Penicillium herquei HGN12. 1C is an endophytic fungus isolated from Dysosma difformis, a native medicinal plant found in the mountainous provinces of northern Vietnam. Previous studies have demonstrated that Penicillium herquei HGN12. 1C (Nguyen et al. , 2024), along with several other endophytic fungi such as Trametes, Purpureocillium, Aspergillus, and Ganoderma (Tran et al. , 2022), as well as the strain Fusarium proliferatum TQN5T (Nguyen et al. , 2023), are capable of synthesizing podophyllotoxin (PTOX) and its derivatives. PTOX is an important natural compound with numerous medical applications, including effective antimicrobial, antifungal, and anticancer properties (Ardalani et al. , 2017;Yu et al. , 2017). PTOX has been found in various plant species such as Podophyllum hexandrum (Anand et al. , 2022), Callitris intratropica (Wanner et al. , 2015), and Juniperus horizontalis Moench (Cantrell et al. , 2014). However, studies on PTOX in fungi remain largely unexplored, especially due to the lack of high-quality genome sequence data in fungi, which would provide valuable resources for comparative taxonomy, as well as for investigating the biosynthetic pathways and mechanisms of bioactive compounds like PTOX. Therefore, sequencing and exploring the genome of the fungal strain Penicillium herquei HGN12. 1C is considered a crucial step for genomic analysis, comparison, and the search for genes involved in the biosynthesis of PTOX and other bioactive compounds. Here, we present the complete genome dataset of Penicillium herquei HGN12. 1C to provide a valuable resource for comparative genomics and biosynthetic pathway investigations. Previous studies have established the biochemical features and synthesis pathway of podophyllotoxin in plants. In this work, we provide the high-quality genome of an endophytic fungus capable of biosynthesizing PTOX. The genome has been assembled and annotated with high quality, enabling further exploration of taxonomic, genetic, metabolic characteristics, and genes related to the biosynthetic pathways of secondary metabolites, especially PTOX, in fungi. The complete genome consists of nine contigs with a total length of 34, 960, 691 bp, an average read depth of 195x, and a GC content of 46. 38% (Figure 1). It has an N50 value of 6, 172, 464, an L50 of 3, and the largest contig measures 8, 398, 835 bp. Among these, one contig (62, 425 bp) was identified as the mitochondrial genome (Table S1, Figure S1). The nuclear genome comprises eight contigs, consisting of seven chromosome-level assemblies and one smaller unplaced scaffold (Table 1). The dataset includes BUSCO assessment results showing 98. 4% completeness metrics (1, 291 of 1, 312 core genes detected), while repetitive sequences identified using standard fungal libraries accounted for 20, 550 bp, representing 0. 06% of the total assembled genome size. It should be noted that this value likely underestimates the total repetitive content as de novo repeat identification was not performed. The dataset includes annotation files generated by the Funannotate pipeline integrating AUGUSTUS, GlimmerHMM, and SNAP predictors, with final gene counts summarized in Table 1. After removing overlapping and redundant genes, 11, 054 protein-coding genes were identified. Combined with 249 tRNA genes and 19 rRNA genes, the Penicillium herquei HGN12. 1C genome was annotated with a total of 11, 322 genes (Table 1). S1). The mitogenome encodes 44 genes, comprising 15 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, and 27 transfer RNA (tRNA) genes (Table S1). The overall base composition is 36. 9% A, 38. 0% T, 11. 6% C, and 13. 4% G, resulting in a low GC content of 25. 0%, which is consistent with other Penicillium species. The 15 PCGs include seven NADH dehydrogenase subunits (nad1-6, nad4L), one cytochrome c reductase subunit (cob), three cytochrome c oxidase subunits (cox1-3), three ATP synthase subunits (atp6, atp8, atp9), and one ribosomal protein (rps5). The total length of these PCGs is approximately 16, 500 bp, accounting for 55. 7% of the entire mitogenome. The two rRNA genes include the small subunit (rns, 16S) and the large subunit (rnl, 23S). Notably, the rnl gene is fragmented into exons by the insertion of the rps5 gene and introns. The set of 27 tRNA genes ranges in length from 71 to 86 bp, sufficient to decode all 20 standard amino acids. The complete mitogenome sequence of Penicillium herquei strain HGN12. 1C has been submitted to the GenBank database under accession number CP098395. 1. The dataset enables researchers to investigate fungal genomics, comparative analyses, and secondary metabolite biosynthesis pathways. All data files are publicly accessible and can be downloaded from the respective repositories for further analysis and validation. The endophytic fungal strain was isolated from D. difformis collected in Ha Giang Province, Vietnam, and preserved at -20°C at the Vietnam Academy of Science and Technology (VAST) -Culture Collection of Microorganisms (VCCM code: VCCM44283), Institute of Biology. The isolation and cultivation were carried out according to the method previously described by Tran et al. (2022). In this study, fungal genomic DNA was extracted using the E. Z. N. A. ® Fungal DNA Mini Kit (OMEGA, USA) following the manufacturer's instructions. The quantity and quality of the extracted DNA were assessed using a Qubit™ dsDNA HS Assay Kit (on a QUBIT 3. 0Fluorometer) and by running 0. 8% agarose gel electrophoresis, respectively. Library preparation was performed with the SMRTbell Express Template Prep Kit 2. 0 (PacBio), followed by polymerase attachment and purification using the Sequel Binding and Internal Ctrl Kit 3. 0 (PacBio). Finally, the fungal genome was sequenced using the PacBio SEQUEL platform, with the Sequel SMRT Cell 1M v3 Tray chip and the Sequel Sequencing Kit 3. 0 (PacBio). Read quality control and de novo genome assembly were performed using FastQC (http: //www. bioinformatics. babraham. ac. uk/projects/fastqc/) and the Hierarchical Genome-Assembly Process (HGAP) version 4 (Chin et al. , 2013). The completeness of the assembled genome was evaluated using BUSCO version 5. 8. 0 (Simão et al. , 2015) based on 1, 312 singlecopy ortholog groups in the fungiₒdb10 database, while assembly parameters were checked using QUAST version 5. 3. 0 (Gurevich et al. , 2013). Repeat sequences in the fungal genome were detected using RepeatMasker-4. 2. 1 (https: //www. repeatmasker. org/) (Tarailo-Graovac and Chen, 2009). Annotation and gene prediction from the assembled genome were performed using the Funannotate pipeline version 1. 8. 17 (Palmer and Stajich, 2020), which integrates multiple gene predictors including AUGUSTUS version 3. 5. 0 (Stanke and Morgenstern, 2005), GlimmerHMM version 3. 0. 4 (Majoros et al. , 2004), and the Semi-HMM-based Nucleic Acid Parser (SNAP version 2. 68. 5+ubuntu24. 04. 1) (Korf, 2004). In this pipeline, AUGUSTUS was trained using BUSCO genes with the Aspergillus nidulans species model as the closely related reference to predict gene structures with high accuracy. Additionally, AUGUSTUS gene prediction models were refined using high-quality protein sequence datasets from two closely related Penicillium species: Penicillium chrysogenum Wisconsin 54-1255 (GCF₀00226395. 1) and Penicillium rubens Wisconsin 54-1255 (GCA₀00226395. 1), which were used as training references to enhance the accuracy of protein-coding gene prediction and annotation specific to the Penicillium genus. GlimmerHMM was employed to identify genes with simple exon-intron structures and detect short genes, while SNAP was used to predict genes with complex structures and alternative splicing patterns, trained using the BUSCO Dikarya lineage dataset. Diamond version 2. 1. 11 was used to filter out low-quality gene models, while Evidence Modeler version 2. 1. 0 (EVM) (Haas et al. , 2008) was used to remove redundant genes and integrate the data from the three predictors, forming a comprehensive genome annotation. The final gene predictions were based on a consensus from all predictors to maximize accuracy and completeness. tRNA and rRNA were annotated using tRNAscan-SE version 2. 0. 12 (https: //github. com/UCSC-LoweLab/tRNAscan-SE) and Barrnap version 0. 9 (https: //github. com/tseemann/barrnap), respectively. The mitochondrial genome assembly was annotated locally using the MITOS2 pipeline (Donath et al. , 2019) within a Conda environment. To ensure high-specificity annotation, the analysis was performed using the RefSeq 89f reference database (fungi-specific) and the Mold, Protozoan, and Coelenterate Mitochondrial Code (NCBI Translation Table 4). The annotation outputs were manually curated to ensure correct nomenclature for ribosomal RNAs (16S and 23S) and to resolve gene fragmentation boundaries. Finally, the circular physical map of the mitochondrial genome was generated using OrganellarGenomeDRAW (OGDRAW) (Greiner et al. , 2019). The complete genome of strain Penicillium herquei HGN12. 1C was visualized as a Circos plot using the pyCirclize package (https: //moshi4. github. io/pyCirclize/).
Nguyen et al. (Mon,) studied this question.