Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development

<p>Abstract</p> <p>Background</p> <p>The Gene Ontology project supports categorization of gene products according to their location of action, the molecular functions that they carry out, and the processes that they are involved in. Although the ontologies are intentionally developed to be taxon neutral, and to cover all species, there are inherent taxon specificities in some branches. For example, the process 'lactation' is specific to mammals and the location 'mitochondrion' is specific to eukaryotes. The lack of an explicit formalization of these constraints can lead to errors and inconsistencies in automated and manual annotation.</p> <p>Results</p> <p>We have formalized the taxonomic constraints implicit in some GO classes, and specified these at various levels in the ontology. We have also developed an inference system that can be used to check for violations of these constraints in annotations. Using the constraints in conjunction with the inference system, we have detected and removed errors in annotations and improved the structure of the ontology.</p> <p>Conclusions</p> <p>Detection of inconsistencies in taxon-specificity enables gradual improvement of the ontologies, the annotations, and the formalized constraints. This is progressively improving the quality of our data. The full system is available for download, and new constraints or proposed changes to constraints can be submitted online at <url>https://sourceforge.net/tracker/?atid=605890&group_id=36855</url>.</p

Heterodera schachtii nematodes interfere with aphid-plant relations on Brassica oleracea

Aboveground and belowground herbivore species modify plant defense responses differently. Simultaneous attack can lead to non-additive effects on primary and secondary metabolite composition in roots and shoots. We previously found that aphid (Brevicoryne brassicae) population growth on Brassica oleracea was reduced on plants that were infested with nematodes (Heterodera schachtii) prior (4 weeks) to aphid infestation. Here, we examined how infection with root-feeding nematodes affected primary and secondary metabolites in the host plant and whether this could explain the increase in aphid doubling time from 3.8 to 6.7 days. We hypothesized that the effects of herbivores on plant metabolites would depend on the presence of the other herbivore and that nematode-induced changes in primary metabolites would correlate with reduced aphid performance. Total glucosinolate concentration in the leaves was not affected by nematode presence, but the composition of glucosinolates shifted, as gluconapin concentrations were reduced, while gluconapoleiferin concentrations increased in plants exposed to nematodes. Aphid presence increased 4-methoxyglucobrassicin concentrations in leaves, which correlated positively with the number of aphids per plant. Nematodes decreased amino acid and sugar concentrations in the phloem. Aphid population doubling time correlated negatively with amino acids and glucosinolate levels in leaves, whereas these correlations were non-significant when nematodes were present. In conclusion, the effects of an herbivore on plant metabolites were independent of the presence of another herbivore. Nematode presence reduced aphid population growth and disturbed feeding relations between plants and aphids.

Proteomic Analysis of Pea (Pisum sativum L.) Response During Compatible and Incompatible Interactions with the Pea Aphid (Acyrthosiphon pisum H.)

Acyrthosiphon pisum (pea aphid) is considered to be one of the most agronomically damaging pests on pea and alfalfa crops, and is responsible for significant yield losses in agriculture. For the efficient control of the parasite, a better understanding of its interaction and associated resistance mechanisms at the molecular level is required. We used two-dimensional gel electrophoresis (2DE) coupled to mass spectrometry (MSMS) analysis to compare the leaf proteome of two pea accessions displaying different phenotypes to A. pisum infestation. Multivariate statistical analysis identified 203 differential proteins under the experimental conditions, 81 of which were identified using a combination of peptide mass fingerprinting (PMF) and MSMS fragmentation. Most of the identified proteins corresponded to amino acid and carbohydrate metabolism, photosynthesis, folding/degradation, stress response, signal transduction and transcription/translation. Results suggested the involvement of different metabolic pathways that may be activated in order to overcome pea aphid attack in the resistant accession (P665): reduction of photosynthesis and amino acid biosynthesis that may be helpful in tackling pea aphid attack by limiting access to nutrients, up-accumulation of wound signal molecules such as LOXs and LAPs, and activation of the antioxidant ASC-GSH cycle. In contrast, the susceptible accession (cv. Messire) showed an increase in primary metabolism pathways (especially amino acid biosynthesis), from which a relationship to the successful performance of aphids on this accession could be inferred. Results are also discussed with regard to differences in management of photoassimilates against the strong sinks produced by aphid feeding. © 2013 Springer Science+Business Media New York.This research was supported by the Spanish AGL2011-22524 project. E. Carrillo was funded by a grant from Cabildo de La Palma- CSIC PhD and Mª Angeles Castillejo by a postdoctoral fellowship from the Spanish Ministry of Education, through the Mobility Program R-D + I 2008–2011.Peer Reviewe