Plant Public RNA‐seq Database: a comprehensive online database for expression analysis of ~45 000 plant public RNA‐Seq libraries

Yu, Yiming; Hong, Zhang; Long, Yanping; Shu, Yi; Zhai, Jixian

doi:10.1111/pbi.13798

Cited by 68 publications

(53 citation statements)

References 12 publications

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“…The SNPs with the most significant associations in a block were identified as the leading SNPs, and LD blocks containing significantly associated SNPs were defined as candidate genomic regions. Differentially expressed genes were identified using the Plant Public RNA-seq Database (Yu et al, 2022). The expression patterns of the differentially expressed genes were analyzed using publicly available microarray data (http://www.genevestigator.…”

Section: Candidate Gene Analysesmentioning

confidence: 99%

Genome-Wide Association Study Reveals a Genetic Mechanism of Salt Tolerance Germinability in Rice (Oryza sativa L.)

Zou

et al. 2022

Front. Plant Sci.

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Salt stress is one of the factors that limits rice production, and an important task for researchers is to cultivate rice with strong salt tolerance. In this study, 211 rice accessions were used to determine salt tolerance germinability (STG) indices and conduct a genome-wide association study (GWAS) using 36,727 SNPs. The relative germination energy (RGE), relative germination index (RGI), relative vigor index (RVI), relative mean germination time (RMGT), relative shoot length (RSL), and relative root length (RRL) were used to determine the STG indices in rice. A total of 43 QTLs, including 15 for the RGE, 6 for the RGI, 7 for the RVI, 3 for the RMGT, 1 for the RSL, and 11 for the RRL, were identified on nine chromosome regions under 60 and 100 mM NaCl conditions. For these STG-related QTLs, 18 QTLs were co-localized with previous studies, and some characterized salt-tolerance genes, such as OsCOIN, OsHsp17.0, and OsDREB2A, are located in these QTL candidates. Among the 25 novel QTLs, qRGE60-1-2 co-localized with qRGI60-1-1 on chromosome 1, and qRGE60-3-1 and qRVI60-3-1 co-localized on chromosome 3. According to the RNA-seq database, 16 genes, including nine for qRGE60-1-2 (qRGI60-1-1) and seven for qRGE60-3-1 (qRVI60-3-1), were found to show significant differences in their expression levels between the control and salt treatments. Furthermore, the expression patterns of these differentially expressed genes were analyzed, and nine genes (five for qRGE60-1-2 and four for qRGE60-3-1) were highly expressed in embryos at the germination stage. Haplotype analysis of these nine genes showed that the rice varieties with elite haplotypes in the LOC_Os03g13560, LOC_Os03g13840, and LOC_Os03g14180 genes had high STG. GWAS validated the known genes underlying salt tolerance and identified novel loci that could enrich the current gene pool related to salt tolerance. The resources with high STG and significant loci identified in this study are potentially useful in breeding for salt tolerance.

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Section: Candidate Gene Analysesmentioning

confidence: 99%

Genome-Wide Association Study Reveals a Genetic Mechanism of Salt Tolerance Germinability in Rice (Oryza sativa L.)

Zou

et al. 2022

Front. Plant Sci.

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“…edu. cn/ pub/ plant rna/), which integrated all publicly available RNA-seq rice libraries (11,726) [31]. The results revealed that all the E3 genes were expressed (Additional file 5, Table S4).…”

Section: Construction Of a High-quality Ube3 Yeast Library Using Pcr ...mentioning

confidence: 99%

An ORFeome of rice E3 ubiquitin ligases for global analysis of the ubiquitination interactome

et al. 2022

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Background Ubiquitination is essential for many cellular processes in eukaryotes, including 26S proteasome-dependent protein degradation, cell cycle progression, transcriptional regulation, and signal transduction. Although numerous ubiquitinated proteins have been empirically identified, their cognate ubiquitin E3 ligases remain largely unknown. Results Here, we generate a complete ubiquitin E3 ligase-encoding open reading frames (UbE3-ORFeome) library containing 98.94% of the 1515 E3 ligase genes in the rice (Oryza sativa L.) genome. In the test screens with four known ubiquitinated proteins, we identify both known and new E3s. The interaction and degradation between several E3s and their substrates are confirmed in vitro and in vivo. In addition, we identify the F-box E3 ligase OsFBK16 as a hub-interacting protein of the phenylalanine ammonia lyase family OsPAL1–OsPAL7. We demonstrate that OsFBK16 promotes the degradation of OsPAL1, OsPAL5, and OsPAL6. Remarkably, we find that overexpression of OsPAL1 or OsPAL6 as well as loss-of-function of OsFBK16 in rice displayed enhanced blast resistance, indicating that OsFBK16 degrades OsPALs to negatively regulate rice immunity. Conclusions The rice UbE3-ORFeome is the first complete E3 ligase library in plants and represents a powerful proteomic resource for rapid identification of the cognate E3 ligases of ubiquitinated proteins and establishment of functional E3–substrate interactome in plants.

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“…Wheat transcriptome data for different tissues were downloaded from the Plant Public RNA-seq database [22]. RNA-seq data were obtained for five different tissues in Chinese Spring Wheat under normal growth conditions.…”

Section: Rna-seq Data Analysismentioning

confidence: 99%

“…Figure 8. Cluster analysis of TaPKS gene expression in different tissues from Chinese Spring wheat.The tissue expression data used for mapping were obtained from Plant Public RNA-seq Database[22]. The change in the color of the box from green to red indicates that the gene expression level changes from low to high.…”

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confidence: 99%

Genome-Wide Analysis of Type-III Polyketide Synthases in Wheat and Possible Roles in Wheat Sheath-Blight Resistance

Geng

Chen

Zhang

et al. 2022

IJMS

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The enzymes in the chalcone synthase family, also known as type-III polyketide synthases (PKSs), play important roles in the biosynthesis of various plant secondary metabolites and plant adaptation to environmental stresses. There have been few detailed reports regarding the gene and tissue expression profiles of the PKS (TaPKS) family members in wheat (Triticum aestivum L.). In this study, 81 candidate TaPKS genes were identified in the wheat genome, which were designated as TaPKS1–81. Phylogenetic analysis divided the TaPKS genes into two groups. TaPKS gene family expansion mainly occurred via tandem duplication and fragment duplication. In addition, we analyzed the physical and chemical properties, gene structures, and cis-acting elements of TaPKS gene family members. RNA-seq analysis showed that the expression of TaPKS genes was tissue-specific, and their expression levels differed before and after infection with Rhizoctonia cerealis. The expression levels of four TaPKS genes were also analyzed via qRT-PCR after treatment with methyl jasmonate, salicylic acid, abscisic acid, and ethylene. In the present study, we systematically identified and analyzed TaPKS gene family members in wheat, and our findings may facilitate the cloning of candidate genes associated with resistance to sheath blight in wheat.

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Plant Public RNA‐seq Database: a comprehensive online database for expression analysis of ~45 000 plant public RNA‐Seq libraries

Cited by 68 publications

References 12 publications

Genome-Wide Association Study Reveals a Genetic Mechanism of Salt Tolerance Germinability in Rice (Oryza sativa L.)

Genome-Wide Association Study Reveals a Genetic Mechanism of Salt Tolerance Germinability in Rice (Oryza sativa L.)

An ORFeome of rice E3 ubiquitin ligases for global analysis of the ubiquitination interactome

Genome-Wide Analysis of Type-III Polyketide Synthases in Wheat and Possible Roles in Wheat Sheath-Blight Resistance

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