Genome assembly and geospatial phylogenomics of the bed bug Cimex lectularius.

The common bed bug (Cimex lectularius) has been a persistent pest of humans for thousands of years, yet the genetic basis of the bed bug's basic biology and adaptation to dense human environments is largely unknown. Here we report the assembly, annotation and phylogenetic mapping of the 697.9-Mb Cimex lectularius genome, with an N50 of 971 kb, using both long and short read technologies.

Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics.

The panoply of microorganisms and other species present in our environment influence human health and disease, especially in cities, but have not been profiled with metagenomics at a city-wide scale. We sequenced DNA from surfaces across the entire New York City (NYC) subway system, the Gowanus Canal, and public parks. Nearly half of the DNA (48%) does not match any known organism; identified organisms spanned 1,688 bacterial, viral, archaeal, and eukaryotic taxa, which were enriched for harmless genera associated with skin (e.

Fungal high-throughput taxonomic identification tool for use with next-generation sequencing (FHiTINGS).

Improvements in DNA sequencing technology provide unprecedented opportunities to explore fungal diversity, but also present challenges in data analysis due to the large number of sequences generated. Here, we describe an open source software program "FHiTINGS" that utilizes the output of a BLASTn (blastall) search to rapidly identify, classify, and parse internal transcribed spacer (ITS) DNA sequences produced in fungal ecology studies that utilize next-generation DNA sequencing. This tool was designed for use with 454 pyrosequencing and is also appropriate for use with any sequencing platform that allows for BLAST searches against the indicated ITS database.

Optimization of de novo transcriptome assembly from high-throughput short read sequencing data improves functional annotation for non-model organisms.

Background: The k-mer hash length is a key factor affecting the output of de novo transcriptome assembly packages using de Bruijn graph algorithms. Assemblies constructed with varying single k-mer choices might result in the loss of unique contiguous sequences (contigs) and relevant biological information. A common solution to this problem is the clustering of single k-mer assemblies.

A genome sequence resource for the aye-aye (Daubentonia madagascariensis), a nocturnal lemur from Madagascar.

We present a high-coverage draft genome assembly of the aye-aye (Daubentonia madagascariensis), a highly unusual nocturnal primate from Madagascar. Our assembly totals ~3.0 billion bp (3.