The maize single-nucleus transcriptome comprehensively describes signaling networks governing movement and development of grass stomata DOI Open Access
Guiling Sun,

Mingzhang Xia,

Jieping Li

et al.

The Plant Cell, Journal Year: 2022, Volume and Issue: unknown

Published: Feb. 9, 2022

The unique morphology of grass stomata enables rapid responses to environmental changes. Deciphering the basis for these is critical improving food security. We have developed a planta platform single-nucleus RNA-sequencing by combined fluorescence-activated nuclei flow sorting, and used it identify cell types in mature developing from 33,098 maize epidermis-enriched tissues. Guard cells (GCs) subsidiary (SCs) displayed differential expression genes, besides those encoding transporters, involved abscisic acid, CO2, Ca2+, starch metabolism, blue light signaling pathways, implicating coordinated signal integration speedy stomatal responses, genes affecting wall plasticity, implying more sophisticated relationship between GCs SCs development dumbbell-shaped guard formation. trajectory identified young tissues, comparison bulk RNA-seq data MUTE defective mutant development, confirmed known features, shed on key participants development. Our study provides valuable, comprehensive, fundamental foundation further insights into function.

Language: Английский

ShinyGO: a graphical gene-set enrichment tool for animals and plants DOI
Xijin Ge, Dongmin Jung,

Runan Yao

et al.

Bioinformatics, Journal Year: 2019, Volume and Issue: 36(8), P. 2628 - 2629

Published: Dec. 23, 2019

Abstract Motivation Gene lists are routinely produced from various omic studies. Enrichment analysis can link these gene with underlying molecular pathways and functional categories such as ontology (GO) other databases. Results To complement existing tools, we developed ShinyGO based on a large annotation database derived Ensembl STRING-db for 59 plant, 256 animal, 115 archeal 1678 bacterial species. ShinyGO’s novel features include graphical visualization of enrichment results characteristics, application program interface access to KEGG STRING the retrieval pathway diagrams protein–protein interaction networks. is an intuitive, web that help researchers gain actionable insights gene-sets. Availability implementation http://ge-lab.org/go/. Supplementary information data available at Bioinformatics online.

Language: Английский

Citations

3175
A chromosome conformation capture ordered sequence of the barley genome DOI Creative Commons
Martin Mascher, Heidrun Gundlach, Axel Himmelbach

et al.

Nature, Journal Year: 2017, Volume and Issue: 544(7651), P. 427 - 433

Published: April 1, 2017

Cereal grasses of the Triticeae tribe have been major food source in temperate regions since dawn agriculture. Their large genomes are characterized by a high content repetitive elements and pericentromeric that virtually devoid meiotic recombination. Here we present high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive linear order sequences across space investigate spatial organization chromatin nucleus at megabase resolution. The composition genes differs between distal proximal regions. Gene family analyses reveal lineage-specific duplications involved transport nutrients developing seeds mobilization carbohydrates grains. demonstrate importance sequence breeding inspecting genomic partitioning variation modern elite germplasm, highlighting vulnerable genetic erosion. International Barley Genome Sequencing Consortium reports sequencing barley, Hordeum vulgare. grasses, which include wheat rye, widely cultivated plants with particularly complex evolutionary histories. has challenging owing its size particular features, such as an abundance elements. Nils Stein colleagues report (Hordeumvulgare L). They combined approach hierarchical shotgun bacterial artificial chromosomes, on nanochannel arrays chromosome-scale scaffolding Hi-C sequencing. This brings first comprehensive, completely ordered genome. authors also sequenced examined diversity exomes 96 European lines spring or winter growth habit, highlight utility this resource cereal genomics programs.

Language: Английский

Citations

1334
iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data DOI Creative Commons
Xijin Ge,

Eun Son,

Runan Yao

et al.

BMC Bioinformatics, Journal Year: 2018, Volume and Issue: 19(1)

Published: Dec. 1, 2018

RNA-seq is widely used for transcriptomic profiling, but the bioinformatics analysis of resultant data can be time-consuming and challenging, especially biologists. We aim to streamline bioinformatic analyses gene-level by developing a user-friendly, interactive web application exploratory analysis, differential expression, pathway analysis.iDEP (integrated Differential Expression Pathway analysis) seamlessly connects 63 R/Bioconductor packages, 2 services, comprehensive annotation databases 220 plant animal species. The workflow reproduced downloading customized R code related files. As an example, we analyzed RNA-Seq dataset lung fibroblasts with Hoxa1 knockdown revealed possible roles SP1 E2F1 their target genes, including microRNAs, in blocking G1/S transition. In another our shows that mouse B cells without functional p53, ionizing radiation activates MYC its downstream genes involved cell proliferation, ribosome biogenesis, non-coding RNA metabolism. wildtype cells, induces p53-mediated apoptosis DNA repair while suppressing E2F1, leads growth cycle arrest. iDEP helps unveil multifaceted functions p53 involvement several microRNAs such as miR-92a, miR-504, miR-30a. both examples, validated known molecular pathways generated novel, testable hypotheses.Combining analytic functionalities massive databases, ( http://ge-lab.org/idep/ ) enables biologists easily translate proteomic into actionable insights.

Language: Английский

Citations

1242
PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics DOI Creative Commons
Michiel Van Bel, Tim Diels, Emmelien Vancaester

et al.

Nucleic Acids Research, Journal Year: 2017, Volume and Issue: 46(D1), P. D1190 - D1196

Published: Oct. 12, 2017

PLAZA (https://bioinformatics.psb.ugent.be/plaza) is a plant-oriented online resource for comparative, evolutionary and functional genomics. The platform consists of multiple independent instances focusing on different plant clades, while also providing access to consistent set reference species. Each instance contains structural gene annotations, family data phylogenetic trees detailed colinearity information. A user-friendly web interface makes the necessary tools visualizations accessible, specific each type. Here we present 4.0, latest iteration framework. This version two new (Dicots 4.0 Monocots 4.0) large increase in newly available species, offers updated implemented visualizations, helping users with ever-increasing demands complex in-depth analyzes. total number species across both nearly doubles from 37 3.0 71 much broader coverage crop (e.g. wheat, palm oil) interest spruce, Marchantia). can be accessed by programming through RESTful service, thus allowing bioinformaticians optimally leverage power platform.

Language: Английский

Citations

461
MapMan4: A Refined Protein Classification and Annotation Framework Applicable to Multi-Omics Data Analysis DOI Creative Commons

Rainer Schwacke,

Gabriel Yaxal Ponce‐Soto, Kirsten Krause

et al.

Molecular Plant, Journal Year: 2019, Volume and Issue: 12(6), P. 879 - 892

Published: Jan. 9, 2019

Language: Английский

Citations

414
Expression Atlas: gene and protein expression across multiple studies and organisms DOI Creative Commons
Irene Papatheodorou, Nuno A. Fonseca, Maria Keays

et al.

Nucleic Acids Research, Journal Year: 2017, Volume and Issue: 46(D1), P. D246 - D251

Published: Nov. 6, 2017

Expression Atlas (http://www.ebi.ac.uk/gxa) is an added value database that provides information about gene and protein expression in different species contexts, such as tissue, developmental stage, disease or cell type. The available public controlled access data sets from sources are curated re-analysed using standardized, open source pipelines made for queries, download visualization. As of August 2017, holds 3,126 studies across 33 species, including 731 plants. Data large-scale RNA sequencing Blueprint, PCAWG, ENCODE, GTEx HipSci can be visualized next to each other. In Atlas, users query genes gene-sets interest explore their within tissues, stages a constitutive differential context, representing the effects diseases, conditions experimental interventions. All processed matrices direct tab-delimited format R-data. addition web interface, now searched downloaded through R package. Novel features visualizations include on-the-fly analysis set overlaps option view co-expression experiments investigating tissues other conditions.

Language: Английский

Citations

388
Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data DOI Creative Commons
Michaël Alaux,

Jane Rogers,

Thomas Letellier

et al.

Genome biology, Journal Year: 2018, Volume and Issue: 19(1)

Published: Aug. 14, 2018

The Wheat@URGI portal has been developed to provide the international community of researchers and breeders with access bread wheat reference genome sequence produced by International Wheat Genome Sequencing Consortium. browsers, BLAST, InterMine tools have established for in-depth exploration together additional linked datasets including physical maps, variations, gene expression, genetic phenomic data from other collaborative projects already stored in GnpIS information system. provides enhanced search browser features that will facilitate deployment latest genomics resources improvement.

Language: Английский

Citations

235
A Collinearity-Incorporating Homology Inference Strategy for Connecting Emerging Assemblies in the Triticeae Tribe as a Pilot Practice in the Plant Pangenomic Era DOI Creative Commons
Yongming Chen,

Wanjun Song,

Xiaoming Xie

et al.

Molecular Plant, Journal Year: 2020, Volume and Issue: 13(12), P. 1694 - 1708

Published: Sept. 23, 2020

Language: Английский

Citations

186
Technological advances in maize breeding: past, present and future DOI Open Access
Carson M. Andorf, William D. Beavis, Matthew B. Hufford

et al.

Theoretical and Applied Genetics, Journal Year: 2019, Volume and Issue: 132(3), P. 817 - 849

Published: Feb. 23, 2019

Language: Английский

Citations

153
Functional genomics of Brassica napus: Progress, challenges, and perspectives DOI Open Access
Zengdong Tan,

Xu Han,

Cheng Dai

et al.

Journal of Integrative Plant Biology, Journal Year: 2024, Volume and Issue: 66(3), P. 484 - 509

Published: March 1, 2024

ABSTRACT Brassica napus , commonly known as rapeseed or canola, is a major oil crop contributing over 13% to the stable supply of edible vegetable worldwide. Identification and understanding gene functions in B. genome crucial for genomic breeding. A group genes controlling agronomic traits have been successfully cloned through functional genomics studies . In this review, we present an overview progress made including availability germplasm resources, omics databases genes. Based on current progress, also highlight main challenges perspectives field. The advances contribute better genetic basis underlying complex will expedite breeding high quality, resistance yield varieties.

Language: Английский

Citations

18