Dataset Information

Genome-Wide Identification and Expression Analysis of the PLATZ Transcription Factor in Tomato.

ABSTRACT: The PLATZ (plant AT protein and zinc-binding protein) transcription factor family is involved in the regulation of plant growth and development and plant stress response. In this study, 24 SlPLATZs were identified from the cultivated tomato genome and classified into four groups based on the similarity of conserved patterns among members of the same subfamily. Fragment duplication was an important way to expand the SlPLATZ gene family in tomatoes, and the sequential order of tomato PLATZ genes in the evolution of monocotyledonous and dicotyledonous plants and the roles they played were hypothesized. Expression profiles based on quantitative real-time reverse transcription PCR showed that SlPLATZ was involved in the growth of different tissues in tomatoes. SlPLATZ21 acts mainly in the leaves. SlPLATZ9, SlPLATZ21, and SlPLATZ23 were primarily involved in the red ripening, expanding, and mature green periods of fruit, respectively. In addition, SlPLATZ1 was found to play an important role in salt stress. This study will lay the foundation for the analysis of the biological functions of SlPLATZ genes and will also provide a theoretical basis for the selection and breeding of new tomato varieties and germplasm innovation.

SUBMITTER: Zhang L

PROVIDER: S-EPMC10384190 | biostudies-literature | 2023 Jul

REPOSITORIES: biostudies-literature

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Genome-Wide Identification and Expression Analysis of the PLATZ Transcription Factor in Tomato.

Zhang Lifang L Yang Tao T Wang Zepeng Z Zhang Fulin F Li Ning N Jiang Weijie W

Plants (Basel, Switzerland) 20230713 14

The PLATZ (plant AT protein and zinc-binding protein) transcription factor family is involved in the regulation of plant growth and development and plant stress response. In this study, 24 <i>SlPLATZs</i> were identified from the cultivated tomato genome and classified into four groups based on the similarity of conserved patterns among members of the same subfamily. Fragment duplication was an important way to expand the <i>SlPLATZ</i> gene family in tomatoes, and the sequential order of tomato ...[more]

PMID: 37514247

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Project description:NAC [no apical meristem (NAM), Arabidopsis transcription activation factor [ATAF1/2] and cup-shaped cotyledon (CUC2)] proteins is one of the largest groups of plant specific transcription factors and plays a crucial role in plant growth, development, and adaption to the environment. Currently, no information is known about the NAC family in cassava. In this study, 96 NAC genes (MeNACs) were identified from the cassava genome. Phylogenetic analysis of the NACs from cassava and Arabidopsis showed that MeNAC proteins can be clustered into 16 subgroups. Gene structure analysis found that the number of introns of MeNAC genes varied from 0 to 5, with the majority of MeNAC genes containing two introns, indicating a small gene structure diversity of cassava NAC genes. Conserved motif analysis revealed that all of the identified MeNACs had the conserved NAC domain and/or NAM domain. Global expression analysis suggested that MeNAC genes exhibited different expression profiles in different tissues between wild subspecies and cultivated varieties, indicating their involvement in the functional diversity of different accessions. Transcriptome analysis demonstrated that MeNACs had a widely transcriptional response to drought stress and that they had differential expression profiles in different accessions, implying their contribution to drought stress resistance in cassava. Finally, the expression of twelve MeNAC genes was analyzed under osmotic, salt, cold, ABA, and H2O2 treatments, indicating that cassava NACs may represent convergence points of different signaling pathways. Taken together, this work found some excellent tissue-specific and abiotic stress-responsive candidate MeNAC genes, which would provide a solid foundation for functional investigation of the NAC family, crop improvement and improved understanding of signal transduction in plants. These data bring new insight on the complexity of the transcriptional control of MeNAC genes and support the hypothesis that NACs play an important role in plant growth, development, and adaption of environment.

Project description:BackgroundPlant AT-rich sequence and zinc-binding (PLATZ) proteins belong to a novel class of plant-specific zinc-finger-dependent DNA-binding proteins that play essential roles in plant growth and development. Although the PLATZ gene family has been identified in several species, systematic identification and characterization of this gene family has not yet been carried out for Tartary buckwheat, which is an important medicinal and edible crop with high nutritional value. The recent completion of Tartary buckwheat genome sequencing has laid the foundation for this study.ResultsA total of 14 FtPLATZ proteins were identified in Tartary buckwheat and were classified into four phylogenetic groups. The gene structure and motif composition were similar within the same group, and evident distinctions among different groups were detected. Gene duplication, particularly segmental duplication, was the main driving force in the evolution of FtPLATZs. Synteny analysis revealed that Tartary buckwheat shares more orthologous PLATZ genes with dicotyledons, particularly soybean. In addition, the expression of FtPLATZs in different tissues and developmental stages of grains showed evident specificity and preference. FtPLATZ3 may be involved in the regulation of grain size, and FtPLATZ4 and FtPLATZ11 may participate in root development. Abundant and variable hormone-responsive cis-acting elements were distributed in the promoter regions of FtPLATZs, and almost all FtPLATZs were significantly regulated after exogenous hormone treatments, particularly methyl jasmonate treatment. Moreover, FtPLATZ6 was significantly upregulated under all exogenous hormone treatments, which may indicate that this gene plays a critical role in the hormone response of Tartary buckwheat.ConclusionsThis study lays a foundation for further exploration of the function of FtPLATZ proteins and their roles in the growth and development of Tartary buckwheat and contributes to the genetic improvement of Tartary buckwheat.

Project description:Background and aimsIn recent years, increasing numbers of long non-coding RNAs (lncRNAs) have been identified in humans, animals and plants, and several of them have been shown to play important roles in diverse biological processes. However, little work has been performed on the regulation mechanism of lncRNA biogenesis and expression, especially in plants. Compared with studies of tomato MADS-box transcription factor RIPENING INHIBITOR (RIN) target coding genes, there are few reports on its relationship to non-coding RNAs. The aim of the present study was to identify and explore the specific role of RIN target lncRNAs in tomato fruit development and ripening.MethodslncRNA targets of RIN were identified by chromatin immunoprecipitation sequencing (ChIP-seq) combined with RNA deep sequencing analysis. Six selected lncRNA targets were validated by quantitative real-time PCR, ChIP and electrophoretic mobility shift assays, and we further confirmed differential expression between wild-type and ripening-deficient mutant fruit, and RIN direct binding in the promoter regions. By means of virus-induced gene silencing (VIGS) assays and a clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) genome editing strategy, the ripening-related function of a specific target lncRNA (lncRNA2155) was studied.Key resultsWe identified 187 lncRNAs as direct RIN targets, which exhibited RIN binding sites in their promoters and showed different expression between the wild-type and rin mutant. Six target lncRNAs were shown to bind with RIN directly in their promoters in vivo and in vitro. Moreover, using CRISPR/Cas9 technology to knock out the locus of the target lncRNA2155 indicated that it delayed fruit ripening in tomato.ConclusionsCollectively, these findings provide new insight into RIN in the transcriptional regulation of lncRNAs and suggest that lncRNAs will contribute to a better understanding of the RIN regulatory network that controls fruit ripening.

Dataset Information

Genome-Wide Identification and Expression Analysis of the PLATZ Transcription Factor in Tomato.

Publications

Genome-Wide Identification and Expression Analysis of the PLATZ Transcription Factor in Tomato.

Similar Datasets

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