Draft genome sequence of a black yeast fungus Exophiala xenobiotica isolated from La Brea Tar Pits

ABSTRACT A 30.28 Mb draft genome sequence was assembled and annotated for the melanized ascomycetous fungus Exophiala xenobiotica NRRL_64630 (Pezizomycotina; Chaetothyriales) isolated from La Brea Tar Pits, Los Angeles, California. Species identification was made by phylogenetic assessment of the Internal Transcribed Spacer. This is the first isolated fungal species from this historic space.

and tar are similar hydrocarbon substrates, asphalt is released into seeps and collected in large viscous pools while tar is man-made (2).Seeps are found in many parts of the world, from Peru's Talara Tar Pits to the La Brea Tar Pits (LBTP) (3).Culturally, the indigenous Los Angeles Native Gabrieleño-Tongva used tar as an adhesive on their boats and tools as far back as 10,000 years ago (3).
The role microbes and fungi can play in the remediation of tar-soaked soils remains an important opportunity for new technology.Fossils were collected from the LBTP in the early 1900s by UC Berkeley, LA High School, and the Southern California Academy of Sciences eventually leading to LBTP in the 1970s (4).
First, 5 mm of soil was collected from the La Brea site "Project 23" neighboring the Los Angeles County Museum of Art parking structure Box 5B (now found within the museum grounds).Cultures of fungi were obtained by plating dilutions of soils on nutrient-rich Malt Extract Yeast Extract (MEYE) media.Culturing followed steps enriching for melanized fungi and the addition of antibiotics to exclude bacteria (5).Growth of one black yeast strain was isolated and subcultured on MEYE at room temperature twice for axenic confirmation and designated TK_68.Genomic DNA was extracted from yeast colonies grown for 1 week on MEYE plates using a cetyltrimethylammonium bromide (CTAB) protocol (6).Genomic DNA was measured by Nanodrop and Qubit and diluted to ~28 ng/L.DNA sequencing libraries were prepared in the Institute for Integrative Genome Biology Genomics Core at University of California, Riverside (Riverside, CA) with Nextera DNA Flex Library kit and sequenced with 2 × 150 bp on Illumina NovoSeq 6000 in the QB3 Genomics Facility at the University of California, Berkeley.

FIG 1
FIG1 Agar culture of Exophiala xenobiotica, axenically isolated from the soil collected in box 5B-P23 C2A, and a phylogenetic tree describing our species along with respective 22 NCBI isolates.(A) Species identity was inferred from the phylogenetic tree constructed from ITS region sequences for our species from this study (in blue), 21 reference sequences from Exophiala genera, and rooted with one sequence of outgroup taxa.

TABLE 1
Strain and species designation, isolation source, sequencing read, assembly, and annotation statistics a al. 2021).