Search results for " GENOMICS"
showing 10 items of 390 documents
Lightweight LCP construction for next-generation sequencing datasets
2012
The advent of "next-generation" DNA sequencing (NGS) technologies has meant that collections of hundreds of millions of DNA sequences are now commonplace in bioinformatics. Knowing the longest common prefix array (LCP) of such a collection would facilitate the rapid computation of maximal exact matches, shortest unique substrings and shortest absent words. CPU-efficient algorithms for computing the LCP of a string have been described in the literature, but require the presence in RAM of large data structures. This prevents such methods from being feasible for NGS datasets. In this paper we propose the first lightweight method that simultaneously computes, via sequential scans, the LCP and B…
Genomic and Proteomic Analysis of Wine Yeasts
2011
Publisher Summary Saccharomyces cerevisiae is the main microorganism involved in wine fermentation. It has been used as a model organism in molecular biology for many years and is the only wine yeast species for which abundant genomic and proteomic information is available. Most of the techniques currently used in functional genomics and proteomics were initially developed in this yeast. The fact that S. cerevisiae was the first microorganism to be widely used in the development of genome technology allowed other phylogenetically related yeasts to be analyzed subsequently in global sequencing projects, and the use of comparative genomics has since led to important conclusions regarding gene…
Effects of postharvest partial dehydration and prolonged treatments with ethylene on transcript profiling in skins of wine grape berries.
2010
For certain food products, postharvest controlled stresses or treatments with specific elicitors are applied to induce desired physical/chemical changes and/or to positively affect phytochemical content. This is the case of wine grapes where both strategies, singularly applied or coupled, can be used to modulate berry composition and, as a consequence, affect wine quality traits. Since the knowledge of the effects of these postharvest treatments on berry metabolism and the regulation of gene expression is very limited, a large-scale transcriptome analysis has been carried out, using an oligo-based microarray (14,562 probes) on skins of wine grape (Vitis vinifera L.) berries subjected to deh…
Distinct Clones of Yersinia pestis Caused the Black Death
2010
From AD 1347 to AD 1353, the Black Death killed tens of millions of people in Europe, leaving misery and devastation in its wake, with successive epidemics ravaging the continent until the 18th century. The etiology of this disease has remained highly controversial, ranging from claims based on genetics and the historical descriptions of symptoms that it was caused by Yersinia pestis to conclusions that it must have been caused by other pathogens. It has also been disputed whether plague had the same etiology in northern and southern Europe. Here we identified DNA and protein signatures specific for Y. pestis in human skeletons from mass graves in northern, central and southern Europe that …
The underlying processes governing seed size plasticity: Impact of endoploidy on seed coat development and cell expansion in Medicago truncatula
2019
Prod 2019-55a BAP GEAPSI CT1 BAP; Abstract Bigger seeds represent an agronomic and economic benefit but the breeding and ecological balance between seed size and number is difficult to find. Large seeds associated with other practices can improve crop competitiveness as they are more vigorous and result in healthier crops with higher yields, even under stressful conditions. Applying genomic research and genome-wide association studies to breeding is generating new strategies to improve seed traits and novel insights into the biology of seed development and metabolism that are discussed in this chapter. The DNA amount differs among the seed tissues and amplifying genomic DNA by endocycle ind…
Identification of the VvFLS2 grapevine flagellin receptor by a functional genomics strategy
2012
Population Structure and Comparative Genome Hybridization of European Flor Yeast Reveal a Unique Group of Saccharomyces cerevisiae Strains with Few G…
2014
Wine biological aging is a wine making process used to produce specific beverages in several countries in Europe, including Spain, Italy, France, and Hungary. This process involves the formation of a velum at the surface of the wine. Here, we present the first large scale comparison of all European flor strains involved in this process. We inferred the population structure of these European flor strains from their microsatellite genotype diversity and analyzed their ploidy. We show that almost all of these flor strains belong to the same cluster and are diploid, except for a few Spanish strains. Comparison of the array hybridization profile of six flor strains originating from these four co…
Achievements from GLIP functional genomics platforms
2008
Format du poster : N° W212 Format du poster : N° W212; absent
Genome‐phenotype‐environment associations identify signatures of selection in a panmictic population of threespine stickleback
2023
Adaptive genetic divergence occurs when selection imposed by the environment causes the genomic component of the phenotype to differentiate. However, genomic signatures of natural selection are usually identified without information on which trait is responding to selection by which selective agent(s). Here we integrate whole-genome-sequencing with phenomics and measures of putative selective agents to assess the extent of adaptive divergence in threespine stickleback occupying the highly heterogeneous lake Mývatn, NE Iceland. We find negligible genome wide divergence, yet multiple traits (body size, gill raker structure and defence traits) were divergent along known ecological gradients (t…