Draft Genome Sequence of Byssochlamys sp. Isolate BYSS01, a Filamentous Fungus Adapted to the Fuel Environment.

Byssochlamys sp. isolate BYSS01 (anamorph, Paecilomyces sp.), which was isolated from jet fuel, is highly adapted to grow in hydrocarbons, having predicted genes involved in degradation of n-alkanes, branched alkanes, and aromatic compounds. The draft genome size is estimated at 29 Mb, containing 8,509 proteins.

GENOME ANNOUNCEMENT

The filamentous fungus Byssochlamys sp. isolate BYSS01 was recovered from Jet A fuel and identified based on morphological characteristics and sequence similarity (94%) to the 18S rRNA gene of Byssochlamys fulva. Byssochlamys sp. (teleomorph) belongs to the genus Paecilomyces, which comprises formaldehyde-resistant and heat-resistant food spoilage fungi (1–4). It was confirmed that the BYSS01 isolate metabolizes alkanes and aromatic hydrocarbons efficiently; this is the first report of a Byssochlamys species adapted to kerosene fuel. Therefore, to gain a deeper understanding of the adaptive mechanisms in isolate BYSS01, its genome was sequenced.

A whole-genome shotgun (WGS) approach on a HiSeq 2000 platform was used to generate TruSeq paired-end libraries, resulting in 47,245,046 paired-end reads (150× sequence coverage), with a read length of 100 bp (∼4.72 Gb). The raw sequences were trimmed using Trimmomatic (5), and reads shorter than 50 bp were removed. The sequence reads were de novo assembled with SPAdes software (6), generating a draft assembly comprised of 394 scaffolds greater than 500 bp, with an N50 value of 463,366, an L50 value of 20 scaffolds, and a G+C content of 49.3%. BUSCO (7) identified 1,425 out of 1,438 ultraconserved eukaryotic genes in Byssochlamys sp. isolate BYSS01 (99.1%). Repetitive sequences (3.09%) were masked using the RepeatMasker program (8), and the masked genome was used for gene prediction by Augustus 2.5.5 (9) with an option set for Aspergillus oryzae parameters, resulting in 8,509 protein-encoding genes. The average gene density is one gene per 1.67 kb, with an average of 3.45 exons per gene. Approximately 21,244 introns, ranging from 34 to 6,725 bp in length, are present in the genome, with 140 bp as an average intron size and 2.5 as the average number of introns per open reading frame.

A BLASTP search against UniProt and the annotated genomes of Hormoconis resinae, Aspergillus fumigatus, and Byssochlamys spectabilis (4) revealed significant matches (E value, 1 × 10−5) for 6,646, 7,578, 7,808, and 7,508 proteins, respectively. Using the Carbohydrate-Active Enzymes (CAZy) database (10), a total of 334 fungal enzymes involved in carbohydrate metabolism and assimilation were identified (E value, 1 × 10−4), including glycoside hydrolases (n = 113), carbohydrate esterases (n = 77), glycosyl transferases (n = 76), enzymes involved in auxiliary activities (n = 46), carbohydrate-binding modules (n = 21), and polysaccharide lyases (n = 1). The Transporter Classification Database (TCDB; http://www.tcdb.org/) identified 283 major facilitator superfamily (MSF) transporters with an E value of 1 × 10−5, reflecting the ability of the BYSS01 isolate to extrude toxic compounds; efflux pumps have been shown to aid in adaptation to hydrocarbons in bacteria (11, 12).

The Kyoto Encyclopedia of Genes and Genomes (KEGG) database and BLASTP searches identified important proteins involved in carbon and energy metabolism (n = 49). In agreement with the ability of BYSS01 to grow in fuel, genes involved in the degradation of aromatics and n-alkanes, including cytochrome P450 alkane hydroxylase, cytochrome P450 monooxygenase, aromatic ring-opening dioxygenase, salicylate hydroxylase, 2-haloacid dehalogenase, benzyl alcohol dehydrogenase, benzoate 4-monooxygenase, and dimethyl-sulfide monooxygenase, were found. This genome sequence will help to understand the adaptive mechanisms employed by fungi to survive and proliferate in hydrocarbon-based fuels.

Accession number(s).

This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number NIXA00000000.