Comprehensive regulatory networks for tomato organ development based on the genome and RNAome of MicroTom tomato

The varied effects of different microplastics on stem development and carbon-nitrogen metabolism in tomato

Microplastics (MPs) pollution negatively impacts agricultural production, posing serious challenges to food security. However, research on the effects of different MPs types on plant growth, particularly on anatomical structures and carbon-nitrogen metabolism, is limited. This study investigates the effects of six MPs types on tomato (Solanum lycopersicum cv. Micro Tom) seedlings, including four non-degradable plastics (polyethylene [PE], polypropylene [PP], polystyrene [PS], and polyvinyl chloride [PVC]) and two biodegradable plastics (polybutylene succinate [PBS] and polylactic acid [PLA]). Results showed that MPs exposure inhibited seedling growth, with the degree of inhibition dependent on both the concentration and MPs type. MPs exert a significant negative impact on the development of the cortex (ct), vascular bundles (VBs), and pith tissues (pi) in tomato stems. Among them, PS-MPs induce relatively weaker negative effects. Analyses of key enzyme activities and gene expression revealed that MPs inhibited glycolysis pathway (EMP) and the tricarboxylic acid cycle (TCA), while enhancing the pentose phosphate pathway (PPP). Specifically, PBS-MPs and PVC-MPs strongly suppressed carbon assimilation, while PBS-MPs severely inhibited nitrogen assimilation. The results indicate that the negative impacts of biodegradable plastics on plants are comparable to those of traditional plastics. This study improves our understanding of the specific toxic effects of various MPs types on plant growth and metabolism.

Mitigating Response of SlCSE06 Induced by 2-Ethylfuran to Botrytis cinerea Infection

Tomato (Solanum lycopersicum L.) is a major economic vegetable crop globally, yet it is prone to gray mold disease caused by Botrytis cinerea infection during cultivation. Caffeoyl shikimate esterase (CSE) is a crucial component of the lignin biosynthesis pathway, which significantly contributes to plant stress resistance. Therefore, investigating the expression patterns of SlCSE after Botrytis cinerea infection may offer a theoretical foundation for breeding resistant tomato varieties. In this study, 11 SlCSE family members were identified from the tomato genome using bioinformatics analyses. Public transcriptome databases and RT-qPCR experiments were used to analyze gene expression in tomato tissues, responses to Botrytis cinerea infection, and the temporal characteristics of the response to 2-ethylfuran treatment during infection. These experiments resulted in the identification of the key gene SlCSE06. Transgenic tomato lines that overexpressed SlCSE06 were constructed to examine their resistance levels to gray mold disease. Many SlCSE genes were upregulated when tomato fruit were infected with Botrytis cinerea during the ripening stage. Furthermore, 24 h after treatment with 2-ethylfuran, most SlCSE genes exhibited increased expression levels compared with the control group, but they exhibited significantly lower levels at other time points. Thus, 2-ethylfuran treatment may enhance the responsiveness of SlCSEs. Based on this research, SlCSE06 was identified as the key gene involved in the response to Botrytis cinerea infection. The SlCSE06-overexpressing (OE6) tomato plants exhibited a 197.94% increase in expression levels compared to the wild type (WT). Furthermore, the lignin content in OE6 was significantly higher than in WT, suggesting that the overexpression of SlCSE06 enhanced lignin formation in tomato plants. At 5 days post-inoculation with Botrytis cinerea, the lesion diameter in OE6 decreased by 31.88% relative to the WT, whereas the lignin content increased by 370.90%. Furthermore, the expression level of SlCSE06 was significantly upregulated, showing a 17.08-fold increase compared with the WT. These findings suggest that 2-ethylfuran enhances the activation of the critical tomato disease resistance gene SlCSE06 in response to gray mold stress, thereby promoting lignin deposition to mitigate further infection by Botrytis cinerea.

Salicylic acid represses VdMYB31 expression to enhance grape resistance to Colletotrichum viniferum

Grape (Vitis vinifera) production globally faces significant challenges from grape ripe rot (Colletotrichum viniferum). MYB transcription factors (TFs) play a crucial role in mediating plant responses to biotic stresses. However, their involvement in grapevine responses to ripe rot remains unclarified. This study employed bioinformatics to identify MYB TF genes within the grapevine genome and assessed their expression profiles post C. viniferum infection via transcriptome analysis. Among the 121 R2R3-MYB genes identified, VdMYB31, predominantly expressed in mature fruits, was notably downregulated in responding to C. viniferum infection. Heterologous expression of VdMYB31 in tomato (Solanum lycopersicum) fruits increased susceptibility to C. acutatum by suppressing salicylic acid (SA)-related gene expression. Silencing MYB31 in grape berries conferred resistance to C. viniferum. Additionally, exogenous SA application bolstered grape resistance to C. viniferum infection. These findings underscore the involvement of R2R3-MYB TFs in defending against C. viniferum, positioning VdMYB31 as a promising target for breeding grape varieties with improved resistance to ripe rot in viticulture.

Prediction of transcript isoforms and identification of tissue-specific genes in cucumber

BACKGROUND

Identification of global transcriptional events is crucial for genome annotation, as accurate annotation enhances the efficiency and comparability of genomic information across species. However, the annotation of transcripts in the cucumber genome remains to be improved, and many transcriptional events have not been well studied.

RESULTS

We collected 1,904 high-quality public cucumber transcriptome samples from the National Center for Biotechnology Information (NCBI) to identify and annotate transcript isoforms in the cucumber genome. Over 44.26 billion Q30 clean reads were mapped to the cucumber genome with an average mapping rate of 92.75%. Transcriptome assembly identified 151,453 transcripts spanning 20,442 loci. Among these, 12.7% of transcripts exactly matched annotated genes in the cucumber reference genome. More than 80% of the transcripts were classified as novel isoforms. Approximately 96.6% of these isoforms originated from known gene loci, while around 3.3% were derived from novel gene loci. Coding potential prediction identified 4,543 long non-coding RNAs (lncRNAs) across 3,376 loci. Building on these results, we identified tissue-specific transcripts in 10 tissues. Among that, 1,655 annotated genes and 4,214 predicted transcripts were considered as tissue-specific. The root exhibited the highest number of tissue-specific transcripts, followed by shoot apex. Subsequent selective pressure analysis revealed that tissue-specific regions experienced stronger directional selection compared to non-specific regions.

CONCLUSIONS

By analyzing thousands of published transcriptome data, we identified abundant transcriptional events and tissue-specific transcripts in cucumbers. This study presented here adds the great value to the public data and offers insights for further exploration of a more comprehensive tissue regulatory network in cucumber.

Deciphering the biosynthetic pathway of triterpene saponins in Prunella vulgaris

The traditional Chinese medicinal plant Prunella vulgaris contains numerous triterpene saponin metabolites, notably ursolic and oleanolic acid saponins, which have significant pharmacological values. Despite their importance, the genes responsible for synthesizing these triterpene saponins in P. vulgaris remain unidentified. This study used a comprehensive screening methodology, combining phylogenetic analysis, gene expression assessment, metabolome-transcriptome correlation and co-expression analysis, to identify candidate genes involved in triterpene saponins biosynthesis. Nine candidate genes - two OSCs, three CYP716s and four UGT73s - were precisely identified from large gene families comprising hundreds of members. These genes were subjected to heterologous expression and functional characterization, with enzymatic activity assays confirming their roles in the biosynthetic pathway, aligning with bioinformatics predictions. Analysis revealed that these genes originated from a whole-genome duplication (WGD) event in P. vulgaris, highlighting the potential importance of WGD for plant metabolism. This study addresses the knowledge gap in the biosynthesis of triterpene saponins in P. vulgaris, establishing a theoretical foundation for industrial production via synthetic biology. Additionally, we present an efficient methodological protocol that integrates evolutionary principles and bioinformatics techniques in metabolite biosynthesis research. This approach holds significant value for studies focused on unraveling various biosynthetic pathways.

Near-complete genome assembly of tomato (Solanum lycopersicum) cultivar Micro-Tom

We present a near-complete genome assembly of tomato (Solanum lycopersicum) cultivar Micro-Tom, which has been recognized as a model cultivar for fruit research. The genome DNA of Micro-Tom, provided by the National BioResource Project (NBRP) Tomato of Japan, was sequenced to obtain 72 Gb of high-fidelity long reads. These reads were assembled into 140 contigs, spanning 832.8 Mb, with an N50 length of 39.6 Mb. The contigs were aligned against the tomato reference genome sequence SL4.0 to establish a chromosome-level assembly. The genome assembly of Micro-Tom contained 98.5% complete BUSCOs and a total of 31,429 genes. Comparative genome structure analysis revealed that Micro-Tom possesses a cluster of ribosomal DNA genes spanning a 15 Mb stretch at the short arm of chromosome 2. This region was not found in the genome assemblies of previously sequenced tomato cultivars, possibly because of the inability of previous technologies to sequence such repetitive DNA. In conclusion, the near-complete genome assembly of Micro-Tom reported in this study would advance the genomics and genetics research on tomato and facilitate the breeding of improved tomato cultivars.

Chitosan from Mushroom Improves Drought Stress Tolerance in Tomatoes

Chitosan is a derivative of chitin that is one of the most abundant biopolymers in nature, found in crustacean shells as well as in fungi cell walls. Most of the commercially available chitosans are produced from the exoskeletons of crustaceans. The extraction process involves harsh chemicals, has limited potential due to the seasonal and limited supply and could cause allergic reactions. However, chitosan has been shown to alleviate the negative effect of environmental stressors in plants, but there is sparse evidence of how chitosan source affects this bioactivity. The aim of this study was to investigate the ability of chitosan from mushroom in comparison to crustacean chitosan in enhancing drought stress tolerance in tomato plants (cv. MicroTom). Chitosan treatment was applied through foliar application and plants were exposed to two 14-day drought stress periods at vegetative and fruit set growth stages. Phenotypic (e.g., fruit number and weight), physiological (RWC) and biochemical-stress-related markers (osmolytes, photosynthetic pigments and malondialdehyde) were analyzed at different time points during the crop growth cycle. Our hypothesis was that this drought stress model will negatively impact tomato plants while the foliar application of chitosan extracted from either crustacean or mushroom will alleviate this effect. Our findings indicate that drought stress markedly decreased the leaf relative water content (RWC) and chlorophyll content, increased lipid peroxidation, and significantly reduced the average fruit number. Chitosan application, regardless of the source, improved these parameters and enhanced plant tolerance to drought stress. It provides a comparative study of the biostimulant activity of chitosan from diverse sources and suggests that chitosan sourced from fungi could serve as a more sustainable and environmentally friendly alternative to the current chitosan from crustaceans.