PHI-base in 2022: a multi-species phenotype database for Pathogen–Host Interactions

Nucleic Acids Research, Journal Year: 2021, Volume and Issue: 50(D1), P. D837 - D847

Published: Nov. 8, 2021

Abstract Since 2005, the Pathogen–Host Interactions Database (PHI-base) has manually curated experimentally verified pathogenicity, virulence and effector genes from fungal, bacterial protist pathogens, which infect animal, plant, fish, insect and/or fungal hosts. PHI-base (www.phi-base.org) is devoted to identification presentation of phenotype information on pathogenicity their host interactions. Specific gene alterations that did not alter in interaction are also presented. invaluable for comparative analyses discovery candidate targets medically agronomically important species intervention. Version 4.12 (September 2021) contains 4387 references, provides 8411 279 tested 228 hosts 18, 190 This a 24% increase content since 4.8 2019). Bacterial pathogens represent majority data, with 54:46 split entries, whilst protists, protozoa, nematodes insects 3.6% entries. Host consist approximately 54% plants 46% others medical, veterinary environmental importance. data disseminated UniProtKB, FungiDB Ensembl Genomes. will migrate new gene-centric version (version 5.0) early 2022. major development briefly described.

Language: Английский

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The Arabidopsis Information Resource in 2024

Genetics, Journal Year: 2024, Volume and Issue: 227(1)

Published: March 8, 2024

Since 1999, The Arabidopsis Information Resource (www.arabidopsis.org) has been curating data about the thaliana genome. Its primary focus is integrating experimental gene function information from peer-reviewed literature and codifying it as controlled vocabulary annotations. Our goal to produce a "gold standard" functional annotation set that reflects current state of knowledge At same time, resource serves nexus for community-based collaborations aimed at improving quality, access, reuse. For past decade, our work made possible by subscriptions global user base. This update covers ongoing biocuration work, some modernization efforts contribute first major infrastructure overhaul since 2011, introduction JBrowse2, resource's role in community activities such organizing structural reannotation assessment, we used ontology annotations metric evaluate: (1) what currently known (2) "unknown" genes. Currently, 74% proteome annotated least one term. Of those loci, half have support following aspects: molecular function, biological process, or cellular component. sheds light on genes which not yet identified any published no annotation. Drawing attention these unknown highlights gaps potential sources novel discoveries.

Language: Английский

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KnetMiner: a comprehensive approach for supporting evidence‐based gene discovery and complex trait analysis across species

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

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KG-COVID-19: A Framework to Produce Customized Knowledge Graphs for COVID-19 Response

Patterns, Journal Year: 2020, Volume and Issue: 2(1), P. 100155 - 100155

Published: Nov. 9, 2020

Integrated, up-to-date data about SARS-CoV-2 and COVID-19 is crucial for the ongoing response to pandemic by biomedical research community. While rich biological knowledge exists related viruses (SARS-CoV, MERS-CoV), integrating this difficult time-consuming, since much of it in siloed databases or textual format. Furthermore, required community vary drastically different tasks; optimal a machine learning task, example, from used populate browsable user interface clinicians. To address these challenges, we created KG-COVID-19, flexible framework that ingests integrates heterogeneous produce graphs (KGs), applied create KG response. This also can be other problems which must quickly integrated applications, including future pandemics.

Language: Английский

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Modelling of gene loss propensity in the pangenomes of three Brassica species suggests different mechanisms between polyploids and diploids

Plant Biotechnology Journal, Journal Year: 2021, Volume and Issue: 19(12), P. 2488 - 2500

Published: July 26, 2021

Summary Plant genomes demonstrate significant presence/absence variation (PAV) within a species; however, the factors that lead to this have not been studied systematically in Brassica across diploids and polyploids. Here, we developed pangenomes of polyploid napus its two diploid progenitor B. rapa oleracea infer how PAV may differ between Modelling gene loss suggests propensity is primarily associated with transposable elements while napus, homoeologous recombination. We use these results gain insights into different causes loss, both following polyploidization, pave way for application machine learning methods understanding underlying biological physical presence/absence.

Language: Английский

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GrainGenes: a data-rich repository for small grains genetics and genomics

Database, Journal Year: 2022, Volume and Issue: 2022

Published: Jan. 1, 2022

Abstract As one of the US Department Agriculture—Agricultural Research Service flagship databases, GrainGenes (https://wheat.pw.usda.gov) serves data and community needs globally distributed small grains researchers for genetic improvement Triticeae family Avena species that include wheat, barley, rye oat. accomplishes its mission by continually enriching cross-linked content following findable, accessible, interoperable reusable principles, enhancing maintaining an intuitive web interface, creating tools to enable easy access establishing connections within between other biological databases facilitate knowledge discovery. operates database community, collaborates with curators genome sequencing groups contributes AgBioData Consortium International Wheat Initiative through Information System (WheatIS). Interactive linked is paramount successful now has 2917 manually curated gene records, including 289 genes 254 alleles from Gene Catalogue (WGC). There are >4.8 million models in 51 browser assemblies, 6273 quantitative trait loci >1.4 on 4756 physical maps contained 443 mapping sets, complete standardized metadata. Most notably, 50 new browsers outputs Barley PanGenome projects have been created. We provide example expression track Genome Sequencing Chinese Spring wheat demonstrate how tracks can be adapted different types. To help users benefit more data, created four tutorials available YouTube. executing vision service continuously responding global a centralized, long-term, interconnected repository. Database URL:https://wheat.pw.usda.gov

Language: Английский

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Exotic alleles contribute to heat tolerance in wheat under field conditions

Communications Biology, Journal Year: 2023, Volume and Issue: 6(1)

Published: Jan. 9, 2023

Global warming poses a major threat to food security and necessitates the development of crop varieties that are resilient future climatic instability. By evaluating 149 spring wheat lines in field under yield potential heat stressed conditions, we demonstrate how strategic integration exotic material significantly increases stress compared elite lines, with no significant penalty favourable conditions. Genetic analyses reveal three exotic-derived genetic loci underlying this tolerance which together increase by over 50% reduce canopy temperature approximately 2 °C. We identified an Ae. tauschii introgression most these associations extracted introgressed genes, revealing candidates for further dissection. Incorporating alleles into breeding programmes could serve as pre-emptive strategy produce high yielding cultivars effects uncertainty.

Language: Английский

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Accelerating crop improvement via integration of transcriptome-based network biology and genome editing

Planta, Journal Year: 2025, Volume and Issue: 261(4)

Published: March 17, 2025

Language: Английский

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A Dual Strategy of Breeding for Drought Tolerance and Introducing Drought-Tolerant, Underutilized Crops into Production Systems to Enhance Their Resilience to Water Deficiency

Plants, Journal Year: 2020, Volume and Issue: 9(10), P. 1263 - 1263

Published: Sept. 24, 2020

Water scarcity is the primary constraint on crop productivity in arid and semiarid tropical areas suffering from climate alterations; accordance, agricultural systems have to be optimized. Several concepts strategies should considered improve yield quality, particularly vulnerable regions where such environmental changes cause a risk of food insecurity. In this work, we review two aiming increase drought stress tolerance: (i) use natural genes that evolved over time are preserved wild relatives landraces for tolerance breeding using conventional molecular methods (ii) exploiting reservoir neglected underutilized species identify those known more drought-tolerant than staple crops while possessing other desired agronomic nutritive characteristics, as well introducing them into existing cropping make resilient water deficiency conditions. past, existence was either unknown or difficult exploit traditional techniques secure potential long-term solutions. Today, with advances genomics phenomics, there number new tools available facilitate discovery resistance their relatively easy transfer advanced lines, thus accelerating progress creating varieties can withstand prolonged periods. Among marker-assisted selection (MAS), genomic (GS), targeted gene editing (clustered regularly interspaced short palindromic repeat (CRISPR) technology). The integration these major strategies, crops, introduction production has enhance resilience under conditions scarcity.

Language: Английский

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Pangenomics in crop improvement—from coding structural variations to finding regulatory variants with pangenome graphs

The Plant Genome, Journal Year: 2021, Volume and Issue: 15(1)

Published: Dec. 13, 2021

Abstract Since the first reported crop pangenome in 2014, advances high‐throughput and cost‐effective DNA sequencing technologies facilitated multiple such studies including pangenomes of oilseed rape ( Brassica napus L.), soybean [ Glycine max (L.) Merr.], rice Oryza sativa wheat Triticum aestivum barley Hordeum vulgare L.). Compared with single‐reference genomes, provide a more accurate representation genetic variation present species. By combining genomic data accessions, allow for detection annotation complex polymorphisms as structural variations (SVs), one major determinants diversity within In this review we summarize current literature on pangenomics, focusing their application to find candidate SVs involved traits agronomic interest. We then highlight potential discovery functional characterization noncoding regulatory sequences variations. conclude summary outlook innovative structures representing complete content plant annotations coding elements outcomes transcriptomic epigenomic experiments.

Language: Английский

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