Cytogenetic characterization of Hydrangea involucrata Sieb. and H. aspera D. Don complex (Hydrangeaceae): genetic, evolutional, and taxonomic implications

The subsection Asperae of genus Hydrangea L. (Hydrangeaceae) has been investigated for three reasons: several ambiguous classifications concerning Hydrangea aspera have been published, unexpected differences in genome size among seven accessions have been reported Cerbah et al. (Theor Appl Genet 103:45–51, 2001), and two atypical chromosome numbers (2n = 30 for Hydrangea involucrata and 2n = 34 for H. aspera) have been found when all other species of the genus present 2n = 36. Therefore, these two species and four subspecies of Hydrangea in all 29 accessions were analyzed for their genome size, chromosome number, and karyotype features. This investigation includes flow cytometric measurements of nuclear DNA content and bases composition (GC%), fluorochrome banding for detection of GC- and AT-rich DNA regions, and fluorescent in situ hybridisation (FISH) for chromosome mapping of 5 S and 18 S-5.8 S-26 S rDNA genes. In the H. aspera complex, the genome size ranged from 2.98 (subsp. sargentiana) to 4.67 pg/2C (subsp. aspera), an exceptional intraspecific variation of 1.57-fold. The mean base composition was 40.5% GC. Our report establishes the first karyotype for the species H. involucrata, and for the subspecies of H. aspera which indeed present different formulae, offering an element of discrimination. FISH and fluorochrome banding revealed the important differentiation between these two species (H. involucrata and H. aspera) and among four subspecies of the H. aspera complex. Our results are in agreement with the Chinese classification that places the groups Kawakami and Villosa as two different species: Hydrangea villosa Rehder and Hydrangea kawakami Hayata. This knowledge can contribute to effective germplasm management and horticultural use

Karyotype differentiation of four Cestrum species (Solanaceae) revealed by fluorescent chromosome banding and FISH

The karyotypes of four South American species of Cestrum (C. capsulare,C. corymbosum,C. laevigatum and C. megalophylum) were studied using conventional staining, C-CMA/DAPI chromosome banding and FISH with 45S and 5S rDNA probes. The karyotypes showed a chromosome number of 2n = 2x = 16, with metacentric chromosomes, except for the eighth submeta- to acrocentric pair. Several types of heterochromatin were detected, which varied in size, number, distribution and base composition. The C-CMA+ bands and 45S rDNA were located predominantly in terminal regions. The C-CMA + /DAPI + bands appeared in interstitial and terminal regions, and the C-DAPI + bands were found in all chromosome regions. The 5S rDNA sites were observed on the long arm of pair 8 in all species except C. capsulare, where they were found in the paracentromeric region of the long arm of pair 4. The differences in band patterns among the species studied here, along with data from other nine species reported in the literature, suggest that the bands are dispersed in an equilocal and non-equilocal manner and that structural rearrangements can be responsible for internal karyotype diversification. However, it is important to point out that the structural changes involving repetitive segments did not culminate in substantial changes in the general karyotype structure concerning chromosome size and morphology

Chromosomal polymorphism of ribosomal genes in the genus Oryza

The genes encoding for 18S–5.8S–28S ribosomal RNA (rDNA) are both conserved and diversified. We used rDNA as probe in the fluorescent in situ hybridization (rDNA-FISH) to localized rDNAs on chromosomes of 15 accessions representing ten Oryza species. These included cultivated and wild species of rice, and four of them are tetraploids. Our results reveal polymorphism in the number of rDNA loci, in the number of rDNA repeats, and in their chromosomal positions among Oryza species. The numbers of rDNA loci varies from one to eight among Oryza species. The rDNA locus located at the end of the short arm of chromosome 9 is conserved among the genus Oryza. The rDNA locus at the end of the short arm of chromosome 10 was lost in some of the accessions. In this study, we report two genome specific rDNA loci in the genus Oryza. One is specific to the BB genome, which was localized at the end of the short arm of chromosome 4. Another may be specific to the CC genome, which was localized in the proximal region of the short arm of chromosome 5. A particular rDNA locus was detected as stretched chromatin with bright signals at the proximal region of the short arm of chromosome 4 in O.grandiglumis by rDNA-FISH. We suggest that chromosomal inversion and the amplification and transposition of rDNA might occur during Oryza species evolution. The possible mechanisms of cyto-evolution in tetraploid Oryza species are discussed

Annotation of protein residues based on a literature analysis: cross-validation against UniProtKb

<p>Abstract</p> <p>Background</p> <p>A protein annotation database, such as the Universal Protein Resource knowledge base (UniProtKb), is a valuable resource for the validation and interpretation of predicted 3D structure patterns in proteins. Existing studies have focussed on point mutation extraction methods from biomedical literature which can be used to support the time consuming work of manual database curation. However, these methods were limited to point mutation extraction and do not extract features for the annotation of proteins at the residue level.</p> <p>Results</p> <p>This work introduces a system that identifies protein residues in MEDLINE abstracts and annotates them with features extracted from the context written in the surrounding text. MEDLINE abstract texts have been processed to identify protein mentions in combination with taxonomic species and protein residues (F1-measure 0.52). The identified protein-species-residue triplets have been validated and benchmarked against reference data resources (UniProtKb, average F1-measure of 0.54). Then, contextual features were extracted through shallow and deep parsing and the features have been classified into predefined categories (F1-measure ranges from 0.15 to 0.67). Furthermore, the feature sets have been aligned with annotation types in UniProtKb to assess the relevance of the annotations for ongoing curation projects. Altogether, the annotations have been assessed automatically and manually against reference data resources.</p> <p>Conclusion</p> <p>This work proposes a solution for the automatic extraction of functional annotation for protein residues from biomedical articles. The presented approach is an extension to other existing systems in that a wider range of residue entities are considered and that features of residues are extracted as annotations.</p

LinkedGeoData -- Adding a Spatial Dimension to the Web of Data

In order to employ the Web as a medium for data and information integration, comprehensive datasets and vocabularies are required as they enable the disambiguation and alignment of other data and information. Many real-life information integration and aggregation tasks are impossible without comprehensive background knowledge related to spatial features of the ways, structures and landscapes surrounding us. In this paper we contribute to the generation of a spatial dimension for the Data Web by elaborating on how the collaboratively collected OpenStreetMap data can be transformed and represented adhering to the RDF data model, how this data can be interlinked with other spatial data sets, how it can be made accessible for machines according to the linked data paradigm and for humans by means of a faceted geo-data browser