4 research outputs found
ATGC transcriptomics : a web-based application to integrate, explore and analyze de novo transcriptomic data
Background: In the last years, applications based on massively parallelized RNA sequencing (RNA-seq) have become valuable approaches for studying non-model species, e.g., without a fully sequenced genome. RNA-seq is a useful tool for detecting novel transcripts and genetic variations and for evaluating differential gene expression by digital measurements. The large and complex datasets resulting from functional genomic experiments represent a challenge in data processing, management, and analysis. This problem is especially significant for small research groups working with non-model species.
Results: We developed a web-based application, called ATGC transcriptomics, with a flexible and adaptable interface that allows users to work with new generation sequencing (NGS) transcriptomic analysis results using an
ontology-driven database. This new application simplifies data exploration, visualization, and integration for a better comprehension of the results.
Conclusions: ATGC transcriptomics provides access to non-expert computer users and small research groups to a scalable storage option and simple data integration, including database administration and management. The
software is freely available under the terms of GNU public license at http://atgcinta.sourceforge.net.Inst. de BiotecnologĂaFil: Gonzalez, Sergio Alberto. Instituto Nacional de TecnologĂa Agropecuaria (INTA). Instituto de BiotecnologĂa; ArgentinaFil: Clavijo, Bernardo. Norwich Research Park. Earlham Institute; Reino UnidoFil: Rivarola, Maximo Lisandro. Instituto Nacional de TecnologĂa Agropecuaria (INTA). Instituto de BiotecnologĂa; Argentina. Consejo Nacional de Investigaciones CientĂficas y TĂ©cnicas; ArgentinaFil: Moreno, Patricio. Universidad de Buenos Aires. Facultad de IngenierĂa. Instituto de IngenierĂa BiomĂ©dica; ArgentinaFil: FernĂĄndez, Paula. Instituto Nacional de TecnologĂa Agropecuaria (INTA). Instituto de BiotecnologĂa; Argentina. Consejo Nacional de Investigaciones CientĂficas y TĂ©cnicas; Argentina.Universidad Nacional de San MartĂn. Escuela de Ciencia y TecnologĂa; ArgentinaFil: Dopazo, JoaquĂn Centro de InvestigaciĂłn PrĂncipe Felipe. Computational Genomics Department; EspañaFil: Paniego, Norma Beatriz. Instituto Nacional de TecnologĂa Agropecuaria (INTA). Instituto de BiotecnologĂa; Argentina. Consejo Nacional de Investigaciones CientĂficas y TĂ©cnicas; Argentin
Usefulness of a New Large Set of High Throughput EST-SNP Markers as a Tool for Olive Germplasm Collection Management
Germplasm collections are basic tools for conservation, characterization, and efficient use of olive genetic resources. The identification of the olive cultivars maintained in the collections is an important ongoing task which has been performed by both, morphological and molecular markers. In the present study, based on the sequencing results of previous genomic projects, a new set of 1,043 EST-SNP markers has been identified. In order to evaluate its discrimination capacity and utility in diversity studies, this set of markers was used in a representative number of accessions from 20 different olive growing countries and maintained at the World Olive Germplasm Collection of IFAPA Centre âAlameda del Obispoâ (CĂłrdoba, Spain), one of the worldâs largest olive germplasm bank. Thus, the cultivated material included: cultivars belonging to previously defined core collections by means of SSR markers and agronomical traits, well known homonymy cases, possible redundancies previously identified in the collection, and recently introduced accessions. Marker stability was tested in repeated analyses of a selected number of accessions, as well as in different trees and accessions belonging to the same cultivar. In addition, 15 genotypes from a cross âPicualâ Ă âArbequinaâ cultivars from the IFAPA olive breeding program and a set of 89 wild genotypes were also included in the study. Our results indicate that, despite their relatively wide variability, the new set of EST-SNPs displayed lower levels of genetic diversity than SSRs in the set of olive core collections tested. However, the EST-SNP markers displayed consistent and reliable results from different plant material sources and plant propagation events. The EST-SNPs revealed a clear cut off between inter- and intra-cultivar variation in olive. Besides, they were able to reliably discriminate among different accessions, to detect possible homonymy cases as well as efficiently ascertain the presence of redundant germplasm in the collection. Additionally, these markers were highly transferable to the wild genotypes. These results, together with the low genotyping error rates and the easy and fully automated procedure used to get the genotyping data, validate the new set of EST-SNPs as possible markers of choice for olive cultivar identification