White-nose syndrome has recently emerged as one of the most devastating

White-nose syndrome has recently emerged as one of the most devastating wildlife diseases recorded, causing common mortality in numerous bat species throughout eastern North America. hibernacula (4). The growth of this fungus on bats and subsequent invasion of epidermal tissues can cause a cascade of deleterious physiological changes resulting in high mortality rates (5, 6). The fungus is usually common in Eurasia (7,C9), and initial genetic and experimental results suggest that it was recently launched to GW1929 IC50 North America (10, 11). Critically missing, however, are detailed genomic analyses of to shed light on the origins, development, global dispersal, and pathogenicity of this fungus. Initial genome sequencing efforts for used 454 and Illumina platforms; however, unresolved repeat regions in the genome resulted in fragmented draft assemblies (12). Therefore, to generate a high-quality contiguous assembly of the genome, we utilized a combination of data from PacBio SMRT reads, Illumina MiSeq 250-bp paired-end reads (SRR1952982), 8-kb 454 jumping libraries (SRP001346), and end sequences from an unbiased random shear bacterial artificial chromosome (BAC) library with an average place size of 100?kb (13). The PacBio reads were assembled with the PacBio SMRT version 2.2 analysis pipeline (14) and yielded 153 contigs. Using Illumina 250-bp paired-end MiSeq reads quality-trimmed to Q30 with ea-utils version 1.1.2 (15) and error-corrected with Hammer (16), 454 8-kb jumping reads, and >100-kb BAC library end sequences, the contigs were extended and scaffolded with SSPACE version 3.0 (17); gaps were removed with GapFiller version 1.10 (18). Twenty iterations of SSPACE/GapFiller were followed by Pilon version 1.8 (19) to correct local misalignments and indels from your assembly, resulting in 96 scaffolds. A self-query of the improved scaffolds GW1929 IC50 with the NUCmer application of MUMmer version 3.23 (20) indicated that the smaller scaffolds (<42,633?bp) and a few larger scaffolds were complete or nearly complete duplications of the sequence in other scaffolds. Thirteen scaffolds, which experienced a >95% identity over 95% of their length with a larger scaffold in the assembly, were removed. The final assembly contains 83 scaffolds, is usually 35.818201 Mb in size, has an (AEFC01: 1,847 scaffolds, 30.6849?Mb, genome contains 38.17% repetitive sequence elements (RepeatModeler version 1.08, RepeatMasker version 4.05, http://www.repeatmasker.org), which required a combination of long-read and large-insert sequencing technologies to scaffold. The nearly total assembly presented here should serve as a valuable resource to facilitate fungal disease research. Nucleotide sequence accession figures. This whole-genome shotgun project has been deposited in DDBJ/ ENA/GenBank under the accession number “type”:”entrez-protein”,”attrs”:”text”:”LAJJ00000000″,”term_id”:”1026911300″LAJJ00000000. The version described in this paper is the first version, “type”:”entrez-nucleotide”,”attrs”:”text”:”LAJJ01000000″,”term_id”:”1026910631″LAJJ01000000. ACKNOWLEDGMENTS We would like to thank Katy Parise for preparing the Rabbit polyclonal to SRP06013 DNA sequenced in this study. Use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government. Notes This paper was supported by the following grant(s): National Science Foundation (NSF) DEB-1336290 to . DOI | U.S. Geological Survey (USGS) to . DOI | U.S. Fish and Wildlife Support (USFWS) to . Footnotes Citation Drees KP, Palmer JM, Sebra R, Lorch GW1929 IC50 JM, Chen C, Wu C-C, Bok JW, Keller NP, Blehert DS, Cuomo CA, Lindner DL, Foster JT. 2016. Use of multiple sequencing technologies to produce a high-quality genome of the fungus causes white-nose syndrome. Nature 480:376C378. doi:10.1038/nature10590. [PubMed] [Cross Ref] 3. Blehert DS, Hicks AC, Behr M, Meteyer CU, Berlowski-Zier BM, Buckles EL, Coleman JTH, Darling SR, Gargas A, Niver R, Okoniewski JC, Rudd RJ, Stone WB. 2009. Bat white-nose syndrome: an emerging fungal pathogen? Science 323:227. doi:10.1126/science.1163874. [PubMed] [Cross Ref] 4. Verant ML, Boyles JG, Waldrep W, Wibbelt G, Blehert DS. 2012. Temperature-dependent growth of contamination tolerated in Europe and palearctic GW1929 IC50 Asia but not in North America. Sci Rep 6:19829. doi:10.1038/srep19829. [PMC free article] [PubMed] [Cross Ref] 10. Leopardi S, Blake D, Puechmaille SJ. 2015. White-nose syndrome fungus launched from Europe to North America. Curr Biol 25:R217CR219. doi:10.1016/j.cub.2015.01.047. [PubMed] [Cross Ref] 11. Warnecke L, Turner JM, Bollinger TK, Lorch JM, Misra V, Cryan PM, Wibbelt G, Blehert DS, Willis CKR. 2012. Inoculation of bats with European supports the novel pathogen hypothesis for the origin of white-nose syndrome. Proc Natl Acad.