A Bioinformatics Framework for plant pathologists to deliver global food security outcomes

Bioinformatics applies information technologies to the allied fields of agriculture, horticulture, forestry, biotechnology, microbiology, plant physiology and molecular biology. Bioinformatics devises strategies for data management, analysis and integration tools that enable rapid scientific discovery and informed decision making. In plant pathology, the 'contemporary' application stage of bioinformatics is typically after a pathogen has been identified as a causative agent for a given plant host and subjected to biotechnological studies. In contrast, this paper contends that a broader bioinformatics framework should also integrate data/reports and interpretations/treatments as soon as potential pathogen incursions are encountered on a farm or forestry plot: capturing in real-time, elements of the incursion, sampling/survey, diagnostics, remedial treatments and field/laboratory work leading to the development of new cultivars or multiple disease resistance. Data currently captured/generated are managed in disparate formats: field/laboratory books, spreadsheets maintained independently by growers, extension officers and scientists, located in geographically disperse locations (e.g. farms, offices, institutions, archival repositories). Bioinformatics solutions provide the opportunity for a more coordinated electronic basis to manage/integrate this information. In this paper, a Bioinformatics Framework is proposed that enables improved cross-border, trans-discipline collaborative efforts that will enable more informed decision making by relevant stakeholders. In this way a shared biosecurity infrastructure can be developed that caters for sustainable global food and fibre production in the context of global climatic changes and increased opportunities for accidental disease incursions through the global plant trade

CattleTickBase: An integrated Internet-based bioinformatics resource for Rhipicephalus (Boophilus) microplus

The Rhipicephalus microplus genome is large and complex in structure, making it difficult to assemble a genome sequence and costly to resource the required bioinformatics. In light of this, a consortium of international collaborators was formed to pool resources to begin sequencing this genome. We have acquired and assembled genomic DNA into contigs that represent over 1.8 Gigabase pairs of DNA from gene-enriched regions of the R. microplus genome. We also have several datasets containing transcript sequences from a number of gene expression experiments conducted by the consortium. A web-based resource was developed to enable the scientific community to access our datasets and conduct analysis through a web-based bioinformatics environment called YABI. The collective bioinformatics resource is termed CattleTickBase. Our consortium has acquired genomic and transcriptomic sequence data at approximately 0.9X coverage of the gene-coding regions of the R. microplus genome. The YABI tool will facilitate access and manipulation of cattle tick genome sequence data as the genome sequencing of R. microplus proceeds. During this process the CattleTickBase resource will continue to be updated

Targeted studies of the genome, transcriptome and microbiome of the cattle tick, Rhipicephalus miroplus

No abstract availabl

Prediction of G protein-coupled receptor encoding sequences from the synganglion transcriptome of the cattle tick, Rhipicephalus microplus

The cattle tick, Rhipicephalus (Boophilus) microplus, is a pest which causes multiple health complications in cattle. The G protein-coupled receptor (GPCR) super-family presents a candidate target for developing novel tick control methods. However, GPCRs share limited sequence similarity among orthologous family members, and there is no reference genome available for R. microplus. This limits the effectiveness of alignment-dependent methods such as BLAST and Pfam for identifying GPCRs from R. microplus. However, GPCRs share a common structure consisting of seven transmembrane helices. We present an analysis of the R. microplus synganglion transcriptome using a combination of structurally-based and alignment-free methods which supplement the identification of GPCRs by sequence similarity. TMHMM predicts the number of transmembrane helices in a protein sequence. GPCRpred is a support vector machine-based method developed to predict and classify GPCRs using the dipeptide composition of a query amino acid sequence. These two bioinformatic tools were applied to our transcriptome assembly of the cattle tick synganglion. Together, BLAST and Pfam identified 85 unique contigs as encoding partial or full length candidate cattle tick GPCRs. Collectively, TMHMM and GPCRpred identified 27 additional GPCR candidates that BLAST and Pfam missed. This demonstrates that the addition of structurally-based and alignment-free bioinformatic approaches to transcriptome annotation and analysis produces a greater collection of prospective GPCRs than an analysis based solely upon methodologies dependent upon sequence alignment and similarity

Spore density and root colonization by arbuscular mycorrhizal fungi in preserved or disturbed Araucaria angustifolia (Bert.) O. Ktze. ecosystems Densidade de esporos e colonização radicular por fungos microrrízicos arbusculares em ecossistemas de Araucaria angustifolia (Bert.) O. Ktze. preservados e impactados

Araucaria angustifolia (Bert.) O. Ktze., a native forest tree from Brazil, is under extinction risk. This tree depends on arbuscular mycorrhizal fungi for growth and development, especially in tropical low-P soils but, despite being a conifer, Araucaria does not form ectomycorrhiza, but only the arbuscular endomycorrhiza. This study aimed at surveying data on the spore density and root colonization (CR) by arbuscular mycorrhizal fungi (AMF) in Araucaria angustifolia forest ecosystems, in order to discriminate natural, implemented, and anthropic action-impacted ecosystems, by means of Canonical Discriminant Analysis (CDA). Three ecosystems representative of the Campos do Jordão (SP, Brazil) region were selected: 1. a native forest (FN); 2. a replanted Araucaria forest (R); and 3. a replanted Araucaria forest, submitted to accidental fire (RF). Rhizosphere soil and roots were sampled in May and October, 2002, for root colonization, AMF identification, and spores counts. Root percent colonization rates at first collection date were relatively low and did not differ amongst ecosystems. At the second period, FN presented higher colonization than the other two areas, with much higher figures than during the first period, for all areas. Spore density was lower in FN than in the other areas. A total of 26 AMF species were identified. The percent root colonization and spore numbers were inversely related to each other in all ecosystems. CDA indicated that there is spatial distinction among the three ecosystems in regard to the evaluated parameters.<br>A Araucaria angustifolia (Bert.) O. Ktze. é uma espécie florestal nativa do Brasil e encontra-se ameaçada de extinção. É altamente dependente de fungos micorrízicos arbusculares para seu desenvolvimento, principalmente em solos com baixos teores de fósforo. Embora sendo uma conífera, esta árvore não forma ectomicorriza, mas sim a endomicorriza arbuscular. O presente estudo teve como objetivo levantar dados sobre a densidade de esporos e a colonização radicular de fungos micorrízicos arbusculares (FMAs) em ecossistemas florestais de Araucaria angustifolia, visando discriminar os ecossistemas natural, implantado e impactado pela ação antrópica, através da Análise Canônica Discriminante (ACD). Foram selecionados três ecossistemas representativos da região de Campos do Jordão (SP): 1. floresta nativa (FN); 2. floresta replantada de araucária (R); e 3. floresta replantada de araucária, submetida a uma queima acidental (RF). As coletas de solo rizosférico e de raízes foram realizadas em maio e outubro de 2002. Determinaram-se a densidade de esporos, taxa de colonização radicular e identificaram-se os gêneros de FMAs presentes. O número de esporos na FN foi sempre inferior aos reflorestamentos. Foram identificadas ao todo 26 espécies de FMAs. A colonização radicular na primeira coleta apresentou valores os quais não diferiram entre as três áreas estudadas. Entretanto, na segunda coleta, a FN apresentou plantas com maior valor de colonização que aquelas dos reflorestamentos, sendo todos os valores superiores aos encontrados na primeira coleta. Houve uma relação inversa entre colonização e número de esporos em todas as áreas. Ocorreu uma separação espacial entre as três áreas de estudo, baseada em análise canônica discriminante das variáveis estudadas