loading page

Haplotype-phased and chromosome-level assembly of Puccinia polysora, a giga-scale fungal pathogen causing southern corn rust
  • +8
  • junmin Liang,
  • Yuanjie Li,
  • Peter Dodds,
  • Melania Figueroa,
  • Jana Sperschneider,
  • Shiling Han,
  • Kin-Ming (Clement) Tsui,
  • Keyu Zhang,
  • Leifu Li,
  • Zhanhong Ma,
  • Lei Cai
junmin Liang
Institute of Microbiology Chinese Academy of Sciences

Corresponding Author:liangjm@im.ac.cn

Author Profile
Yuanjie Li
Institute of Microbiology Chinese Academy of Sciences
Author Profile
Peter Dodds
Commonwealth Scientific and Industrial Research Organisation
Author Profile
Melania Figueroa
Commonwealth Scientific and Industrial Research Organisation
Author Profile
Jana Sperschneider
Commonwealth Scientific and Industrial Research Organisation
Author Profile
Shiling Han
Institute of Microbiology Chinese Academy of Sciences
Author Profile
Kin-Ming (Clement) Tsui
Tan Tock Seng Hospital
Author Profile
Keyu Zhang
China Agricultural University
Author Profile
Leifu Li
China Agricultural University
Author Profile
Zhanhong Ma
China Agricultural University
Author Profile
Lei Cai
Institute of Microbiology Chinese Academy of Sciences
Author Profile

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 describe 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 the largest fungal genome assembled to chromosome scale. Transcript-based annotation identified 47,512 genes 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 content, with genome-size expansion, gene losses and gene family expansions suggested by multiple copies of species-specific orthogroups. Interestingly, these features did not affect overall synteny with other Puccinia species with 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 drifted from the major population by having mutations on secreted proteins including AvrRppC, indicating the ongoing evolution and population differentiation. The high-quality assembly provides valuable genomic resources for future studies on the evolution of P. polysora.
18 May 2022Submitted to Molecular Ecology Resources
13 Jun 2022Submission Checks Completed
13 Jun 2022Assigned to Editor
21 Jun 2022Reviewer(s) Assigned
09 Sep 2022Review(s) Completed, Editorial Evaluation Pending
15 Sep 2022Editorial Decision: Revise Minor
06 Oct 2022Review(s) Completed, Editorial Evaluation Pending
06 Oct 20221st Revision Received
12 Oct 2022Reviewer(s) Assigned
11 Nov 2022Editorial Decision: Revise Minor
16 Nov 2022Review(s) Completed, Editorial Evaluation Pending
16 Nov 20222nd Revision Received
17 Nov 2022Editorial Decision: Accept