractionation is carried out inside the living organisms, due to their peculiar physiologies...
The common fig tree (Ficus carica L.) is a Mediterranean crop with problematic cultivar identification. The recovery and conservation of possible local varieties for ecological production requires the previous genetic characterization of the available germplasm. In this context, 42 lines corresponding to 12 local varieties and two caprifigs, in add...
In this study, a survey of miRNAs using the next-generation sequencing data was performed at subgenomic level. After analyzing shotgun sequences from chromosome 4A of bread wheat (Triticum aestivum L.), a total of 68 different miRNAs were predicted in silico, of which 37 were identified in wheat for the first time. The long arm of the chromosome wa...
Wheat is the third most important crop for human nutrition in the world. The availability of high-resolution genetic and physical maps and ultimately a complete genome sequence holds great promise for breeding improved varieties to cope with increasing food demand under the conditions of changing global climate. However, the large size of the bread...
Wheat is the third most important crop for human nutrition in the world. The availability of high-resolution genetic and physical maps and ultimately a complete genome sequence holds great promise for breeding improved varieties to cope with increasing food demand under the conditions of changing global climate. However, the large size of the bread...
Complex Triticeae genomes pose a challenge to genome sequencing efforts due to their size and repetitive nature. Genome sequencing can reveal details of conservation and rearrangements between related genomes. We have applied Illumina second generation sequencing technology to sequence and assemble the low copy and unique regions of Triticum aestiv...
The new massive DNA sequencing methods demand both computer hardware and bioinformatics software capable of handling huge amounts of data. This paper shows how the many-core processors (in which each core can execute a whole operating system) can be exploited to address problems which previously required expensive supercomputers. Thus, the Needlema...
Characterisation of plastid genome (or cpDNA) polymorphisms is commonly used for phylogeographic, population genetic and forensic analyses in plants, but detecting cpDNA variation is sometimes challenging, limiting the applications of such an approach. In the present study, we screened cpDNA polymorphism in the olive tree (Olea europaea L.) by sequ...
Plastid DNA variation based on the 64 loci. a) Profiles for the 321 trees characterized in this study (including those for complete cpDNA genomes); and b) Different cpDNA haplotypes.
Nucleotide substitutions between each pair of Olea plastid genomes.
Data matrix of the 26 cpDNA haplotypes for the reduced-median network analysis.
PCR amplification and sequencing primers (5'->3') used to amplify and sequence the complete olive plastid genome.
Loci features. Primers, allele size range, polymorphism type, genome location and corresponding names in previous studies are given
Characterised cultivars and their cpDNA haplotypes.
Current computer engineering evolves at an accelerated pace, with hardware advancing towards new chip multiprocessors (CMP) architectures and with supporting software gearing towards new programming and abstraction paradigms, to obtain the maximum efficiency of the hardware at a low cost. In this context, Tilera Corporation has developed a brand ne...
New analytical methodologies, like the so-called “next-generation sequencing” (NGS), allow the sequencing of full genomes
with high speed and reduced price. Yet, such technologies generate huge amounts of data that demand large raw computational
power. Many-core technologies can be exploited to overcome the involved bioinformatics bottleneck. Indee...
El maíz (Zea mays) es un cereal herbáceo americano extensamente cultivado, que fue domesticado a partir del teocinte suroeste de Méjico hace unos 9.000 años. El maíz fue una piedra angular para el desarrollo y preponderancia de la civilización Maya y Azteca, así como otras culturas antiguas americanas.
Inicialmente, los restos del maíz fueron anali...
Multi-allelic microsatellite markers have become the markers of choice for the determination of genetic structure in plants. Synteny across cereals has allowed the cross-species and cross-genera transferability of SSR markers, which constitute a valuable and cost-effective tool for the genetic analysis and marker-assisted introgression of wild rela...
Mantel test showing the relationship between genetic distance and environmental distance for group II accessions. Plot of genetic distance vs. Ln (environmental distance).
Estimated number of populations from Geneland analysis. (a) Posterior density distribution of the number of clusters estimated from analysis in five replicates; and (b) genetic assignment of H. chilense individuals.
Mantel test showing the relationship between genetic distance and geographic distance. (B1) Relationship between Nei's genetic distance and Napierian logarithm of geographic distances for group I accessions; and (B2) relationship between Nei's genetic distance and Napierian logarithm of geographic distances for group II-Center accessions.
Motivation: Bioinformatics algorithms and computing power are the main bottlenecks for analyzing huge amount of data generated by the current technologies, such as the 'next-generation' sequencing methodologies. At the same time, most powerful microprocessors are based on many-core chips, yet most applications cannot exploit such power, requiring p...
A selection of 147 wheat D-genome and 130 barley genomic simple sequence repeat (gSSR) markers were screened for their utility in Hordeum chilense, as an alien donor genome for cereal breeding. Fifty-eight wheat D-genome and 71 barley PCR primer pairs consistently amplified products from H. chilense. Nineteen wheat D-genome and 20 barley gSSR marke...
The recent developments in life sciences and technology have produced large amounts of data in an extremely fast and cost-efficient way which require the development of new algorithms, coupled with massively parallel computing. Besides, biologists are usually non-programmers, thus demanding intuitive computer applications that are easy to use by me...
Hordeum chilense, a native South American diploid wild barley, is a potential source of useful genes for cereal breeding. The use of this wild species to increase genetic variation in cereals will be greatly facilitated by marker-assisted selection. Different economically feasible approaches have been undertaken for this wild species with limited d...
Recently, EST derived microsatellite markers have become a useful tool to complement existing genomic SSR markers. In the present work, barley EST-derived SSR markers (Varshney et al. 2005) were tested to determine their usefulness for mapping, introgression and variability studies in Hordeum chilense. 100% of the 74 barley EST-derived SSR-markers...
Brachypodium distachyon (L.) Beauv. is a temperate wild grass species; its morphological and genomic characteristics make it a model system when compared to many other grass species. It has a small genome, short growth cycle, self-fertility, many diploid accessions, and simple growth requirements. In addition, it is phylogenetically close to econom...
The public free software (now renamed as open software) is the basis of the open source software (OSS) project. This initiative promotes the use of open standards and platform-independent accessibility. Many OSS products are free or low cost, which allows their deployment even in the absence of large economic resources (developing countries, school...
There is an increasing amount of public sequence information for the main cultivated cereals, such as wheat and barley. It
is not foreseeable that comparable efforts or resources could be devoted to related wild species. However, wild species are
interesting sources of genetic variation through introgression breeding. Comparative genomics can be a...
Interspecific hybridization can occur under natural conditions among species of the Prosopis genus, potentially giving rise to hybrid individuals with increased adaptation values. A study was conducted to assess the
occurrence of interspecific hybridization among Prosopis in the Argentinian Chaco region and the species involved. The survey included...
Abstract In wheat, carotenoids are very important for end-use quality in noodle production. Hexaploid tritordeums are the amphiploids derived from the cross between a wild diploid barley (Hordeum chilense) and durum wheat. Hexaploid tritordeums exhibit a higher carotenoid content than their respective wheat parents. The cross between H1 and H7 line...
In cereals, rust fungi are among the most harmful pathogens. Breeders usually rely on short-lived hypersensitivity resistance. As an alternative, "avoidance" may be a more durable defence mechanism to protect plants to rust fungi. In Hordeum chilense avoidance is based on extensive wax covering of stomata, which interferes with the induction of app...
Hordeum chilense is a potential source of useful genes for wheat breeding. The use of this wild species to increase genetic variation in wheat will be greatly facilitated by marker-assisted introgression. In recent years, the search for the most suitable DNA marker system for tagging H. chilense genomic regions in a wheat background has lead to the...
A selection of 36 wheat and 35 barley simple sequence repeat markers (SSRs) were studied for their utility in Hordeum chilense. Nineteen wheat and nineteen barley primer pairs amplified consistent H. chilense products. Nine wheat and two barley SSRs were polymorphic in a H. chilense mapping population, producing codominant markers that mapped to th...
A range of single tagged site (STS), simple sequence repeat (SSR), and sequence-characterized amplified region (SCAR) markers were screened for their utility in detecting Hordeum vulgare and H. chilense chromosomes in a wheat background. PCR conditions were optimized for specific amplification of the targeted sequences and to avoid cross-species am...
RAPD markers generated by mixtures of two different 10-mer primers were developed for eight different olive cultivars used
as parental lines in olive-breeding programs. Two RAPD bands were converted into dominant SCAR markers by direct sequencing
of the RAPD products, avoiding the costly and time-consuming cloning step. The SCARs generated have mai...
With the aim of determining the effect of different cytoplasms on anther culture response, we analyzed anthers from different tritordeum lines with either Hordeum chilense, Triticum aestivum or T. turgidum cytoplasms for their response in vitro. The use of these tritordeum alloplasmic lines enabled cytoplasms belonging to two different genera to be...
The first genetic map of the wild South Ameri- can barley species Hordeum chilense is presented. The map, based on an F2 population of 114 plants, contains 123 markers, including 82 RAPDs, 13 SSRs, 16 RFLPs, four SCARs, two seed storage proteins
and two STS markers. The map spans 694 cM with an average distance of 5.7 cM between markers. Six additi...
When developing SCARs by sequencing RAPD markers useful for olive variety identification, one RAPD sequence of 407 bp has
been identified that shows significant DNA homology with more than 160 retrotransposon-like sequences. A generally coherent
phylogenetic tree has been constructed based on the homologous retrotransposon-like sequences, reflectin...
A survey of Gramineae markers was carried out with the aim of developing cost-effective methods for the molecular analysis
of Miscanthus species. Ten out of twenty Gramineae RFLP probes from ”anchor” sets hybridized well to Miscanthus DNA while all 15 maize probes tested cross-hybridized successfully, showing similar patterns in both species. Cross...
A selection of 51 barley Sequence-Tagged Sites (STSs) were studied for their utility in Hordeum chilense. They included four primer sets from wheat origin and six primer sets from oat origin. Forty-four primer pairs amplified H. chilense products consistently. Five primer pairs were suitable for studying the introgression of H. chilense in wheat be...
BLAST (Basic Local Alignment Search) analyses of Hordeum chilense RAPD markers have shown DNA sequence similarities with several plant genes. Biologically significant hits were scored for: plastocianin (Hordeum vulgare), alpha-gliadin (Triticum aestivum), Grandel-6 retrotransposon (Zea diploperennis), retrofit (gag/pol) copia-like, transposon-like...
SUMMARY - Hordeum chilense is a wild species, native to Chile and small area in Argentina, which has been successfully crossed with diploid, tetraploid and hexaploid wheats and the intergeneric amphiploids obtained from them have been named tritordeums. Hexaploid tritordeum can be used as bridge species to introgress genetic material from this wild...
RAPD markers generated by mixtures of two different primers were developed for octoploid × Tritordeum (amphiploid Hordeum
chilense × Triticum aestivum) and its parents. Addition lines were used to identify 21 specific RAPD markers for the H.chilense
chromosomes detectable in a wheat background. Ten RAPD bands were selected and eight of them were co...
Alloploidy, one of the most efficient evolutionary mechanisms in nature, has not been extensively exploited in plant breeding programmes. Many genomic combinations remain to be created by plant breeders, to be used directly as new crops or indirectly to widen the genetic basis of crops. The Triticeae tribe, to which wheat belongs, is among the bota...
RAPD markers were developed for octoploid×Tritordeum (amphiploid Hordeum chilense×Triticum aestivum) and its parents. Addition lines were used to identify specific RAPD markers for the Hordeum chilense chromosomes detectable in a wheat background. Twelve RAPD fragments have been cloned, sequenced and converted into STS markers.
Eleven of these STS...
RAPD markers were developed for octoploid X Tritordeum (amphiploid Hordeum chilense × Triticum aestivum) and its parents. Two bread wheats, two H. chilense accessions and the two tritordeums synthesized with them were used. A total of 41 arbitrary decamer primers were tested, yielding 190 products that could be assigned to wheat, 185 to H. chilense...
Immature embryo- and anther-derived suspension and protoplast cultures were established in hexaploid tritordeum. The morphogenic capability of these cultures was studied under different nitrogen regimes. Both embryo- and anther-derived suspensions showed morphogenic capability. Suspension and protoplast cultures established from immature embryos ga...
Complex Triticeae genomes pose a challenge to genome sequencing efforts due to their size and repetitive nature. Recently, second generation sequencing technologies have been applied to genomic portions of both barley and wheat, allowing further investigation of the biology of their genomes. Genome sequencing can reveal details of gene conservation...
Wheat is a major export crop for Australia, but yields are often limited by abiotic stress, with water availability being the major limiting factor. Climate change is likely to impact the reliable production of wheat in Australia and the breeding of cultivars for Australia’s harsh climate is a priority for Australian crop researchers. The genome of...
