Mario Cáccamo
A5044372059- Genomics and Phylogenetic Studies
- Genetic Mapping and Diversity in Plants and Animals
- Chromosomal and Genetic Variations
- Wheat and Barley Genetics and Pathology
- Genetics, Bioinformatics, and Biomedical Research
- Plant Reproductive Biology
- Genetics and Plant Breeding
- Plant Disease Resistance and Genetics
- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- Rice Cultivation and Yield Improvement
- GABA and Rice Research
- Plant Taxonomy and Phylogenetics
- Yeasts and Rust Fungi Studies
- Plant Molecular Biology Research
- Plant nutrient uptake and metabolism
- Research Data Management Practices
- Plant Physiology and Cultivation Studies
- Plant and fungal interactions
- Logic, programming, and type systems
- RNA and protein synthesis mechanisms
- Animal Genetics and Reproduction
- Genetic and phenotypic traits in livestock
- Natural Language Processing Techniques
- Bioenergy crop production and management
National Institute of Agricultural Botany
2016-2025
East Malling Research (United Kingdom)
2021
National Research Institute of Brewing
2021
Earlham Institute
2011-2018
Norwich Research Park
2011-2018
European Bioinformatics Institute
2007-2015
John Innes Centre
2015
Norwich University
2015
Wellcome Sanger Institute
2004-2013
Max Planck Institute for Developmental Biology
2013
Barley (Hordeum vulgare L.) is among the world's earliest domesticated and most important crop plants. It diploid with a large haploid genome of 5.1 gigabases (Gb). Here we present an integrated ordered physical, genetic functional sequence resource that describes barley gene-space in structured whole-genome context. We developed physical map 4.98 Gb, more than 3.90 Gb anchored to high-resolution map. Projecting deep shotgun assembly, complementary DNA RNA data onto this framework supports...
Cereal grasses of the Triticeae tribe have been major food source in temperate regions since dawn agriculture. Their large genomes are characterized by a high content repetitive elements and pericentromeric that virtually devoid meiotic recombination. Here we present high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive linear order sequences across space investigate spatial organization chromatin nucleus at megabase...
The Ensembl (http://www.ensembl.org/) project provides a comprehensive and integrated source of annotation chordate genome sequences. Over the past year number genomes available from has increased 15 to 33, with addition sites for mammalian elephant, rabbit, armadillo, tenrec, platypus, pig, cat, bush baby, common shrew, microbat european hedgehog; fish stickleback medaka second example sea squirt (Ciona savignyi) mosquito (Aedes aegypti). Some major features added during include first...
Low-cost short read sequencing technology has revolutionized genomics, though it is only just becoming practical for the high-quality de novo assembly of a novel large genome. We describe Assemblathon 1 competition, which aimed to comprehensively assess state art in methods when applied current technologies. In collaborative effort, teams were asked assemble simulated Illumina HiSeq data set an unknown, diploid A total 41 assemblies from 17 different groups received. Novel haplotype aware...
The zebrafish has become a widely used model to study disease resistance and immunity. Although the genes encoding many components of immune signaling pathways have been found in teleost fish, it is not clear whether all are present or complexity mechanisms employed by mammals similar fish. We searched genomes Danio rerio two pufferfish for Toll-like receptor interferon pathways, NLR (NACHT-domain leucine rich repeat containing) protein family, related proteins. find that most known also...
The Ensembl project (http://www.ensembl.org) is a comprehensive genome information system featuring an integrated set of annotation, databases and other for chordate selected model organism disease vector genomes. As release 47 (October 2007), fully supports 35 species, with preliminary support six additional species. New species in the past year include platypus horse. Major additions improvements to since our previous report extensive functional genomics data form specialized database,...
Abstract Motivation: For most research approaches, genome analyses are dependent on the existence of a high quality reference assembly. However, local accuracy an assembly remains difficult to assess and improve. The gEVAL browser allows user interrogate in any region by comparing it different datasets evaluating concordance. These include: wide variety sequence alignments, comparative multiple assemblies, consistency with optical other physical maps. highlights allelic variations, regions...
Paul Flicek and colleagues provide an update on the European Genome-phenome Archive (EGA), a service of Bioinformatics Institute (EMBL-EBI) Center for Genome Regulation (CRG). The authors describe EGA policies infrastructure, how access decisions are made, methods data submission future plans expansion this database. (EGA) is permanent archive that promotes distribution sharing genetic phenotypic consented specific approved uses but not fully open, public distribution. follows strict...
Abstract Summary: The design of genetic markers is particular relevance in crop breeding programs. Despite many economically important crops being polyploid organisms, the current primer tools are tailored for diploid species. Bread wheat, instance, a hexaploid comprising three related genomes and performance diminished if primers not genome specific. PolyMarker pipeline that generates SNP by selecting candidate specified using local alignments standard to test viability primers. A command...
The identification of genetic markers linked to genes agronomic importance is a major aim crop research and breeding programmes. Here, we identify for Yr15, disease resistance gene wheat yellow rust, using segregating F2 population. After phenotyping, implemented RNA sequencing (RNA-Seq) bulked pools single-nucleotide polymorphisms (SNP) associated with Yr15. Over 27 000 SNPs were identified between the parents, then classified based on results from sequenced bulks. We calculated bulk...
The genome sequence and genetic diversity of European ash (Fraxinus excelsior) trees reveals the species' varying susceptibility to dieback. Woodlands forests around world are increasingly susceptible spread pests pathogens resulting from climate change global trade. In particular, across Europe North America currently threatened by fungal disease dieback infestation emerald borer beetle, respectively. Against this background, Richard Buggs colleagues report first an tree, Fraxinus...
Abstract Undomesticated wild species, crop relatives, and landraces represent sources of variation for wheat improvement to address challenges from climate change the growing human population. Here, we study 56,342 domesticated hexaploid, 18,946 tetraploid 3,903 relatives in a massive-scale genotyping diversity analysis. Using DArTseq TM technology, identify more than 300,000 high-quality SNPs SilicoDArT markers align them three reference maps: IWGSC RefSeq v1.0 genome assembly, durum...
Abstract Key message Here, we provide an updated set of guidelines for naming genes in wheat that has been endorsed by the research community. The last decade seen a proliferation genomic resources wheat, including reference- and pan-genome assemblies with gene annotations, which new opportunities to detect, characterise, describe influence traits interest. expansion genetic information supported growth community catalysed strong interest control agronomically important traits, such as...
The Ensembl ( http://www.ensembl.org/ ) project provides a comprehensive and integrated source of annotation large genome sequences. Over the last year number genomes available from site has increased by 7 to 16, with addition six vertebrate chimpanzee, dog, cow, chicken, tetraodon frog insect honeybee. majority have been annotated automatically using gene build system, showing its flexibility reliably annotate wide variety genomes. With genomes, comparative analysis provided users greatly...
Red clover (Trifolium pratense L.) is a globally significant forage legume in pastoral livestock farming systems. It an attractive component of grassland farming, because its high yield and protein content, nutritional value ability to fix atmospheric nitrogen. Enhancing role further sustainable agriculture requires genetic improvement persistency, disease resistance, tolerance grazing. To help address these challenges, we have assembled chromosome-scale reference genome for red clover. We...
Abstract Barley ( Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. ‘Morex’ was constructed by International Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report experimental computational procedures to (i) assemble more than 80,000 bacterial artificial chromosome (BAC) clones along minimum tiling path genome-wide physical map, (ii) find...
Wheat occupies a special role in global food security since, addition to providing 20% of our carbohydrates and protein, almost 25% the production is traded internationally. The importance wheat for was recognised by Chief Agricultural Scientists G20 group countries when they endorsed establishment Initiative 2011. tasked with supporting research community facilitating collaboration, information resource sharing helping build capacity address challenges facing an increasingly variable...
The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organize biology around the sequences of large genomes. It is comprehensive and integrated source annotation genome sequences, available via interactive website, web services or flat files. As well as being one leading sources annotation, an open software engineering develop portable system able handle very genomes associated requirements. facilities range from sequence analysis data storage...
<ns4:p>Artificial Intelligence (AI) is increasingly used within plant science, yet it far from being routinely and effectively implemented in this domain. Particularly relevant to the development of novel food agricultural technologies validated, meaningful usable ways integrate, compare visualise large, multi-dimensional datasets different sources scientific approaches. After a brief summary reasons for interest data science AI paper identifies discusses eight key challenges management that...