Plant Transcriptome Research Articles

Refining dual RNA-seq mapping: sequential and combined approaches in host-parasitic plant dynamics.

Transcriptional profiling in host plant-parasitic plant interactions is challenging due to the tight interface between host and parasitic plants and the percentage of homologous sequences shared. Dual RNA-seq offers a solution by enabling in silico separation of mixed transcripts from the interface region. However, it has to deal with issues related to multiple mapping and cross-mapping of reads in host and parasite genomes, particularly as evolutionary divergence decreases. In this paper, we evaluated the feasibility of this technique by simulating interactions between parasitic and host plants and refining the mapping process. More specifically, we merged host plant with parasitic plant transcriptomes and compared two alignment approaches: sequential mapping of reads to the two separate reference genomes and combined mapping of reads to a single concatenated genome. We considered Cuscuta campestris as parasitic plant and two host plants of interest such as Arabidopsis thaliana and Solanum lycopersicum. Both tested approaches achieved a mapping rate of ~90%, with only about 1% of cross-mapping reads. This suggests the effectiveness of the method in accurately separating mixed transcripts in silico. The combined approach proved slightly more accurate and less time consuming than the sequential approach. The evolutionary distance between parasitic and host plants did not significantly impact the accuracy of read assignment to their respective genomes since enough polymorphisms were present to ensure reliable differentiation. This study demonstrates the reliability of dual RNA-seq for studying host-parasite interactions within the same taxonomic kingdom, paving the way for further research into the key genes involved in plant parasitism.

Comparative transcriptome analysis of tobacco plants reveals differences in reactive oxygen species activated defenses following the infestations of non-viruliferous and TYLCCNV-viruliferous whitefly Mediterranean

ABSTRACT Tomato yellow leaf curl China virus (TYLCCNV) viruliferous Mediterranean (MED) whitefly infestation in tobacco plants elevated hydrogen peroxide (H2O2) levels more than non-viruliferous ones. To unravel the underlying mechanisms behind the phenomenon, comparative analyses of plant transcriptome and enzyme activities of reactive oxygen species (ROS) scavengers were conducted in this study. Compared to the control, a total of 4032 and 6853 differentially expressed genes (DEGs) were identified in the plants following the infestations of non-viruliferous and TYLCCNV-viruliferous MED, respectively. Gene ontology analysis of DEGs suggested substantial transcriptional reprogramming of diverse cellular processes, particularly in the biotic stress response pathways of tobacco plants. Respiratory burst oxidase homologs related genes and important kinases putatively involved in plant defense were differentially modulated in tobacco plants in response to the non-viruliferous and TYLCCNV-viruliferous whitefly MED infestation. The analysis reported here lays out a strong foundation for future investigations into the mechanisms of ROS-associated plant defense mediating the interactions between B. tabaci and begomoviruses.

Computational Prediction and Structural Analysis of α-Hairpinins, a Ubiquitous Family of Antimicrobial Peptides, Using the Cysmotif Searcher Pipeline.

α-Hairpinins are a family of antimicrobial peptides, promising antimicrobial agents, which includes only 12 currently revealed members with proven activity, although their real number is supposed to be much higher. α-Hairpinins are short peptides containing four cysteine residues arranged in a specific Cys-motif. These antimicrobial peptides (AMPs) have a characteristic helix-loop-helix structure with two disulfide bonds. Isolation of α-hairpinins by biochemical methods is cost- and labor-consuming, thus requiring reliable preliminary in silico prediction. In this study, we developed a special algorithm for the prediction of putative α-hairpinins on the basis of characteristic motifs with four (4C) and six (6C) cysteines deduced from translated plant transcriptome sequences. We integrated this algorithm into the Cysmotif searcher pipeline and then analyzed all transcriptomes available from the One Thousand Plant Transcriptomes project. We predicted more than 2000 putative α-hairpinins belonging to various plant sources including algae, mosses, ferns, and true flowering plants. These data make α-hairpinins one of the ubiquitous antimicrobial peptides, being widespread among various plants. The largest numbers of α-hairpinins were revealed in the Papaveraceae family and in Papaver somniferum in particular. By analyzing the primary structure of α-hairpinins, we concluded that more predicted peptides with the 6C motif are likely to have potent antimicrobial activity in comparison to the ones possessing 4C motifs. In addition, we found 30 α-hairpinin precursors containing from two to eight Cys-rich modules. A striking similarity between some α-hairpinin modules belonging to diverse plants was revealed. These data allowed us to assume that the evolution of α-hairpinin precursors possibly involved changing the number of Cys-rich modules, leading to some missing middle and C-terminal modules, in particular.

Variability of plant transcriptomic responses under stress acclimation: a review from high throughput studies.

Plant transcriptomes are complex entities shaped spatially and temporally by a multitude of stressors. The aim of this review was to summarize the most relevant transcriptomic responses to selected abiotic (UV radiation, chemical compounds, drought, suboptimal temperature) and biotic (bacteria, fungi, viruses, viroids) stress conditions in a variety of plant species, including model species, crops, and medicinal plants. Selected basic and applicative studies employing RNA-seq from various sequencing platforms and single-cell RNA-seq were involved. The transcriptomic responsiveness of various plant species and the diversity of affected gene families were discussed. Under stress acclimation, plant transcriptomes respond particularly dynamically. Stress response involved both distinct, but also similar gene families, depending on the species, tissue, and the quality and dosage of the stressor. We also noted the over-representation of transcriptomic data for some plant organs. Studies on plant transcriptomes allow for a better understanding of response strategies to environmental conditions. Functional analyses reveal the multitude of stress-affected genes as well as acclimatory mechanisms and suggest metabolome diversity, particularly among medicinal species. Extensive characterization of transcriptomic responses to stress would result in the development of new cultivars that would cope with stress more efficiently. These actions would include modern methodological tools, including advanced genetic engineering, as well as gene editing, especially for the expression of selected stress proteins in planta and for metabolic modifications that allow more efficient synthesis of secondary metabolites.

Identification of nine putative novel members of plant-infecting alphaflexiviruses in public domain plant transcriptomes

Identification of nine putative novel members of plant-infecting alphaflexiviruses in public domain plant transcriptomes

From the discovery of a novel arepavirus in diseased arecanut palms (Areca catechu L.) in India to the identification of known and novel arepaviruses in bee and plant transcriptomes through data-mining

Arecanut palm is a commercially important plantation crop valued for its nut. In this investigation, we report the discovery of a putative novel arepavirus, named areca palm necrotic ringspot virus 2 (ANRSV2), in necrotic ringspot diseased areca palms in Bantwal, Dakshina Kannada, Karnataka, India through RNA-sequencing and transmission electron microscopy. Further, the presence of ANRSV2 in the diseased samples was confirmed through reverse transcriptase-polymerase chain reaction assays. In addition, by mining public domain transcriptome data for arepaviral sequences, we identified a putative novel arepavirus in Psychotria rubra, a non-palm host. We recovered the genome sequences of the areca palm necrotic ringspot virus in honey bees, tomato, Onobrychis viciifolia, and Rhamnus heterophylla. These findings broaden our comprehension of arepaviral diversity and host range, and suggest an intriguing possibility of pollen-mediated arepaviral transmission that necessitates empirical validation. Further studies are needed to understand the biology of identified putative novel arepaviruses.

Presence of vitamin B12 metabolism in the last common ancestor of land plants.

Vitamin B12, also known as cobalamin, is an essential organic cofactor for methionine synthase (METH), and is only synthesized by a subset of bacteria. Plants and fungi have an alternative methionine synthase (METE) that does not need B12 and are typically considered not to utilize it. Some algae facultatively utilize B12 because they encode both METE and METH, while other algae are dependent on B12 as they encode METH only. We performed phylogenomic analyses of METE, METH and 11 further proteins involved in B12 metabolism across more than 1600 plant and algal genomes and transcriptomes (e.g. from OneKp), demonstrating the presence of B12-associated metabolism deep into the streptophytes. METH and five further accessory proteins (MTRR, CblB, CblC, CblD and CblJ) were detected in the hornworts (Anthocerotophyta), and two (CblB and CblJ) were identified in liverworts (Marchantiophyta) in the bryophytes, suggesting a retention of B12-metabolism in the last common land plant ancestor. Our data further show more limited distributions for other B12-related proteins (MCM and RNR-II) and B12 dependency in several algal orders. Finally, considering the collection sites of algae that have lost B12 metabolism, we propose freshwater-to-land transitions and symbiotic associations to have been constraining factors for B12 availability in early plant evolution. This article is part of the theme issue 'The evolution of plant metabolism'.

Rhizosphere microbiomes derived from vermicompost alter gene expression and regulatory pathways in tomato (Solanum lycopersicum, L.).

The gut microbiome of worms from composting facilities potentially harbors organisms that are beneficial to plant growth and development. In this experiment, we sought to examine the potential impacts of rhizosphere microbiomes derived from Eisenia fetida worm castings (i.e. vermicompost) on tomato (Solanum lycopersicum, L.) plant growth and physiology. Our experiment consisted of a greenhouse trial lasting 17weeks total in which tomato plants were grown with one of three inoculant treatments: a microbial inoculant created from vermicompost (V), a microbial inoculant created from sterilized vermicompost (SV), and a no-compost control inoculant (C). We hypothesized that living microbiomes from the vermicompost inoculant treatment would enhance host plant growth and gene expression profiles compared to plants grown in sterile and control treatments. Our data showed that bacterial community composition was significantly altered in tomato rhizospheres, but fungal community composition was highly variable in each treatment. Plant phenotypes that were significantly enhanced in the vermicompost and sterile vermicompost treatments, compared to the control, included aboveground biomass and foliar δ15N nitrogen. RNA sequencing revealed distinct gene expression changes in the vermicompost treatment, including upregulation of nutrient transporter genes such as Solyc06g074995 (high affinity nitrate transporter), which exhibited a 250.2-fold increase in expression in the vermicompost treatment compared to both the sterile vermicompost and control treatments. The plant transcriptome data suggest that rhizosphere microbiomes derived from vermicompost can influence tomato gene expression and growth-related regulatory pathways, which highlights the value of RNA sequencing in uncovering molecular responses in plant microbiome studies.

A land plant phylogenetic framework for GLABROUS INFLORESCENCE STEMS (GIS), SUPERMAN, JAGGED and allies plus their TOPLESS co-repressor

Members of the plant specific family of C1-1i zincfinger transcriptionfactors (ZF-TFs), such as SUPERMAN, JAGGED, KNUCKLES or GIS,regulatediversedevelopmental processes including sexual reproduction. C1-1is consist of one zinc-finger and one to two EAR domains, connected by large intrinsically disordered regions (IDR). While the role of C1-i1 ZF-TFs in development processes is well known for some genes in Arabidopsis, rice or tomatoa comprehensive and broadphylogenetic background is lacking, yet knowledge of orthology is a requirement for a better understanding of C1-1i-Zf-TFs diverse roles in plants. Here, we provide a fine-grained and land plant wide classification of C1-1i sub-families and their known co-repressors TOPLESS and TOPLESS RELATED. Our work combines the identification of orthologous groups with Maximum-Likelihood phylogeny reconstructions and digital gene expression analyses mining high quality land plant genomes and transcriptomes to generate a comprehensive framework of C1-1i ZF-TF evolution. We show that C1-1i’s are low to moderate copy genesand that orthologous genesonly partiallyhaveconserved sub-family and life cycle stage dependent expression pattern across land plants while others are highly diverged. Our workprovides the phylogenetic framework for C1-1i ZF-TFs, s and strengthen C1-1 ZF-TFs as a potential model for IDR-research in plants.

Detection and molecular characterization of a novel mitovirus associated with Passiflora edulis Sims.

Mitoviruses are cryptic capsidless viruses belonging to the family Mitoviridae that replicate and are maintained in the mitochondria of fungi. Complete mitovirus-like sequences were recently assembled from plant transcriptome data and plant leaf tissue samples. Passion fruit (Passiflora spp.) is an economically important crop for numerous tropical and subtropical countries worldwide, and many virus-induced diseases impact its production. From a large-scale genomic study targeting viruses infecting Passiflora spp. in Brazil, we detected a de novo-assembled contig with similarity to other plant-associated mitoviruses. The contig is ∼2.6kb long, with a single open reading frame (ORF) encoding an RNA-dependent RNA polymerase (RdRP). This contig has been named "passion fruit mitovirus-like 1" (PfMv1). An alignment of the predicted amino acid sequence of the RdRP of PfMv1 and those of other plant-associated mitoviruses revealed the presence of the six conserved motifs of mitovirus RdRPs. PfMv1 has 79% coverage and 50.14% identity to Humulus lupulus mitovirus 1. Phylogenetic analysis showed that PfMV1 clustered with other plant-associated mitoviruses in the genus Duamitovirus. Using RT-PCR, we detected a PfMv1-derived fragment, but no corresponding DNA was identified, thus excluding the possibility that this is an endogenized viral-like sequence. This is the first evidence of a replicating mitovirus associated with Passiflora edulis, and it should be classified as a member of a new species, for which we propose the name "Duamitovirus passiflorae".

Three-fold expansion of the genetic diversity of blunerviruses through plant (meta)transcriptome data-mining

Kitaviruses are plant-infecting, non-systemic disease-causing viruses with multipartite single-stranded RNA genomes. Despite their importance, knowledge on kitaviruses is limited in comparison with other plant virus groups, mainly because of the lesser number of identified and characterized kitaviruses and their isolates. In the present study, we explored plant (meta)transcriptome data available in public domain and identified genome sequences of eighteen putative novel blunerviruses in eighteen plant species, including four gymnosperm and four monocot species. Four RNA segments (RNAs 1–4) of eleven identified viruses were recovered, whilst at least two RNA segments were recovered for the remaining viruses. Phylogenetic analysis grouped the identified viruses with known blunerviruses. Based on genome organization, sequence identities of encoded proteins with known blunerviruses and phylogeny, the identified viruses are regarded as new members of the genus Blunervirus. The study paves way for initiating further studies on understanding biological properties, economic importance and geographical distribution of identified blunerviruses.

Biochar modulates the antioxidant system and hormonal signaling in tobacco under continuous-cropping conditions

ABSTRACT As an important economic crop, tobacco faces the common challenges of continuous cropping due to the limited amount of arable land. Biochar has certain preventive and control effects on continuous cropping obstacles and can improve crop yield and quality. This study aims to explore the regulation of the antioxidant system and hormone signaling in tobacco under continuous cropping conditions by biochar. We studied the impact of biochar (Nicotiana tabacum LJ911 and LY101) on plant physiological functions and transcriptomes of tobacco under continuous cropping conditions. The results showed that biochar regulates photosynthetic gas exchange parameters in both tobacco varieties. Biochar significantly increased the activity of antioxidant enzymes in the leaves of both tobacco varieties under continuous-cropping conditions. Additionally, biochar up-regulated endogenous abscisic acid, auxin, and jasmonic acid in the leaves of both tobacco varieties, with higher levels observed in LY101 than in LJ911. Through Weighted Gene Co-expression Network Analysis (WGCNA), it was found that the tobacco antioxidant system and hormones showed a significant response. Biochar improved photosynthetic efficiency, enhanced antioxidant capacity, and promoted tobacco growth through hormone synthesis and signaling. In summary, biochar application can serve as a promising strategy to mitigate the challenges associated with continuous cropping in tobacco cultivation.

Dicranopteris dichotoma rhizosphere-derived Bacillus sp. MQB12 acts as an enhancer of plant growth via increasing phosphorus utilization, hormone synthesis, and rhizosphere microbial abundance

In recent years, microbial inoculants have showed a great potential to replace chemical fertilizers as a new generation of soil amendment agents, however, the understanding of their effects on nutrient cycling within plants and rhizosphere microbial diversity are still limited. In this study, the rhizosphere growth-promoting bacteria MQB12 was used to inoculate Vigna radiata to evaluate the effects of external inoculants on plant transcriptomics and rhizosphere soil microbial diversity. Enrichment analysis using GO and KEGG revealed significant enrichment in DNA-binding transcription factor activity, transcriptional regulatory factor activity, and phenylpropanoid biosynthesis among the differentially expressed genes. MQB12 inoculation positively responded to phosphorus starvation response, increased the expression of phosphorus starvation response genes (PHT/PAP), enhanced the synthesis of ethylene and salicylic acid to cope with external stress, and improved the expression of plant disease resistance genes to strengthen the disease resistance of plants to pathogens. At the same time, microbial diversity analysis further revealed the positive effect of MQB12 inoculum. MQB12 inoculum enriched beneficial flora, improved flora abundance, changed the structure and diversity of V. radiata rhizosphere microbial community, enhanced the interconnections between the flora, and positively promoted growth. MQB12 was found to adjust the microflora of the rhizosphere, which subsequently changed the environment for plant colonization. This change led to the enrichment of beneficial bacteria and removal of pathogenic bacteria, which positively affected the internal pathways of plants. Additionally, changes in gene expression levels of plants resulted in the formation of different phenotypes and various metabolites, further influencing the formation of rhizosphere microbial communities through close contact between roots and soil. This study provides new insights into the effects of microbial agents on plant growth and root environment construction and is conducive to the further development and application of microbial agents.Graphical

Appropriate sulfur fertilization in contaminated soil enhanced the cadmium uptake by hyperaccumulator Sedum alfredii Hance

The biogeochemical processes of sulfur and heavy metals in the environment are closely related to each other. We investigated the influence of sulfur addition on hyperaccumulator Sedum alfredii Hance growth, cadmium (Cd) accumulation, soil Cd bioavailability, soil bacterial communities and plant transcriptome responses. The results showed that an appropriate rate of sulfur addition (1.0 or 2.5 g/kg) enhanced the growth of Sedum alfredii Hance plants as well as their accumulation of Cd. A high rate of sulfur addition (5.0 or 10.0 g/kg) causes toxicity to Sedum alfredii Hance plants. The application of an appropriate amount of sulfur to the soil increased the abundance of sulfur-oxidizing bacteria such as Sulfuriferula and Thiobacillus; acid-fast bacillus such as Alicyclobacillus; and cadmium-tolerant bacteria such as Bacillus and Rhodanobacter. This led to a decrease in pH and an increase in bioavailable Cd in the soil. RNA sequencing revealed that the addition of sulfur to soils led to the up regulation of most of the differentially expressed genes (DEGs) involved in “photosynthesis” and “photosynthesis, light reaction” in Sedum alfredii Hance leaves. Moreover, the “plant hormone signal transduction” pathway was significantly enriched with sulfur addition. Sulfur assimilation in Sedum alfredii Hance plants may promote photosynthesis and hormone synthesis, leading to Cd tolerance in these plants. Our study revealed that sulfur fertilization enhanced the efficiency of Cd phytoremediation in Sedum alfredii Hance plants.

Molecular Responses to Drought and Waterlogging Stresses of Kiwifruit (Actinidia chinensis var. deliciosa) Potted Vines

Environmental extremes, such as drought and flooding, are becoming increasingly common, resulting in significant crop losses. The aim of the present study was to understand the molecular response induced by drought and waterlogging conditions, and to link these responses to the physiological adaptation of plants. For this purpose, leaf RNA expression was analyzed in potted kiwifruit plants by Illumina Next Generation Sequences. Stressed plants showed an impairment of all physiological parameters (leaf-gas exchange and stem-water potential) with a more evident effect in waterlogging condition than in drought condition. However, the impact on the transcriptome in waterlogged plants was less intense than in drought stress. Drought affected several metabolic pathways, among which “plant hormone signal transduction”, “protein processing in endoplasmic reticulum”, and “mitogen-activated protein kinase signaling pathway” were the most representative in terms of number of genes involved. The genes involved in the biosynthesis of phenylpropanoids were positively influenced by both drought and waterlogging. Finally, waterlogging stimulated secondary metabolisms by upregulating the genes responsible for the biosynthesis of terpenoids and flavonoids, such as stilbenoids. The obtained results show that the two contrasting stress conditions share several common physiological responses and molecular mechanisms.

Doubling down on polyploid discoveries: Global advances in genomics and ecological impacts of polyploidy.

All flowering plants are now recognized as diploidized paleopolyploids (Jiao et al., 2011; One Thousand Plant Transcriptomes Initiative, 2019), and polyploid species comprise approximately 30% of contemporary plant species (Wood et al., 2009; Barker et al., 2016a). A major implication of these discoveries is that, to appreciate the evolution of plant diversity, we need to understand the fundamental biology of polyploids and diploidization. This need is broadly recognized by our community as there is a continued, growing interest in polyploidy as a research topic. Over the past 25 years, the sequencing and analysis of plant genomes has revolutionized our understanding of the importance of polyploid speciation to the evolution of land plants.

Molecular Evidence of Crosstalk Between Bacterial Endophytes and Plant Transcriptome in Brassica juncea

Molecular Evidence of Crosstalk Between Bacterial Endophytes and Plant Transcriptome in Brassica juncea

The underground world of plant disease: Rhizosphere dysbiosis reduces above-ground plant resistance to bacterial leaf spot and alters plant transcriptome.

Just as the human gut microbiome is colonized by a variety of microbes, so too is the rhizosphere of plants. An imbalance in this microbial community, known as dysbiosis, can have a negative impact on plant health. This study sought to explore the effect of rhizosphere dysbiosis on the health of tomato plants (Solanum lycopersicum L.), using them and the foliar bacterial spot pathogen Xanthomonas perforans as model organisms. The rhizospheres of 3-week-old tomato plants were treated with either streptomycin or water as a control, and then spray-inoculated with X. perforans after 24 h. Half of the plants that were treated with both streptomycin and X. perforans received soil microbiome transplants from uninfected plant donors 48 h after the streptomycin was applied. The plants treated with streptomycin showed a 26% increase in disease severity compared to those that did not receive the antibiotic. However, the plants that received the soil microbiome transplant exhibited an intermediate level of disease severity. The antibiotic-treated plants demonstrated a reduced abundance of rhizobacterial taxa such as Cyanobacteria from the genus Cylindrospermum. They also showed a down-regulation of genes related to plant primary and secondary metabolism, and an up-regulation of plant defence genes associated with induced systemic resistance. This study highlights the vital role that beneficial rhizosphere microbes play in disease resistance, even against foliar pathogens.

Silicon and Potassium-Induced Modulations in Leaf Carbohydrate Metabolism Confer Freezing Tolerance in Satsuma Mandarin

Freezing temperatures are a severe issue in North Florida, primarily due to occasional cold snaps and frost events in winter and early spring that cause damage to citrus groves, resulting in reduced fruit yield. The apoplasm is the primary cell component that interacts with environmental stress and is essential for plant tolerance to freezing temperatures. The present study was conducted to gain insight into how the application of silicon (Si) and potassium (K) are involved in the leaf apoplasm contributes to freezing stress tolerance, and regulates carbohydrate metabolism. We used Satsuma mandarin (Citrus unshiu Marc.), the most successful commercially grown citrus cultivar in North Florida, and treated trees with two concentrations of Si and K (50 and 100 ppm) both individually and combined as foliar spray to determine their effect as they relate to improving cold hardiness. Freezing stress (-6 °C) caused a severe reduction in photosynthesis, and modulations in leaf carbohydrate metabolism resulted in inhibited plant growth. The exogenous application of Si and K both improved the photosynthesis rate, soluble sugars, and activities of enzymes of carbohydrate metabolism such as fructokinase, phosphofructokinase, hexokinase, sucrose and phosphate synthase, and acid and neutral invertase. Applying Si (100 ppm) and combined treatment (Si + K-50) showed the best response by inducing the maximum tolerance to freeze stress. Our data demonstrated the ameliorative effect of Si and K under freezing stress in citrus is associated with modification in carbohydrate metabolism in the leaf apoplasm. This study provides direction for future research to investigate the effect of Si and K on the transcriptome and metabolome in citrus plants and their tissues under freezing stress.Graphical

Probing of plant transcriptomes reveals the hidden genetic diversity of the family Secoviridae.

Secoviruses are single-stranded RNA viruses that infect plants. In the present study, we identified 61 putative novel secoviral genomes in various plant species by mining publicly available plant transcriptome data. These viral sequences represent the genomes of 13 monopartite and 48 bipartite secovirids. The genome sequences of 52 secovirids were coding-complete, and nine were partial. Except for small open reading frames (ORFs) determined in waikaviral genomes and RNA2 of torradoviruses, all of the recovered genomes/genome segments contained a large ORF encoding a polyprotein. Based on genome organization and phylogeny, all but three of the novel secoviruses were assigned to different genera. The genome organization of two identified waika-like viruses resembled that of the recently identified waika-like virus Triticum aestivum secovirus. Phylogenetic analysis revealed a pattern of host-virus co-evolution in a few waika- and waika-like viruses and increased phylogenetic diversity of nepoviruses. The study provides a basis for further investigation of the biological properties of these novel secoviruses.