Characterization of new IS elements and studies of their dispersion in two subspecies of Leifsonia xyli

<p>Abstract</p> <p>Background</p> <p><it>Leifsonia xyli </it>is a xylem-inhabiting bacterial species comprised of two subspecies: <it>L. xyli </it>subsp. <it>xyli </it>(<it>Lxx</it>) and <it>L. xyli </it>subsp. <it>cynodontis </it>(<it>Lxc</it>). <it>Lxx </it>is the causal agent of ratoon stunting disease in sugarcane commercial fields and <it>Lxc </it>colonizes the xylem of several grasses causing either mild or no symptoms of disease. The completely sequenced genome of <it>Lxx </it>provided insights into its biology and pathogenicity. Since IS elements are largely reported as an important source of bacterial genome diversification and nothing is known about their role in chromosome architecture of <it>L. xyli</it>, a comparative analysis of <it>Lxc </it>and <it>Lxx </it>elements was performed.</p> <p>Results</p> <p>Sample sequencing of <it>Lxc </it>genome and comparative analysis with <it>Lxx </it>complete DNA sequence revealed a variable number of IS transposable elements acting upon genomic diversity. A detailed characterization of <it>Lxc </it>IS elements and a comparative review with IS elements of <it>Lxx </it>are presented. Each genome showed a unique set of elements although related to same IS families when considering features such as similarity among transposases, inverted and direct repeats, and element size. Most of the <it>Lxc </it>and <it>Lxx </it>IS families assigned were reported to maintain transposition at low levels using translation regulatory mechanisms, consistent with our <it>in silico </it>analysis. Some of the IS elements were found associated with rearrangements and specific regions of each genome. Differences were also found in the effect of IS elements upon insertion, although none of the elements were preferentially associated with gene disruption. A survey of transposases among genomes of Actinobacteria showed no correlation between phylogenetic relatedness and distribution of IS families. By using Southern hybridization, we suggested that diversification of <it>Lxc </it>isolates is also mediated by insertion sequences in probably recent events.</p> <p>Conclusion</p> <p>Collectively our data indicate that transposable elements are involved in genome diversification of <it>Lxc </it>and <it>Lxx</it>. The IS elements were probably acquired after the divergence of the two subspecies and are associated with genome organization and gene contents. In addition to enhancing understanding of IS element dynamics in general, these data will contribute to our ongoing comparative analyses aimed at understanding the biological differences of the <it>Lxc </it>and <it>Lxx</it>.</p

Responses of Acidobacteria Granulicella sp. WH15 to High Carbon Revealed by Integrated Omics Analyses

The phylum Acidobacteria is widely distributed in soils, but few representatives have been cultured. In general, Acidobacteria are oligotrophs and exhibit slow growth under laboratory conditions. We sequenced the genome of Granulicella sp. WH15, a strain obtained from decaying wood, and determined the bacterial transcriptome and proteome under growth in poor medium with a low or high concentration of sugar. We detected the presence of 217 carbohydrate-associated enzymes in the genome of strain WH15. Integrated analysis of the transcriptomic and proteomic profiles showed that high sugar triggered a stress response. As part of this response, transcripts related to cell wall stress, such as sigma factor σW and toxin–antitoxin (TA) systems, were upregulated, as were several proteins involved in detoxification and repair, including MdtA and OprM. KEGG metabolic pathway analysis indicated the repression of carbon metabolism (especially the pentose phosphate pathway) and the reduction of protein synthesis, carbohydrate metabolism, and cell division, suggesting the arrest of cell activity and growth. In summary, the stress response of Granulicella sp. WH15 induced by the presence of a high sugar concentration in the medium resulted in the intensification of secretion functions to eliminate toxic compounds and the reallocation of resources to cell maintenance instead of growth

Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire

Background: Pythium ultimum (P. ultimum) is a ubiquitous oomycete plant pathogen responsible for a variety of diseases on a broad range of crop and ornamental species. Results: The P. ultimum genome (42.8 Mb) encodes 15,290 genes and has extensive sequence similarity and synteny with related Phytophthora species, including the potato blight pathogen Phytophthora infestans. Whole transcriptome sequencing revealed expression of 86% of genes, with detectable differential expression of suites of genes under abiotic stress and in the presence of a host. The predicted proteome includes a large repertoire of proteins involved in plant pathogen interactions although surprisingly, the P. ultimum genome does not encode any classical RXLR effectors and relatively few Crinkler genes in comparison to related phytopathogenic oomycetes. A lower number of enzymes involved in carbohydrate metabolism were present compared to Phytophthora species, with the notable absence of cutinases, suggesting a significant difference in virulence mechanisms between P. ultimum and more host specific oomycete species. Although we observed a high degree of orthology with Phytophthora genomes, there were novel features of the P. ultimum proteome including an expansion of genes involved in proteolysis and genes unique to Pythium. We identified a small gene family of cadherins, proteins involved in cell adhesion, the first report in a genome outside the metazoans. Conclusions: Access to the P. ultimum genome has revealed not only core pathogenic mechanisms within the oomycetes but also lineage specific genes associated with the alternative virulence and lifestyles found within the pythiaceous lineages compared to the Peronosporaceae

Pythium vexans DAOM BR484 Genome Assembly and Annotation

Pythium vexans DAOM BR484 Genome Assembly and Annotation Contents: pve1_func_anno.list; pve.maker.proteins.fasta; pve.maker.transcripts.fasta; pve_contigs_asm.fasta; pve_contigs_asm.maker.gff

Data from: Comparative genomics reveals insight into virulence strategies of plant pathogenic oomycetes

The kingdom Stramenopile includes diatoms, brown algae, and oomycetes. Plant pathogenic oomycetes, including Phytophthora, Pythium and downy mildew species, cause devastating diseases on a wide range of host species and have a significant impact on agriculture. Here, we report comparative analyses on the genomes of thirteen straminipilous species, including eleven plant pathogenic oomycetes, to explore common features linked to their pathogenic lifestyle. We report the sequencing, assembly, and annotation of six Pythium genomes and comparison with other stramenopiles including photosynthetic diatoms, and other plant pathogenic oomycetes such as Phytophthora species, Hyaloperonospora arabidopsidis, and Pythium ultimum var. ultimum. Novel features of the oomycete genomes include an expansion of genes encoding secreted effectors and plant cell wall degrading enzymes in Phytophthora species and an over-representation of genes involved in proteolytic degradation and signal transduction in Pythium species. A complete lack of classical RxLR effectors was observed in the seven surveyed Pythium genomes along with an overall reduction of pathogenesis-related gene families in H. arabidopsidis. Comparative analyses revealed fewer genes encoding enzymes involved in carbohydrate metabolism in Pythium species and H. arabidopsidis as compared to Phytophthora species, suggesting variation in virulence mechanisms within plant pathogenic oomycete species. Shared features between the oomycetes and diatoms revealed common mechanisms of intracellular signaling and transportation. Our analyses demonstrate the value of comparative genome analyses for exploring the evolution of pathogenesis and survival mechanisms in the oomycetes. The comparative analyses of seven Pythium species with the closely related oomycetes, Phytophthora species and H. arabidopsidis, and distantly related diatoms provide insight into genes that underlie virulence

Pythium iwayamai DAOM BR242034 Genome Assembly and Annotation

Pythium iwayamai DAOM BR242034 Genome Assembly and Annotation Contents: piw_functional_annotation.txt; piw.maker.proteins.fasta; piw.maker.transcripts.fasta; piw_contigs_asm.fasta; piw_contigs_asm.maker.gff

Pythium aphanidermatum DAOM BR444 Genome Assembly and Annotation

Pythium aphanidermatum DAOM BR444 Genome Assembly and Annotation Contents: pag1_functional_annotation.txt; pag1.maker.proteins.fasta; pag1.maker.transcripts.fasta; pag1_scaffolds_asm.fasta; pag1_scaffolds_asm.maker.gff

Pythium ultimum var. sporangiiferum BR650 Genome Assembly and Annotation

Pythium ultimum var. sporangiiferum BR650 Genome Assembly and Annotation Contents: pug3_functional_annotation.txt; pug3.maker.proteins.fasta; pug3.maker.transcripts.fasta; pug3_contigs_asm.fasta; pug3_contigs_asm.maker.gff

Pythium arrhenomanes ATCC 12531 Genome Assembly and Annotation

Pythium arrhenomanes ATCC 12531 Genome Assembly and Annotation Contents: par_functional_annotation.txt; par.maker.proteins.fasta; par.maker.transcripts.fasta; par_contigs_asm.fasta; par_contigs_asm.maker.gff

Comparative Genomics Reveals Insight into Virulence Strategies of Plant Pathogenic Oomycetes

<div><p>The kingdom Stramenopile includes diatoms, brown algae, and oomycetes. Plant pathogenic oomycetes, including <i>Phytophthora</i>, <i>Pythium</i> and downy mildew species, cause devastating diseases on a wide range of host species and have a significant impact on agriculture. Here, we report comparative analyses on the genomes of thirteen straminipilous species, including eleven plant pathogenic oomycetes, to explore common features linked to their pathogenic lifestyle. We report the sequencing, assembly, and annotation of six <i>Pythium</i> genomes and comparison with other stramenopiles including photosynthetic diatoms, and other plant pathogenic oomycetes such as <i>Phytophthora</i> species, <i>Hyaloperonospora arabidopsidis,</i> and <i>Pythium ultimum</i> var. <i>ultimum</i>. Novel features of the oomycete genomes include an expansion of genes encoding secreted effectors and plant cell wall degrading enzymes in <i>Phytophthora</i> species and an over-representation of genes involved in proteolytic degradation and signal transduction in <i>Pythium</i> species. A complete lack of classical RxLR effectors was observed in the seven surveyed <i>Pythium</i> genomes along with an overall reduction of pathogenesis-related gene families in <i>H. arabidopsidis</i>. Comparative analyses revealed fewer genes encoding enzymes involved in carbohydrate metabolism in <i>Pythium</i> species and <i>H. arabidopsidis</i> as compared to <i>Phytophthora</i> species, suggesting variation in virulence mechanisms within plant pathogenic oomycete species. Shared features between the oomycetes and diatoms revealed common mechanisms of intracellular signaling and transportation. Our analyses demonstrate the value of comparative genome analyses for exploring the evolution of pathogenesis and survival mechanisms in the oomycetes. The comparative analyses of seven <i>Pythium</i> species with the closely related oomycetes, <i>Phytophthora</i> species and <i>H. arabidopsidis</i>, and distantly related diatoms provide insight into genes that underlie virulence.</p></div