194 research outputs found
Haematococcus lacustris genome assembly and annotation reveal diploid genetic traits and stress-induced gene expression patterns
No full textThe green alga Haematococcus lacustris (formerly Haematococcus pluvialis) ) is a primary source of astaxanthin, a ketocarotenoid with high antioxidant activity and several industrial applications. Here, the Haematococcus lacustris highly repetitive genome was reconstructed by exploiting next-generation sequencing integrated with Hi-C scaffolding, obtaining a 151 Mb genome assembly in 32 scaffolds at a near-chromosome level with high continuity. Surprisingly, the distribution of the single-nucleotide-polymorphisms identified demonstrates a diploid configuration for the Haematococcus genome, further validated by Sanger sequencing of heterozygous regions. Functional annotation and RNA-seq data enabled the identification of 13,946 nuclear genes, with >5000 genes not previously identified in this species, providing insights into the molecular basis for metabolic rearrangement in stressing conditions such as high light and/or nitrogen starvation, where astaxanthin biosynthesis is triggered. These data constitute a rich genetic resource for biotechnological manipulation of Haematococcus lacustris highlighting potential targets to improve astaxanthin and carotenoid productivity
CLE peptides control medicago truncatula nodulation locally and systemically
No full textThe CLAVATA3/embryo-surrounding region (CLE) peptides control the fine balance between proliferation and differentiation in plant development. We studied the role of CLE peptides during indeterminate nodule development and identified 25 MtCLE peptide genes in the Medicago truncatula genome, of which two genes, MtCLE12 and MtCLE13, had nodulation-related expression patterns that were linked to proliferation and differentiation. MtCLE13 expression was up-regulated early in nodule development. A high-to-low expression gradient radiated from the inner toward the outer cortical cell layers in a region defining the incipient nodule. At later stages, MtCLE12 and MtCLE13 were expressed in differentiating nodules and in the apical part of mature, elongated nodules. Functional analysis revealed a putative role for MtCLE12 and MtCLE13 in autoregulation of nodulation, a mechanism that controls the number of nodules and involves systemic signals mediated by a leucine-rich repeat receptor-like kinase, SUNN, which is active in the shoot. When MtCLE12 and MtCLE13 were ectopically expressed in transgenic roots, nodulation was abolished at the level of the nodulation factor signal transduction, and this inhibition involved long-distance signaling. In addition, composite plants with roots ectopically expressing MtCLE12 or MtCLE13 had elongated petioles. This systemic effect was not observed in transgenic roots ectopically expressing MtCLE12 and MtCLE13 in a sunn-1 mutant background, although nodulation was still strongly reduced. These results suggest multiple roles for CLE signaling in nodulation.Virginie Mortier, Griet Den Herder, Ryan Whitford, Willem Van de Velde, Stephane Rombauts, Katrien D’haeseleer, Marcelle Holsters, and Sofie Goormachti
‘Nebbiolo’ genome assembly allows surveying the occurrence and functional implications of genomic structural variations in grapevines (Vitis vinifera L.)
No full textBackground: ‘Nebbiolo’ is a grapevine cultivar typical of north-western Italy, appreciated for producing high-quality red wines. Grapevine cultivars are characterized by possessing highly heterozygous genomes, including a great incidence of genomic rearrangements larger than 50 bp, so called structural variations (SVs). Even though abundant, SVs are an under-explored source of genetic variation mainly due to methodological limitations at their detection. Results: We employed a multiple platform approach to produce long-range genomic data for two different ‘Nebbiolo’ clones, namely: optical mapping, long-reads and linked-reads. We performed a haplotype-resolved de novo assembly for cultivar ‘Nebbiolo’ (clone CVT 71) and used an ab-initio strategy to annotate it. The annotated assembly enhanced our ability to detect SVs, enabling the study of genomic regions not present in the grapevines’ reference genome and accounting for their functional implications. We performed variant calling analyses at three different organizational levels: i) between haplotypes of clone CVT 71 (primary assembly vs haplotigs), ii) between ‘Nebbiolo’ and ‘Cabernet Sauvignon’ assemblies and iii) between clones CVT 71 and CVT 185, representing different ‘Nebbiolo’ biotypes. The cumulative size of non-redundant merged SVs indicated a total of 79.6 Mbp for the first comparison and 136.1 Mbp for the second one, while no SVs were detected for the third comparison. Interestingly, SVs differentiating cultivars and haplotypes affected similar numbers of coding genes. Conclusions: Our results suggest that SVs accumulation rate and their functional implications in ‘Nebbiolo’ genome are highly-dependent on the organizational level under study. SVs are abundant when comparing ‘Nebbiolo’ to a different cultivar or the two haplotypes of the same individual, while they turned absent between the two analysed clones.Fil: Maestri, Simone. Universita di Verona; ItaliaFil: Gambino, Giorgio. Centre National de la Recherche Scientifique; FranciaFil: Lopatriello, Giulia. Universita di Verona; ItaliaFil: Minio, Andrea. University of California at Davis; Estados UnidosFil: Perrone, Irene. Centre National de la Recherche Scientifique; FranciaFil: Cosentino, Emanuela. Universita di Verona; ItaliaFil: Giovannone, Barbara. Universita di Verona; ItaliaFil: Marcolungo, Luca. Universita di Verona; ItaliaFil: Alfano, Massimiliano. Universita di Verona; ItaliaFil: Rombauts, Stephane. University of Ghent; BélgicaFil: Cantu, Dario. University of California at Davis; Estados UnidosFil: Rossato, Marzia. Universita di Verona; ItaliaFil: Delledonne, Massimo. Universita di Verona; ItaliaFil: Calderón, Pablo Luciano Sebastian. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; Argentin
Genome annotation: which tools do we have for it?
No full textGenome data have to be converted into knowledge to be useful to biologists. Many valuable computational tools have already been developed to help annotation of plant genome sequences, and these may be improved further, for example by identification of more gene regulatory elements. The lack of a standard computer-assisted annotation platform for eukaryotic genomes remains a major bottle-neck
Analysis of RNA-Seq data with TopHat and Cufflinks for genome-wide expression analysis of jasmonate-treated plants and plant cell cultures
No full textThe recent development of various deep sequencing techniques has led to the most powerful transcript profiling method available to date, RNA sequencing or RNA-Seq. Besides the identification of new genes and new splice variants of known genes, RNA-Seq allows to compare the whole transcriptome of any organism under two or more experimental conditions, such as before and after jasmonate treatment. However, the vast amounts of data generated during RNA-Seq experiments require complex computational methods for read mapping and expression quantification. Here, we describe a detailed protocol for the analysis of deep sequencing data, starting from the raw RNA-Seq reads. First, a quality check is performed on the raw reads to assess the quality of the sequencing. Subsequently, adapters and low-quality sequences are trimmed off the raw reads. The resulting processed reads are mapped to the reference genome, and the mapped reads are counted to generate expression data for the annotated genes for each sample. This method can be used for the analysis of RNA-Seq data of any organism for which a reference genome is available
Génomique et bio-informatique
No full textGenomics projects produce huge amounts of data of different kinds whose interpretation stimulated the development of bioinformatics, a recent discipline based on theoretical aspects of informatics and mathematics, as well as on biology. Bioinformatics enables the staring and organizing of genome-wide molecular data, provides tools to analyze them and to convert raw data into biological knowledge. We illustrate how the combination of data management and of sequence analysis tools has already brought fruitful perspectives for gene discovery
AFLPinSilico, simulating AFLP fingerprints
No full textA drawback of the Amplified Fragment Length Polymorphism (AFLP) fingerprinting method is the difficulty to correlate the different fragments with their DNA sequence. The AFLPinSilico application presented here simulates AFLP experiments run on either cDNA or genomic sequences, producing virtual fingerprints that allow high throughput identification of AFLP fragments. The program also enables biologists to manage experiments through simulations done beforehand, thereby reducing the number of experiments that have to be run. AFLPinSilico is available through the www or as a stand-alone version, through a command line executable (available upon request, for any platform running PERL)
PlantCARE, a plant cis-acting regulatory element database
No full textPlantCARE is a database of plant cis-acting regulatory elements, enhancers and repressors. Besides the transcription motifs found on a sequence, it also offers a link to the EMBL entry that contains the full gene sequence as well as a description of the conditions in which a motif becomes functional. The information on these sites is given by matrices, consensus and individual site sequences on particular genes, depending on the available information
diagnosis
No full text12 p.-4 fig.-2 tab.Background: Allergy to house dust mites (HDM), the most important source of indoor allergens worldwide, is diagnosed and treated using natural extracts from cultures that can contain immunoactive components from the HDM microbiome, including mite-infecting viruses. This study aimed to contribute to the discovery and characterization of RNA viruses from Dermatophagoides pteronyssinus, followed by their detection in different mite-derived sources.Methods: Viruses were assembled after in silico metatranscriptomic analysis of D. pteronyssinus RNA samples, visualized by electron microscopy, and RNA detected by direct RT-PCR or data mining. Mite culture performance was evaluated in vivo.Results: Seven RNA viruses were identified in our laboratory stock colony. Picornavirus-like viral particles were detected in epithelial cells of the digestive system and in fecal pellets. Most of these viruses could be persistently transmitted to an inbred virus-free colony by inoculating fecal material from the stock colony. Upon viral infection, no significant effect could be seen on mite population growth. Transcriptomic screening confirmed the presence of homolog sequences to these viruses in independent laboratory stocks of D. pteronyssinus and in other Astigmata mites. Noteworthy, RNA from most of the viruses could be detected by RT-PCR on house dust samples, reference standards, and/or commercial diagnostic D. pteronyssinus extracts.Conclusions: Our results show that viral infections are common and widespread in D. pteronyssinus, both in natural and culture-based growth conditions. Potential effects on the mites themselves and consequences toward allergenicity in humans whether exposed naturally or after immunotherapy are discussed.Peer reviewedPublisher's versio
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