Cell‐type‐aware regulatory landscapes governing monoterpene indole alkaloid biosynthesis in the medicinal plant Catharanthus roseus DOI Creative Commons
Chenxin Li, Maite Colinas, Joshua C. Wood

et al.

New Phytologist, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 25, 2024

In plants, the biosynthetic pathways of some specialized metabolites are partitioned into or rare cell types, as exemplified by monoterpenoid indole alkaloid (MIA) pathway Catharanthus roseus (Madagascar Periwinkle), source anticancer compounds vinblastine and vincristine. leaf, C. MIA is three types with final known steps expressed in type termed idioblast. How cell-type specificity biosynthesis achieved poorly understood. We generated single-cell multi-omics data from leaves. Integrating gene expression chromatin accessibility profiles across single cells, well transcription factor (TF)-binding site profiles, we constructed a cell-type-aware regulatory network for biosynthesis. showcased cell-type-specific TFs cis-regulatory elements. Using motif enrichment analysis, co-expression functional validation approaches, discovered novel idioblast-specific TF (Idioblast MYB1, CrIDM1) that activates late-stage genes These analyses not only led to discovery first documented regulates two within an idioblast metabolic regulon but also provides insights regulation.

Language: Английский

Genetic factors of grain cadmium concentration in Polish wheat (Triticum polonicum L.) DOI
Yiran Cheng,

R. H. Liu,

Tian Yang

et al.

PLANT PHYSIOLOGY, Journal Year: 2024, Volume and Issue: 196(2), P. 979 - 995

Published: June 25, 2024

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

Language: Английский

Citations

7
A spatially resolved multiomic single-cell atlas of soybean development DOI
Xuan Zhang, Ziliang Luo, Alexandre P. Marand

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 3, 2024

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

Language: Английский

Citations

6
Constraint of accessible chromatins maps regulatory loci involved in maize speciation and domestication DOI Creative Commons
Y Liu, Xiang Gao, Hongjun Liu

et al.

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: March 12, 2025

Comparative genomic studies can identify genes under evolutionary constraint or specialized for trait innovation. Growing evidence suggests that also acts on non-coding regulatory sequences, exerting significant impacts fitness-related traits, although it has yet to be thoroughly explored in plants. Using the assay transposase-accessible chromatin by sequencing (ATAC-seq), we profile over 80,000 maize accessible regions (ACRs), revealing ACRs evolve faster than coding genes, with about one-third being maize-specific and regulating associated speciation. We highlight role of transposable elements (TEs) driving intraspecific innovation hundreds candidate potentially involved transcriptional rewiring during domestication. Additionally, demonstrate importance maintaining subgenome dominance controlling complex variations. This study establishes a framework analyzing trajectory plant sequences offers loci downstream exploration application breeding. Intricate regulation gene expression is important execution biology processes. Here, authors generate comprehensive map integrating ATAC-seq data 12 major tissues explore their interspecific constraints multiple Poaceae genomes.

Language: Английский

Citations

0
Chromatin accessibility and gene expression vary between a new and evolved autopolyploid Arabidopsis arenosa DOI Creative Commons
Thanvi Srikant, Adrián Gonzalo, Kirsten Bomblies

et al.

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(10)

Published: Oct. 1, 2024

Abstract Polyploids arise from whole-genome duplication (WGD) events, which have played important roles in genome evolution across eukaryotes. WGD can increase complexity, yield phenotypic novelty, and influence adaptation. Neo-polyploids been reported to often show seemingly stochastic epigenetic transcriptional changes, but this leaves open the question whether these changes persist evolved polyploids. A powerful approach address is compare diploids, neo-polyploids, polyploids of same species. Arabidopsis arenosa a species that allows us do this—natural diploid autotetraploid populations exist, while neo-tetraploids be artificially generated. Here, we use ATAC-seq assay local chromatin accessibility, RNA-seq study gene expression on matched leaf petal samples diploid, neo-tetraploid tetraploid A. arenosa. We found over 8,000 differentially accessible regions all samples. These are largely tissue specific distinct trends cytotypes, with roughly 70% arising upon WGD. Interestingly, only small proportion associated nearby genes. However, accessibility variation cytotypes associates strongly number transposable elements. Relatively few genes were expressed duplication, ∼60% reverted near-diploid levels tetraploid, suggesting most initial perturbations not last. Our results provide new insights into how epigenomic mechanisms jointly respond subsequent autopolyploids, importantly, one cannot directly predicted other.

Language: Английский

Citations

1
Investigating biological nitrogen fixation via single-cell transcriptomics DOI
Wendell J. Pereira, Daniel Conde, Noé Perron

et al.

Journal of Experimental Botany, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 20, 2024

Abstract The extensive use of nitrogen fertilizers has detrimental environmental consequences, and it is essential for society to explore sustainable alternatives. One promising avenue engineering root nodule symbiosis, a naturally occurring process in certain plant species within the nitrogen-fixing clade, into non-leguminous crops. Advancements single-cell transcriptomics provide unprecedented opportunities dissect molecular mechanisms underlying symbiosis at cellular level. This review summarizes key findings from studies Medicago truncatula, Lotus japonicus, Glycine max. We highlight how these address fundamental questions about development including following findings: (i) revealed conserved transcriptional program hair cortical cells during rhizobial infection, suggesting common infection pathway across legume species; (ii) characterization determinate indeterminate nodules using technologies supports compartmentalization fixation, assimilation, transport distinct cell populations; (iii) data have enabled identification novel genes provided new approaches prioritizing candidate functional characterization; (iv) trajectory inference RNA velocity analyses allowed reconstruction lineages dynamic states symbiosis.

Language: Английский

Citations

1
Cell‐type‐aware regulatory landscapes governing monoterpene indole alkaloid biosynthesis in the medicinal plant Catharanthus roseus DOI Creative Commons
Chenxin Li, Maite Colinas, Joshua C. Wood

et al.

New Phytologist, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 25, 2024

In plants, the biosynthetic pathways of some specialized metabolites are partitioned into or rare cell types, as exemplified by monoterpenoid indole alkaloid (MIA) pathway Catharanthus roseus (Madagascar Periwinkle), source anticancer compounds vinblastine and vincristine. leaf, C. MIA is three types with final known steps expressed in type termed idioblast. How cell-type specificity biosynthesis achieved poorly understood. We generated single-cell multi-omics data from leaves. Integrating gene expression chromatin accessibility profiles across single cells, well transcription factor (TF)-binding site profiles, we constructed a cell-type-aware regulatory network for biosynthesis. showcased cell-type-specific TFs cis-regulatory elements. Using motif enrichment analysis, co-expression functional validation approaches, discovered novel idioblast-specific TF (Idioblast MYB1, CrIDM1) that activates late-stage genes These analyses not only led to discovery first documented regulates two within an idioblast metabolic regulon but also provides insights regulation.

Language: Английский

Citations

0