Molecular Plant, Journal Year: 2017, Volume and Issue: 10(8), P. 1129 - 1132
Published: March 24, 2017
Language: Английский
Molecular Plant, Journal Year: 2023, Volume and Issue: 16(11), P. 1733 - 1742
Published: Sept. 22, 2023
Language: Английский
Citations
1284
Genome biology, Journal Year: 2016, Volume and Issue: 17(1)
Published: April 12, 2016
JBrowse is a fast and full-featured genome browser built with JavaScript HTML5. It easily embedded into websites or apps but can also be served as standalone web page.Overall improvements to speed scalability are accompanied by specific enhancements that support complex interactive queries on large track sets. Analysis functions readily added using the plugin framework; most visual aspects of tracks customized, along clicks, mouseovers, menus, popup boxes. used browse local annotation files offline generate high-resolution figures for publication.JBrowse mature application suitable visualization analysis.
Language: Английский
Citations
738
Nucleic Acids Research, Journal Year: 2018, Volume and Issue: 47(D1), P. D1155 - D1163
Published: Oct. 22, 2018
The Plant Promoter Analysis Navigator (PlantPAN; http://PlantPAN.itps.ncku.edu.tw/) is an effective resource for predicting regulatory elements and reconstructing transcriptional networks plant genes. In this release (PlantPAN 3.0), 17 230 TFs were collected from 78 species. To explore landscapes, genomic locations of TFBSs have been captured 662 public ChIP-seq samples using standard data processing. A total 1 233 999 linkages identified 99 factors (TFs, histones other DNA-binding proteins) their target genes across seven Additionally, new version added 2449 matrices extracted peaks cis-regulatory element prediction. addition to integrated data, four major improvements provided more comprehensive information TF binding events, including (i) 1107 experimentally verified the literature, (ii) gene regulation network comparison between two species, (iii) 3D structures TF-DNA complexes (iv) condition-specific co-expression extended PlantPAN 3.0 can not only be efficiently used investigate critical cis- trans-regulatory in promoters, but also reconstruct high-confidence relationships among TF-targets under specific conditions.
Language: Английский
Citations
394
BMC Genomics, Journal Year: 2017, Volume and Issue: 18(1)
Published: June 7, 2017
Tobacco (Nicotiana tabacum) is an important plant model system that has played a key role in the early development of molecular biology. The tobacco genome large and its characterisation challenging because it allotetraploid, likely arising from hybridisation between diploid N. sylvestris tomentosiformis ancestors. A draft assembly was recently published for tabacum, but aforementioned complexities limited utility due to high level fragmentation. Here we report improved assembly, which, aided by application optical mapping, achieves N50 size 2.17 Mb enables anchoring 64% pseudomolecules; significant increase previous value 19%. We use this identify two homeologous genes explain differentiation burley market class, with potential greater understanding Nitrogen Utilization Efficiency Use plants; trait future sustainability agricultural production. Development tabacum what believe be first successful map-based gene discovery species, demonstrates research commercially-important species.
Language: Английский
Citations
323
Science, Journal Year: 2015, Volume and Issue: 349(6247), P. 540 - 543
Published: July 30, 2015
Obligate parasitic plants in the Orobanchaceae germinate after sensing plant hormones, strigolactones, exuded from host roots. In Arabidopsis thaliana, α/β-hydrolase D14 acts as a strigolactone receptor that controls shoot branching, whereas its ancestral paralog, KAI2, mediates karrikin-specific germination responses. We observed but not D14, is present at higher copy numbers species than nonparasitic relatives. KAI2 paralogs parasites are distributed into three phylogenetic clades. The fastest-evolving clade, KAI2d, contains majority of paralogs. Homology models predict ligand-binding pockets KAI2d resemble D14. transgenes confer strigolactone-specific responses to thaliana. Thus, and underwent convergent evolution recognition, respectively enabling developmental strigolactones angiosperms detection parasites.
Language: Английский
Citations
284
Cell, Journal Year: 2020, Volume and Issue: 182(5), P. 1093 - 1108.e18
Published: Aug. 17, 2020
Language: Английский
Citations
265
New Phytologist, Journal Year: 2018, Volume and Issue: 222(2), P. 966 - 980
Published: Dec. 24, 2018
Most land plant genomes carry genes that encode RPW8-NLR Resistance (R) proteins. Angiosperms two subclasses: ADR1 and NRG1. ADR1s act as 'helper' NLRs for multiple TIR- CC-NLR R proteins in Arabidopsis. In angiosperm families, NRG1 co-occurs with TIR-NLR genes. We tested whether is required signalling of TIR-NLRs. Using CRISPR mutagenesis, we obtained an nrg1a-nrg1b double mutant Arabidopsis accessions, nrg1 Nicotiana benthamiana. These mutants are compromised all TIR-NLRs tested, including WRR4A, WRR4B, RPP1, RPP2, RPP4 the pairs RRS1/RPS4, RRS1B/RPS4B, CHS1/SOC3 CHS3/CSA1. Arabidopsis, hypersensitive cell death response (HR) full oomycete resistance, but not salicylic acid induction or bacterial resistance. By contrast, loss function does compromise RPS5 MLA. RPM1 RPS2 (CC-NLRs) slightly mutant. Thus, contributes to some CC-NLRs. Some NRG1-dependent also signal partially via sister clade, ADR1. propose only, only both neither.
Language: Английский
Citations
252
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2019, Volume and Issue: unknown
Published: Sept. 14, 2019
Abstract The original Heinz 1706 reference genome was produced by a large team of scientists from across the globe variety input sources that included 454 sequences in addition to full-length BACs, BAC and fosmid ends sequenced with Sanger technology. We present here latest tomato (SL4.0) assembled de novo PacBio long reads scaffolded using Hi-C contact maps. assembly validated Bionano optical maps 10X linked-read sequences. This is highly contiguous fewer gaps compared previous builds almost all scaffolds have been anchored oriented 12 chromosomes. found more repeats versions one largest repeat classes identified are LTR retrotransposons. also describe updates annotation since last publication. corresponding ITAG4.0 has 4,794 novel genes along 29,281 preserved ITAG2.4. Most updated extensions 5’ 3’ UTRs resulting doubling annotated per gene. can be accessed SGN through BLAST database, Pathway database (SolCyc), Apollo, JBrowse browser FTP available at https://solgenomics.net .
Language: Английский
Citations
232
eLife, Journal Year: 2019, Volume and Issue: 8
Published: Nov. 27, 2019
The molecular codes underpinning the functions of plant NLR immune receptors are poorly understood. We used in vitro Mu transposition to generate a random truncation library and identify minimal functional region NLRs. applied this method NRC4-a helper that with multiple sensor NLRs within Solanaceae receptor network. This revealed NRC4 N-terminal 29 amino acids sufficient induce hypersensitive cell death. is defined by consensus MADAxVSFxVxKLxxLLxxEx (MADA motif) conserved at N-termini NRC family proteins ~20% coiled-coil (CC)-type MADA motif matches α1 helix Arabidopsis protein ZAR1, which undergoes conformational switch during resistosome activation. Immunoassays functionally across from distantly related species. NRC-dependent lack sequences indicating has degenerated over evolutionary time.
Language: Английский
Citations
208
Trends in Plant Science, Journal Year: 2016, Volume and Issue: 21(6), P. 506 - 515
Published: Feb. 14, 2016
Language: Английский
Citations
185