First Draft Genome Sequence of the Pathogenic Fungus Lomentospora prolificans (Formerly Scedosporium prolificans)

Ruibang Luo; Aleksey Zimin; Rachael Workman; Yunfan Fan; Geo Pertea; Nina Grossman; Maggie P Wear; Bei Jia; Heather Miller; Arturo Casadevall; Winston Timp; Sean X Zhang; Steven L Salzberg

doi:10.1534/g3.117.300107

First Draft Genome Sequence of the Pathogenic Fungus Lomentospora prolificans (Formerly Scedosporium prolificans)

G3 (Bethesda). 2017 Nov 6;7(11):3831-3836. doi: 10.1534/g3.117.300107.

Authors

Ruibang Luo^{1

2}, Aleksey Zimin^{1

3

4}, Rachael Workman⁴, Yunfan Fan⁴, Geo Pertea¹, Nina Grossman⁵, Maggie P Wear⁵, Bei Jia⁶, Heather Miller⁶, Arturo Casadevall⁵, Winston Timp⁴, Sean X Zhang^{7

6

8}, Steven L Salzberg^{7

2

4

9}

Affiliations

¹ Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205.
² Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218.
³ Institute for Physical Sciences and Technology, University of Maryland, College Park, Maryland 20742.
⁴ Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205.
⁵ Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205.
⁶ Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287.
⁷ Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 [email protected] [email protected].
⁸ Microbiology Laboratory, Johns Hopkins Hospital, Baltimore, Maryland 21287.
⁹ Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205.

Abstract

Here we describe the sequencing and assembly of the pathogenic fungus Lomentospora prolificans using a combination of short, highly accurate Illumina reads and additional coverage in very long Oxford Nanopore reads. The resulting assembly is highly contiguous, containing a total of 37,627,092 bp with over 98% of the sequence in just 26 scaffolds. Annotation identified 8896 protein-coding genes. Pulsed-field gel analysis suggests that this organism contains at least 7 and possibly 11 chromosomes, the two longest of which have sizes corresponding closely to the sizes of the longest scaffolds, at 6.6 and 5.7 Mb.

Keywords: fungal genomics; genome assembly; nanopore sequencing; pathogen genomics.

MeSH terms

Fungal Proteins / genetics
Genome, Fungal*
Molecular Sequence Annotation*
Scedosporium / genetics*
Whole Genome Sequencing

Substances

Fungal Proteins

Abstract

MeSH terms

Substances

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