ArticlePLoS genetics2020
Long transposon-rich centromeres in an oomycete reveal divergence of centromere features in Stramenopila-Alveolata-Rhizaria lineages.
Article in PLoS genetics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
19 citing papers in PubMed, 40 citations in OpenAlex.
- Fungi as models of centromere innovation: from DNA sequence to 3-dimensional arrangement.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2025Review
- Recombination landscape and karyotypic variations revealed by linkage mapping in the grapevine downy mildew pathogen Plasmopara viticola.G3 (Bethesda, Md.) · 2025Article
- 3D chromatin maps of a brown alga reveal U/V sex chromosome spatial organization.Nature communications · 2024Article
- Pangenome graph analysis reveals extensive effector copy-number variation in spinach downy mildew.PLoS genetics · 2024Article
- Complete telomere-to-telomere genomes uncover virulence evolution conferred by chromosome fusion in oomycete plant pathogens.Nature communications · 2024Article
- How do emerging long-read sequencing technologies function in transforming the plant pathology research landscape?Plant molecular biology · 2022Review
- The contribution of DNA repair pathways to genome editing and evolution in filamentous pathogens.FEMS microbiology reviews · 2022Review
- Article
- Centromere drive: model systems and experimental progress.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2022Review
- An Efficient Chromatin Immunoprecipitation Protocol for the Analysis of Histone Modification Distributions in the Brown AlgaMethods and protocols · 2022Article
- A Comprehensive Assessment of the Secretome Responsible for Host Adaptation of the Legume Root PathogenJournal of fungi (Basel, Switzerland) · 2022Article
- Chromosome-level assembly of theFrontiers in microbiology · 2022Article
- Remote homology clustering identifies lowly conserved families of effector proteins in plant-pathogenic fungi.Microbial genomics · 2021Article
- Epigenetic dynamics of centromeres and neocentromeres in Cryptococcus deuterogattii.PLoS genetics · 2021Article
- Comparative genomics of Chlamydomonas.The Plant cell · 2021Article
- Functional and Comparative Analysis of Centromeres Reveals Clade-Specific Genome Rearrangements inmBio · 2021Article
- SMARTdenovo: aGigaByte (Hong Kong, China) · 2021Article
- Repetitive Elements Contribute to the Diversity and Evolution of Centromeres in the Fungal GenusmBio · 2020Article
- Comparative Genomic and Proteomic Analyses of Three WidespreadMicroorganisms · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
16 authors at 6 institutions in 4 countries.
Funding
Abstract
Centromeres are chromosomal regions that serve as platforms for kinetochore assembly and spindle attachments, ensuring accurate chromosome segregation during cell division. Despite functional conservation, centromere DNA sequences are diverse and often repetitive, making them challenging to assemble and identify. Here, we describe centromeres in an oomycete Phytophthora sojae by combining long-read sequencing-based genome assembly and chromatin immunoprecipitation for the centromeric histone CENP-A followed by high-throughput sequencing (ChIP-seq). P. sojae centromeres cluster at a single focus at different life stages and during nuclear division. We report an improved genome assembly of the P. sojae reference strain, which enabled identification of 15 enriched CENP-A binding regions as putative centromeres. By focusing on a subset of these regions, we demonstrate that centromeres in P. sojae are regional, spanning 211 to 356 kb. Most of these regions are transposon-rich, poorly transcribed, and lack the histone modification H3K4me2 but are embedded within regions with the heterochromatin marks H3K9me3 and H3K27me3. Strikingly, we discovered a Copia-like transposon (CoLT) that is highly enriched in the CENP-A chromatin. Similar clustered elements are also found in oomycete relatives of P. sojae, and may be applied as a criterion for prediction of oomycete centromeres. This work reveals a divergence of centromere features in oomycetes as compared to other organisms in the Stramenopila-Alveolata-Rhizaria (SAR) supergroup including diatoms and Plasmodium falciparum that have relatively short and simple regional centromeres. Identification of P. sojae centromeres in turn also advances the genome assembly.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.