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| Status |
Public on Jan 07, 2020 |
| Title |
ChIP-seq of phytophthora sojae P6497 |
| Organism |
Phytophthora sojae |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Centromeres are chromosomal regions that serve as platforms for kinetochore assembly and spindle attachments, ensuring accurate chromosome segregation during cell division. Despite functional conservation, centromeric sequences are diverse and usually repetitive across species, making them challenging to assemble and identify. Here, we describe centromeres in the model 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 in the nucleus at different life stages and during nuclear division. We report a highly contiguous genome assembly of the P. sojae reference strain, which enabled identification of 15 highly enriched CENP-A binding regions as putative centromeres. By focusing on 10 intact 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 euchromatin mark H3K4me2 but are embedded within regions with the heterochromatin marks H3K9me3 and H3K27me3.
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| Overall design |
Examination of H3K9me3 and H3K4me2 on centromeres locus in phytophthora sojae
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| Contributor(s) |
Shu H, Chen H, Dong S, Fang Y |
| Citation(s) |
32150559 |
| |
| Submission date |
Jan 05, 2020 |
| Last update date |
Apr 19, 2020 |
| Contact name |
Haidong Shu |
| E-mail(s) |
2018202004@njau.edu.cn
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| Organization name |
Nanjing Agricultural University
|
| Department |
Department of Plant Pathology
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| Lab |
The Lab of Pathogenomics
|
| Street address |
Weigang NO.1
|
| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210095 |
| Country |
China |
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| Platforms (1) |
| GPL25217 |
Illumina HiSeq 4000 (Phytophthora sojae) |
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| Samples (3) |
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| Relations |
| BioProject |
PRJNA599013 |
| SRA |
SRP239493 |
