Manuel Talon

Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research

SUMMARYnWe present here Blast2GO (B2G), a research tool designed with the main purpose of enabling Gene Ontology (GO) based data mining on sequence data for which no GO annotation is yet available. B2G joints in one application GO annotation based on similarity searches with statistical analysis and highlighted visualization on directed acyclic graphs. This tool offers a suitable platform for functional genomics research in non-model species. B2G is an intuitive and interactive desktop application that allows monitoring and comprehension of the whole annotation and analysis process.nnnAVAILABILITYnBlast2GO is freely available via Java Web Start at http://www.blast2go.de.nnnSUPPLEMENTARY MATERIALnhttp://www.blast2go.de -> Evaluation.

High-throughput functional annotation and data mining with the Blast2GO suite

Functional genomics technologies have been widely adopted in the biological research of both model and non-model species. An efficient functional annotation of DNA or protein sequences is a major requirement for the successful application of these approaches as functional information on gene products is often the key to the interpretation of experimental results. Therefore, there is an increasing need for bioinformatics resources which are able to cope with large amount of sequence data, produce valuable annotation results and are easily accessible to laboratories where functional genomics projects are being undertaken. We present the Blast2GO suite as an integrated and biologist-oriented solution for the high-throughput and automatic functional annotation of DNA or protein sequences based on the Gene Ontology vocabulary. The most outstanding Blast2GO features are: (i) the combination of various annotation strategies and tools controlling type and intensity of annotation, (ii) the numerous graphical features such as the interactive GO-graph visualization for gene-set function profiling or descriptive charts, (iii) the general sequence management features and (iv) high-throughput capabilities. We used the Blast2GO framework to carry out a detailed analysis of annotation behaviour through homology transfer and its impact in functional genomics research. Our aim is to offer biologists useful information to take into account when addressing the task of functionally characterizing their sequence data.

maSigPro: a method to identify significantly differential expression profiles in time-course microarray experiments

MOTIVATIONnMulti-series time-course microarray experiments are useful approaches for exploring biological processes. In this type of experiments, the researcher is frequently interested in studying gene expression changes along time and in evaluating trend differences between the various experimental groups. The large amount of data, multiplicity of experimental conditions and the dynamic nature of the experiments poses great challenges to data analysis.nnnRESULTSnIn this work, we propose a statistical procedure to identify genes that show different gene expression profiles across analytical groups in time-course experiments. The method is a two-regression step approach where the experimental groups are identified by dummy variables. The procedure first adjusts a global regression model with all the defined variables to identify differentially expressed genes, and in second a variable selection strategy is applied to study differences between groups and to find statistically significant different profiles. The methodology is illustrated on both a real and a simulated microarray dataset.

Spatial differentiation in the vegetative mycelium of Aspergillus niger.

ABSTRACT Fungal mycelia are exposed to heterogenic substrates. The substrate in the central part of the colony has been (partly) degraded, whereas it is still unexplored at the periphery of the mycelium. We here assessed whether substrate heterogeneity is a main determinant of spatial gene expression in colonies of Aspergillus niger. This question was addressed by analyzing whole-genome gene expression in five concentric zones of 7-day-old maltose- and xylose-grown colonies. Expression profiles at the periphery and the center were clearly different. More than 25% of the active genes showed twofold differences in expression between the inner and outermost zones of the colony. Moreover, 9% of the genes were expressed in only one of the five concentric zones, showing that a considerable part of the genome is active in a restricted part of the colony only. Statistical analysis of expression profiles of colonies that had either been or not been transferred to fresh xylose-containing medium showed that differential expression in a colony is due to the heterogeneity of the medium (e.g., genes involved in secretion, genes encoding proteases, and genes involved in xylose metabolism) as well as to medium-independent mechanisms (e.g., genes involved in nitrate metabolism and genes involved in cell wall synthesis and modification). Thus, we conclude that the mycelia of 7-day-old colonies of A. niger are highly differentiated. This conclusion is also indicated by the fact that distinct zones of the colony grow and secrete proteins, even after transfer to fresh medium.

A reference genetic map of C. clementina hort. ex Tan.; citrus evolution inferences from comparative mapping

BackgroundMost modern citrus cultivars have an interspecific origin. As a foundational step towards deciphering the interspecific genome structures, a reference whole genome sequence was produced by the International Citrus Genome Consortium from a haploid derived from Clementine mandarin. The availability of a saturated genetic map of Clementine was identified as an essential prerequisite to assist the whole genome sequence assembly. Clementine is believed to be a ‘Mediterranean’ mandarin × sweet orange hybrid, and sweet orange likely arose from interspecific hybridizations between mandarin and pummelo gene pools. The primary goals of the present study were to establish a Clementine reference map using codominant markers, and to perform comparative mapping of pummelo, sweet orange, and Clementine.ResultsFive parental genetic maps were established from three segregating populations, which were genotyped with Single Nucleotide Polymorphism (SNP), Simple Sequence Repeats (SSR) and Insertion-Deletion (Indel) markers. An initial medium density reference map (961 markers for 1084.1 cM) of the Clementine was established by combining male and female Clementine segregation data. This Clementine map was compared with two pummelo maps and a sweet orange map. The linear order of markers was highly conserved in the different species. However, significant differences in map size were observed, which suggests a variation in the recombination rates. Skewed segregations were much higher in the male than female Clementine mapping data. The mapping data confirmed that Clementine arose from hybridization between ‘Mediterranean’ mandarin and sweet orange. The results identified nine recombination break points for the sweet orange gamete that contributed to the Clementine genome.ConclusionsA reference genetic map of citrus, used to facilitate the chromosome assembly of the first citrus reference genome sequence, was established. The high conservation of marker order observed at the interspecific level should allow reasonable inferences of most citrus genome sequences by mapping next-generation sequencing (NGS) data in the reference genome sequence. The genome of the haploid Clementine used to establish the citrus reference genome sequence appears to have been inherited primarily from the ‘Mediterranean’ mandarin. The high frequency of skewed allelic segregations in the male Clementine data underline the probable extent of deviation from Mendelian segregation for characters controlled by heterozygous loci in male parents.

Discovering gene expression patterns in time course microarray experiments by ANOVA–SCA

MOTIVATIONnDesigned microarray experiments are used to investigate the effects that controlled experimental factors have on gene expression and learn about the transcriptional responses associated with external variables. In these datasets, signals of interest coexist with varying sources of unwanted noise in a framework of (co)relation among the measured variables and with the different levels of the studied factors. Discovering experimentally relevant transcriptional changes require methodologies that take all these elements into account.nnnRESULTSnIn this work, we develop the application of the Analysis of variance-simultaneous component analysis (ANOVA-SCA) Smilde et al. Bioinformatics, (2005) to the analysis of multiple series time course microarray data as an example of multifactorial gene expression profiling experiments. We denoted this implementation as ASCA-genes. We show how the combination of ANOVA-modeling and a dimension reduction technique is effective in extracting targeted signals from data by-passing structural noise. The methodology is valuable for identifying main and secondary responses associated with the experimental factors and spotting relevant experimental conditions. We additionally propose a novel approach for gene selection in the context of the relation of individual transcriptional patterns to global gene expression signals. We demonstrate the methodology on both real and synthetic datasets.nnnAVAILABILITYnASCA-genes has been implemented in the statistical language R and is available at http://www.ivia.es/centrodegenomica/bioinformatics.htm.nnnSUPPLEMENTARY INFORMATIONnSupplementary data are available at Bioinformatics online.

Diversity in the trifoliate orange taxon reveals two main genetic groups marked by specific morphological traits and water deficit tolerance properties

Trifoliate orange (Poncirus trifoliata (L.) Raf.) is a very useful taxon for the citrus industry since this rootstock is immune to the Citrus Tristeza virus and confers cold tolerance. Numerous trifoliate orange varieties exist but little is known regarding their behavioural variability when subjected to abiotic constraints. The diversity of 74 P. trifoliata accessions maintained in the INRA-CIRAD Citrus Germplasm Collection was investigated using simple sequence repeat markers. Two major genetic groups were clearly identified as a few homonyms, intergroup or intra-group hybrids and doubled-chromosome tetraploid forms. The Group 1 phenotype was characterized by larger flowers and leaves and smaller seeds than Group 2. Tetraploid accessions showed larger leaves and heavier seeds than all other diploid accessions, regardless of genetic classification. Eight genotypes belonging to both genetic groups, as well as two hybrids between the two groups, were selected to investigate their water deficit tolerance. Stress was applied by withdrawing irrigation for 4 weeks. Physiological parameters such as leaf stomatal conductance, quantum yield of photosystem II electron transport, soil water potential, leaf osmotic potential and transpiration rate were estimated. Some varieties, such as Rubidoux 0101033, were clearly more tolerant to water deficit than others, such as Pomeroy 0101040 and Pomeroy 0110081. Interestingly, accessions that had the highest soil water potential and were the least affected by stress belonged to genetic Group 2. Conversely, trifoliate oranges of genetic Group 1 were the least tolerant. (Resume dauteur)

Salt stress tolerance in acidic and sweet mandarins

Mandarin genotypes can be split in two main groups: the acidic and the sweet mandarins. Commonly, acidic are used as rootstocks when sweet mandarins are the varieties that are consumed as fruits. The acidic ‘Cleopatra’ mandarin (Citrus reshni Hort. ex Tan.) is considered to be the most salt stress tolerant rootstock since it is able to limit the absorption of chloride and sodium at root level. As a consequence, limited amount of toxic ions are translocated from root to leaves. If salt stress tolerance of ‘Cleopatra’ mandarin and its hybrids has been well documented, little data exist for sweet mandarins. We investigated 16 genotypes representing a large diversity in mandarins subjected to salt stress. Physiological parameters such as stomatal conductance and leaf chloride contents were analyzed. If most of the acidic varieties were tolerant, also some sweet varieties presented traits of tolerance. Taking into account the results of leaf ion contents, we observed that large leaf chloride contents were not always associated with sensitivity. (Resume dauteur)

Physiological responses of diploid and doubled diploid 'Rangpur' lime under water deficit

In citrus, the use of rootstocks promotes productivity, improves fruit quality and may confer resistance or tolerance to biotic and abiotic stress. ‘Rangpur’ lime (Citrus limonia, Osbeck) is one of the most tolerant rootstock to drought and is largely used by the Brazilian citrus industry. Previous studies have shown that, when grafted with a variety citrus doubled diploid (4x) ‘Rangpur’ lime rootstock is more tolerant to drought stress than the respective diploid (2x). In the present study, we characterized the water deficit tolerance in 2x and 4x ‘Rangpur’ lime seedlings. Water deficit was applied respectively for 21 days, followed by recovery irrigation. Physiological and biochemical parameters were measured periodically during the experiment and samples were collected for biochemical analysis. Doubled diploid seedlings were showed to be more water deficit tolerant than 2x. Water deficit caused a greater reduction in stomatal conductance in 2x compared to 4x. The 21st day of stress, leaf water potential in 2x was lower. Analyses of the activity of enzymes involved in detoxification process suggest that the better tolerance of 4x genotypes may be related to better scavenging of reactive oxygen species. (Resume dauteur)

Transcriptional profile analysis of young and mature leaves of citrus trees acclimated to salinity

11 paginas.-- 3 figuras.-- 2 tablas.-- 32 referencias.-- Articulo publicado en XII International Citrus Congress - International Society of Citriculture