Genomic Sequencing and Functional Analysis of the Ex-Type Strain of Malbranchea zuffiana

Abstract

Malbranchea is a genus within the order Onygenales (phylum Ascomycota) that includes predominantly saprobic cosmopolitan species. Despite its ability to produce diverse secondary metabolites, no genomic data for Malbranchea spp. are currently available in databases. Therefore, in this study, we obtained, assembled, and annotated the genomic sequence of the ex-type strain of Malbranchea zuffiana (CBS 219.58). For the genomic sequencing, we employed both the Illumina and PacBio platforms, followed by hybrid assembly using MaSuRCA. Quality assessment of the assembly was performed using QUAST and BUSCO tools. Annotation was conducted using BRAKER2, and functional annotation was completed with InterProScan. The resulting genome was of high quality, with a size of 26.46 Mbp distributed across 38 contigs and a BUSCO completion rate of 95.7%, indicating excellent contiguity and assembly completeness. A total of 8248 protein-encoding genes were predicted, with functional annotations assigned to 73.9% of them. Moreover, 82 genes displayed homology with entries in the Pathogen Host Interactions (PHI) database, while 494 genes exhibited similarity to entries in the Carbohydrate-Active Enzymes (CAZymes) database. Furthermore, 30 biosynthetic gene clusters (BGCs) were identified, suggesting significant potential for the biosynthesis of diverse secondary metabolites. Comparative functional analysis with closely related species unveiled a considerable abundance of domains linked to enzymes involved in keratin degradation, alongside a restricted number of domains associated with enzymes engaged in plant cell wall degradation in all studied species of the Onygenales. This genome-based elucidation not only enhances our comprehension of the biological characteristics of M. zuffiana but also furnishes valuable insights for subsequent investigations concerning Malbranchea species and the order Onygenales.

Keywords: Malbranchea zuffiana; Onygenales; genes; genome assembly; keratin degradation; phylogenomics; proteins.

Figure 1

Functional annotation of CBS 219.52. A—RNA processing and modification; B—chromatin structure and dynamics; C—energy production and conversion; D—cell cycle control, cell division, chromosome partitioning; E—amino acid transport and metabolism; F—nucleotide transport and metabolism; G—carbohydrate transport and metabolism; H—coenzyme transport and metabolism; I—lipid transport and metabolism; J—translation, ribosomal structure, and biogenesis; K—transcription; L—replication, recombination, and repair; M—cell wall/membrane/envelope biogenesis; N—cell motility; O—post-translational modification, protein turnover, chaperones; P—inorganic ion transport and metabolism; Q—secondary metabolite biosynthesis, transport, and catabolism; R—general function prediction only; S—function unknown; T—signal transduction mechanisms; U—intracellular trafficking, secretion, and vesicular transport; V—defense mechanisms; X—mobilome: prophages, transposons; Z—cytoskeleton.

Figure 2

Most prevalent CAZyme families (in number of genes) identified per class in the strain CBS 219.58.

Figure 3

Sequence alignment of amino acid sequences of malA protein from Malbranchea aurantiaca RRC1813 and Malbranchea zuffiana CBS 219.58.

Figure 4

Maximum likelihood (ML) phylogenetic tree of fifty concatenated single-copy orthologous using RAxML with the JTT+I+G4+F model and 1000 ultrafast bootstrap replicates.