Plastid genomes of two brown algae, Ectocarpus siliculosus and Fucus vesiculosus: further insights on the evolution of red-algal derived plastids

<p>Abstract</p> <p>Background</p> <p>Heterokont algae, together with cryptophytes, haptophytes and some alveolates, possess red-algal derived plastids. The chromalveolate hypothesis proposes that the red-algal derived plastids of all four groups have a monophyletic origin resulting from a single secondary endosymbiotic event. However, due to incongruence between nuclear and plastid phylogenies, this controversial hypothesis remains under debate. Large-scale genomic analyses have shown to be a powerful tool for phylogenetic reconstruction but insufficient sequence data have been available for red-algal derived plastid genomes.</p> <p>Results</p> <p>The chloroplast genomes of two brown algae, <it>Ectocarpus siliculosus </it>and <it>Fucus vesiculosus</it>, have been fully sequenced. These species represent two distinct orders of the Phaeophyceae, which is a major group within the heterokont lineage. The sizes of the circular plastid genomes are 139,954 and 124,986 base pairs, respectively, the size difference being due principally to the presence of longer inverted repeat and intergenic regions in <it>E. siliculosus</it>. Gene contents of the two plastids are similar with 139-148 protein-coding genes, 28-31 tRNA genes, and 3 ribosomal RNA genes. The two genomes also exhibit very similar rearrangements compared to other sequenced plastid genomes. The tRNA-Leu gene of <it>E. siliculosus </it>lacks an intron, in contrast to the <it>F. vesiculosus </it>and other heterokont plastid homologues, suggesting its recent loss in the Ectocarpales. Most of the brown algal plastid genes are shared with other red-algal derived plastid genomes, but a few are absent from raphidophyte or diatom plastid genomes. One of these regions is most similar to an apicomplexan nuclear sequence. The phylogenetic relationship between heterokonts, cryptophytes and haptophytes (collectively referred to as chromists) plastids was investigated using several datasets of concatenated proteins from two cyanobacterial genomes and 18 plastid genomes, including most of the available red algal and chromist plastid genomes.</p> <p>Conclusion</p> <p>The phylogenetic studies using concatenated plastid proteins still do not resolve the question of the monophyly of all chromist plastids. However, these results support both the monophyly of heterokont plastids and that of cryptophyte and haptophyte plastids, in agreement with nuclear phylogenies.</p

Features of the ancestral bilaterian inferred from Platynereis dumerilii ParaHox genes

Background The ParaHox gene cluster is the evolutionary sister to the Hox cluster. Whilst the role of the Hox cluster in patterning the anterior-posterior axis of bilaterian animals is well established, and the organisation of vertebrate Hox clusters is intimately linked to gene regulation, much less is known about the more recently discovered ParaHox cluster. ParaHox gene clustering, and its relationship to expression, has only been described in deuterostomes. Conventional protostome models (Drosophila melanogaster and Caenorhabditis elegans) are secondarily derived with respect to ParaHox genes, suffering gene loss and cluster break-up. Results We provide the first evidence for ParaHox gene clustering from a less-derived protostome animal, the annelid Platynereis dumerilii. Clustering of these genes is thus not a sole preserve of the deuterostome lineage within Bilateria. This protostome ParaHox cluster is not entirely intact however, with Pdu-Cdx being on the opposite end of the same chromosome arm from Pdu-Gsx and Pdu-Xlox. From the genomic sequence around the P. dumerilii ParaHox genes the neighbouring genes are identified, compared with other taxa, and the ancestral arrangement deduced. Conclusion We relate the organisation of the ParaHox genes to their expression, and from comparisons with other taxa hypothesise that a relatively complex pattern of ParaHox gene expression existed in the protostome-deuterostome ancestor, which was secondarily simplified along several invertebrate lineages. Detailed comparisons of the gene content around the ParaHox genes enables the reconstruction of the genome surrounding the ParaHox cluster of the protostome-deuterostome ancestor, which existed over 550 million years ago.Publisher PDFPeer reviewe

Cadherin-11 localizes to focal adhesions and promotes cell-substrate adhesion

Cadherin receptors have a well-established role in cell–cell adhesion, cell polarization and differentiation. However, some cadherins also promote cell and tissue movement during embryonic development and tumour progression. In particular, cadherin-11 is upregulated during tumour and inflammatory cell invasion, but the mechanisms underlying cadherin-11 stimulated cell migration are still incompletely understood. Here, we show that cadherin-11 localizes to focal adhesions and promotes adhesion to fibronectin in Xenopus neural crest, a highly migratory embryonic cell population. Transfected cadherin-11 also localizes to focal adhesions in different mammalian cell lines, while endogenous cadherin-11 shows focal adhesion localization in primary human fibroblasts. In focal adhesions, cadherin-11 co-localizes with β1-integrin and paxillin and physically interacts with the fibronectin-binding proteoglycan syndecan-4. Adhesion to fibronectin mediated by cadherin-11/syndecan-4 complexes requires both the extracellular domain of syndecan-4, and the transmembrane and cytoplasmic domains of cadherin-11. These results reveal an unexpected role of a classical cadherin in cell–matrix adhesion during cell migration

Complete genome sequence of the entomopathogenic and metabolically versatile soil bacterium Pseudomonas entomophila

Pseudomonas entomophila is an entomopathogenic bacterium that, upon ingestion, kills Drosophila melanogaster as well as insects from different orders. The complete sequence of the 5.9-Mb genome was determined and compared to the sequenced genomes of four Pseudomonas species. P. entomophila possesses most of the catabolic genes of the closely related strain P. putida KT2440, revealing its metabolically versatile properties and its soil lifestyle. Several features that probably contribute to its entomopathogenic properties were disclosed. Unexpectedly for an animal pathogen, P. entomophila is devoid of a type III secretion system and associated toxins but rather relies on a number of potential virulence factors such as insecticidal toxins, proteases, putative hemolysins, hydrogen cyanide and novel secondary metabolites to infect and kill insects. Genome-wide random mutagenesis revealed the major role of the two-component system GacS/GacA that regulates most of the potential virulence factors identified

Caractérisation et analyse bioinformatique comparative des profils génomiques de mutagénèse chez Saccharomyces cerevisiae

Des altérations de l'ADN se produisent en conditions physiologiques normales au cours du cycle cellulaire. Des systèmes de maintien de l intégrité de l ADN contiennent ces altérations qui représentent une menace pour la cellule, voire l organisme. Les gènes impliqués dans ces processus ont un rôle dans des fonctions de réplication, réparation et recombinaison de l ADN (fonctions 3R). Ces fonctions fondamentales confèrent aux gènes qu elles impliquent un pouvoir potentiellement mutateur intervenant précocement dans le processus d accumulation de mutations de la tumorigenèse qui a lieu dans les cancers. Dans le projet MUTome , 11 mutants de délétion de Saccharomyces cerevisiae ont été construits pour des gènes impliqués dans des fonctions du cycle cellulaire et des fonctions 3R. Le séquençage à haut débit de lignées d accumulation de mutations de ces mutants, suivi de l analyse bioinformatique, a permis d établir des spectres de mutations relatifs à des substitutions de base, des insertions/délétions et à des variations structurales. Parce que les répétitions génomiques bruitent les analyses, j ai développé une stratégie bioinformatique qui aborde ce problème. J ai identifié dans la séquence de référence les régions répétées, sources d alignements multiples. Dans ces régions j ai établi la liste des polymorphismes de substitution de base intra-génomiques qui existent entre répétitions non exactes. L utilisation de cette liste est le principe de base du filtre g-deNoise que j ai développé. Appliqué aux données du MUTome, il a permis d identifier des SNP robustes dans les régions génomiques uniques mais aussi dans des régions répétées comme les gènes multi-copies.DNA mutations arise during the cell growth, even under normal physiological conditions. Processes related to the maintaining of DNA integrity prevent appearance of mutations that represent a threat for the cell life and even for the whole organism. Genes implied in these processes play a role in DNA replication, recombination and reparation (3R functions). They also potentially play a role in the early stage of tumorigenesis occurring in cancers. In the MUTome project 11 mutants of Saccharomyces cerevisiae were deleted for genes implicated in the 3R and cell cycle functions. High throughput sequencing of these accumulation mutation lines followed by bioinformatics analysis permitted to define the catalogue of DNA alterations induced by gene inactivation in the 11 mutants, related to base substitution, insertions/deletions and structural variations. Because genomic repetitions noise analyses, I set up a strategy to address this problem. To do so, I first identified in the reference sequence of S. cerevisiae, the repetitive regions, covered by multi-aligned reads after the reads mapping step. In these repetitive regions, I identified intra-genomic base substitution polymorphisms existing between near exact repetitions. Consecutively, I developed an alignment filter, named g-deNoise , that uses information of intra-genomic polymorphism. This filter applied to MUTome data allowed SNP identification in unique genomic regions, but also in polymorphic repeated regions such as multicopy genesPARIS-BIUSJ-Biologie recherche (751052107) / SudocSudocFranceF

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Sequence Profiling of the Saccharomyces cerevisiae Genome Permits Deconvolution of Unique and Multialigned Reads for Variant Detection

International audienceAdvances in high-throughput sequencing (HTS) technologies have accelerated our knowledge of genomes in hundreds of organisms, but the presence of repetitions found in every genome raises challenges to unambiguously map short reads. In particular, short polymorphic reads that are multialigned hinder our capacity to detect mutations. Here, we present two complementary bioinformatics strategies to perform more robust analyses of genome content and sequencing data, validated by use of the Saccharo-myces cerevisiae fully sequenced genome. First, we created an annotated HTS profile for the reference genome, based on the production of virtual HTS reads. Using variable read lengths and different numbers of mismatches, we found that 35 nt-reads, with a maximum of 6 mismatches, targets 89.5% of the genome to unique (U) regions. Longer reads consisting of 502100 nt provided little additional benefits on the U regions extent. Second, to analyze the remaining multialigned (M) regions, we identified the intragenomic single-nucleotide variants and thus defined the unique (M U) and multialigned (M M) subregions, as exemplified for the polymorphic copies of the six flocculation genes and the 50 Ty retrotransposons. As a resource , the coordinates of the U and M regions of the yeast genome have been added to the Saccharomyces Genome Database (www.yeastgenome.org). The benefit of this advanced method of ge-nome annotation was confirmed by our ability to identify acquired single nucleotide polymorphisms in the U and M regions of an experimentally sequenced variant wild-type yeast strain

In vitro propagation of the microsporidian pathogen Brachiola algerae and studies of its chromosome and ribosomal DNA organization in the context of the complete genome sequencing project

International audienceBrachiola algerae has a broad host spectrum from human to mosquitoes. The successful infection of two mosquito cell lines (Mos55: embryonic cells and Sua 4.0: hemocyte-like cells) and a human cell line (HFF) highlights the efficient adaptive capacity of this microsporidian pathogen. The molecular karyotype of this microsporidian species was determined in the context of the B. algerae genome sequencing project, showing that its haploid genome consists of 30 chromosomal-sized DNAs ranging from 160 to 2240 kbp giving an estimated genome size of 23 Mbp. A contig of 12,269 bp including the DNA sequence of the B. algerae ribosomal transcription unit has been built from initial genomic sequences and the secondary structure of the large subunit rRNA constructed. The data obtained indicate that B. algerae should be an excellent parasitic model to understand genome evolution in relation to infectious capacity