Plant buffering against the high-light stress-induced accumulation of CsGA2ox8 transcripts via alternative splicing to finely tune gibberellin levels and maintain hypocotyl elongation

Relevance and regulation of alternative splicing in plant secondary metabolism: current understanding and future directions

The secondary metabolism of plants is an essential life process enabling organisms to navigate various stages of plant development and cope with ever-changing environmental stresses. Secondary metabolites, abundantly found in nature, possess significant medicinal value. Among the regulatory mechanisms governing these metabolic processes, alternative splicing stands out as a widely observed post-transcriptional mechanism present in multicellular organisms. It facilitates the generation of multiple mRNA transcripts from a single gene by selecting different splicing sites. Selective splicing events in plants are widely induced by various signals, including external environmental stress and hormone signals. These events ultimately regulate the secondary metabolic processes and the accumulation of essential secondary metabolites in plants by influencing the synthesis of primary metabolites, hormone metabolism, biomass accumulation, and capillary density. Simultaneously, alternative splicing plays a crucial role in enhancing protein diversity and the abundance of the transcriptome. This paper provides a summary of the factors inducing alternative splicing events in plants and systematically describes the progress in regulating alternative splicing with respect to different secondary metabolites, including terpenoid, phenolic compounds, and nitrogen-containing compounds. Such elucidation offers critical foundational insights for understanding the role of alternative splicing in regulating plant metabolism and presents novel avenues and perspectives for bioengineering.

Metabolic, transcriptomic, and genetic analyses of candidate genes for seed size in watermelon

Seed size (SS) constitutes a pivotal trait in watermelon breeding. In this study, we present findings from an examination of two watermelon accessions, namely, BW85 and F211. Seeds from BW85 exhibited a significant enlargement compared to those of F211 at 13 days after pollination (DAP), with the maximal disparity in seed length and width manifesting at 17 DAP. A comprehensive study involving both metabolic and transcriptomic analyses indicated a significant enrichment of the ubiquinone and other terpenoid-quinone biosynthesis KEGG pathways. To detect the genetic region governing seed size, a BSA-seq analysis was conducted utilizing the F2 (BW85 × F211) population, which resulted in the identification of two adjacent QTLs, namely, SS6.1 and SS6.2, located on chromosomes 6. SS6.1 spanned from Chr06:4847169 to Chr06:5163486, encompassing 33 genes, while SS6.2 ranged from Chr06:5379337 to Chr06:5419136, which included only one gene. Among these genes, 11 exhibited a significant differential expression between BW85 and F211 according to transcriptomic analysis. Notably, three genes (Cla97C06G113960, Cla97C06G114180, and Cla97C06G114000) presented a differential expression at both 13 and 17 DAP. Through annotation, Cla97C06G113960 was identified as a ubiquitin-conjugating enzyme E2, playing a role in the ubiquitin pathway that mediates seed size control. Taken together, our results provide a novel candidate gene influencing the seed size in watermelon, shedding light on the mechanism underlying seed development.

A nanopore-based cucumber genome assembly reveals structural variations at two QTLs controlling hypocotyl elongation

The Xishuangbanna (XIS) cucumber (Cucumis sativus var. xishuangbannanesis) is a semiwild variety that has many distinct agronomic traits. Here, long reads generated by Nanopore sequencing technology helped assembling a high-quality genome (contig N50 = 8.7 Mb) of landrace XIS49. A total of 10,036 structural/sequence variations (SVs) were identified when comparing with Chinese Long (CL), and known SVs controlling spines, tubercles, and carpel number were confirmed in XIS49 genome. Two QTLs of hypocotyl elongation under low light, SH3.1 and SH6.1, were fine-mapped using introgression lines (donor parent, XIS49; recurrent parent, CL). SH3.1 encodes a red-light receptor Phytochrome B (PhyB, CsaV3_3G015190). A ∼4 kb region with large deletion and highly divergent regions (HDRs) were identified in the promoter of the PhyB gene in XIS49. Loss of function of this PhyB caused a super-long hypocotyl phenotype. SH6.1 encodes a CCCH-type zinc finger protein FRIGIDA-ESSENTIAL LIKE (FEL, CsaV3_6G050300). FEL negatively regulated hypocotyl elongation but it was transcriptionally suppressed by long terminal repeats retrotransposon insertion in CL cucumber. Mechanistically, FEL physically binds to the promoter of CONSTITUTIVE PHOTOMORPHOGENIC 1a (COP1a), regulating the expression of COP1a and the downstream hypocotyl elongation. These above results demonstrate the genetic mechanism of cucumber hypocotyl elongation under low light.

Evidence Supporting a Role of Alternative Splicing Participates in Melon (Cucumis melo L.) Fruit Ripening

One key post-transcriptional modification mechanism that dynamically controls a number of physiological processes in plants is alternative splicing (AS). However, the functional impacts of AS on fruit ripening remain unclear. In this research, we used RNA-seq data from climacteric (VED, Harukei 3) and non-climacteric (PI, PS) melon cultivars to explore alternative splicing (AS) in immature and mature fruit. The results revealed dramatic changes in differential AS genes (DAG) between the young and mature fruit stages, particularly in genes involved in fruit development/ripening, carotenoid and capsaicinoid biosynthesis, and starch and sucrose metabolism. Serine/arginine-rich (SR) family proteins are known as important splicing factors in AS events. From the melon genome, a total of 17 SR members were discovered in this study. These genes could be classified into eight distinct subfamilies based on gene structure and conserved motifs. Promoter analysis detected various cis-acting regulatory elements involved in hormone pathways and fruit development. Interestingly, these SR genes exhibited specific expression patterns in reproductive organs such as flowers and ovaries. Additionally, concurrent with the increase in AS levels in ripening fruit, the transcripts of these SR genes were activated during fruit maturation in both climacteric and non-climacteric melon varieties. We also found that most SR genes were under selection during domestication. These results represent a novel finding of increased AS levels and SR gene expression during fruit ripening, indicating that alternative splicing may play a role in fruit maturation.

Overexpression of SlCRF6 in tomato inhibits leaf development and affects plant morphology

Cytokinin response factors (CRFs) are transcription factors (TFs) that are specific to plants and have diverse functions in plant growth and stress responses. However, the precise roles of CRFs in regulating tomato plant architecture and leaf development have not been comprehensively investigated. Here, we identified a novel CRF, SlCRF6, which is involved in the regulation of plant growth via the gibberellin (GA) signaling pathway. SlCRF6-overexpressing (SlCRF6-OE) plants displayed pleiotropic phenotypic changes, including reduced internode length and leaf size, which caused dwarfism in tomato plants. This dwarfism could be alleviated by application of exogenous GA3. Remarkably, quantitative real-time PCR (qRTPCR), a dual luciferase reporter assay and a yeast one-hybrid (Y1H) assay revealed that SlCRF6 promoted the expression of SlDELLA (a GA signal transduction inhibitor) in vivo. Furthermore, transgenic plants displayed variegated leaves and diminished chlorophyll content, resulting in decreased photosynthetic efficiency and less starch than in wild-type (WT) plants. The results of transient expression assays and Y1H assays indicated that SlCRF6 suppressed the expression of SlPHAN (leaf morphology-related gene). Collectively, these findings suggest that SlCRF6 plays a crucial role in regulating tomato plant morphology, leaf development, and the accumulation of photosynthetic products.

Characterization of Almond Scion/Rootstock Communication in Cultivar and Rootstock Tissues through an RNA-Seq Approach

The rootstock genotype plays a crucial role in determining various aspects of scion development, including the scion three-dimensional structure, or tree architecture. Consequently, rootstock choice is a pivotal factor in the establishment of new almond (Prunus amygdalus (L.) Batsch, syn P. dulcis (Mill.)) intensive planting systems, demanding cultivars that can adapt to distinct requirements of vigor and shape. Nevertheless, considering the capacity of the rootstock genotype to influence scion development, it is likely that the scion genotype reciprocally affects rootstock performance. In the context of this study, we conducted a transcriptomic analysis of the scion/rootstock interaction in young almond trees, with a specific focus on elucidating the scion impact on the rootstock molecular response. Two commercial almond cultivars were grafted onto two hybrid rootstocks, thereby generating four distinct combinations. Through RNA-Seq analysis, we discerned that indeed, the scion genotype exerts an influence on the rootstock expression profile. This influence manifests through the modulation of genes associated with hormonal regulation, cell division, root development, and light signaling. This intricate interplay between scion and rootstock communication plays a pivotal role in the development of both scion and rootstock, underscoring the critical importance of a correct choice when establishing new almond orchards.

Physiological and Transcriptomic Analyses Uncover the Reason for the Inhibition of Photosynthesis by Phosphate Deficiency in Cucumis melo L

Phosphate (Pi) deficiency is a common phenomenon in agricultural production and limits plant growth. Recent work showed that long-term Pi deficiency caused the inhibition of photosynthesis and inefficient electron transport. However, the underlying mechanisms are still unknown. In this study, we used the physiological, histochemical, and transcriptomic methods to investigate the effect of low-Pi stress on photosynthetic gas exchange parameters, cell membrane lipid, chloroplast ultrastructure, and transcriptional regulation of key genes in melon seedlings. The results showed that Pi deficiency significantly downregulated the expression of aquaporin genes, induced an increase in ABA levels, and reduced the water content and free water content of melon leaves, which caused physiological drought in melon leaves. Therefore, gas exchange was disturbed. Pi deficiency also reduced the phospholipid contents in leaf cell membranes, caused the peroxidation of membrane lipids, and destroyed the ultrastructure of chloroplasts. The transcriptomic analysis showed that 822 differentially expressed genes (DEGs) were upregulated and 1254 downregulated by Pi deficiency in leaves. GO and KEGG enrichment analysis showed that DEGs significantly enriched in chloroplast thylakoid membrane composition (GO:0009535), photosynthesis-antenna proteins (map00196), and photosynthesis pathways (map00195) were downregulated by Pi deficiency. It indicated that Pi deficiency regulated photosynthesis-related genes at the transcriptional level, thereby affecting the histochemical properties and physiological functions, and consequently causing the reduced light assimilation ability and photosynthesis efficiency. It enriches the mechanism of photosynthesis inhibition by Pi deficiency.

The Role of the GSTF11 Gene in Resistance to Powdery Mildew Infection and Cold Stress

Oilseed rape (Brassica napus) is an economically important crop. In a temperate climate, powdery mildew Erysiphe crucifertaum can drastically reduce its yield. Nevertheless, cultivars resistant to this fungal disease have not yet been selected. Glutathione S-transferase GSTF11 is involved in glucosinolate (GSL) biosynthesis and response to stress, including fungal deceases. However, the impact of exogenous GSTF11 gene expression on resistance to powdery mildew has not yet been confirmed and requires further investigation. Transgenic B. napus was generated for this purpose. It demonstrated increased GST activity and a higher GSH:GSSG ratio under normal conditions. Powdery mildew Erysiphe crucifertaum caused 50% mortality in wild type (WT) plants. In most of transgenic plants, mycelium growth was inhibited. The infection contributed to higher GSTF11 expression and increased levels of glutathione (GSH) and oxidized glutathione (GSSG) in both transgenic and WT plants. In contrast, GSTF11 mRNA content, GST activity and GSSG level were lower only in WT plants. In transgenic plants, increased resistance to powdery mildew correlated with a lower GSH:GSSG ratio, indicating a higher content of neutralized toxic molecules. GSTF11 expression was also affected by cold stress, but not drought. At -1 °C, the expression level increased only in transgenic plants. Therefore, GSTF11 appears to be nonspecific and is able to protect plants under several types of stress. This gene could be used as a target in the production of stress tolerant cultivars.

Transcriptome sequencing revealed the influence of blue light on the expression levels of light-stress response genes in Centella asiatica

Centella asiatica is rich in medical and cosmetic properties. While physiological responses of C. asiatica to light have been widely reported, the knowledge of the effects of light on its gene expression is sparse. In this study, we used RNA sequencing (RNA-seq) to investigate the expression of the C. asiatica genes in response to monochromatic red and blue light. Most of the differentially expressed genes (DEGs) under blue light were up-regulated but those under red light were down-regulated. The DEGs encoded for CRY-DASH and UVR3 were among up-regulated genes that play significant roles in responses under blue light. The DEGs involved in the response to photosystem II photodamages and in the biosynthesis of photoprotective xanthophylls were also up-regulated. The expression of flavonoid biosynthetic DEGs under blue light was up-regulated but that under red light was down-regulated. Correspondingly, total flavonoid content under blue light was higher than that under red light. The ABI5, MYB4, and HYH transcription factors appeared as hub nodes in the protein-protein interaction network of the DEGs under blue light while ERF38 was a hub node among the DEGs under red light. In summary, stress-responsive genes were predominantly up-regulated under blue light to respond to stresses that could be induced under high energy light. The information obtained from this study can be useful to better understand the responses of C. asiatica to different light qualities.

Light Deficiency Inhibits Growth by Affecting Photosynthesis Efficiency as well as JA and Ethylene Signaling in Endangered Plant Magnolia sinostellata

The endangered plant Magnolia sinostellata largely grows in the understory of forest and suffers light deficiency stress. It is generally recognized that the interaction between plant development and growth environment is intricate; however, the underlying molecular regulatory pathways by which light deficiency induced growth inhibition remain obscure. To understand the physiological and molecular mechanisms of plant response to shading caused light deficiency, we performed photosynthesis efficiency analysis and comparative transcriptome analysis in M. sinostellata leaves, which were subjected to shading treatments of different durations. Most of the parameters relevant to the photosynthesis systems were altered as the result of light deficiency treatment, which was also confirmed by the transcriptome analysis. Gene Ontology and KEGG pathway enrichment analyses illustrated that most of differential expression genes (DEGs) were enriched in photosynthesis-related pathways. Light deficiency may have accelerated leaf abscission by impacting the photosynthesis efficiency and hormone signaling. Further, shading could repress the expression of stress responsive transcription factors and R-genes, which confer disease resistance. This study provides valuable insight into light deficiency-induced molecular regulatory pathways in M. sinostellata and offers a theoretical basis for conservation and cultivation improvements of Magnolia and other endangered woody plants.

Genetic regulation of shoot architecture in cucumber

Cucumber (Cucumis sativus L.) is an important vegetable crop species with great economic value. Shoot architecture determines the visual appearance of plants and has a strong impact on crop management and yield. Unlike most model plant species, cucumber undergoes vegetative growth and reproductive growth simultaneously, in which leaves are produced from the shoot apical meristem and flowers are generated from leaf axils, during the majority of its life, a feature representative of the Cucurbitaceae family. Despite substantial advances achieved in understanding the regulation of plant form in Arabidopsis thaliana, rice, and maize, our understanding of the mechanisms controlling shoot architecture in Cucurbitaceae crop species is still limited. In this review, we focus on recent progress on elucidating the genetic regulatory pathways underlying the determinant/indeterminant growth habit, leaf shape, branch outgrowth, tendril identity, and vine length determination in cucumber. We also discuss the potential of applying biotechnology tools and resources for the generation of ideal plant types with desired architectural features to improve cucumber productivity and cultivation efficiency.

Transcriptomic Analysis of Seasonal Gene Expression and Regulation during Xylem Development in “Shanxin” Hybrid Poplar (Populus davidiana × Populus bolleana)

Xylem development is a key process for wood formation in woody plants. To study the molecular regulatory mechanisms related to xylem development in hybrid poplar P. davidiana × P. bolleana, transcriptome analyses were conducted on developing xylem at six different growth stages within a single growing season. Xylem development and differentially expressed genes in the six time points were selected for a regulatory analysis. Xylem development was observed in stem sections at different growth stages, which showed that xylem development extended from the middle of April to early August and included cell expansion and secondary cell wall biosynthesis. An RNA-seq analysis of six samples with three replicates was performed. After transcriptome assembly and annotation, the differentially expressed genes (DEGs) were identified, and a Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and expression analysis of the DEGs were performed on each sample. On average, we obtained >20 million clean reads per sample, which were assembled into 84,733 nonredundant transcripts, of which there were 17,603 unigenes with lengths >1 kb. There were 14,890 genes that were differentially expressed among the six stages. The upregulated DEGs were enriched in GO terms related to cell wall biosynthesis between S1 vs. S2 or S3 vs. S4 and, in GO terms, related to phytohormones in the S1 vs. S2 or S4 vs. S5 comparisons. The downregulated DEGs were enriched in GO terms related to cell wall biosynthesis between S4 vs. S5 or S5 vs. S6 and, in GO terms, related to hormones between S1 vs. S2 or S2 vs. S3. The KEGG pathways in the DEGs related to “phenylpropanoid biosynthesis”, “plant hormone signal transduction” and “starch and sucrose metabolism” were significantly enriched among the different stages. The DEGs related to cell expansion, polysaccharide metabolism and synthesis, lignin synthesis, transcription factors and hormones were identified. The identification of genes involved in the regulation of xylem development will increase our understanding of the molecular regulation of wood formation in trees and, also, offers potential targets for genetic manipulation to improve the properties of wood.

Integrated Transcriptomics and Metabolomics Analyses Provide Insights Into the Response of Chongyi Wild Mandarin to Candidatus Liberibacter Asiaticus Infection

Candidatus Liberibacter asiaticus (CLas) is the causative agent of Huanglongbing (HLB), which has caused great economic losses to the citrus industry. The molecular mechanism of the host response to CLas in wild citrus germplasm has been reported less. Eighteen weeks after inoculation via grafting, all the CLas-inoculated Chongyi wild mandarin (Citrus reticulata) were positive and showed severe anatomical aberrations, suggesting its susceptibility to HLB. Transcriptomics and metabolomics analyses of leaves, barks, and roots from mock-inoculated (control) and CLas-inoculated seedlings were performed. Comparative transcriptomics identified 3,628, 3,770, and 1,716 differentially expressed genes (DEGs) between CLas-infected and healthy tissues in the leaves, barks, and roots, respectively. The CLas-infected tissues had higher transcripts per kilobase per million values and more genes that reached their maximal expression, suggesting that HLB might cause an overall increase in transcript accumulation. However, HLB-triggered transcriptional alteration showed tissue specificity. In the CLas-infected leaves, many DEGs encoding immune receptors were downregulated. In the CLas-infected barks, nearly all the DEGs involved in signaling and plant-pathogen interaction were upregulated. In the CLas-infected roots, DEGs encoding enzymes or transporters involved in carotenoid biosynthesis and nitrogen metabolism were downregulated. Metabolomics identified 71, 62, and 50 differentially accumulated metabolites (DAMs) in the CLas-infected leaves, barks and roots, respectively. By associating DEGs with DAMs, nitrogen metabolism was the only pathway shared by the three infected tissues and was depressed in the CLas-infected roots. In addition, 26 genes were determined as putative markers of CLas infection, and a hypothesized model for the HLB susceptibility mechanism in Chongyi was proposed. Our study may shed light on investigating the molecular mechanism of the host response to CLas infection in wild citrus germplasm.