Evolution of plant cell-type-specific<i>cis</i>-regulatory elements

Yan, Haidong; Mendieta, John P.; Zhang, Xuan; Marand, Alexandre P.; Liang, Yan; Luo, Ziliang; Minow, Mark A.A.; Jang, Hosung; Li, Xiang; Roulé, Thomas; Wagner, Doris; Tu, Xiaoyu; Wang, Yonghong; Jiang, Daiquan; Zhong, Silin; Huang, Linkai; Wessler, Susan R.; Schmitz, Robert J.

doi:10.1101/2024.01.08.574753

Cited by 4 publications

(1 citation statement)

References 165 publications

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“…11–17 To date, only three atlas-scale single-cell transcriptomes or chromatin accessibility maps have been reported in Arabidopsis thaliana , Oryza sativa ( rice) and Zea mays (maize), each limited to a single modality. 18–20 However, while extremely valuable, these resources are limited by challenges inherent in single-cell genomic technologies, where the cell types are extracted from their origin in a complex tissue, potentially losing critical biological information, and increasing the difficulty of proper cell-type annotation. 21…”

Section: Introductionmentioning

confidence: 99%

A spatially resolved multiomic single-cell atlas of soybean development

Zhang,

Luo,

Marand

et al. 2024

Preprint

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SummaryCis-regulatory elements (CREs) precisely control spatiotemporal gene expression in cells. Using a spatially resolved single-cell atlas of gene expression with chromatin accessibility across ten soybean tissues, we identified 103 distinct cell types and 303,199 accessible chromatin regions (ACRs). Nearly 40% of the ACRs showed cell-type-specific patterns and were enriched for transcription factor (TF) motifs defining diverse cell identities. We identifiedde novoenriched TF motifs and explored conservation of gene regulatory networks underpinning legume symbiotic nitrogen fixation. With comprehensive developmental trajectories for endosperm and embryo, we uncovered the functional transition of the three sub-cell types of endosperm, identified 13 sucrose transporters sharing the DOF11 motif that were co-up-regulated in late peripheral endosperm and identified key embryo cell-type specification regulators during embryogenesis, including a homeobox TF that promotes cotyledon parenchyma identity. This resource provides a valuable foundation for analyzing gene regulatory programs in soybean cell types across tissues and life stages.

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Section: Introductionmentioning

confidence: 99%

A spatially resolved multiomic single-cell atlas of soybean development

Zhang,

Luo,

Marand

et al. 2024

Preprint

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Chromatin Accessibility and Gene Expression Vary Between a New and Evolved Autopolyploid of Arabidopsis arenosa

Srikant,

Gonzalo,

Bomblies

2024

Molecular Biology and Evolution

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Polyploids arise from whole-genome duplication (WGD) events, which have played important roles in genome evolution across eukaryotes. WGD can increase genome complexity, yield phenotypic novelty and influence adaptation. Neo-polyploids have been reported to often show seemingly stochastic epigenetic and transcriptional changes, but this leaves open the question whether these changes persist in evolved polyploids. A powerful approach to address this is to compare diploids, neo-polyploids, and evolved polyploids of the same species. Arabidopsis arenosa is a species that allows us to do this - natural diploid and autotetraploid populations exist, while neo-tetraploids can be artificially generated. Here we use ATAC-seq to assay local chromatin accessibility, and RNA-seq to study gene expression on matched leaf and petal samples from diploid, neo-tetraploid and evolved tetraploid A. arenosa. We found over 8000 differentially accessible chromatin regions across all samples. These are largely tissue-specific and show distinct trends across cytotypes, with roughly 70% arising upon WGD. Interestingly, only a small proportion are associated with expression changes in nearby genes. However, accessibility variation across cytotypes associates strongly with the number of nearby transposable elements (TEs). Relatively few genes were differentially expressed upon genome duplication, and approximately 60% of these reverted to near-diploid levels in the evolved tetraploid, suggesting that most initial perturbations do not last. Our results provide new insights into how epigenomic and transcriptional mechanisms jointly respond to genome duplication and subsequent evolution of autopolyploids, and importantly, show that one cannot be directly predicted from the other.

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Genetic factors of grain cadmium concentration in Polish wheat (Triticum polonicum L.)

Cheng,

Liu,

Yang

et al. 2024

Plant Physiology

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Wheat (Triticum aestivum L.) is one of the most important crops worldwide and a major source of human cadmium (Cd) intake. Limiting grain Cd concentration (Gr_Cd_Conc) in wheat is necessary to ensure food safety. However, the genetic factors associated with Cd uptake, translocation and distribution and Gr_Cd_Conc in wheat are poorly understood. Here, we mapped quantitative trait loci (QTLs) for Gr_Cd_Conc and its related transport pathway using a recombinant inbred line (RIL) population derived from 2 Polish wheat varieties (RIL_DT; dwarf Polish wheat [DPW] and tall Polish wheat [TPW]). We identified 29 novel major QTLs for grain and tissue Cd concentration; 14 novel major QTLs for Cd uptake, translocation, and distribution; and 27 major QTLs for agronomic traits. We also analyzed the pleiotropy of these QTLs. Six novel QTLs (QGr_Cd_Conc-1A, QGr_Cd_Conc-3A, QGr_Cd_Conc-4B, QGr_Cd_Conc-5B, QGr_Cd_Conc-6A, and QGr_Cd_Conc-7A) for Gr_Cd_Conc explained 8.16% to 17.02% of the phenotypic variation. QGr_Cd_Conc-3A, QGr_Cd_Conc-6A, and QGr_Cd_Conc-7A pleiotropically regulated Cd transport; 3 other QTLs were organ-specific for Gr_Cd_Conc. We fine-mapped the locus of QGr_Cd_Conc-4B and identified the candidate gene as Cation/Ca exchanger 2 (TpCCX2-4B), which was differentially expressed in DPW and TPW. It encodes an endoplasmic reticulum membrane/plasma membrane–localized Cd efflux transporter in yeast. Overexpression of TpCCX2-4B reduced Gr_Cd_Conc in rice. The average Gr_Cd_Conc was significantly lower in TpCCX2-4BDPW genotypes than in TpCCX2-4BTPW genotypes of the RIL_DT population and 2 other natural populations, based on a Kompetitive allele-specific PCR marker derived from the different promoter sequences between TpCCX2-4BDPW and TpCCX2-4BTPW. Our study reveals the genetic mechanism of Cd accumulation in wheat and provides valuable resources for genetic improvement of low–Cd-accumulating wheat cultivars.

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Evolution of plant cell-type-specificcis-regulatory elements

Cited by 4 publications

References 165 publications

A spatially resolved multiomic single-cell atlas of soybean development

A spatially resolved multiomic single-cell atlas of soybean development

Chromatin Accessibility and Gene Expression Vary Between a New and Evolved Autopolyploid of Arabidopsis arenosa

Genetic factors of grain cadmium concentration in Polish wheat (Triticum polonicum L.)

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