{"doi":"10.1101/2021.09.14.460278","title":"Ancestral chromosomes for the Peronosporaceae inferred from a telomere-to-telomere genome assembly of <i>Peronospora effusa</i>","abstract":"Abstract We report the first telomere-to-telomere genome assembly for an oomycete. This assembly has extensive synteny with less complete genome assemblies of other oomycetes and will therefore serve as a reference genome for this taxon. Downy mildew disease of spinach, caused by the oomycete Peronospora effusa , causes major losses to spinach production. The 17 chromosomes of P. effusa were assembled telomere-to-telomere using Pacific Biosciences High Fidelity reads. Sixteen chromosomes are complete and gapless; Chromosome 15 contains one gap bridging the nucleolus organizer region. Putative centromeres were identified on all chromosomes. This new assembly enables a re-evaluation of the genomic composition of Peronospora spp.; the assembly was almost double the size and contained more repeat sequences than previously reported for any Peronospora spp. Genome fragments consistently under-represented in six previously reported assemblies of P. effusa typically encoded repeats. Some genes annotated as encoding effectors were organized into multigene clusters on several chromosomes. At least two effector-encoding genes were annotated on every chromosome. The intergenic distances between annotated genes were consistent with the two-speed genome hypothesis, with some effectors located in gene-sparse regions. The near-gapless assembly revealed apparent horizontal gene transfer from Ascomycete fungi. Gene order was highly conserved between P. effusa and the genetically oriented assembly of the oomycete Bremia lactucae . High levels of synteny were also detected with Phytophthora sojae . Many oomycete species may have similar chromosome organization; therefore, this genome assembly provides the foundation for genomic analyses of diverse oomycetes.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2021,"id":215194,"datarank":0.39182130928421877,"base_score":2.0794415416798357,"endowment":2.0794415416798357,"self_citation_contribution":0.31191623125197543,"citation_network_contribution":0.07990507803224332,"self_endowment_contribution":0.31191623125197543,"citer_contribution":0.07990507803224332,"corpus_percentile":53.48495397230602,"corpus_rank":6014,"citation_count":7,"citer_count":6,"citers_with_citation_signal":4,"citers_with_endowment":4,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.7893,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":809893,"name":"Oon-Ha Shin","orcid":null,"position":1,"is_corresponding":false},{"id":809438,"name":"Kelley J. Clark","orcid":"0000-0002-4824-5862","position":2,"is_corresponding":false},{"id":809439,"name":"Chunda Feng","orcid":"0000-0003-0451-9531","position":3,"is_corresponding":false},{"id":739618,"name":"Alexander I. Putman","orcid":"0000-0002-1151-1987","position":4,"is_corresponding":false},{"id":809440,"name":"James C. Correll","orcid":"0000-0002-3800-9655","position":5,"is_corresponding":false},{"id":809441,"name":"Steven J. Klosterman","orcid":"0000-0002-0571-5051","position":6,"is_corresponding":false},{"id":806732,"name":"Allen Van Deynze","orcid":"0000-0002-2093-0577","position":7,"is_corresponding":false},{"id":571313,"name":"Richard W. Michelmore","orcid":"0000-0002-7512-592X","position":8,"is_corresponding":false},{"id":571309,"name":"Kyle Fletcher","orcid":"0000-0003-1191-9939","position":0,"is_corresponding":true}],"reference_count":53,"raw_metadata":null,"created_at":"2026-07-18T23:52:51.201033Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}