PlantGSAD: a comprehensive gene set annotation database for plant species

Ma, Xuelian; Yan, Hengyu; Yang, Jiaotong; Liu, Yue; Li, Zhongqiu; Sheng, Minghao; Cao, Yaxin; Yu, Xinyue; Yi, Xin; Xu, Wenying

doi:10.1093/nar/gkab794

Cited by 32 publications

(23 citation statements)

References 82 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…For further analysis of HOS59‐binding genes, we applied the PlantGSAD platform (Ma et al., 2022), especially the TO category, to predict the potential functions of HOS59 from the perspective of agronomic traits. TO terms contain information of agronomic traits in crops (Cooper et al., 2018; Oellrich et al., 2015; Pan et al., 2019).…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

KNOX II transcription factor HOS59 functions in regulating rice grain size

Sheng

Wang

et al. 2022

The Plant Journal

Self Cite

View full text Add to dashboard Cite

Plant Knotted1-like homeobox (KNOX) genes encode homeodomain-containing transcription factors. In rice (Oryza sativa L.), little is known about the downstream target genes of KNOX Class II subfamily proteins.Here we generated chromatin immunoprecipitation (ChIP)-sequencing datasets for HOS59, a member of the rice KNOX Class II subfamily, and characterized the genome-wide binding sites of HOS59. We conducted trait ontology (TO) analysis of 9705 identified downstream target genes, and found that multiple TO terms are related to plant structure morphology and stress traits. ChIP-quantitative PCR (qPCR) was conducted to validate some key target genes. Meanwhile, our IP-MS datasets showed that HOS59 was closely associated with BELL family proteins, some grain size regulators (OsSPL13, OsSPL16, OsSPL18, SLG, etc.), and some epigenetic modification factors such as OsAGO4a and OsAGO4b, proteins involved in small interfering RNAmediated gene silencing. Furthermore, we employed CRISPR/Cas9 editing and transgenic approaches to generate hos59 mutants and overexpression lines, respectively. Compared with wild-type plants, the hos59 mutants have longer grains and increased glume cell length, a loose plant architecture, and drooping leaves, while the overexpression lines showed smaller grain size, erect leaves, and lower plant height. The qRT-PCR results showed that mutation of the HOS59 gene led to upregulation of some grain size-related genes such as OsSPL13, OsSPL18, and PGL2. In summary, our results indicate that HOS59 may be a repressor of the downstream target genes, negatively regulating glume cell length, rice grain size, plant architecture, etc. The identified downstream target genes and possible interaction proteins of HOS59 improve our understanding of the KNOX regulatory networks.

show abstract

Section: Resultsmentioning

confidence: 99%

“…GO enrichment analysis of ChIP‐seq data was performed using agriGOv2 (Tian et al., 2017) and REVIGO (Supek et al., 2011). Through the analysis tool of PlantGSAD (Ma et al., 2022), the TO category was selected to perform gene set enrichment analysis. Terms with a P ‐value of less than 0.05 were considered to be significantly enriched.…”

Section: Methodsmentioning

confidence: 99%

KNOX II transcription factor HOS59 functions in regulating rice grain size

Sheng

Wang

et al. 2022

The Plant Journal

Self Cite

View full text Add to dashboard Cite

show abstract

“…The latter offers an impressive array of new features for functional and evolutionary exploration including gene regulatory elements, target annotations, variants and phylogenetic trees. Finally, welcome new arrivals include PlantGSAD ( 104 ) which provides >200 000 gene sets across 44 families, sets based on a notably diverse set of properties; and qPTMplants ( 105 ) which curates data, including quantitative information, on post-translational modifications (PTM) across 43 species. The latter features an interesting discussion of PTM crosstalk identified in the database.…”

Section: New and Updated Databasesmentioning

confidence: 99%

The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection

Rigden

Fernández

2021

Nucleic Acids Research

View full text Add to dashboard Cite

The 2022 Nucleic Acids Research Database Issue contains 185 papers, including 87 papers reporting on new databases and 85 updates from resources previously published in the Issue. Thirteen additional manuscripts provide updates on databases most recently published elsewhere. Seven new databases focus specifically on COVID-19 and SARS-CoV-2, including SCoV2-MD, the first of the Issue's Breakthrough Articles. Major nucleic acid databases reporting updates include MODOMICS, JASPAR and miRTarBase. The AlphaFold Protein Structure Database, described in the second Breakthrough Article, is the stand-out in the protein section, where the Human Proteoform Atlas and GproteinDb are other notable new arrivals. Updates from DisProt, FuzDB and ELM comprehensively cover disordered proteins. Under the metabolism and signalling section Reactome, ConsensusPathDB, HMDB and CAZy are major returning resources. In microbial and viral genomes taxonomy and systematics are well covered by LPSN, TYGS and GTDB. Genomics resources include Ensembl, Ensembl Genomes and UCSC Genome Browser. Major returning pharmacology resource names include the IUPHAR/BPS guide and the Therapeutic Target Database. New plant databases include PlantGSAD for gene lists and qPTMplants for post-translational modifications. The entire Database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). Our latest update to the NAR online Molecular Biology Database Collection brings the total number of entries to 1645. Following last year's major cleanup, we have updated 317 entries, listing 89 new resources and trimming 80 discontinued URLs. The current release is available at http://www.oxfordjournals.org/nar/database/c/.

show abstract

“…Metabolic pathways and biochemical signals transduction pathways were predicted by the Kyoto Encyclopedia of Genes and Genomes (KEGG) and KOBAS 3.0 ( Kanehisa and Goto, 2000 ; Bu et al, 2021 ). PlantCyc enrichment analysis was performed by PlantGSAD ( Ma et al, 2021 ). p -Value < 0.05 (Fisher’s exact test) was used as the threshold to determine the significant enrichments of GO and KEGG pathways.…”

Section: Methodsmentioning

confidence: 99%

Global analysis of lysine 2-hydroxyisobutyrylation during Fusarium graminearum infection in maize

Zhang

Cao

et al. 2022

Front. Plant Sci.

View full text Add to dashboard Cite

Proteins post-translational modification (PTMs) is necessary in the whole life process of organisms. Among them, lysine 2-hydroxyisobutyrylation (Khib) plays an important role in protein synthesis, transcriptional regulation, and cell metabolism. Khib is a newly identified PTM in several plant species. However, the function of Khib in maize was unclear. In this study, western blotting results showed that Khib modification level increased significantly after Fusarium graminearum infection, and 2,066 Khib modified sites on 728 proteins were identified in maize, among which 24 Khib sites occurred on core histones. Subcellular localization results showed that these Khib modified proteins were localized in cytoplasm, chloroplast, and nucleus. Then, comparative proteomic analysis of the defense response to F. graminearum infection showed that Khib modification participated in plant resistance to pathogen infection by regulating glycolysis, TCA cycle, protein synthesis, peroxisome, and secondary metabolic processes, such as benzoxazinoid biosynthesis, phenylpropanoid biosynthesis, jasmonic acid synthesis, and tyrosine and tryptophan biosynthesis. In addition, we also demonstrated that lysine 2-hydroxyisobutyrylation sites on histones were involved in the gene expression of pathogenesis-related proteins. Our results provide a new perspective for the study of plant disease resistance, and had directive significance of maize disease resistance for molecular breeding.

show abstract

PlantGSAD: a comprehensive gene set annotation database for plant species

Cited by 32 publications

References 82 publications

KNOX II transcription factor HOS59 functions in regulating rice grain size

KNOX II transcription factor HOS59 functions in regulating rice grain size

The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection

Global analysis of lysine 2-hydroxyisobutyrylation during Fusarium graminearum infection in maize

Contact Info

Product

Resources

About