Bidirectional best hit r-window gene clusters

<p>Abstract</p> <p>Background</p> <p><it>Conserved gene clusters </it>are groups of genes that are located close to one another in the genomes of several species. They tend to code for proteins that have a functional interaction. The identification of conserved gene clusters is an important step towards understanding genome evolution and predicting gene function.</p> <p>Results</p> <p>In this paper, we propose a novel pairwise gene cluster model that combines the notion of bidirectional best hits with the <it>r</it>-window model introduced in 2003 by Durand and Sankoff. The bidirectional best hit (BBH) constraint removes the need to specify the minimum number of shared genes in the <it>r</it>-window model and improves the relevance of the results. We design a subquadratic time algorithm to compute the set of BBH <it>r</it>-window gene clusters efficiently.</p> <p>Conclusion</p> <p>We apply our cluster model to the comparative analysis of <it>E. coli </it>K-12 and <it>B. subtilis </it>and perform an extensive comparison between our new model and the gene teams model developed by Bergeron <it>et al</it>. As compared to the gene teams model, our new cluster model has a slightly lower recall but a higher precision at all levels of recall when the results were ranked using statistical tests. An analysis of the most significant BBH <it>r</it>-window gene cluster show that they correspond to known operons.</p

Conserved gene cluster discovery and applications in comparative genomics

Ph.DDOCTOR OF PHILOSOPH

Identification and annotation of conserved promoters and macrophage-expressed genes in the pig genome.

BACKGROUND: The FANTOM5 consortium used Cap Analysis of Gene Expression (CAGE) tag sequencing to produce a comprehensive atlas of promoters and enhancers within the human and mouse genomes. We reasoned that the mapping of these regulatory elements to the pig genome could provide useful annotation and evidence to support assignment of orthology. RESULTS: For human transcription start sites (TSS) associated with annotated human-mouse orthologs, 17% mapped to the pig genome but not to the mouse, 10% mapped only to the mouse, and 55% mapped to both pig and mouse. Around 17% did not map to either species. The mapping percentages were lower where there was not clear orthology relationship, but in every case, mapping to pig was greater than to mouse, and the degree of homology was also greater. Combined mapping of mouse and human CAGE-defined promoters identified at least one putative conserved TSS for >16,000 protein-coding genes. About 54% of the predicted locations of regulatory elements in the pig genome were supported by CAGE and/or RNA-Seq analysis from pig macrophages. CONCLUSIONS: Comparative mapping of promoters and enhancers from humans and mice can provide useful preliminary annotation of other animal genomes. The data also confirm extensive gain and loss of regulatory elements between species, and the likelihood that pigs provide a better model than mice for human gene regulation and function

Clades of huge phages from across Earth's ecosystems.

Bacteriophages typically have small genomes1 and depend on their bacterial hosts for replication2. Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200&nbsp;kilobases (kb), including a genome of 735&nbsp;kb, which is-to our knowledge-the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR-Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR-Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR-Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth's ecosystems

Comparative pan-genome analysis of Piscirickettsia salmonis reveals genomic divergences within genogroups

Indexación: Scopus.Piscirickettsia salmonis is the etiological agent of salmonid rickettsial septicemia, a disease that seriously affects the salmonid industry. Despite efforts to genomically characterize P. salmonis, functional information on the life cycle, pathogenesis mechanisms, diagnosis, treatment, and control of this fish pathogen remain lacking. To address this knowledge gap, the present study conducted an in silico pan-genome analysis of 19 P. salmonis strains from distinct geographic locations and genogroups. Results revealed an expected open pan-genome of 3,463 genes and a core-genome of 1,732 genes. Two marked genogroups were identified, as confirmed by phylogenetic and phylogenomic relationships to the LF-89 and EM-90 reference strains, as well as by assessments of genomic structures. Different structural configurations were found for the six identified copies of the ribosomal operon in the P. salmonis genome, indicating translocation throughout the genetic material. Chromosomal divergences in genomic localization and quantity of genetic cassettes were also found for the Dot/Icm type IVB secretion system. To determine divergences between core-genomes, additional pan-genome descriptions were compiled for the so-termed LF and EM genogroups. Open pan-genomes composed of 2,924 and 2,778 genes and core-genomes composed of 2,170 and 2,228 genes were respectively found for the LF and EM genogroups. The core-genomes were functionally annotated using the Gene Ontology, KEGG, and Virulence Factor databases, revealing the presence of several shared groups of genes related to basic function of intracellular survival and bacterial pathogenesis. Additionally, the specific pan-genomes for the LF and EM genogroups were defined, resulting in the identification of 148 and 273 exclusive proteins, respectively. Notably, specific virulence factors linked to adherence, colonization, invasion factors, and endotoxins were established. The obtained data suggest that these genes could be directly associated with inter-genogroup differences in pathogenesis and host-pathogen interactions, information that could be useful in designing novel strategies for diagnosing and controlling P. salmonis infection. © 2017 Nourdin-Galindo, Sánchez, Molina, Espinoza-Rojas, Oliver, Ruiz, Vargas-Chacoff, Cárcamo, Figueroa, Mancilla, Maracaja-Coutinho and Yañez.https://www.frontiersin.org/articles/10.3389/fcimb.2017.00459/ful

EDGAR: A software framework for the comparative analysis of prokaryotic genomes

Blom J, Albaum S, Doppmeier D, et al. EDGAR: a software framework for the comparative analysis of prokaryotic genomes. BMC Bioinformatics. 2009;10(1): 154.Background:The introduction of next generation sequencing approaches has caused a rapid increase in the number of completely sequenced genomes. As one result of this development, it is now feasible to analyze large groups of related genomes in a comparative approach. A main task in comparative genomics is the identification of orthologous genes in different genomes and the classification of genes as core genes or singletons. Results: To support these studies EDGAR – ''Efficient Database framework for comparative Genome Analyses using BLAST score Ratios'' – was developed. EDGAR is designed to automatically perform genome comparisons in a high throughput approach. Comparative analyses for 582 genomes across 75 genus groups taken from the NCBI genomes database were conducted with the software and the results were integrated into an underlying database. To demonstrate a specific application case, we analyzed ten genomes of the bacterial genus Xanthomonas, for which phylogenetic studies were awkward due to divergent taxonomic systems. The resultant phylogeny EDGAR provided was consistent with outcomes from traditional approaches performed recently and moreover, it was possible to root each strain with unprecedented accuracy. Conclusion: EDGAR provides novel analysis features and significantly simplifies the comparative analysis of related genomes. The software supports a quick survey of evolutionary relationships and simplifies the process of obtaining new biological insights into the differential gene content of kindred genomes. Visualization features, like synteny plots or Venn diagrams, are offered to the scientific community through a web-based and therefore platform independent user interface http://edgar.cebitec.uni-bielefeld.de webcite, where the precomputed data sets can be browsed

Long-term balancing selection drives evolution of immunity genes in Capsella.

Genetic drift is expected to remove polymorphism from populations over long periods of time, with the rate of polymorphism loss being accelerated when species experience strong reductions in population size. Adaptive forces that maintain genetic variation in populations, or balancing selection, might counteract this process. To understand the extent to which natural selection can drive the retention of genetic diversity, we document genomic variability after two parallel species-wide bottlenecks in the genus Capsella. We find that ancestral variation preferentially persists at immunity related loci, and that the same collection of alleles has been maintained in different lineages that have been separated for several million years. By reconstructing the evolution of the disease-related locus MLO2b, we find that divergence between ancient haplotypes can be obscured by referenced based re-sequencing methods, and that trans-specific alleles can encode substantially diverged protein sequences. Our data point to long-term balancing selection as an important factor shaping the genetics of immune systems in plants and as the predominant driver of genomic variability after a population bottleneck

De novo transcriptome sequencing in Bixa orellana to identify genes involved in methylerythritol phosphate, carotenoid and bixin biosynthesis.

BackgroundBixin or annatto is a commercially important natural orange-red pigment derived from lycopene that is produced and stored in seeds of Bixa orellana L. An enzymatic pathway for bixin biosynthesis was inferred from homology of putative proteins encoded by differentially expressed seed cDNAs. Some activities were later validated in a heterologous system. Nevertheless, much of the pathway remains to be clarified. For example, it is essential to identify the methylerythritol phosphate (MEP) and carotenoid pathways genes.ResultsIn order to investigate the MEP, carotenoid, and bixin pathways genes, total RNA from young leaves and two different developmental stages of seeds from B. orellana were used for the construction of indexed mRNA libraries, sequenced on the Illumina HiSeq 2500 platform and assembled de novo using Velvet, CLC Genomics Workbench and CAP3 software. A total of 52,549 contigs were obtained with average length of 1,924&nbsp;bp. Two phylogenetic analyses of inferred proteins, in one case encoded by thirteen general, single-copy cDNAs, in the other from carotenoid and MEP cDNAs, indicated that B. orellana is closely related to sister Malvales species cacao and cotton. Using homology, we identified 7 and 14 core gene products from the MEP and carotenoid pathways, respectively. Surprisingly, previously defined bixin pathway cDNAs were not present in our transcriptome. Here we propose a new set of gene products involved in bixin pathway.ConclusionThe identification and qRT-PCR quantification of cDNAs involved in annatto production suggest a hypothetical model for bixin biosynthesis that involve coordinated activation of some MEP, carotenoid and bixin pathway genes. These findings provide a better understanding of the mechanisms regulating these pathways and will facilitate the genetic improvement of B. orellana