Biased gene retention during diploidization in Brassica linked to three-dimensional genome organization

Xie, Ting; Zhang, Fugui; Zhang, Hongyu; Wang, Xiaotao; Hu, Jihong; Wu, Xiaoming

doi:10.1038/s41477-019-0479-8

Cited by 55 publications

(70 citation statements)

References 71 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…As previously reported in B. rapa (Wang et al, 2011) and B. oleracea (Liu et al, 2014), the three subgenomes of Korso and OX-heart, LF (the least fractionated), MF1 (the medium fractionated) and MF2 (the most fractionated), showed the same biased retention pattern of duplicated genes during diploidization (Xie et al, 2019) ( Supplementary Fig. 8a,b).…”

Section: Genome Annotation and Comparative Genomicssupporting

confidence: 82%

Genome sequencing sheds light on the contribution of structural variants toBrassica oleraceadiversification

Guo

Wang

Gao

et al. 2020

Preprint

View full text Add to dashboard Cite

Brassica oleracea includes several morphologically diverse, economically important vegetable crops. Here we present high-quality chromosome-scale genome assemblies for two B. oleracea morphotypes, cauliflower and cabbage. Direct comparison of these two assemblies identifies ~120 K high-confidence structural variants (SVs). Population analysis of 271 B. oleracea accessions using these SVs clearly separates different morphotypes, suggesting the association of SVs with B. oleracea intraspecific divergence. Genes affected by SVs selected between cauliflower and cabbage are enriched with functions related to response to stress and stimulus and meristem and flower development. Furthermore, genes affected by selected SVs and involved in the switch from vegetative to generative growth that defines curd initiation, inflorescence meristem proliferation for curd formation, maintenance and enlargement, are identified, providing insights into the regulatory network of curd development. This study reveals the important roles of SVs in diversification of different morphotypes of B. oleracea, and the newly assembled genomes and the SVs provide rich resources for future research and breeding.

show abstract

Section: Genome Annotation and Comparative Genomicssupporting

confidence: 82%

Genome sequencing sheds light on the contribution of structural variants toBrassica oleraceadiversification

Guo

Wang

Gao

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…Topologically associating domain (TADs), one of these organizational features, was originally discovered in Hi-C contact maps as domains within which DNA sequences physically contact each other more densely than they are outside (Sexton et al 2012;Dixon et al 2012) . TADs or similar domains have been widely observed across the kingdom of life, from yeast (Mizuguchi et al 2014) and bacteria (Le et al 2013) to plants (Liu et al 2017;Xie et al 2019) and animals (Fishman et al 2019) .…”

Section: Introductionmentioning

confidence: 99%

Topologically associating domains and their role in the evolution of genome structure and function inDrosophila

Liao¹,

Zhang²,

Chakraborty³

et al. 2020

Preprint

View full text Add to dashboard Cite

Topologically associating domains (TADs) are regarded as functional and structural units of higher-order spatial genome organization of many eukaryotic genomes. However, our knowledge of how evolution affects TADs remains limited. To decipher the evolutionary significance of TADs, we de novo assembled the genome of D. pseudoobscura and created a high-resolution (~800 bp) Hi-C contact map to annotate TADs. Remarkably, more than 40% of TADs between D. pseudoobscura and D. melanogaster are conserved, despite extensive chromosomal rearrangement in the ~49 million years since they shared a common ancestor. Comparison of 17 diverse Drosophila species genomes revealed enrichment of genome rearrangement breakpoints at the TAD boundaries but depletion of such breaks inside the TADs themselves. We show that conservation of TADs is associated with gene expression stability across tissues. Surprisingly, despite being larger mutational targets, a substantial proportion of long (>50kb) genes in D. melanogaster (42%) and D. pseudoobscura (26%) are individually spanned by complete TADs, implying the formation and maintenance of TADs via 3D cis-regulatory interactions commonly found within long genes. U sing high-confidence genome-wide structural variant datasets from 14 D. melanogaster strains, its 3 closest sibling species from the D. simulans species complex, and two obscura clade species, we show evidence of natural selection operating on structural variants at the TAD boundaries, but with the nature of selection differing between the SV types. Deletions are significantly depleted at TAD boundaries for both divergent and polymorphic SVs, suggesting that deletions at TAD boundaries are under purifying selection, whereas divergent duplications are enriched at the TAD boundaries, pointing to positive selection. Our results offer novel insights into the evolutionary role and maintenance of TADs and their significance in genome structure evolution and gene regulation.

show abstract

“…status switching between A and B under different conditions (Wang et al, 2018a;Xie et al, 2019;Zhang et al, 2019a).…”

Section: Accepted Articlementioning

confidence: 99%

Plant 3D genomics: the exploration and application of chromatin organization

Pei

Lindsey

et al. 2021

New Phytologist

View full text Add to dashboard Cite

Eukaryotic genomes are highly folded for packing into higher-order chromatin structures in the nucleus. With the emergence of state-of-the-art chromosome conformation capture methods and microscopic imaging techniques, the spatial organization of chromatin and its functional implications have been interrogated. Our knowledge of three-dimensional (3D) chromatin organization in plants has improved dramatically in the past few years, building on the early advances in animal systems. Here, we review recent advances in 3D genome mapping approaches, our understanding of the sophisticated organization of spatial structures, and the application of 3D genomic principles in plants. We also discuss directions for future developments in 3D genomics in plants.

show abstract

Biased gene retention during diploidization in Brassica linked to three-dimensional genome organization

Cited by 55 publications

References 71 publications

Genome sequencing sheds light on the contribution of structural variants toBrassica oleraceadiversification

Genome sequencing sheds light on the contribution of structural variants toBrassica oleraceadiversification

Topologically associating domains and their role in the evolution of genome structure and function inDrosophila

Plant 3D genomics: the exploration and application of chromatin organization

Contact Info

Product

Resources

About