A highly quality genome sequence of Penicillium oxalicum species isolated from the root of Ixora chinensis in Vietnam

Abstract

Penicillium oxalicum has been reported as a multienzyme-producing fungus and is widely used in industry due to great potential for cellulase release. Until now, there are only 10 available genome assemblies of P. oxalicum species deposited in the GenBank database. In this study, the genome of the I1R1 strain isolated from the root of Ixora chinensis was completely sequenced by Pacbio Sequel sequencing technology, assembled into 8 chromosomes with the genome size of 30.8 Mb, as well as a mitogenome of 26 kb. The structural and functional analyses of the I1R1 genome revealed gene model annotations encoding an enzyme set involved in significant metabolic processes, along with cytochrome P450s and secondary metabolite biosynthesis. The comparative analysis of the P. oxalicum species based on orthology and gene family duplications indicated their large and closed pan-genome of 9,500 orthologous groups. This is valuable data for future phylogenetic and population genomics studies.

Keywords: Penicillium; chromosome-level assembly; fungal genome; long-read sequencing; reference genome.

Fig. 1.

Genome features of the chromosome-scale assembly the P. oxalicum I1R1 genome. a) Graphic representation of the 8 P. oxalicum I1R1–assembled chromosomes containing centromeric regions. b) Whole-genome alignment between the I1R1 strain and the reference CCTCC M 20211203 strain. The blocks represent the LCBs of the 2 genomes and the numbers within blocks are the chromosomes which these LCBs belong to. c) Syntenic regions between the I1R1 and CCTCC M 20211203 scaffolds.

Fig. 2.

The circular mitochondrial genome and comparison visualization of the P. oxalicum I1R1. a)The circular map shows the core genes as part of the NADH dehydrogenase, ubiquinol cytochrome c reductase, cytochrome c oxidase, and ATP synthase protein complexes. The RNAseP subunit (rnpB), small and large rRNAs (rns and rnl), as well as tRNAs are also displayed. Additional ORFs are shown along the circular map. b) The identity plot comparing the mitogenomes of I1R1 with 3 other Penicillium species and 2 Aspergillus species.

Fig. 3.

Bootstrap maximum-likelihood phylogenetic trees of Penicillium sp. based on ITS region sequences (a) and complete mitogenome (b). The graph shows clustering I1R1 with P. oxalicum.

Fig. 4.

Carbohydrate-active enzyme (CAZyme) analysis results of P. oxalicum I1R1 genome. A total of 653 genes encoding CAZymes include glycoside hydrolases (GHs), auxiliary activities (AAs), carbohydrate-binding modules (CBMs), carbohydrate esterases (CEs), glycosyl transferases (GTs), and polysaccharide lyases (PLs). The y-axis shows the number of protein-coding genes in each CAZy term.

Fig. 5.

Typical smBGCs found in P. oxalicum I1R1 genomes compared with other reference smBGCs from MIBiG database. a) MIBiG comparison of protocluster to region. b) NRPS/PKS domain organization. A, adenylation domain; ACP, acyl-carrier protein domain; AT, acyltransferase domain; C, condensation domain linking an L-amino acid to a peptide ending with an L-amino acid; cMT, carbon methyltransferase; DH, dehydratase domain; KR, ketoreductase domain; KS, ketosynthase domain; nMT, nitrogen methyltransferase; PCP, peptidyl-carrier protein domain; PP, phosphopantetheine acyl-carrier protein group; PT, product template domain; SAT, Starter unit—ACP transacylase in aflatoxin biosynthesis; TD, terminal reductase domain; TE, thioesterase domain.