MtNIP5;1, a novel Medicago truncatula boron diffusion facilitator induced under deficiency DOI Creative Commons
Sara Granado‐Rodríguez, Luis Bolaños, María Reguera

et al.

Research Square (Research Square), Journal Year: 2020, Volume and Issue: unknown

Published: Oct. 30, 2020

Abstract Background: Legumes comprise important crops that offer major agronomic benefits, including the capacity of establishing symbiosis with rhizobia, fixing atmospheric N2. It has been proven legumes are particularly susceptible to boron (B) stress, which leads yield penalties. Boron deficiency or toxicity in plants causes inhibition growth and an altered development. Under such conditions, participation two distinct protein families (the intrinsic family MIP transporter BOR) is required minimize detrimental effects caused by B stress. However, legumes, little known about transport mechanisms responsible for uptake distribution, especially under deficiency. Results: A Medicago truncatula protein, MtNIP5;1 (Medtr1g097840) (homologous Arabidopsis thaliana AtNIP5;1) was identified as a novel legume involved Further analyses revealed this M. aquaporin expression boron-regulated roots, being induced repressed toxicity. localizes at plasma membrane root epidermal cells nodules, where plays pivotal roles symbiosis. Furthermore, partial complementation nip5;1-1 A. mutant phenotype supports functional role model plant. Conclusions: The results here presented support provides new insights into species.

Language: Английский

Detecting novel plant pathogen threats to food system security by integrating the Plant Reactome and remote sensing DOI
Seth C. Murray, Aart Verhoef, Alper Adak

et al.

Current Opinion in Plant Biology, Journal Year: 2025, Volume and Issue: 83, P. 102684 - 102684

Published: Jan. 5, 2025

Language: Английский

Citations

0
Genome-wide identification and characterization of annexin family in cowpea (Vigna unguiculata (L.) Walp.) DOI
Bharati Swain, Deepanker Yadav

Genetic Resources and Crop Evolution, Journal Year: 2025, Volume and Issue: unknown

Published: April 9, 2025

Language: Английский

Citations

0
Genome-wide identification of SnRK gene family and functional characterization of AcSnRK2.4 in response to heat stress in kiwifruit DOI Creative Commons
Yi Wang,

Xueling Wen,

H. Lv

et al.

Environmental and Experimental Botany, Journal Year: 2025, Volume and Issue: unknown, P. 106146 - 106146

Published: April 1, 2025

Language: Английский

Citations

0
Identification and characterization of the RcTCP gene family and its expression in response to abiotic stresses in castor bean DOI Creative Commons
Yanxiao Li, Xingyang Liu,

Xing-Yuan Xu

et al.

BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)

Published: July 4, 2024

The TCP (teosinte branched1/cincinnata/proliferating cell factor) family plays a prominent role in plant development and stress responses. However, genes have thus far not been identified castor bean, therefore an understanding of the expression functional aspects bean is lacking. To identify potential biological functions (RcTCP) members, composition RcTCP their basic physicochemical properties, subcellular localizations, interacting proteins, miRNA target sites, gene patterns under were assessed.

Language: Английский

Citations

1
Single feature polymorphism (SFP)-based selective sweep identification and association mapping of growth-related metabolic traits in Arabidopsis thaliana DOI Creative Commons
Liam Childs,

Hanna Witucka‐Wall,

Torsten Günther

et al.

BMC Genomics, Journal Year: 2010, Volume and Issue: 11(1), P. 188 - 188

Published: Jan. 1, 2010

Natural accessions of Arabidopsis thaliana are characterized by a high level phenotypic variation that can be used to investigate the extent and mode selection on primary metabolic traits. A collection 54 A. natural accession-derived lines were subjected deep genotyping through Single Feature Polymorphism (SFP) detection via genomic DNA hybridization Tiling 1.0 Arrays for selective sweeps, identification associations between sweep regions growth-related total 1,072,557 high-quality SFPs detected indications 3,943 deletions 1,007 duplications obtained. significantly lower than expected SFP frequency was observed in protein-, rRNA-, tRNA-coding non-repetitive intergenic regions, while pseudogenes, transposons, non-coding RNA genes enriched with SFPs. Gene families involved plant defence or signalling identified as highly polymorphic, several other including transcription factors depleted 198 significant 9 traits annotation hinting at nature relationship. Five also which one associated trait. We generated density polymorphism map highlights variability resistance across geographic ranges it identify sweeps phenotypes. Several show clear biological relationship, many remain requiring further investigation.

Language: Английский

Citations

14
Analysis of CATMA transcriptome data identifies hundreds of novel functional genes and improves gene models in the Arabidopsis genome DOI Creative Commons
Santiago P. Aubourg, Marie‐Laure Martin‐Magniette, Véronique Brunaud

et al.

BMC Genomics, Journal Year: 2007, Volume and Issue: 8(1), P. 401 - 401

Published: Jan. 1, 2007

Since the finishing of sequencing Arabidopsis thaliana genome, community and annotator centers have been working on improvement gene annotation at structural functional levels. In this context, we used large CATMA resource transcriptome to search for genes missed by different processes. Probes microarrays are specific sequence tags (GSTs) based CDS models predicted Eugene software. Among 24 576 v2 GSTs, 677 in regions considered as intergenic TAIR annotation. We analyzed cognate data carried out data-mining characterize novel improve models. The statistical analysis results more than 500 hybridized samples distributed among 12 organs provides an experimental validation 465 genes. hybridization evidence was confirmed RT-PCR approaches 88% Comparisons with current show that these often encode small proteins, average size 137 aa. Our approach has also led pre-existing through both extension 16 identification 13 erroneously constituted two merged CDS. This work is a noticeable step forward genome increased number validated transcribed which associated several annotations such expression profiles, conservation plants, transcripts protein motifs.

Language: Английский

Citations

14
Investigating low frequency somatic mutations inArabidopsiswith Duplex Sequencing DOI Creative Commons
Gus Waneka,

B. J. Pate,

J. Grey Monroe

et al.

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

Published: Feb. 1, 2024

Mutations are the source of novel genetic diversity but can also lead to disease and maladaptation. The conventional view is that mutations occur randomly with respect their environment-specific fitness consequences. However, intragenomic mutation rates vary dramatically due transcription coupled repair based on local epigenomic modifications, which non-uniformly distributed across genomes. One sequence feature associated decreased higher expression level, depending environmental cues. To understand whether association between level rate creates a systematic relationship effects, we perturbed through heat treatment in

Language: Английский

Citations

0
FuncFetch: An LLM-assisted workflow enables mining thousands of enzyme-substrate interactions from published manuscripts DOI Creative Commons
Nathaniel Smith, Xinyu Yuan, Chesney Melissinos

et al.

Bioinformatics, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 20, 2024

Abstract Motivation Thousands of genomes are publicly available, however, most genes in those have poorly defined functions. This is partly due to a gap between previously published, experimentally-characterized protein activities and deposited databases. activity deposition bottlenecked by the time-consuming biocuration process. The emergence large language models (LLMs) presents an opportunity speed up text-mining for biocuration. Results We developed FuncFetch—a workflow that integrates NCBI E-Utilities, OpenAI’s GPT-4 Zotero—to screen thousands manuscripts extract enzyme activities. Extensive validation revealed high precision recall determining whether abstract given paper indicates presence characterized paper. Provided manuscript, FuncFetch extracted data such as species information, names, sequence identifiers, substrates products, which were subjected extensive quality analyses. Comparison this against manually curated dataset BAHD acyltransferase demonstrated precision/recall 0.86/0.64 extracting substrates. further deployed on nine plant families. Screening 26,543 papers, retrieved 32,605 entries from 5,459 selected papers. also identified multiple extraction errors including incorrect associations, non-target enzymes, hallucinations, highlight need manual curation. verified, resulting comprehensive functional fingerprint family revealing ∼70% experimentally enzymes uncurated public domain. represents advance lays groundwork predicting functions uncharacterized enzymes. Availability Implementation Code minimally-curated available at: https://github.com/moghelab/funcfetch https://tools.moghelab.org/funczymedb. Supplementary information at Bioinformatics online.

Language: Английский

Citations

0
MtNIP5;1, a novel Medicago truncatula boron diffusion facilitator induced under deficiency DOI Creative Commons
Sara Granado‐Rodríguez, Luis Bolaños, María Reguera

et al.

Research Square (Research Square), Journal Year: 2020, Volume and Issue: unknown

Published: Oct. 30, 2020

Abstract Background: Legumes comprise important crops that offer major agronomic benefits, including the capacity of establishing symbiosis with rhizobia, fixing atmospheric N2. It has been proven legumes are particularly susceptible to boron (B) stress, which leads yield penalties. Boron deficiency or toxicity in plants causes inhibition growth and an altered development. Under such conditions, participation two distinct protein families (the intrinsic family MIP transporter BOR) is required minimize detrimental effects caused by B stress. However, legumes, little known about transport mechanisms responsible for uptake distribution, especially under deficiency. Results: A Medicago truncatula protein, MtNIP5;1 (Medtr1g097840) (homologous Arabidopsis thaliana AtNIP5;1) was identified as a novel legume involved Further analyses revealed this M. aquaporin expression boron-regulated roots, being induced repressed toxicity. localizes at plasma membrane root epidermal cells nodules, where plays pivotal roles symbiosis. Furthermore, partial complementation nip5;1-1 A. mutant phenotype supports functional role model plant. Conclusions: The results here presented support provides new insights into species.

Language: Английский

Citations

1