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bioRxiv · 10.1101/2022.05.18.492400

The largest haplotype-phased and chromosome-scale genome assembly of the fungal pathogen, Puccinia polysora, by HiFi reads and Hi-C data

Liang, j.·Li, y.·Dodds, P. N.·Figueroa, M.·Sperschneider, J.·Han, S.·Tsui, C. K. M.·Zhang, K.·Li, L.·Ma, Z.·Cai, L.
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Abstract

Rust fungi are characterized by large genomes with high repeat content and have two haploid nuclei in most life stages, which makes achieving high-quality genome assemblies challenging. Here, we described a pipeline using HiFi reads and Hi-C data to assemble a gigabase-sized fungal pathogen, Puccinia polysora f.sp. zeae, to haplotype-phased and chromosome-scale. The final assembled genome is 1.71 Gbp, with ~850 Mbp and 18 chromosomes in each haplotype, being currently one of the two giga-scale fungi assembled to chromosome level. Transcript-based annotation identified 47,512 genes for dikaryotic genome with a similar number for each haplotype. A high level of interhaplotype variation was found with 10% haplotype-specific BUSCO genes, 5.8 SNPs/kbp and structural variation accounting for 3% of the genome size. The P. polysora genome displayed over 85% repeat contents, with genome-size expansion and copy number increasing of species-specific orthogroups. Interestingly, these features did not affect overall synteny with other Puccinia species having smaller genomes. Fine-time-point transcriptomics revealed seven clusters of co-expressed secreted proteins that are conserved between two haplotypes. The fact that candidate effectors interspersed with all genes indicated the absence of a "two-speed genome" evolution in P. polysora. Genome resequencing of 79 additional isolates revealed a clonal population structure of P. polysora in China with low geographic differentiation. Nevertheless, a minor population differentiated from the major population by having mutations on secreted proteins including AvrRppC, indicating the ongoing virulence to evade recognition by RppC, a major resistance gene in Chinese corn cultivars. The high-quality assembly provides valuable genomic resources for future studies on disease management and the evolution of P. polysora.

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Liang, j., Li, y., Dodds, P. N., Figueroa, M., Sperschneider, J., Han, S., Tsui, C. K. M., Zhang, K., Li, L., Ma, Z., Cai, L.. 2022-05-19. The largest haplotype-phased and chromosome-scale genome assembly of the fungal pathogen, Puccinia polysora, by HiFi reads and Hi-C data. https://doi.org/10.1101/2022.05.18.492400

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