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Biased gene retention during diploidization in Brassica linked to three-dimensional genome organization
- Source :
- Nature Plants. 5:822-832
- Publication Year :
- 2019
- Publisher :
- Springer Science and Business Media LLC, 2019.
-
Abstract
- The non-random three-dimensional (3D) organization of the genome in the nucleus is critical to gene regulation and genome function. Using high-throughput chromatin conformation capture, we generated chromatin interaction maps for Brassica rapa and Brassica oleracea at a high resolution and characterized the conservation and divergence of chromatin organization in these two species. Large-scale chromatin structures, including A/B compartments and topologically associating domains, are notably conserved between B. rapa and B. oleracea, yet their KNOT structures are highly divergent. We found that genes retained in less fractionated subgenomes exhibited stronger interaction strengths, and diploidization-resistant duplicates retained in pairs or triplets are more likely to be colocalized in both B. rapa and B. oleracea. These observations suggest that spatial constraint in duplicated genes is correlated to their biased retention in the diploidization process. In addition, we found strong similarities in the epigenetic modification and Gene Ontology terms of colocalized paralogues, which were largely conserved across B. rapa and B. oleracea, indicating functional constraints on their 3D positioning in the nucleus. This study presents an investigation of the spatial organization of genomes in Brassica and provides insights on the role of 3D organization in the genome evolution of this genus.
- Subjects :
- 0106 biological sciences
0301 basic medicine
Genome evolution
Protein Conformation
Brassica
Plant Science
Biology
01 natural sciences
Genome
Evolution, Molecular
Chromosome conformation capture
03 medical and health sciences
Brassica rapa
Protein Interaction Maps
Gene
Genomic organization
biology.organism_classification
Diploidy
Chromatin
030104 developmental biology
Evolutionary biology
Nucleic Acid Conformation
Brassica oleracea
Genome, Plant
010606 plant biology & botany
Subjects
Details
- ISSN :
- 20550278
- Volume :
- 5
- Database :
- OpenAIRE
- Journal :
- Nature Plants
- Accession number :
- edsair.doi.dedup.....c999e78261125dad610a9521fdf29fbb