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

Draft genome sequence of Burkholderia ambifaria RZ2MS16, a plant growth-promoting rhizobacterium isolated from guarana, a tropical plant

Burkholderia ambifaria strain RZ2MS16 was isolated from the rhizosphere of Amazon guarana in Brazil. This bacterium exhibits a remarkable capacity to promote the growth of corn and soybean. Here, we report the draft genome sequence of RZ2MS16 and some genes related to multiple traits involved in plant growth promotion

Xylella fastidiosa comparative genomic database is an information resource to explore the annotation, genomic features, and biology of different strains

The Xylella fastidiosa comparative genomic database is a scientific resource with the aim to provide a user-friendly interface for accessing high-quality manually curated genomic annotation and comparative sequence analysis, as well as for identifying and mapping prophage-like elements, a marked feature of Xylella genomes. Here we describe a database and tools for exploring the biology of this important plant pathogen. The hallmarks of this database are the high quality genomic annotation, the functional and comparative genomic analysis and the identification and mapping of prophage-like elements. It is available from web site http://www.xylella.lncc.br

O Papel do ensino do português como língua estrangeira na defesa do multicultarismo

As política actuais existentes a nível oficial para a implementação e defesa do ensino da Língua Portuguesa como Língua Estrangeira (L. E.) na Europa e no resto do mundo levam-nos a pensar que são, sobretudo, os casos isolados de leitores portugueses pioneiros, inspirados e marginais que na sua missão individual e afastada lutam pela implementação e defesa desta língua nos seus países de acolhimento. Segundo Volfgram, “cabe ensinar a alguns que o multiculturalismo não está apenas na teoria e sim ao nosso redor, nos elevando realmente à condição de seres humanos” (2005), e o mesmo é dizer que o multiculturalismo começa nas suas bases pela aprendizagem desinteressada e não interesseira das crianças na sua mais tenra idade. Não é impunemente que em países multiculturais como a Bélgica, a Língua Portuguesa ensinada como segunda língua ou como língua estrangeira desempenha um papel preponderante na defesa e na preservação do Português e, em simultâneo, pugna pela defesa incontestável da necessidade incontornável que o multiculturalismo é hoje. É indubitável que a luta contra a xenofobia, a luta pela tolerância e o respeito mútuo, bem como o diálogo profícuo biunívoco não podem sobreviver actualmente sem uma consciencialização da importância das línguas minoritárias, da crioulização, da relação com as línguas maioritárias e da conquista da defesa do multiculturalismo hic et nunc. Abordando algumas opiniões avisadas, esperamos trazer à discussão temas importantes, tais como, a necessidade de articulação de políticas de difusão da língua portuguesa na Europa e no Mundo concertadamente com o Brasil e outros Países Lusófonos, a necessidade de implementação de medidas concretas no terreno para defesa da Língua de Camões fora de Portugal, a sobrevivência do Português que embora sendo minoritária na Europa é uma das línguas mais faladas no mundo, a necessidade da consciencialização para a crescente importância geo-estratégica do Português paralelamente com o recrudescimento do multiculturalismo à escala global

Metabolome Dynamics of Smutted Sugarcane Reveals Mechanisms Involved in Disease Progression and Whip Emission

Sugarcane smut disease, caused by the biotrophic fungus Sporisorium scitamineum, is characterized by the development of a whip-like structure from the plant meristem. The disease causes negative effects on sucrose accumulation, fiber content and juice quality. The aim of this study was to exam whether the transcriptomic changes already described during the infection of sugarcane by S. scitamineum result in changes at the metabolomic level. To address this question, an analysis was conducted during the initial stage of the interaction and through disease progression in a susceptible sugarcane genotype. GC-TOF-MS allowed the identification of 73 primary metabolites. A set of these compounds was quantitatively altered at each analyzed point as compared with healthy plants. The results revealed that energetic pathways and amino acid pools were affected throughout the interaction. Raffinose levels increased shortly after infection but decreased remarkably after whip emission. Changes related to cell wall biosynthesis were characteristic of disease progression and suggested a loosening of its structure to allow whip growth. Lignin biosynthesis related to whip formation may rely on Tyr metabolism through the overexpression of a bifunctional PTAL. The altered levels of Met residues along with overexpression of SAM synthetase and ACC synthase genes suggested a role for ethylene in whip emission. Moreover, unique secondary metabolites antifungal-related were identified using LC-ESI-MS approach, which may have potential biomarker applications. Lastly, a putative toxin was the most important fungal metabolite identified whose role during infection remains to be established

Data_Sheet_1.XLSX

<p>Host specialization is a key evolutionary process for the diversification and emergence of new pathogens. However, the molecular determinants of host range are poorly understood. Smut fungi are biotrophic pathogens that have distinct and narrow host ranges based on largely unknown genetic determinants. Hence, we aimed to expand comparative genomics analyses of smut fungi by including more species infecting different hosts and to define orphans and positively selected genes to gain further insights into the genetics basis of host specialization. We analyzed nine lineages of smut fungi isolated from eight crop and non-crop hosts: maize, barley, sugarcane, wheat, oats, Zizania latifolia (Manchurian rice), Echinochloa colona (a wild grass), and Persicaria sp. (a wild dicot plant). We assembled two new genomes: Ustilago hordei (strain Uhor01) isolated from oats and U. tritici (strain CBS 119.19) isolated from wheat. The smut genomes were of small sizes, ranging from 18.38 to 24.63 Mb. U. hordei species experienced genome expansions due to the proliferation of transposable elements and the amount of these elements varied among the two strains. Phylogenetic analysis confirmed that Ustilago is not a monophyletic genus and, furthermore, detected misclassification of the U. tritici specimen. The comparison between smut pathogens of crop and non-crop hosts did not reveal distinct signatures, suggesting that host domestication did not play a dominant role in shaping the evolution of smuts. We found that host specialization in smut fungi likely has a complex genetic basis: different functional categories were enriched in orphans and lineage-specific selected genes. The diversification and gain/loss of effector genes are probably the most important determinants of host specificity.</p