Simulation Modeling

Simulation Modelin

STRUCTURE

STRUCTUR

USA_map

USA_ma

README

READM

Metadata_for_specimens

Metadata_for_specimen

Cline_analysis

Cline_analysi

RAD data processing files

RAD data processing file

Whole-Genome Shotgun Sequencing of Two β‑Proteobacterial Species in Search of the Bulgecin Biosynthetic Cluster

We have produced draft whole-genome sequences for two bacterial strains reported to produce the bulgecins as well as NRPS-derived monobactam β-lactam antibiotics. We propose classification of ATCC 31363 as <i>Paraburkholderia acidophila.</i> We further reaffirm that ATCC 31433 (<i>Burkholderia ubonensis subsp. mesacidophila</i>) is a taxonomically distinct producer of bulgecins with notable gene regions shared with <i>Paraburkholderia acidophila.</i> We use RAST multiple-gene comparison and MASH distancing with published genomes to order the draft contigs and identify unique gene regions for characterization. Forty-eight natural-product gene clusters are presented from PATRIC (RASTtk) and antiSMASH annotations. We present evidence that the 10 genes that follow the sulfazecin and isosulfazecin pathways in both species are likely involved in bulgecin A biosynthesis

MAF TBA genome alignment of reference assemblies from the An gambiae complex

Whole genome alignment of the of the reference assemblies from the members of the Anopheles gambiae species complex (AGC). The reference assemblies are mostly derived from colonized anopheline mosquitoes. This multiple genome alignment, in MAF format, include the new reference assemblies from six genomes of the AGC, plus the assemblies of An. gambiae PEST, An. gambiae Pimperena S, An. coluzzii, and two outgroup Pyretophorus species (An. christyi and An epiroticus). MAF for each chromosome arm are provided. See the SOM, section S1 for a full description of the methodology

VCF files of field individual samples from the AGC complex

This is a tar archive including the VCF files (one per chromosome arm) for the 69 individual mosquito samples sequenced at low-depth that passed QC filters, plus 2 outgroups (see SOM, section 2.2)