Mitochondrial DNA variation in the Yemeni populations: the role of the regional based sampling and the genetic structure of the South Arabia

Katedra antropologie a genetiky člověkaDepartment of Anthropology and Human GeneticsPřírodovědecká fakultaFaculty of Scienc

Metagenomic profiling of microbial consortia

Methods of molecular biology enable studies on microbial diversity based on analysis of genes encoding processes and biochemical pathways of individual microorganisms and also complete microbial consortia. For this a crucial step was elaboration of new technologies of high-throughput DNA sequencing. These methods made it possible to advance studies of diversity from analysis of genomes of model microorganisms easily cultivated in laboratories to simple communities living in extreme environments and further to complex microbial consortia. This experimental approach is based on metagenomic analyses. Important are studies on ecosystems negatively affected by human activity where microorganisms not only survive but they can convert their metabolism to degrade compounds toxic for higher organisms. An example is bacterium Achromobacter xylosoxidans A8 isolated form soils contaminated by toxic chlorobenzoates. Sequencing and analysis of Achromobacter xylosoxidans A8 genome made it possible to study genes coding for enzymes that are involved in chlorobenzoates degradation in the context of the complete genetic background. An interesting microbial biofilm - gelatinous stalactites - was discovered in an extremely acidic environment of the abandoned mine in Zlaté Hory (the Czech Republic). It is formed by a simple..

Mitochondrial DNA variation in the Yemeni populations: the role of the regional based sampling and the genetic structure of the South Arabia

Katedra antropologie a genetiky člověkaDepartment of Anthropology and Human GeneticsPřírodovědecká fakultaFaculty of Scienc

Luscinia transcriptome reads.

A bzip2 archive containing reads in fastq fromat and sample and species assignment tables in tsv format

Rapid gene content turnover on the germline-restricted chromosome in songbirds

Abstract The germline-restricted chromosome (GRC) of songbirds represents a taxonomically widespread example of programmed DNA elimination. Despite its apparent indispensability, we still know very little about the GRC’s genetic composition, function, and evolutionary significance. Here we assemble the GRC in two closely related species, the common and thrush nightingale. In total we identify 192 genes across the two GRCs, with many of them present in multiple copies. Interestingly, the GRC appears to be under little selective pressure, with the genetic content differing dramatically between the two species and many GRC genes appearing to be pseudogenized fragments. Only one gene, cpeb1, has a complete coding region in all examined individuals of the two species and shows no copy number variation. The acquisition of this gene by the GRC corresponds with the earliest estimates of the GRC origin, making it a good candidate for the functional indispensability of the GRC in songbirds

Table S6. Oocyte analysis

For each female we indicate her biotype, origin, allozyme profile and the number of analyzed eggs

Four reference samples for exome capture and SNP calling_1.zip

To extract the contents of 'Four reference samples for exome capture and SNP calling_1.zip', first concatenate the parts 001 through 006 -- On a Unix or Linux machine, you may use the "cat" command as $ cat Four* > Four_reference_samples_for_exome_capture_and_SNP_calling.zip -- On a Windows machine, you may use the copy command, or a software such as HJSplit