A database of amphibian karyotypes.

One of the first characteristics that we learn about the genome of many species is the number of chromosomes it is divided among. Despite this, many questions regarding the evolution of chromosome number remain unanswered. Testing hypotheses of chromosome number evolution using comparative approaches requires trait data to be readily accessible and associated with currently accepted taxonomy. The lack of accessible karyotype data that can be linked to phylogenies has limited the application of comparative approaches that could help us understand the evolution of genome structure. Furthermore, for taxonomists, the significance of new karyotype data can only be determined with reference to records for other species. Here, we describe a curated database (karyotype.org) developed to facilitate access to chromosome number and sex chromosome system data for amphibians. The open web interface for this database allows users to generate customized exploratory plots and tables of selected clades, as well as downloading CSV files for offline analyses.

Retrogene survival is not impacted by linkage relationships.

In retrogene evolution, the out-of-the-X pattern is the retroduplication of X-linked housekeeping genes to autosomes, hypothesized to be driven by meiotic sex chromosome inactivation during spermatogenesis. This pattern suggests that some retrogene survival is driven by selection on X-linkage. We asked if selection on linkage constitutes an important evolutionary force in retrogene survival, including for autosomal parents. Specifically, is there a correlation between retrogene survival and changes in linkage with parental gene networks? To answer this question, we compiled data on retrogenes in both Homo sapiens and Drosophila melanogaster and using Monte Carlo methods, we tested whether retrogenes exhibit significantly different linkage relationships than expected under a null assumption of uniform distribution in the genome. Overall, after excluding genes involved in the out-of-the-X pattern, no general pattern was found associating genetic linkage and retrogene survival. This demonstrates that selection on linkage may not represent an overarching force in retrogene survival. However, it remains possible that this type of selection still influences the survival of specific retrogenes.

Complete Genome Sequence of Stenotrophomonas maltophilia Podophage Pepon.

Stenotrophomonas maltophilia is an opportunistic bacterium that is commonly associated with respiratory infections in immunocompromised patients, including cystic fibrosis patients. In this report, we introduce the complete genome sequence of S. maltophilia podophage Pepon, which is a T7-like phage closely related to the previously reported phage Ponderosa.

Complete Genome Sequence of Klebsiella pneumoniae Podophage Pone.

Klebsiella pneumoniae is a Gram-negative pathogen that has become increasingly antibiotic resistant. Phage therapy is potentially a useful approach to controlling this pathogen. Here, we present the genome sequence of the phiKMV-like K. pneumoniae podophage Pone.

Mode and Tempo of Microsatellite Evolution across 300 Million Years of Insect Evolution.

Microsatellites are short, repetitive DNA sequences that can rapidly expand and contract due to slippage during DNA replication. Despite their impacts on transcription, genome structure, and disease, relatively little is known about the evolutionary dynamics of these short sequences across long evolutionary periods. To address this gap in our knowledge, we performed comparative analyses of 304 available insect genomes. We investigated the impact of sequence assembly methods and assembly quality on the inference of microsatellite content, and we explored the influence of chromosome type and number on the tempo and mode of microsatellite evolution across one of the most speciose clades on the planet. Diploid chromosome number had no impact on the rate of microsatellite evolution or the amount of microsatellite content in genomes. We found that centromere type (holocentric or monocentric) is not associated with a difference in the amount of microsatellite content; however, in those species with monocentric chromosomes, microsatellite content tends to evolve faster than in species with holocentric chromosomes.

micRocounter: Microsatellite Characterization in Genome Assemblies.

Microsatellites are repetitive DNA sequences usually found in non-coding regions of the genome. Their quantification and analysis have applications in fields from population genetics to evolutionary biology. As genome assemblies become commonplace, the need for software that can facilitate analyses has never been greater. In particular, R packages that can analyze genomic data are particularly important since this is one of the most popular software environments for biologists. We created an R package, micRocounter, to quantify microsatellites. We have optimized our package for speed, accessibility, and portability, making the automated analysis of large genomic data sets feasible. Computationally intensive algorithms were built in C++ to increase speed. Tests using benchmark datasets show a 200-fold improvement in speed over existing software. A moderately sized genome of 500 Mb can be processed in under 50 sec. Results are output as an object in R increasing accessibility and flexibility for practitioners.