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| Status |
Public on Jun 17, 2022 |
| Title |
The 3D architecture of the pepper genome and its relationship to function and evolution |
| Organism |
Capsicum annuum |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
The organization of chromatin into self-interacting domains is universal among eukaryotic genomes, though how and why they form varies considerably. Here we report a chromosome-scale reference genome assembly of pepper (Capsicum annuum) and explore its 3D organization through integrating high-resolution Hi-C maps with epigenomic, transcriptomic, and genetic variation data. Chromatin folding domains in pepper are as prominent as TADs in mammals but exhibit unique characteristics. They tend to coincide with heterochromatic regions enriched with retrotransposons and are frequently embedded in loops, which may correlate with transcription factories. Their boundaries are hotspots for chromosome rearrangements but are otherwise depleted for genetic variation. While chromatin conformation broadly affects transcription variance, it does not predict differential gene expression between tissues. Our results suggest that pepper genome organization is explained by a model of heterochromatin-driven folding promoted by transcription factories and that such spatial architecture is under structural and functional constraints.
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| Overall design |
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for the histone modifications YZ-H3K27me3, YZ-H3K4me3 and YZ-H3K9me2 in Pepper leaves.
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| Contributor(s) |
Liao Y, Wang J, Zhu Z, Liu Y, Chen J, Zhou Y, Liu F, Lei J, Gaut BS, Cao B, Emersion J, Chen C |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| BioProject |
PRJNA788020 |
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| Submission date |
Jun 13, 2022 |
| Last update date |
Jun 19, 2022 |
| Contact name |
Juntao Wang |
| E-mail(s) |
[email protected]
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| Organization name |
South China Agricultural University
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| Department |
Collage of Horticulture
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| Street address |
Wushan Street
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| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510642 |
| Country |
China |
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| Platforms (1) |
| GPL29650 |
Illumina NovaSeq 6000 (Capsicum annuum) |
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| Samples (12)
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| GSM6239272 |
YZ, H3K27me3, rep2 |
| GSM6239273 |
YZ, H3K4me3, rep1 input |
| GSM6239274 |
YZ, H3K4me3, rep1 |
| GSM6239275 |
YZ, H3K4me3, rep2 input |
| GSM6239276 |
YZ, H3K4me3, rep2 |
| GSM6239277 |
YZ, H3K9me2, rep1 input |
| GSM6239278 |
YZ, H3K9me2, rep1 |
| GSM6239279 |
YZ, H3K9me2, rep2 input |
| GSM6239280 |
YZ, H3K9me2, rep2 |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSE206031_RAW.tar |
23.1 Mb |
(http)(custom) |
TAR (of BEDGRAPH, BW, NARROWPEAK) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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