The Plant Journal, Год журнала: 2023, Номер 116(4), С. 967 - 973
Опубликована: Ноя. 1, 2023
Over the last 10 years, The Plant Journal has published a wide number of Resource Articles not including those in this collection. currently standing at 262. These have covered genomes, transcriptomes and epigenomics, proteogenomics, translatomics, proteomics post-translational modifications, metabolomics, lipidomics, ionomics, flux profiling, large-scale phenotyping novel genetic cell biological resources as well modeling databases. In recent pan-transcriptomes (including plant gene atlases), pangenomes single-cell biology become major focal points for biology. first articles series were by Sierro et al. (2013), Niarchou (2013) Dorn (2013). these reported physical genome map tobacco Hicks Broadleaf been cited 21 times, while second provided cross-species database predicted antimicrobial peptides 32 times third describing transcriptomics potential development pennycress winter cover crop being 63 (at time going to press). (Virtual) Special Issue, we celebrate decade with collection resource covering databases, high-resolution haplotype-phased resources, databases horticultural fruit crops, expression atlases soybean sweet potato sprouting ABA responses lateral root development. addition, special issue contains four focused on combined stress evaluation which is becoming increasingly prevalent current prospective climate change scenarios. Before briefly issue, however, felt it timely review some key community prior relaunch. To do so separated 57 previously papers that chosen highlight into seven groups basis experimental techniques they employ- namely (i) sequencing, (ii) population trait analysis, (iii) alternative splicing, non-coding RNA, transposons epigenome investigation, (iv) atlases, (v) modifications interactomics, (vi) lipidomics ionomics (vii) miscellaneous resources. A high TPJ years report genomes model species minor crops. For example, article Cheng (2017), complete reannotation Arabidopsis thaliana reference genome, sequence Aethionema arabicum valuable seed dormancy Brassicaceae evolution (Fernandez-Pozo al., 2021). Similarly, resequencing Brachipodium inbred lines massively improve annotation important grass (Gordon 2014), sequencing Spirodela polyrhiza fast-growing aquatic monocot (Michael 2017). also assemblies cereals; sorghum (McCormick 2018), rye (Bauer 2017), flax (You 2018) bread wheat (Montenegro 2017; Zhu 2021); tree walnut (Martínez-García 2016), scots pine (Kastally 2022), Jatropha (Wu 2015), white spruce (Warren 2015) tolerant forest Casuarina equisetifolia (Ye 2019); more tomato (Aflitos black raspberry (VanBuren bottle gourde Chinese liquorice (Mochida 2017) pomegranate (Qin studies span range sizes, technologies computational approaches optical mapping complement differ regard genotypes sequenced many providing high-quality only single genotype, others such 2014) up 1000. keeping expansion breadth (Gui pan-genome Another category extensively featured since inception focuses generation/collection broad populations their subsequent availability. Such often tandem methods involved genotyping and/or phenotyping. We believe are particularly worthy highlighting. 2016 validation an apple array was (Bianco highly both tool research template establishment similar other S. pennellii backcross line (Ofner 2016). Important less well-characterized include cowpea (Vigna unguiculate). whole sequences 37 accessions supporting SNP-based platform (Muñoz-Amatriaín described generation multi-parent advanced inter-cross (MAGIC) analysis improvement (Huynh 2018). further Soybean (Song 2020), cotton (Gossypium hirsutum) ethyl methanesulfonate mutant library provides significant species. Finally, paper Li (2023) reports traits associated loci conferring radiation use efficiency importantly delivers much-touted promise using quantitative genetics means improving photosynthesis. While above largely applied aspects considerable advances our understanding fundamental processes among series. chose six here. global identification splicing via comparative SMRT- Illumina-based RNA-seq strawberry. Evaluation epigenetic changes chromatin accessibility Brassica napus Shen (2017) Sijacic (2018), staying within Brassicaea, Huang (2018) performed systematic long RNAs during pollen fertilization rapa. two contributions role study maize Anderson (2019) diversification closely related almond peach (Alioto 2020). Within period launched type unprecedented torrent data from RNA generated. term atlas relatively recently adopted common usage, several years. transcriptome dynamics sequential biotic abiotic stresses across presented pair early (Coolen 2016; Klepikova With later (Zouine Physcomitrella 2020; Perroud (Hoopes 2019), rice (Kawakatsu 2021), Norway (Bag 2021) barley (Coulter 2022). At most basic level, provide information concerning genes expressed certain tissues, but sophisticated now contain developmental cues or a(biotic stresses). Berkowitz (2021) laser micro-dissected leaf epidermis, mesophyll vasculature defines tissue-specific transcriptional multiple treatments rich resource. comprehensive transcriptomic datasets technical increased coverage sensitivity over notable various technology. Two focus mitochondrial proteome. Senker studied complexome two-dimensional electrophoretic gels sequencing. More recently, fascinating Fuchs (2020) explored protein composition individual mitochondrion deduce principles functional structural organization estimating total 1.4 million molecules make copy numbers proteins five orders magnitude. note Cao who generated ABA-T3SE interactome network between Pseudomonas syringae T3SEs encoded ABA-regulated unique insight interaction same year, ‘The PTM Viewer’ (Willems central exploring received community. Less than still data-rich ionomics. Of topic would like one each discipline. Drapal (2022), chemotype core genus Nicotiana 17 benthamiana enabling measurement 360 metabolites chemical classes thousands unknowns dedicated spectral chromatographic properties. As represents exemplary metabolomics year before 1135 ionomes (Campos revealed pattern mineral nutrient trace element diversity Even earlier PlantFAdb (Ohlrogge allowing researchers explore hundreds fatty acid structures synthesized different plants alongside phylogenetic relationships. really fit readily categories. want better way order them will discuss chronologically. genome-scale metabolic brown algae Ectocarpus siliculosus Prigent 2014 (Prigent 2014). This consists 1866 reactions 2020 metabolites, its construction integrative approach identifying pathways, gap filling manual refinement. capability produce biomass validated balance enabled 56 genes. primary metabolism diatom Phaeodactylum tricornutum Kim (Kim study, constructed P. biochemical literature online bioinformatic Intracellular fluxes subsequently calculated autotrophic, mixotrophic heterotrophic growth conditions. unusual features metabolism, presence lower glycolysis pathways mitochondrion, differences photosynthetic organisms. next resource, Depuydt Vandepoele (2021), function prediction outperformed state-of-the-art expression-based approaches. Utilizing method assign least 5054 (42.6%) then-unknown genome. Grau Franco-Zorrilla TDTHub, web server transcription factor binding sites plants. uses precomputed 40 effectiveness demonstrated respect anthocyanin biosynthetic pathway jasmonate responses. date manuscript Jaiswal (2022) used integrated identify γ-glutamyl based signature mass fragments shifts 13C 15N enriched metabolite extracts. be powerful assignment turnover likely increasing utility begin attain greater time-resolution events. addition reviewing contribution made date, wanted showcase articles. Therefore, remainder Issue comprises 4 new issues containing databasing 9 research-based start Weil describe PLANTdataHUB management FAIR-compliant sharing (Weil 2023). consortium-based effort FAIR digital objects called annotated contexts (ARCs) tools scientific planning, communication, collaboration, publication reuse simultaneously quality control insights. allows scaling personal communities borrowing much properties software should facilitate transition science age. Mansfield contribute high-quality, haplotype-resolved, chromosome-scale assembly Pacific crabapple Malus fusca (Mansfeld M. extremely hardy wild relative commercial untapped cultivars enhanced resistance. high-fidelity long-reads scaffolding maps high-throughput conformation capture resulting contiguous date. However, insights invaluable general facilitating DNA-informed introgression breeding. similarly Zhou telomere-to-telomere Populus tremula × alba chromosome-scale, haplotype-resolved (Zhou They additionally evaluated origins repetitive landscapes 147 bp monomer abundant repeat frequently exceeding length excess 1 megabase. work thus greatly improves design editing experiments opens questions aspen-specific satellite DNA. data-mining nearly 13 000 uniformly omics libraries spanning 150 fruits, vegetables ornamental (Cheng conserved can rapidly identified equipped allow assessment expression, in-species regulation, coexpression, enrichment/pathway analysis. case authors functions CmEIN3 flower transgenic chrysanthemum illustrating generating testable hypotheses. Liu regulatory networks determining (Liu developed Gene Improvements Fruit Trait Database (GIFTdb) 35 365 derived 30 2021, supplemented 236 UniProt almost 34 homology furthermore supports aids facile searches rendering putative facile. Almeida-Silva present Expression Atlas v2, updated version agronomically legume 4-fold increase samples, featuring transcript- gene-level transcript abundance matrices 5481 publicly available samples(Almeida-Silva New availability transcript-level estimates equivalence differential bias-corrected counts accuracy analyses, interface improved visualization user experience, reproducible scalable pipeline R package. It undoubtedly huge interested legumes alike. Motte co-workers inducible systems induce roots synchronously rice, Medicago courses stages primordium three displayed temporal patterns elements AUX/IAA LBD families identified, thereby collectively contributing (Motte Global warming driving alarming frequency intensity extreme events, droughts, heat waves combination, inflicting heavy losses agricultural production. address phenomenon, Sinha tissue/stress tissues water deficit, combination stresses. detailed dataset includes response leaf, pod, anther, stigma, ovary sepal singular Mining set stress-response transcripts tissue had findings crucial importance when attempting enhance overall resilience crops (see Zsögön 2022 review) imply could require coordinated alters stress-specific manner (Sinha – C4 considered environmental extremes. how molecular genotype-specific context day unknown. assess Bonnot examined whether temperature impact cold-sensitive heat-sensitive finding influencing (Bonnot On subject Stress combinations Interactions Plants (SCIPDb) Priya (2023). collates morpho-physio (phenome) (transcriptome metabolome) combinations. phenome 939 delineate effects yield candidate drought pathogen tolerance. opportunities tackle pressing problem developing climate-resilient vein Da Ros multi-omics combinatorial (Da investigated physio-metabolic adjustments reprogramming acclimations heat, drought, salinity all therein. complexity altered considerably assessed agronomic losses, proline levels. assembled open-access browser interrogation WRKY33 leading tolerance stress. wheat-specific highlights strength discovery. above-mentioned feature metabolomics. these, multi-year yield-associated phenotype-guided screen 7900 around world, associations complex weight soluble solids (Brix) (Zemach Intriguingly, taking able isolate individuals Brix values compromised terms yield. Bulut gas chromatography–mass spectrometry (GC–MS) liquid chromatography-mass (LC–MS) commonly grown Europe, bean, chickpea, lentil, pearl lupin level. contained therein future integration metabolomics-assisted breeding metabolite-based GWAS. Giese light-dependent proteome (and rosettes, focusing phosphorylation, lysine acetylation cysteine-based redox switches. 24 modification (PTMs) detected, 1700 changed dark light known yet unreported light-responsive PTMs investigating (Giese Writing editorial reinforced view great best transformative fields. Journal, remain keen publish promote not, default, mechanistic insight. main criterion instead wide-enough interest broader continue welcome submissions fields species, pan genomes; analysis; Transposons epigenomes; atlases; interactomics; indeed any satisfies above-stated criteria. convinced (as amply demonstrates), underpin hope remains journal choice engaged
Язык: Английский
