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.

Background: Population-specific reference genomes are essential for improving the accuracy and reliability of genomic analyses across diverse human populations. Although Vietnam ranks as the 16th most populous country in the world, with more than 86% of its population identifying as Kinh, studies specifically focusing on the Kinh Vietnamese reference genome remain scarce. Therefore, constructing a Kinh Vietnamese reference genome is valuable in the genetic research of Vietnamese. Methods: In this study, we combined PacBio long-read sequencing and Bionano optical mapping data to generate a de novo assembly of a Kinh Vietnamese genome (VHG), which was subsequently polished using multiple Kinh Vietnamese short-read whole-genome sequences (WGSs). Results: The final assembly, named VHG1.2, comprised 3.22 gigabase pairs of high-quality sequence data, demonstrating high accuracy (QV: 48), completeness (BUSCO: 92%), and continuity (295 super scaffolds, super scaffold N50: 50 Kbp). Using multiple bioinformatic tools for variant calling, we observed significant variants when the population-specific reference VHG1.2 was used compared to the standard reference genome hg38. Conclusions: Overall, our genome assembly demonstrates the advantages of a long-read hybrid sequencing approach for de novo assembly and highlights the benefit of using population-specific reference genomes in population genomic analysis.