Genomic Analysis of Talaromyces verruculosus SJ9: An Efficient Tetracycline-, Enrofloxacin-, and Tylosin-Degrading Fungus

Abstract

Background/objectives: Many fungi related to Talaromyces verruculosus can degrade a wide range of pollutants and are widely distributed globally. T. verruculosus SJ9 was enriched from fresh strawberry inter-root soil to yield fungi capable of degrading tetracycline, enrofloxacin, and tylosin.

Methods: T. verruculosus SJ9 genome was sequenced, assembled, and annotated in this study utilizing bioinformatics software, PacBio, and the Illumina NovaSeq PE150 technology.

Results: The genome size is 40.6 Mb, the N50 scaffold size is 4,534,389 bp, and the predicted number of coding genes is 8171. The T. verruculosus TS63-9 genome has the highest resemblance to the T. verruculosus SJ9 genome, according to a comparative genomic analysis of seven species. In addition, we annotated many genes encoding antibiotic-degrading enzymes in T. verruculosus SJ9 through genomic databases, which also provided strong evidence for its ability to degrade antibiotics.

Conclusions: Through the correlation analysis of the whole-genome data of T. verruculosus SJ9, we identified a number of genes capable of encoding antibiotic-degrading enzymes in its gene function annotation database. These antibiotic-related enzymes provide some evidence that T. verruculosus SJ9 can degrade fluoroquinolone antibiotics, tetracycline antibiotics, and macrolide antibiotics. In summary, the complete genome sequence of T. verruculosus SJ9 has now been published, and this resource constitutes a significant dataset that will inform forthcoming transcriptomic, proteomic, and metabolic investigations of this fungal species. In addition, genomic studies of other filamentous fungi can utilize it as a reference. Thanks to the discoveries made in this study, the future application of this fungus in industrial production will be more rapid.

Keywords: T. verruculosus; antibiotic degradation; functional annotation; whole-genome sequencing.

Figure 1

Morphological characteristics of T. verruculosus SJ9. (a) Colony morphology of strain SJ9 on PDA plate. (b) Identification of strain SJ9 based on phylogenomic analyses. The phylogenetic tree reveals that strain SJ9 is closely related to T. verruculosus. The red star indicates the SJ9 strain.

Figure 2

Clusters of orthologous groups of proteins (KOG) function classification of proteins in T. verruculosus SJ9. The x-axis shows the function of the class and the y-axis shows the number of matching genes. KOG functional classification is divided into 26 groups classified as A–Z, and each group has its own function. Different colors with their names and number of genes are also mentioned in the figure.

Figure 3

Gene Ontology (GO) functional annotation of T. verruculosus SJ9. (a) Biological Process: Biological processes accomplished through multiple molecular activities. (b) Cellular Component: The location of the cellular structure in which the gene product performs its function. (c) Molecular Function: Activity of individual gene products (including proteins and RNA) or complexes of multiple gene products at the molecular level.

Figure 4

Kyoto Encyclopedia of Genes and Genomes (KEGG) functional annotation of the T. verruculosus SJ9 genome. The figure indicates the number of genes in the major categories and their names and associated subcategory divisions. The x-axis indicates the scale from a few genes to 1000 genes. KEGG Functions The annotations are grouped into six major categories: cellular processes, environmental information processing, genetic information, human diseases, metabolism, and organismal systems. There are 40 subcategories. Each subcategory is represented by a different color.

Figure 5

The Non-Redundant Protein Database functional annotation of the T. verruculosus SJ9 genome. In this figure, the x-axis represents the top 20 of 1–20 species, while the y-axis represents the number of matching genes between species on a scale of up to 2500. NR annotations were split into 20 classes. The different colors depict the top 20 species, their names, and values.

Figure 6

Core and pan gene orthological petals diagram of GXJ.SJ9, 11CN.20.091, W13939, ATCC.10500, CIB, IBT.11181, PMI.201, and TS63.9.

Figure 7

Species evolutionary analysis of SJ9 (a) T. verruculosus TS63-9, T. marneffei 11CN-20-091, T. rugulosus W13939, T. stipitatus ATCC 10500, T. amestolkiae CIB, T. atroroseus IBT 11181, T. proteolyticus PMI_201, and T. verruculosus GXJ-SJ9 phylogenetic tree among species. (b) Plot of ANI correlation coefficients for SJ9 and seven other reference genomes.