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 enrichment tool for ani-mals and plants DOI Creative Commons
Xijin Ge, Dongmin Jung

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2018, Volume and Issue: unknown

Published: May 4, 2018

Abstract Motivation Gene lists are routinely produced from various genome-wide studies. Enrichment analysis can link these gene with underlying molecular pathways by using functional categories such as ontology (GO). Results To complement existing tools, we developed ShinyGO several features: (1) large annotation database GO and many other sources for over 200 plant animal species, (2) graphical visualization of enrichment results characteristics, (3) application program interface (API) access to KEGG STRING the retrieval pathway diagrams protein-protein interaction networks. is an intuitive, web that help researchers gain actionable insights lists. Availability http://ge-lab.org/go/ Contact [email protected] Supplementary information data available at Bioinformatics online.

Language: Английский

Citations

124
Genome-wide association mapping for resistance to leaf rust, stripe rust and tan spot in wheat reveals potential candidate genes DOI Creative Commons
Philomin Juliana, Ravi P. Singh, P. K. Singh

et al.

Theoretical and Applied Genetics, Journal Year: 2018, Volume and Issue: 131(7), P. 1405 - 1422

Published: March 27, 2018

Genome-wide association mapping in conjunction with population sequencing map and Ensembl plants was used to identify markers/candidate genes linked leaf rust, stripe rust tan spot resistance wheat. Leaf (LR), (YR) (TS) are some of the important foliar diseases wheat (Triticum aestivum L.). To candidate for these CIMMYT's (International Maize Wheat Improvement Center) International bread screening nurseries, we genome-wide studies (GWAS) information from plants. entries were genotyped using genotyping-by-sequencing phenotyped replicated trials. Using a mixed linear model, observed that seedling LR associated 12 markers on chromosomes 1DS, 2AS, 2BL, 3B, 4AL, 6AS 6AL, TS 14 1AS, 2AL, 3AS, 3AL, 6AL. Seedling adult plant (APR) YR several at distal end chromosome 2AS. In addition, APR also 2DL, 3B 7DS. The potential included genes, receptor-like serine/threonine-protein kinases defense-related enzymes. However, extensive LD decays about 5 × 107 bps, poses huge challenge delineating gene intervals candidates should be further mapped, functionally characterized validated. We explored segment 2AS multiple disease identified seventeen genes. conclude identifying significant GWAS is feasible wheat, thus creating opportunities accelerating molecular breeding.

Language: Английский

Citations

113
The AP2/ERF Gene Family in Triticum durum: Genome-Wide Identification and Expression Analysis under Drought and Salinity Stresses DOI Open Access

Sahar Faraji,

Ertuğrul Filiz, Seyed Kamal Kazemitabar

et al.

Genes, Journal Year: 2020, Volume and Issue: 11(12), P. 1464 - 1464

Published: Dec. 7, 2020

Members of the AP2/ERF transcription factor family play critical roles in plant development, biosynthesis key metabolites, and stress response. A detailed study was performed to identify TtAP2s/ERFs durum wheat (Triticum turgidum ssp. durum) genome, which resulted identification 271 genes distributed on chromosomes 1A-7B. By carrying 27 genes, chromosome 6A had highest number TtAP2s/ERFs. Furthermore, a duplication assay demonstrated that 70 duplicated gene pairs undergone purifying selection. According RNA-seq analysis, expression levels all tissues response stimuli were associated with DRF ERF subfamily genes. In addition, results revealed TtAP2/ERF have tissue-specific patterns, most significantly induced root tissue. Additionally, 13 (six ERFs, three DREBs, two DRFs, one AP2, RAV) selected for further analysis via qRT-PCR their potential coping drought salinity stresses. The belonging DREB markedly under both drought-stress salinity-stress conditions. docking simulations several residues pocket sites proteins response, may be useful future site-directed mutagenesis studies increase tolerance wheat. This could provide valuable insights evolutionary functional assays this important

Language: Английский

Citations

103
Applying the latest advances in genomics and phenomics for trait discovery in polyploid wheat DOI Creative Commons
Philippa Borrill, Sophie A. Harrington, Cristóbal Uauy

et al.

The Plant Journal, Journal Year: 2018, Volume and Issue: 97(1), P. 56 - 72

Published: Nov. 8, 2018

Improving traits in wheat has historically been challenging due to its large and polyploid genome, limited genetic diversity in-field phenotyping constraints. However, within recent years many of these barriers have lowered. The availability a chromosome-level assembly the genome now facilitates step-change genetics provides common platform for resources, including variation data, gene expression data markers. development sequenced mutant populations gene-editing techniques enables rapid assessment function directly. ability alter targeted manner will unmask effects homoeolog redundancy allow hidden potential this be discovered. New identify exploit wild relatives enable breeders take advantage additional sources address challenges facing food production. Finally, advances phenomics unlocked screening interest both greenhouses field. Looking forwards, integrating diverse types, genomic, epigenetic big approaches machine learning understand trait biology unprecedented detail.

Language: Английский

Citations

97
CANTATAdb 2.0: Expanding the Collection of Plant Long Noncoding RNAs DOI
Michał Wojciech Szcześniak,

Oleksii Bryzghalov,

Joanna Ciomborowska-Basheer

et al.

Methods in molecular biology, Journal Year: 2019, Volume and Issue: unknown, P. 415 - 429

Published: Jan. 1, 2019

Language: Английский

Citations

93
KnetMiner: a comprehensive approach for supporting evidence‐based gene discovery and complex trait analysis across species DOI Creative Commons
Keywan Hassani‐Pak, Ajit Singh, Marco Brandizi

et al.

Plant Biotechnology Journal, Journal Year: 2021, Volume and Issue: 19(8), P. 1670 - 1678

Published: March 22, 2021

The generation of new ideas and scientific hypotheses is often the result extensive literature database searches, but, with growing wealth public private knowledge, process searching diverse interconnected data to generate insights into genes, gene networks, traits diseases becoming both more complex time-consuming. To guide this technically challenging integration task make discovery easier for researchers, we have developed a comprehensive software package called KnetMiner which open-source containerized easy use. an integrated, intelligent, interactive network platform that supports scientists explore understand biological stories across species. It features fast algorithms generating rich networks prioritizing candidate genes based on knowledge mining approaches. used in many plant science institutions has been adopted by several breeding organizations accelerate discovery. generic customizable can therefore be readily applied species types; example, it pest insects fungal pathogens; most recently repurposed support COVID-19 research. Here, give overview main approaches behind report plant-centric case studies identifying trait relationships Triticum aestivum (bread wheat), as well as, evidence-based approach rank under large Arabidopsis thaliana QTL. available at: https://knetminer.org.

Language: Английский

Citations

90
Plant genome and transcriptome annotations: from misconceptions to simple solutions DOI Creative Commons
Marie Bolger, Borjana Arsova, Björn Usadel

et al.

Briefings in Bioinformatics, Journal Year: 2016, Volume and Issue: unknown, P. bbw135 - bbw135

Published: Dec. 2, 2016

Next-generation sequencing has triggered an explosion of available genomic and transcriptomic resources in the plant sciences. Although genome transcriptome become orders magnitudes cheaper more efficient, often functional annotation process is lagging behind. This might be hampered by lack a comprehensive enumeration simple-to-use tools to researcher. In this review, we present (i) typical ontologies used sciences, (ii) useful databases for annotation, (iii) what expect from annotated genome, (iv) automated pipeline (v) recipe reference chart outlining steps annotate genomes/transcriptomes using publicly resources.

Language: Английский

Citations

86
Plant Reactome: a knowledgebase and resource for comparative pathway analysis DOI Creative Commons
Sushma Naithani, Parul Gupta, Justin Preece

et al.

Nucleic Acids Research, Journal Year: 2019, Volume and Issue: unknown

Published: Oct. 15, 2019

Abstract Plant Reactome (https://plantreactome.gramene.org) is an open-source, comparative plant pathway knowledgebase of the Gramene project. It uses Oryza sativa (rice) as a reference species for manual curation pathways and extends knowledge to another 82 via gene-orthology projection using data model framework. currently hosts 298 pathways, including metabolic transport transcriptional networks, hormone signaling developmental processes. In addition browsing users can upload analyze their omics data, such gene-expression overlay curated or experimental gene-gene interaction extend knowledge. The team actively engages researchers students on gene by offering workshops online tutorials. supports, implements collaborates with wider community make tools related genes, genomes, Findable, Accessible, Interoperable Re-usable (FAIR).

Language: Английский

Citations

83
Edit at will: Genotype independent plant transformation in the era of advanced genomics and genome editing DOI Creative Commons

Albert P. Kausch,

Kimberly Nelson‐Vasilchik,

Joel Hague

et al.

Plant Science, Journal Year: 2019, Volume and Issue: 281, P. 186 - 205

Published: Jan. 14, 2019

Language: Английский

Citations

79
Tissue-specific transcriptome profiling of the Arabidopsis inflorescence stem reveals local cellular signatures DOI Creative Commons
Dongbo Shi, Virginie Jouannet, Javier Agustí

et al.

The Plant Cell, Journal Year: 2020, Volume and Issue: 33(2), P. 200 - 223

Published: Dec. 2, 2020

Abstract Genome-wide gene expression maps with a high spatial resolution have substantially accelerated plant molecular science. However, the number of characterized tissues and growth stages is still small due to limited accessibility most for protoplast isolation. Here, we provide profiles mature inflorescence stem Arabidopsis thaliana covering comprehensive set distinct tissues. By combining fluorescence-activated nucleus sorting laser-capture microdissection next-generation RNA sequencing, transcriptomes xylem vessels, fibers, proximal distal cambium, phloem, phloem cap, pith, starch sheath, epidermis cells. Our analyses classified more than 15,000 genes as being differentially expressed among different revealed known novel tissue-specific cellular signatures. determining overrepresented transcription factor binding regions in promoters genes, identified candidate transcriptional regulators. datasets predict an exceptional allow hypotheses be generated about organization physiological processes. Moreover, demonstrate that information broad range can established at by nuclear mRNA profiling. Tissue-specific values accessed online https://arabidopsis-stem.cos.uni-heidelberg.de/.

Language: Английский

Citations

74