A chromosome-scale genome assembly of the tomato pathogen Cladosporium fulvum reveals a compartmentalized genome architecture and the presence of a dispensable chromosome

Abstract

Cladosporium fulvum is a fungal pathogen that causes leaf mould of tomato. The reference genome of this pathogen was released in 2012 but its high repetitive DNA content prevented a contiguous assembly and further prohibited the analysis of its genome architecture. In this study, we combined third generation sequencing technology with the Hi-C chromatin conformation capture technique, to produce a high-quality and near complete genome assembly and gene annotation of a Race 5 isolate of C. fulvum. The resulting genome assembly contained 67.17 Mb organized into 14 chromosomes (Chr1-to-Chr14), all of which were assembled telomere-to-telomere. The smallest of the chromosomes, Chr14, is only 460 kb in size and contains 25 genes that all encode hypothetical proteins. Notably, PCR assays revealed that Chr14 was absent in 19 out of 24 isolates of a world-wide collection of C. fulvum, indicating that Chr14 is dispensable. Thus, C. fulvum is currently the second species of Capnodiales shown to harbour dispensable chromosomes. The genome of C. fulvum Race 5 is 49.7 % repetitive and contains 14 690 predicted genes with an estimated completeness of 98.9%, currently one of the highest among the Capnodiales. Genome structure analysis revealed a compartmentalized architecture composed of gene-dense and repeat-poor regions interspersed with gene-sparse and repeat-rich regions. Nearly 39.2 % of the C. fulvum Race 5 genome is affected by Repeat-Induced Point (RIP) mutations and evidence of RIP leakage toward non-repetitive regions was observed in all chromosomes, indicating the RIP plays an important role in the evolution of this pathogen. Finally, 345 genes encoding candidate effectors were identified in C. fulvum Race 5, with a significant enrichment of their location in gene-sparse regions, in accordance with the ‘two-speed genome’ model of evolution. Overall, the new reference genome of C. fulvum presents several notable features and is a valuable resource for studies in plant pathogens.

Characterization of two conserved cell death elicitor families from the Dothideomycete fungal pathogens Dothistroma septosporum and Fulvia fulva (syn. Cladosporium fulvum)

“…Genomes from the two species are mesosyntenic (de Wit et al, 2012;Zaccaron et al, 2022) and, in keeping with this, we found conservation of chromosome location between the two species for each of the Ds/FfEcp20 and Ds/FfEcp32 gene pairs (Supplementary Figure S3). Taken together, sequence similarity, intron position and chromosome localization suggest a common evolutionary origin for the Ecp20 and Ecp32 genes from both species.…”

“…Members of the Ecp20 and Ecp32 protein families were identified from the predicted proteomes and/or genomes of D. septosporum NZE10 and F. fulva 0WU ( de Wit et al, 2012 ). Chromosome locations of the FfEcp20 and FfEcp32 genes were identified using the F. fulva Race 5 genome assembly ( Zaccaron et al, 2022 ). Gene family members were also identified from genome sequences of 18 other D. septosporum isolates ( Bradshaw et al, 2019 ) and D. pini CBS 116487 (GenBank assembly accession GCA_002116355.1), using reciprocal BLASTp and tBLASTn searches in conjunction with an E-value cut-off of <10 −5 .…”

Chromosome-level assembly of the Phytophthora agathidicida genome reveals adaptation in effector gene families

“…Although chromosome-level assemblies of Phytophthora species are currently rare, repeat-rich genomes of fungal pathogens have been fully assembled using long-read and Hi-C sequence data. For example, the 67 Mb genome sequence of the fungal tomato pathogen Cladosporium fulvum (now called Fulvia fulva ) was assembled to 14 chromosomes using these technologies ( Zaccaron et al, 2022 ), representing a considerable advance over the 4,865 scaffolds of the earlier assembly, albeit from a different isolate of this species ( de Wit et al, 2012 ). However, the 1 Gb genome sequence of the fungal myrtle rust pathogen Austropuccinia psidii , of which 91% is repetitive sequence, was assembled into 66 scaffolds rather than to chromosome-level ( Tobias et al, 2021 ), highlighting the ongoing limitations to complete assembly imposed by repeats.…”

“…Such dispensable or accessory chromosomes are often found in fungi. This includes Fulvia fulva , where only five of 24 isolates examined were found to contain the smallest chromosome, chromosome 14 ( Zaccaron et al, 2022 ).…”

Differences in fungal communities in the fur of two- and three-toed sloths revealed by ITS metabarcoding

“…Cladosporiaceae was mainly represented by the genus Cladosporium (). Cladosporium has been reported to be a highly diverse genus found in most non-extreme habitats around the globe, including plants, animals and soils [19, 20]; nevertheless, they are particularly abundant in indoor environments. Some species are important in human health, particularly in allergic lung mycoses [21].…”