@article {406, title = {The first complete genomic structure of Butyrivibrio fibrisolvens and its chromid.}, journal = {Microb Genom}, volume = {4}, year = {2018}, month = {2018 Oct}, abstract = {

Butyrivibrio fibrisolvens forms part of the gastrointestinal microbiome of ruminants and other mammals, including humans. Indeed, it is one of the most common bacteria found in the rumen and plays an important role in ruminal fermentation of polysaccharides, yet, to date, there is no closed reference genome published for this species in any ruminant animal. We successfully assembled the nearly complete genome sequence of B. fibrisolvens strain INBov1 isolated from cow rumen using Illumina paired-end reads, 454 Roche single-end and mate pair sequencing technology. Additionally, we constructed an optical restriction map of this strain to aid in scaffold ordering and positioning, and completed the first genomic structure of this species. Moreover, we identified and assembled the first chromid of this species (pINBov266). The INBov1 genome encodes a large set of genes involved in the cellulolytic process but lacks key genes. This seems to indicate that B. fibrisolvens plays an important role in ruminal cellulolytic processes, but does not have autonomous cellulolytic capacity. When searching for genes involved in the biohydrogenation of unsaturated fatty acids, no linoleate isomerase gene was found in this strain. INBov1 does encode oleate hydratase genes known to participate in the hydrogenation of oleic acids. Furthermore, INBov1 contains an enolase gene, which has been recently determined to participate in the synthesis of conjugated linoleic acids. This work confirms the presence of a novel chromid in B. fibrisolvens and provides a new potential reference genome sequence for this species, providing new insight into its role in biohydrogenation and carbohydrate degradation.

}, keywords = {Animals, Butyrivibrio fibrisolvens, Cattle, Genome, Bacterial, Genomics, Humans, Milk, Rumen, Sequence Analysis, DNA}, issn = {2057-5858}, doi = {10.1099/mgen.0.000216}, author = {Rodr{\'\i}guez Hern{\'a}ez, Javier and Cer{\'o}n Cucchi, Maria Esperanza and Cravero, Silvio and Martinez, Maria Carolina and Gonzalez, Sergio and Puebla, Andrea and Dopazo, Joaquin and Farber, Marisa and Paniego, Norma and Rivarola, M{\'a}ximo} } @article {432, title = {ATGC transcriptomics: a web-based application to integrate, explore and analyze de novo transcriptomic data.}, journal = {BMC Bioinformatics}, volume = {18}, year = {2017}, month = {2017 Feb 22}, pages = {121}, abstract = {

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 .

}, keywords = {Animals, Databases, Genetic, Gene Expression Profiling, High-Throughput Nucleotide Sequencing, Internet, Sequence Analysis, RNA, Transcriptome, User-Computer Interface}, issn = {1471-2105}, doi = {10.1186/s12859-017-1494-2}, author = {Gonzalez, Sergio and Clavijo, Bernardo and Rivarola, M{\'a}ximo and Moreno, Patricio and Fernandez, Paula and Dopazo, Joaquin and Paniego, Norma} }