Comparative genomic study of the Penicillium genus elucidates a diverse pangenome and 15 lateral gene transfer events

Abstract

The Penicillia are known to produce a wide range natural products—some with devastating outcome for the agricultural industry and others with unexploited potential in different applications. However, a large-scale overview of the biosynthetic potential of different species has been lacking. In this study, we sequenced 93 Penicillium isolates and, together with eleven published genomes that hold similar assembly characteristics, we established a species phylogeny as well as defining a Penicillium pangenome. A total of 5612 genes were shared between ≥ 98 isolates corresponding to approximately half of the average number of genes a Penicillium genome holds. We further identified 15 lateral gene transfer events that have occurred in this collection of Penicillium isolates, which might have played an important role, such as niche adaption, in the evolution of these fungi. The comprehensive characterization of the genomic diversity in the Penicillium genus supersedes single-reference genomes, which do not necessarily capture the entire genetic variation.

Gene acquisition by giant transposons primes eukaryotes for rapid evolution via horizontal gene transfer

“…In addition to looking at Starships carrying genes associated with formaldehyde tolerance, we also have identified an additional HGT of the original metal resistance Hφ - Starship via BLAST searches in the recently released genome of Penicillium chermesinum IBT 19713 [54] (Figure S4). This Penicillium Starship is nearly identical to the original P. variotii Starship except for the insertion of a retrotransposon (99.8% identical).…”

“…The small amount of variation is mostly single nucleotide indels. Given that the P. chermesinum genome was generated using nanopore technology without additional polishing using Illumina reads, indel sequencing errors are expected and may account for the small amount of divergence observed [54].…”

“…The sister species of P. variotii , P. paravariotii (only recently delimited from P. variotii ) also contains apparent HGT mediated acquisition of the element [45]. Finally, examination of the recently released Penicillium chermesium IBT 19713 genome reveals yet another HGT of this element (Figure S4) [54]. We thus have evidence for at least four HGT events of this Starship just in publicly available genomes.…”

“…"Pencillium sp." strain IBT 35674x [54] was identified as A. rudallense based on comparison of the RPB2 sequence to those examined by Houbraken et al [52]. Similarly, "Aspergillus sp."…”

“…“ Pencillium sp.” strain IBT 35674x [54] was identified as A. rudallense based on comparison of the RPB2 sequence to those examined by Houbraken et al [52]. Similarly, “ Aspergillus sp.” PB4102 was taxonomically identified as A. sydowii based on a phylogenetic comparison of the RPB2 sequence to those examined by Jurjevic et al [47].…”