The hidden elasticity of avian and mammalian genomes, bioRxiv, 2016-10-17

AbstractGenome size in mammals and birds shows remarkably little interspecific variation compared to other taxa. Yet, genome sequencing has revealed that many mammal and bird lineages have experienced differential rates of transposable element (TE) accumulation, which would be predicted to cause substantial variation in genome size between species. Thus, we hypothesize that there has been co-variation between the amount of DNA gained by transposition and lost by deletion during mammal and avian evolution, resulting in genome size homeostasis. To test this model, we develop a computational pipeline to quantify the amount of DNA gained by TE expansion and lost by deletion over the last 100 million years (My) in the lineages of 10 species of eutherian mammals and 24 species of birds. The results reveal extensive variation in the amount of DNA gained via lineage-specific transposition, but that DNA loss counteracted this expansion to various extent across lineages. Our analysis of the rate and size spectrum of deletion events implies that DNA removal in both mammals and birds has proceeded mostly through large segmental deletions (>10 kb). These findings support a unified ‘accordion’ model of genome size evolution in eukaryotes whereby DNA loss counteracting TE expansion is a major determinant of genome size. Furthermore, we propose that extensive DNA loss, and not necessarily a dearth of TE activity, has been the primary force maintaining the greater genomic compaction of flying birds and bats relative to their flightless relatives.

biorxiv evolutionary-biology 0-100-users 2016

Nanopore DNA Sequencing and Genome Assembly on the International Space Station, bioRxiv, 2016-09-28

AbstractThe emergence of nanopore-based sequencers greatly expands the reach of sequencing into low-resource field environments, enabling in situ molecular analysis. In this work, we evaluated the performance of the MinION DNA sequencer (Oxford Nanopore Technologies) in-flight on the International Space Station (ISS), and benchmarked its performance off-Earth against the MinION, Illumina MiSeq, and PacBio RS II sequencing platforms in terrestrial laboratories. Samples contained mixtures of genomic DNA extracted from lambda bacteriophage, Escherichia coli (strain K12) and Mus musculus (BALBc). The in-flight sequencing experiments generated more than 80,000 total reads with mean 2D accuracies of 85 – 90%, mean 1D accuracies of 75 – 80%, and median read lengths of approximately 6,000 bases. We were able to construct directed assemblies of the ~4.7 Mb E. coli genome, ~48.5 kb lambda genome, and a representative M. musculus sequence (the ~16.3 kb mitochondrial genome), at 100%, 100%, and 96.7% pairwise identity, respectively, and de novo assemblies of the lambda and E. coli genomes generated solely from nanopore reads yielded 100% and 99.8% genome coverage, respectively, at 100% and 98.5% pairwise identity. Across all surveyed metrics (base quality, throughput, staysbase, skipsbase), no observable decrease in MinION performance was observed while sequencing DNA in space. Simulated runs of in-flight nanopore data using an automated bioinformatic pipeline and cloud or laptop based genomic assembly demonstrated the feasibility of real-time sequencing analysis and direct microbial identification in space. Applications of sequencing for space exploration include infectious disease diagnosis, environmental monitoring, evaluating biological responses to spaceflight, and even potentially the detection of extraterrestrial life on other planetary bodies.

biorxiv genomics 100-200-users 2016

 

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