Evolution of F-box genes in plants: different modes of sequence divergence and their relationships with functional diversification

Nematode-resistance loci in upland cotton genomes are associated with structural differences

Reniform and root-knot nematode are two of the most destructive pests of conventional upland cotton, Gossypium hirsutum L., and continue to be a major threat to cotton fiber production in semiarid regions of the Southern United States and Central America. Fortunately, naturally occurring tolerance to these nematodes has been identified in the Pima cotton species (Gossypium barbadense) and several upland cotton varieties (G. hirsutum), which has led to a robust breeding program that has successfully introgressed and stacked these independent resistant traits into several upland cotton lineages with superior agronomic traits, e.g. BAR 32-30 and BARBREN-713. This work identifies the genomic variations of these nematode-tolerant accessions by comparing their respective genomes to the susceptible, high-quality fiber-producing parental line of this lineage: Phytogen 355 (PSC355). We discover several large genomic differences within marker regions that harbor putative resistance genes as well as expression mechanisms shared by the two resistant lines, with respect to the susceptible PSC355 parental line. This work emphasizes the utility of whole-genome comparisons as a means of elucidating large and small nuclear differences by lineage and phenotype.

An Arabidopsis Kinesin-14D motor is associated with midzone microtubules for spindle morphogenesis

The acentrosomal spindle apparatus has kinetochore fibers organized and converged toward opposite poles; however, mechanisms underlying the organization of these microtubule fibers into an orchestrated bipolar array were largely unknown. Kinesin-14D is one of the four classes of Kinesin-14 motors that are conserved from green algae to flowering plants. In Arabidopsis thaliana, three Kinesin-14D members displayed distinct cell cycle-dependent localization patterns on spindle microtubules in mitosis. Notably, Kinesin-14D1 was enriched on the midzone microtubules of prophase and mitotic spindles and later persisted in the spindle and phragmoplast midzones. The kinesin-14d1 mutant had kinetochore fibers disengaged from each other during mitosis and exhibited hypersensitivity to the microtubule-depolymerizing herbicide oryzalin. Oryzalin-treated kinesin-14d1 mutant cells had kinetochore fibers tangled together in collapsed spindle microtubule arrays. Kinesin-14D1, unlike other Kinesin-14 motors, showed slow microtubule plus end-directed motility, and its localization and function were dependent on its motor activity and the novel malectin-like domain. Our findings revealed a Kinesin-14D1-dependent mechanism that employs interpolar microtubules to regulate the organization of kinetochore fibers for acentrosomal spindle morphogenesis.

Identification and expression analysis of nuclear factor Y transcription factor genes under drought, cold and Eldana infestation in sugarcane (Saccharum spp. hybrid)

BACKGROUND

The Nuclear Factor Y (NF-Y) transcription factor (TF) gene family plays a crucial role in plant development and response to stress. Limited information is available on this gene family in sugarcane.

OBJECTIVES

To identify sugarcane NF-Y genes through bioinformatic analysis and phylogenetic association and investigate the expression of these genes in response to abiotic and biotic stress.

METHODS

Sugarcane NF-Y genes were identified using comparative genomics from functionally annotated Poaceae and Arabidopsis species. Quantitative PCR and transcriptome analysis assigned preliminary functional roles to these genes in response to water deficit, cold and African sugarcane borer (Eldana saccharina) infestation.

RESULTS

We identify 21 NF-Y genes in sugarcane. Phylogenetic analysis revealed three main branches representing the subunits with potential discrepancies present in the assignment of numerical names of some NF-Y putative orthologs across the different species. Gene expression analysis indicated that three genes, ShNF-YA1, A3 and B3 were upregulated and two genes, NF-YA4 and A7 were downregulated, while three genes were upregulated, ShNF-YB2, B3 and C4, in the plants exposed to water deficit and cold stress, respectively. Functional involvement of NF-Y genes in the biotic stress response were also detected where three genes, ShNF-YA6, A3 and A7 were downregulated in the early resistant (cv. N33) response to Eldana infestation whilst only ShNF-YA6 was downregulated in the susceptible (cv. N11) early response.

CONCLUSIONS

Our research findings establish a foundation for investigating the function of ShNF-Ys and offer candidate genes for stress-resistant breeding and improvement in sugarcane.

TaMIR397-6A and -6B Homoeologs Encode Active miR397 Contributing to the Regulation of Grain Size in Hexaploid Wheat

Wheat is one of the most important food crops globally, and understanding the regulation of grain size is crucial for wheat breeding to achieve a higher grain yield. MicroRNAs (miRNAs) play vital roles in plant growth and development. However, the miRNA-mediated mechanism underlying grain size regulation remains largely elusive in wheat. Here, we report the characterization and functional validation of a miRNA, TamiR397a, associated with grain size regulation in wheat. The function of three TaMIR397 homoeologs was determined through histochemical β-glucuronidase-dependent assay. MiRNA expression was detected using quantitative reverse transcription polymerase chain reaction (qRT-PCR), and the function of TamiR397a was validated through its transgenic overexpression and repression in wheat. It was found that TaMIR397-6A and TaMIR397-6B encode active TamiR397a. The expression profiling indicated that TamiR397a was differentially expressed in various tissues and gradually up-regulated during grain filling. The inhibition of TamiR397a perturbed grain development, leading to a decrease in grain size and weight. Conversely, the overexpression of TamiR397a resulted in increased grain size and weight by accelerating the grain filling process. Transcriptome analysis revealed that TamiR397a regulates a set of genes involved in hormone response, desiccation tolerance, regulation of cellular senescence, seed dormancy, and seed maturation biological processes, which are important for grain development. Among the down-regulated genes in the grains of the TamiR397a-overexpressing transgenic plants, 11 putative targets of the miRNA were identified. Taken together, our results demonstrate that TamiR397a is a positive regulator of grain size and weight, offering potential targets for breeding wheat with an increased grain yield.

The PHYB-FOF2-VOZ2 module functions to fine-tune flowering in response to changes in light quality by modulating FLC expression in Arabidopsis

Proper timing of flowering under different environmental conditions is critical for plant propagation. Light quality is a pivotal environmental cue that plays a critical role in flowering regulation. Plants tend to flower late under light with a high red (R)/far-red (FR) light ratio but early under light with a low R/FR light ratio. However, how plants fine-tune flowering in response to changes in light quality is not well understood. Here, we demonstrate that F-box of Flowering 2 (FOF2), an autonomous pathway-related regulator, physically interacts with VASCULAR PLANT ONE-ZINC FINGER 1 and 2 (VOZ1 and VOZ2), which are direct downstream factors of the R/FR light receptor phytochrome B (PHYB). We show that PHYB physically interacts with FOF2, mediates stabilization of the FOF2 protein under FR light and end-of-day FR light, and enhances FOF2 binding to VOZ2, which leads to degradation of VOZ2 by SCFFOF2 E3 ligase. By contrast, PHYB mediates degradation of FOF2 protein under R light and end-of-day R light. Genetic interaction studies demonstrated that FOF2 functions downstream of PHYB to promote FLC expression and inhibit flowering under both high R/FR light and simulated shade conditions, processes that are partially dependent on VOZ proteins. Taken together, our findings suggest a novel mechanism whereby plants fine-tune flowering time through a PHYB-FOF2-VOZ2 module that modulates FLC expression in response to changes in light quality.

Single-cell transcriptome landscape elucidates the cellular and developmental responses to tomato chlorosis virus infection in tomato leaf

Plant viral diseases compromise the growth and yield of the crop globally, and they tend to be more serious under extreme temperatures and drought climate changes. Currently, regulatory dynamics during plant development and in response to virus infection at the plant cell level remain largely unknown. In this study, single-cell RNA sequencing on 23 226 individual cells from healthy and tomato chlorosis virus-infected leaves was established. The specific expression and epigenetic landscape of each cell type during the viral infection stage were depicted. Notably, the mesophyll cells showed a rapid function transition in virus-infected leaves, which is consistent with the pathological changes such as thinner leaves and decreased chloroplast lamella in virus-infected samples. Interestingly, the F-box protein SKIP2 was identified to play a pivotal role in chlorophyll maintenance during virus infection in tomato plants. Knockout of the SlSKIP2 showed a greener leaf state before and after virus infection. Moreover, we further demonstrated that SlSKIP2 was located in the cytomembrane and nucleus and directly regulated by ERF4. In conclusion, with detailed insights into the plant responses to viral infections at the cellular level, our study provides a genetic framework and gene reference in plant-virus interaction and breeding in the future research.

Deciphering the mechanism of E3 ubiquitin ligases in plant responses to abiotic and biotic stresses and perspectives on PROTACs for crop resistance

With global climate change, it is essential to find strategies to make crops more resistant to different stresses and guarantee food security worldwide. E3 ubiquitin ligases are critical regulatory elements that are gaining importance due to their role in selecting proteins for degradation in the ubiquitin-proteasome proteolysis pathway. The role of E3 Ub ligases has been demonstrated in numerous cellular processes in plants responding to biotic and abiotic stresses. E3 Ub ligases are considered a class of proteins that are difficult to control by conventional inhibitors, as they lack a standard active site with pocket, and their biological activity is mainly due to protein-protein interactions with transient conformational changes. Proteolysis-targeted chimeras (PROTACs) are a new class of heterobifunctional molecules that have emerged in recent years as relevant alternatives for incurable human diseases like cancer because they can target recalcitrant proteins for destruction. PROTACs interact with the ubiquitin-proteasome system, principally the E3 Ub ligase in the cell, and facilitate proteasome turnover of the proteins of interest. PROTAC strategies harness the essential functions of E3 Ub ligases for proteasomal degradation of proteins involved in dysfunction. This review examines critical advances in E3 Ub ligase research in plant responses to biotic and abiotic stresses. It highlights how PROTACs can be applied to target proteins involved in plant stress response to mitigate pathogenic agents and environmental adversities.

Functional role of geminivirus encoded proteins in the host: Past and present

During plant-pathogen interaction, plant exhibits a strong defense system utilizing diverse groups of proteins to suppress the infection and subsequent establishment of the pathogen. However, in response, pathogens trigger an anti-silencing mechanism to overcome the host defense machinery. Among plant viruses, geminiviruses are the second largest virus family with a worldwide distribution and continue to be production constraints to food, feed, and fiber crops. These viruses are spread by a diverse group of insects, predominantly by whiteflies, and are characterized by a single-stranded DNA (ssDNA) genome coding for four to eight proteins that facilitate viral infection. The most effective means to managing these viruses is through an integrated disease management strategy that includes virus-resistant cultivars, vector management, and cultural practices. Dynamic changes in this virus family enable the species to manipulate their genome organization to respond to external changes in the environment. Therefore, the evolutionary nature of geminiviruses leads to new and novel approaches for developing virus-resistant cultivars and it is essential to study molecular ecology and evolution of geminiviruses. This review summarizes the multifunctionality of each geminivirus-encoded protein. These protein-based interactions trigger the abrupt changes in the host methyl cycle and signaling pathways that turn over protein normal production and impair the plant antiviral defense system. Studying these geminivirus interactions localized at cytoplasm-nucleus could reveal a more clear picture of host-pathogen relation. Data collected from this antagonistic relationship among geminivirus, vector, and its host, will provide extensive knowledge on their virulence mode and diversity with climate change.

Identification of candidate genes for Fusarium head blight resistance from QTLs using RIL population in wheat

Fusarium head blight (FHB) stands out as one of the most devastating wheat diseases and leads to significantly grain yield losses and quality reductions in epidemic years. Exploring quantitative trait loci (QTL) for FHB resistance is a critical step for developing new FHB-resistant varieties. We previously constructed a genetic map of unigenes (UG-Map) according to the physical positions using a set of recombinant-inbred lines (RILs) derived from the cross of 'TN18 × LM6' (TL-RILs). Here, the number of diseased spikelets (NDS) and relative disease index (RDI) for FHB resistance were investigated under four environments using TL-RILs, which were distributed across 13 chromosomes. A number of 36 candidate genes for NDS and RDI from of 19 stable QTLs were identified. The average number of candidate genes per QTL was 1.89, with 14 (73.7%), two (10.5%), and three (15.8%) QTLs including one, two, and 3-10 candidate genes, respectively. Among the 24 candidate genes annotated in the reference genome RefSeq v1.1, the homologous genes of seven candidate genes, including TraesCS4B02G227300 for QNds/Rdi-4BL-4553, TraesCS5B02G303200, TraesCS5B02G303300, TraesCS5B02G303700, TraesCS5B02G303800 and TraesCS5B02G304000 for QNds/Rdi-5BL-9509, and TraesCS7A02G568400 for QNds/Rdi-7AL-14499, were previously reported to be related to FHB resistance in wheat, barely or Brachypodium distachyon. These genes should be closely associated with FHB resistance in wheat. In addition, the homologous genes of five genes, including TraesCS1A02G037600LC for QNds-1AS-2225, TraesCS1D02G017800 and TraesCS1D02G017900 for QNds-1DS-527, TraesCS1D02G018000 for QRdi-1DS-575, and TraesCS4B02G227400 for QNds/Rdi-4BL-4553, were involved in plant defense responses against pathogens. These genes should be likely associated with FHB resistance in wheat.

The F-box protein RhSAF destabilizes the gibberellic acid receptor RhGID1 to mediate ethylene-induced petal senescence in rose

Roses are among the most popular ornamental plants cultivated worldwide for their great economic, symbolic, and cultural importance. Nevertheless, rapid petal senescence markedly reduces rose (Rosa hybrida) flower quality and value. Petal senescence is a developmental process tightly regulated by various phytohormones. Ethylene accelerates petal senescence, while gibberellic acid (GA) delays this process. However, the molecular mechanisms underlying the crosstalk between these phytohormones in the regulation of petal senescence remain largely unclear. Here, we identified SENESCENCE-ASSOCIATED F-BOX (RhSAF), an ethylene-induced F-box protein gene encoding a recognition subunit of the SCF-type E3 ligase. We demonstrated that RhSAF promotes degradation of the GA receptor GIBBERELLIN INSENSITIVE DWARF1 (RhGID1) to accelerate petal senescence. Silencing RhSAF expression delays petal senescence, while suppressing RhGID1 expression accelerates petal senescence. RhSAF physically interacts with RhGID1s and targets them for ubiquitin/26S proteasome-mediated degradation. Accordingly, ethylene-induced RhGID1C degradation and RhDELLA3 accumulation are compromised in RhSAF-RNAi lines. Our results demonstrate that ethylene antagonizes GA activity through RhGID1 degradation mediated by the E3 ligase RhSAF. These findings enhance our understanding of the phytohormone crosstalk regulating petal senescence and provide insights for improving flower longevity.

The F-box protein encoding genes of the leaf-rust fungi Puccinia triticina: genome-wide identification, characterization and expression dynamics during pathogenesis

The F-box proteins in fungi perform diverse functions including regulation of cell cycle, circadian clock, development, signal transduction and nutrient sensing. Genome-wide analysis revealed 10 F-box genes in Puccinia triticina, the causal organism for the leaf rust disease in wheat and were characterized using in silico approaches for revealing phylogenetic relationships, gene structures, gene ontology, protein properties, sequence analysis and gene expression studies. Domain analysis predicted functional domains like WD40 and LRR at C-terminus along with the obvious presence of F-box motif in N-terminus. MSA showed amino acid replacements, which might be due to nucleotide substitution during replication. Phylogenetic analysis revealed the F-box proteins with similar domains to be clustered together while some sequences were spread out in different clades, which might be due to functional diversity. The clustering of Puccinia triticina GG705409 with Triticum aestivum TaAFB4/TaAFB5 in a single clade suggested the possibilities of horizontal gene transfer during the coevolution of P. triticina and wheat. Gene ontological annotation categorized them into three classes and were functionally involved in protein degradation through the protein ubiquitination pathway. Protein-protein interaction network revealed F-box proteins to interact with other components of the SCF complex involved in protein ubiquitination. Relative expression analysis of five F-box genes in a time course experiment denoted their involvement in leaf rust susceptible wheat plants. This study provides information on structure elucidation of F-box proteins of a basidiomycetes plant pathogenic fungi and their role during pathogenesis.

Dynamic interactions between SPX proteins, the ubiquitination machinery, and signalling molecules for stress adaptation at a whole-plant level

The plant macronutrient phosphorus is a scarce resource and plant-available phosphate is limiting in most soil types. Generally, a gene regulatory module called the phosphate starvation response (PSR) enables efficient phosphate acquisition by roots and translocation to other organs. Plants growing on moderate to nutrient-rich soils need to co-ordinate availability of different nutrients and repress the highly efficient PSR to adjust phosphate acquisition to the availability of other macro- and micronutrients, and in particular nitrogen. PSR repression is mediated by a small family of single SYG1/Pho81/XPR1 (SPX) domain proteins. The SPX domain binds higher order inositol pyrophosphates that signal cellular phosphorus status and modulate SPX protein interaction with PHOSPHATE STARVATION RESPONSE1 (PHR1), the central transcriptional regulator of PSR. Sequestration by SPX repressors restricts PHR1 access to PSR gene promoters. Here we focus on SPX4 that primarily acts in shoots and sequesters many transcription factors other than PHR1 in the cytosol to control processes beyond the classical PSR, such as nitrate, auxin, and jasmonic acid signalling. Unlike SPX1 and SPX2, SPX4 is subject to proteasomal degradation not only by singular E3 ligases, but also by SCF-CRL complexes. Emerging models for these different layers of control and their consequences for plant acclimation to the environment will be discussed.

The Identification and Expression Analysis of the Liriodendron chinense F-Box Gene Family

The F-box gene family is one of the largest gene families in plants, and it plays a crucial role in regulating plant development, reproduction, cellular protein degradation, and response to biotic and abiotic stresses. Despite their significance, a comprehensive analysis of the F-box gene family in Liriodendron chinense and other magnoliaceae species has not been reported. In this study, we report for the first time the identification of 144 full-length F-box genes in L. chinense. Based on specific domains and phylogenetic analyses, these genes were divided into 10 distinct subfamilies. We further analyzed their gene structure, conserved domain and chromosome distribution, genome-wide replication events, and collinearity. Additionally, based on GO analysis, we found that F-box genes exhibit functional specificity, with a significant proportion of them being involved in protein binding (GO:0005515), suggesting that F-box genes may play an important role in gene regulation in L. chinense. Transcriptome data and q-PCR results also showed that F-box genes are involved in the development of multiple tissues in L. chinense, regulate the somatic embryogenesis of Liriodendron hybrids, and play a pivotal role in abiotic stress. Altogether, these findings provide a foundation for understanding the biological function of F-box genes in L. chinense and other plant species.

Phosphoproteome analyses pinpoint the F-box protein SLOW MOTION as a regulator of warm temperature-mediated hypocotyl growth in Arabidopsis

Hypocotyl elongation is controlled by several signals and is a major characteristic of plants growing in darkness or under warm temperature. While already several molecular mechanisms associated with this process are known, protein degradation and associated E3 ligases have hardly been studied in the context of warm temperature. In a time-course phosphoproteome analysis on Arabidopsis seedlings exposed to control or warm ambient temperature, we observed reduced levels of diverse proteins over time, which could be due to transcription, translation, and/or degradation. In addition, we observed differential phosphorylation of the LRR F-box protein SLOMO MOTION (SLOMO) at two serine residues. We demonstrate that SLOMO is a negative regulator of hypocotyl growth, also under warm temperature conditions, and protein-protein interaction studies revealed possible interactors of SLOMO, such as MKK5, DWF1, and NCED4. We identified DWF1 as a likely SLOMO substrate and a regulator of warm temperature-mediated hypocotyl growth. We propose that warm temperature-mediated regulation of SLOMO activity controls the abundance of hypocotyl growth regulators, such as DWF1, through ubiquitin-mediated degradation.

GhFB15 is an F-box protein that modulates the response to salinity by regulating flavonoid biosynthesis

An exposure to extremely saline conditions can lead to significant oxidative damage in plants. Flavonoids, which are potent antioxidants, are critical for the scavenging of reactive oxygen species caused by abiotic stress. In the present study, the cotton F-box gene GhFB15 was isolated and characterized. The expression of GhFB15 was rapidly induced by salt as well as by exogenous hormones (ETH, MeJA, ABA, and GA). An analysis of subcellular localization revealed GhFB15 is mainly distributed in nuclei. Overexpression of GhFB15 adversely affected the salt tolerance of transgenic Arabidopsis plants as evidenced by decreased seed germination and seedling growth, whereas the silencing of GhFB15 improved the salt tolerance of cotton plants. Furthermore, we analyzed the gene expression profiles of VIGS-GhFB15 and TRV:00 plants. Many of the differentially expressed genes were associated with the flavonoid biosynthesis pathway. Moreover, lower flavonoid contents and higher levels of H2O2 and O2- were observed in the transgenic Arabidopsis plants. Conversely, the VIGS-GhFB15 cotton plants had relatively higher flavonoid contents, but lower H2O2 and O2- levels. These results suggest that GhFB15 negatively regulates salt tolerance, and silencing GhFB15 results in increased flavonoid accumulation and improved ROS scavenging.

Deciphering genetic basis of developmental and agronomic traits by integrating high-throughput optical phenotyping and genome-wide association studies in wheat

Dissecting the genetic basis of complex traits such as dynamic growth and yield potential is a major challenge in crops. Monitoring the growth throughout growing season in a large wheat population to uncover the temporal genetic controls for plant growth and yield-related traits has so far not been explored. In this study, a diverse wheat panel composed of 288 lines was monitored by a non-invasive and high-throughput phenotyping platform to collect growth traits from seedling to grain filling stage and their relationship with yield-related traits was further explored. Whole genome re-sequencing of the panel provided 12.64 million markers for a high-resolution genome-wide association analysis using 190 image-based traits and 17 agronomic traits. A total of 8327 marker-trait associations were detected and clustered into 1605 quantitative trait loci (QTLs) including a number of known genes or QTLs. We identified 277 pleiotropic QTLs controlling multiple traits at different growth stages which revealed temporal dynamics of QTLs action on plant development and yield production in wheat. A candidate gene related to plant growth that was detected by image traits was further validated. Particularly, our study demonstrated that the yield-related traits are largely predictable using models developed based on i-traits and provide possibility for high-throughput early selection, thus to accelerate breeding process. Our study explored the genetic architecture of growth and yield-related traits by combining high-throughput phenotyping and genotyping, which further unravelled the complex and stage-specific contributions of genetic loci to optimize growth and yield in wheat.

Rice florigens control a common set of genes at the shoot apical meristem including the F-BOX BROADER TILLER ANGLE 1 that regulates tiller angle and spikelet development

Rice flowering is triggered by transcriptional reprogramming at the shoot apical meristem (SAM) mediated by florigenic proteins produced in leaves in response to changes in photoperiod. Florigens are more rapidly expressed under short days (SDs) compared to long days (LDs) and include the HEADING DATE 3a (Hd3a) and RICE FLOWERING LOCUS T1 (RFT1) phosphatidylethanolamine binding proteins. Hd3a and RFT1 are largely redundant at converting the SAM into an inflorescence, but whether they activate the same target genes and convey all photoperiodic information that modifies gene expression at the SAM is currently unclear. We uncoupled the contribution of Hd3a and RFT1 to transcriptome reprogramming at the SAM by RNA sequencing of dexamethasone-inducible over-expressors of single florigens and wild-type plants exposed to photoperiodic induction. Fifteen highly differentially expressed genes common to Hd3a, RFT1, and SDs were retrieved, 10 of which still uncharacterized. Detailed functional studies on some candidates revealed a role for LOC_Os04g13150 in determining tiller angle and spikelet development and the gene was renamed BROADER TILLER ANGLE 1 (BRT1). We identified a core set of genes controlled by florigen-mediated photoperiodic induction and defined the function of a novel florigen target controlling tiller angle and spikelet development.

Tissues and mechanisms associated with Verticillium wilt resistance in tomato using bi-grafted near-isogenic lines

Host resistance is the primary means to control Verticillium dahliae, a soil-borne pathogen causing major losses on a broad range of plants, including tomato. The tissues and mechanisms responsible for resistance remain obscure. In the field, resistant tomato used as rootstocks does not confer resistance. Here, we created bi-grafted plants with near-isogenic lines (NILs) exhibiting (Ve1) or lacking (ve1) resistance to V. dahliae race 1. Ten days after inoculation, scion and rootstock tissues were subjected to differential gene expression and co-expression network analyses. Symptoms only developed in susceptible scions regardless of the rootstock. Infection caused more dramatic alteration of tomato gene expression in susceptible compared with resistant tissues, including pathogen receptor, signaling pathway, pathogenesis-related protein, and cell wall modification genes. Differences were observed between scions and rootstocks, primarily related to physiological processes in these tissues. Gene expression in scions was influenced by the rootstock genotype. A few genes were associated with the Ve1 genotype, which was independent of infection or tissue type. Several were physically clustered, some near the Ve1 locus on chromosome 9. Transcripts mapped to V. dahliae were dominated by secreted candidate effector proteins. These findings advance knowledge of molecular mechanisms underlying the tomato-V. dahliae interaction.

Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes

Fruiting bodies (sporocarps, sporophores or basidiomata) of mushroom-forming fungi (Agaricomycetes) are among the most complex structures produced by fungi. Unlike vegetative hyphae, fruiting bodies grow determinately and follow a genetically encoded developmental program that orchestrates their growth, tissue differentiation and sexual sporulation. In spite of more than a century of research, our understanding of the molecular details of fruiting body morphogenesis is still limited and a general synthesis on the genetics of this complex process is lacking. In this paper, we aim at a comprehensive identification of conserved genes related to fruiting body morphogenesis and distil novel functional hypotheses for functionally poorly characterised ones. As a result of this analysis, we report 921 conserved developmentally expressed gene families, only a few dozens of which have previously been reported to be involved in fruiting body development. Based on literature data, conserved expression patterns and functional annotations, we provide hypotheses on the potential role of these gene families in fruiting body development, yielding the most complete description of molecular processes in fruiting body morphogenesis to date. We discuss genes related to the initiation of fruiting, differentiation, growth, cell surface and cell wall, defence, transcriptional regulation as well as signal transduction. Based on these data we derive a general model of fruiting body development, which includes an early, proliferative phase that is mostly concerned with laying out the mushroom body plan (via cell division and differentiation), and a second phase of growth via cell expansion as well as meiotic events and sporulation. Altogether, our discussions cover 1 480 genes of Coprinopsis cinerea, and their orthologs in Agaricus bisporus, Cyclocybe aegerita, Armillaria ostoyae, Auriculariopsis ampla, Laccaria bicolor, Lentinula edodes, Lentinus tigrinus, Mycena kentingensis, Phanerochaete chrysosporium, Pleurotus ostreatus, and Schizophyllum commune, providing functional hypotheses for ~10 % of genes in the genomes of these species. Although experimental evidence for the role of these genes will need to be established in the future, our data provide a roadmap for guiding functional analyses of fruiting related genes in the Agaricomycetes. We anticipate that the gene compendium presented here, combined with developments in functional genomics approaches will contribute to uncovering the genetic bases of one of the most spectacular multicellular developmental processes in fungi. Citation: Nagy LG, Vonk PJ, Künzler M, Földi C, Virágh M, Ohm RA, Hennicke F, Bálint B, Csernetics Á, Hegedüs B, Hou Z, Liu XB, Nan S, M. Pareek M, Sahu N, Szathmári B, Varga T, Wu W, Yang X, Merényi Z (2023). Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes. Studies in Mycology 104: 1-85. doi: 10.3114/sim.2022.104.01.

Role of F-box E3-ubiquitin ligases in plant development and stress responses

KEY MESSAGE

F-box E3-ubiquitin ligases regulate critical biological processes in plant development and stress responses. Future research could elucidate why and how plants have acquired a large number of F-box genes. The ubiquitin-proteasome system (UPS) is a predominant regulatory mechanism employed by plants to maintain the protein turnover in the cells and involves the interplay of three classes of enzymes, E1 (ubiquitin-activating), E2 (ubiquitin-conjugating), and E3 ligases. The diverse and most prominent protein family among eukaryotes, F-box proteins, are a vital component of the multi-subunit SCF (Skp1-Cullin 1-F-box) complex among E3 ligases. Several F-box proteins with multifarious functions in different plant systems have evolved rapidly over time within closely related species, but only a small part has been characterized. We need to advance our understanding of substrate-recognition regulation and the involvement of F-box proteins in biological processes and environmental adaptation. This review presents a background of E3 ligases with particular emphasis on the F-box proteins, their structural assembly, and their mechanism of action during substrate recognition. We discuss how the F-box proteins regulate and participate in the signaling mechanisms of plant development and environmental responses. We highlight an urgent need for research on the molecular basis of the F-box E3-ubiquitin ligases in plant physiology, systems biology, and biotechnology. Further, the developments and outlooks of the potential technologies targeting the E3-ubiquitin ligases for developing crop improvement strategies have been discussed.

Insights of auxin signaling F-box genes in wheat (Triticum aestivum L.) and their dynamic expression during the leaf rust infection

The TRANSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALING F-BOX (TIR1/AFB) protein serves as auxin receptor and links with Aux/IAA repressor protein leading to its degradation via SKP-Cullin-F box (SCF^TIR1/AFB) complex in the auxin signaling pathway. Present study revealed 11 TIR1/AFB genes in wheat by genome-wide search using AFB HMM profile. Phylogenetic analysis clustered these genes in two classes. Several phytohormone, abiotic, and biotic stress responsive cis-elements were detected in promoter regions of TIR1/AFB genes. These genes were localized on homoeologous chromosome groups 2, 3, and 5 showing orthologous relation with other monocot plants. Most genes were interrupted by introns and the gene products were localized in cytoplasm, nucleus, and cell organelles. TaAFB3, TaAFB5, and TaAFB8 had nuclear localization signals. The evolutionary constraint suggested paralogous sister pairs and orthologous genes went through strong purifying selection process and are slowly evolving at protein level. Functional annotation revealed all TaAFB genes participated in auxin activated signaling pathway and SCF-mediated ubiquitination process. Furthermore, in silico expression study revealed their diverse expression profiles during various developmental stages in different tissues and organs as well as during biotic and abiotic stress. QRT-PCR based studies suggested distinct expression pattern of TIR1-1, TIR1-3, TaAFB1, TaAFB2, TaAFB3, TaAFB4, TaAFB5, TaAFB7, and TaAFB8 displaying maximum expression at 24 and 48 h post inoculation in both susceptible and resistant near isogenic wheat lines infected with leaf rust pathogen. Importantly, this also reflects coordinated responses in expression patterns of wheat TIR1/AFB genes during progression stages of leaf rust infection.

Identification of F-box gene family in Brassica oleracea and expression analysis in response to low-temperature stress

Unfavorable climatic conditions, such as low temperatures, often hinder the growth and production of crops worldwide. The F-box protein-encoding gene family performs an essential role in plant stress resistance. However, a comprehensive analysis of the F-box gene family in cabbage (Brassica oleracea var capitata L.) has not been reported yet. In this study, genome-wide characterization of F-box proteins in cabbage yielded 303 BoFBX genes and 224 BoFBX genes unevenly distributed on 9 chromosomes of cabbage. Phylogenetic analysis of 303 BoFBX genes was classified into nine distinct subfamily groups (GI-GIX). Analysis of the gene structure of BoFBX genes indicated that most genes within the same clade are highly conserved. In addition, tissue-specific expression analysis revealed that six F-box genes in cabbage showed the highest expression in rosette leaves, followed by roots and stems and the lowest expression was observed in the BoFBX156 gene. In contrast, the expression of the other five genes, BoFBX100, BoFBX117, BoFBX136, BoFBX137 and BoFBX213 was observed to be upregulated in response to low-temperature stress. Moreover, we found that the expression level of the BoFBX gene in the cold-tolerant cultivar "ZG" was higher than that in cold-sensitive "YC" with the extension of stress duration, while expression levels of each gene in "ZG" were higher than "YC" at 24 h. Knowledge of the various functions provided by BoFBXs genes and their expression patterns provides a firm theoretical foundation for explaining the functions of BoFBXs, thereby contributing to the molecular breeding process of cabbage.

Jasmonate perception: Ligand-receptor interaction, regulation, and evolution

Phytohormones integrate external environmental and developmental signals with internal cellular responses for plant survival and multiplication in changing surroundings. Jasmonate (JA), which might originate from prokaryotes and benefit plant terrestrial adaptation, is a vital phytohormone that regulates diverse developmental processes and defense responses against various environmental stresses. In this review, we first provide an overview of ligand-receptor binding techniques used for the characterization of phytohormone-receptor interactions, then introduce the identification of the receptor COI1 and active JA molecules, and finally summarize recent advances on the regulation of JA perception and its evolution.

An F-box protein attenuates fungal xylanase-triggered immunity by destabilizing LRR-RLP NbEIX2 in a SOBIR1-dependent manner

Receptor-like proteins (RLPs) lacking the cytoplasmic kinase domain play crucial roles in plant growth, development and immunity. However, what remains largely elusive is whether RLP protein levels are fine-tuned by E3 ubiquitin ligases, which are employed by receptor-like kinases for signaling attenuation. Nicotiana benthamiana NbEIX2 is a leucine-rich repeat RLP (LRR-RLP) that mediates fungal xylanase-triggered immunity. Here we show that NbEIX2 associates with an F-box protein NbPFB1, which promotes NbEIX2 degradation likely by forming an SCF E3 ubiquitin ligase complex, and negatively regulates NbEIX2-mediated immune responses. NbEIX2 undergoes ubiquitination and proteasomal degradation in planta. Interestingly, NbEIX2 without its cytoplasmic tail is still associated with and destabilized by NbPFB1. In addition, NbPFB1 also associates with and destabilizes NbSOBIR1, a co-receptor of LRR-RLPs, and fails to promote NbEIX2 degradation in the sobir1 mutant. Our findings reveal a distinct model of NbEIX2 degradation, in which an F-box protein destabilizes NbEIX2 indirectly in a SOBIR1-dependent manner.

KARRIKIN UPREGULATED F-BOX 1 negatively regulates drought tolerance in Arabidopsis

The karrikin (KAR) receptor and several related signaling components have been identified by forward genetic screening, but only a few studies have reported on upstream and downstream KAR signaling components and their roles in drought tolerance. Here, we characterized the functions of KAR UPREGULATED F-BOX 1 (KUF1) in drought tolerance using a reverse genetics approach in Arabidopsis (Arabidopsis thaliana). We observed that kuf1 mutant plants were more tolerant to drought stress than wild-type (WT) plants. To clarify the mechanisms by which KUF1 negatively regulates drought tolerance, we performed physiological, transcriptome, and morphological analyses. We found that kuf1 plants limited leaf water loss by reducing stomatal aperture and cuticular permeability. In addition, kuf1 plants showed increased sensitivity of stomatal closure, seed germination, primary root growth, and leaf senescence to abscisic acid (ABA). Genome-wide transcriptome comparisons of kuf1 and WT rosette leaves before and after dehydration showed that the differences in various drought tolerance-related traits were accompanied by differences in the expression of genes associated with stomatal closure (e.g. OPEN STOMATA 1), lipid and fatty acid metabolism (e.g. WAX ESTER SYNTHASE), and ABA responsiveness (e.g. ABA-RESPONSIVE ELEMENT 3). The kuf1 mutant plants had higher root/shoot ratios and root hair densities than WT plants, suggesting that they could absorb more water than WT plants. Together, these results demonstrate that KUF1 negatively regulates drought tolerance by modulating various physiological traits, morphological adjustments, and ABA responses and that the genetic manipulation of KUF1 in crops is a potential means of enhancing their drought tolerance.

GWAS, MWAS and mGWAS provide insights into precision agriculture based on genotype-dependent microbial effects in foxtail millet

Genetic and environmental factors collectively determine plant growth and yield. In the past 20 years, genome-wide association studies (GWAS) have been conducted on crops to decipher genetic loci that contribute to growth and yield, however, plant genotype appears to be insufficient to explain the trait variations. Here, we unravel the associations between genotypic, phenotypic, and rhizoplane microbiota variables of 827 foxtail millet cultivars by an integrated GWAS, microbiome-wide association studies (MWAS) and microbiome genome-wide association studies (mGWAS) method. We identify 257 rhizoplane microbial biomarkers associated with six key agronomic traits and validated the microbial-mediated growth effects on foxtail millet using marker strains isolated from the field. The rhizoplane microbiota composition is mainly driven by variations in plant genes related to immunity, metabolites, hormone signaling and nutrient uptake. Among these, the host immune gene FLS2 and transcription factor bHLH35 are widely associated with the microbial taxa of the rhizoplane. We further uncover a plant genotype-microbiota interaction network that contributes to phenotype plasticity. The microbial-mediated growth effects on foxtail millet are dependent on the host genotype, suggesting that precision microbiome management could be used to engineer high-yielding cultivars in agriculture systems.

Genome-Wide Identification and Expression Patterns of the F-box Family in Poplar under Salt Stress

The F-box family exists in a wide variety of plants and plays an extremely important role in plant growth, development and stress responses. However, systematic studies of F-box family have not been reported in populus trichocarpa. In the present study, 245 PtrFBX proteins in total were identified, and a phylogenetic tree was constructed on the basis of their C-terminal conserved domains, which was divided into 16 groups (A–P). F-box proteins were located in 19 chromosomes and six scaffolds, and segmental duplication was main force for the evolution of the F-box family in poplar. Collinearity analysis was conducted between poplar and other species including Arabidopsis thaliana, Glycine max, Anemone vitifolia Buch, Oryza sativa and Zea mays, which indicated that poplar has a relatively close relationship with G. max. The promoter regions of PtrFBX genes mainly contain two kinds of cis-elements, including hormone-responsive elements and stress-related elements. Transcriptome analysis indicated that there were 82 differentially expressed PtrFBX genes (DEGs), among which 64 DEGs were in the roots, 17 in the leaves and 26 in the stems. In addition, a co-expression network analysis of four representative PtrFBX genes indicated that their co-expression gene sets were mainly involved in abiotic stress responses and complex physiological processes. Using bioinformatic methods, we explored the structure, evolution and expression pattern of F-box genes in poplar, which provided clues to the molecular function of F-box family members and the screening of salt-tolerant PtrFBX genes.

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

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.

Annotation and Analysis of 3902 Odorant Receptor Protein Sequences from 21 Insect Species Provide Insights into the Evolution of Odorant Receptor Gene Families in Solitary and Social Insects

The gene family of insect olfactory receptors (ORs) has expanded greatly over the course of evolution. ORs enable insects to detect volatile chemicals and therefore play an important role in social interactions, enemy and prey recognition, and foraging. The sequences of several thousand ORs are known, but their specific function or their ligands have only been identified for very few of them. To advance the functional characterization of ORs, we have assembled, curated, and aligned the sequences of 3902 ORs from 21 insect species, which we provide as an annotated online resource. Using functionally characterized proteins from the fly Drosophila melanogaster, the mosquito Anopheles gambiae and the ant Harpegnathos saltator, we identified amino acid positions that best predict response to ligands. We examined the conservation of these predicted relevant residues in all OR subfamilies; the results showed that the subfamilies that expanded strongly in social insects had a high degree of conservation in their binding sites. This suggests that the ORs of social insect families are typically finely tuned and exhibit sensitivity to very similar odorants. Our novel approach provides a powerful tool to exploit functional information from a limited number of genes to study the functional evolution of large gene families.

Bulk RNA-Seq Analysis Reveals Differentially Expressed Genes Associated with Lateral Branch Angle in Peanut

Lateral branch angle (LBA), or branch habit, is one of the most important agronomic traits in peanut. To date, the underlying molecular mechanisms of LBA have not been elucidated in peanut. To acquire the differentially expressed genes (DEGs) related to LBA, a TI population was constructed through the hybridization of a bunch-type peanut variety Tifrunner and prostrate-type Ipadur. We report the identification of DEGs related to LBA by sequencing two RNA pools, which were composed of 45 F₃ lines showing an extreme opposite bunch and prostrate phenotype. We propose to name this approach Bulk RNA-sequencing (BR-seq) as applied to several plant species. Through BR-seq analysis, a total of 3083 differentially expressed genes (DEGs) were identified, including 13 gravitropism-related DEGs, 22 plant hormone-related DEGs, and 55 transcription factors-encoding DEGs. Furthermore, we also identified commonly expressed alternatively spliced (AS) transcripts, of which skipped exon (SE) and retained intron (RI) were most abundant in the prostrate and bunch-type peanut. AS isoforms between prostrate and bunch peanut highlighted important clues to further understand the post-transcriptional regulatory mechanisms of branch angle regulation. Our findings provide not only important insights into the landscape of the regulatory pathway involved in branch angle formation but also present practical information for peanut molecular breeding in the future.

Genome-wide identification and characterization of the tomato F-box associated (FBA) protein family and expression analysis of their responsiveness to Phytophthora infestans

Late blight caused by Phytophthora infestans brings huge economic losses to the production of tomato (Solanum lycopersicum) every year. F-box proteins participate in plants response to phytohormones and biotic stress, whereas as the largest subfamily of F-box superfamily, the detailed information about F-box associated (SlFBA) family in tomato has been rarely reported. In this study, a total of 46 tomato FBA genes were identified based on the latest genome annotation. Phylogenetic analysis revealed that the FBA proteins from tomato and 6 different plant species were clustered into 7 distinct clades. The SlFBA genes were unevenly distributed on 11 chromosomes of tomato, mainly concentrated in the regions with high gene density. Tandem duplications and purification selection contribute to the expansion and evolution of the SlFBA gene family. Transcriptome analysis revealed that the SlFBA genes were differentially expressed in different tissues with obvious tissue-specific expression patterns. There were 18 SlFBA genes differentially expressed in P. infestans-resistant and -susceptible tomato, among which, 3 SlFBA genes might play positive roles in tomato resistance to P. infestans. Taken together, this study systematically analyzed the SlFBA genes family for the first time and identified the candidate SlFBA genes that affect tomato resistance to P. infestans, which provided important genetic and breeding resources for improving tomato resistance to pathogens.

Genome-wide identification, evolutionary and functional analyses of KFB family members in potato

BACKGROUND

Kelch repeat F-box (KFB) proteins play vital roles in the regulation of multitudinous biochemical and physiological processes in plants, including growth and development, stress response and secondary metabolism. Multiple KFBs have been characterized in various plant species, but the family members and functions have not been systematically identified and analyzed in potato.

RESULTS

Genome and transcriptome analyses of StKFB gene family were conducted to dissect the structure, evolution and function of the StKFBs in Solanum tuberosum L. Totally, 44 StKFB members were identified and were classified into 5 groups. The chromosomal localization analysis showed that the 44 StKFB genes were located on 12 chromosomes of potato. Among these genes, two pairs of genes (StKFB15/16 and StKFB40/41) were predicted to be tandemly duplicated genes, and one pair of genes (StKFB15/29) was segmentally duplicated genes. The syntenic analysis showed that the KFBs in potato were closely related to the KFBs in tomato and pepper. Expression profiles of the StKFBs in 13 different tissues and in potato plants with different treatments uncovered distinct spatial expression patterns of these genes and their potential roles in response to various stresses, respectively. Multiple StKFB genes were differentially expressed in yellow- (cultivar 'Jin-16'), red- (cultivar 'Red rose-2') and purple-fleshed (cultivar 'Xisen-8') potato tubers, suggesting that they may play important roles in the regulation of anthocyanin biosynthesis in potato.

CONCLUSIONS

This study reports the structure, evolution and expression characteristics of the KFB family in potato. These findings pave the way for further investigation of functional mechanisms of StKFBs, and also provide candidate genes for potato genetic improvement.

miRNA Profiling and Its Role in Multi-Omics Regulatory Networks Connected with Somaclonal Variation in Cucumber (Cucumis sativus L.)

The role of miRNAs in connection with the phenomenon of somaclonal variation, which occurs during plant in vitro culture, remains uncertain. This study aims to investigate the possible role of miRNAs in multi-omics regulatory pathways in cucumber somaclonal lines. For this purpose, we performed sRNA sequencing (sRNA-seq) from cucumber fruit samples identified 8, 10 and 44 miRNAs that are differentially expressed between somaclones (S1, S2, S3 lines) and the reference B10 line of Cucumis sativus. For miRNA identification, we use ShortStack software designed to filter miRNAs from sRNAs according to specific program criteria. The identification of predicted in-silico targets revealed 2,886 mRNAs encoded by 644 genes. The functional annotation of miRNA's target genes and gene ontology classification revealed their association with metabolic processes, response to stress, multicellular organism development, biosynthetic process and catalytic activity. We checked with bioinformatic analyses for possible interactions at the level of target proteins, differentially expressed genes (DEGs) and genes affected by genomic polymorphisms. We assume that miRNAs can indirectly influence molecular networks and play a role in many different regulatory pathways, leading to somaclonal variation. This regulation is supposed to occur through the process of the target gene cleavage or translation inhibition, which in turn affects the proteome, as we have shown in the example of molecular networks. This is a new approach combining levels from DNA-seq through mRNA-seq, sRNA-seq and in silico PPI in the area of plants' somaclonal variation.

Genome-wide identification and characterization of F-box family proteins in sweet potato and its expression analysis under abiotic stress

In this study, genome-wide characterization of F-box proteins in sweet potato yielded 243 IbFBX genes, unevenly distributed on the 15 chromosomes of sweet potato. Gene duplication analysis suggested segmental duplication as the principal factor influencing the expansive evolution of IbFBX genes in sweet potato. Phylogenetic analysis clustered F-box proteins in sweet potato, Arabidopsis, and rice into six clades (I-VI). Gene structure analysis of the IbFBX genes revealed that most of the genes within the same clade were highly conserved. Expression profiles of IbFBX family genes in 9 different tissues and under stress conditions revealed that the IbFBXs were highly upregulated or downregulated in response to salt and drought stress, suggesting their significant roles in abiotic stress response and adaptation. Knowledge of the diverse functions and expression patterns of IbFBXs presents a solid theoretical basis for annotating the functions of IbFBXs and further facilitate the molecular breeding of sweet potato.

A common F-box gene regulates the leucine homeostasis of Medicago truncatula and Arabidopsis thaliana

The F-box domain is a conserved structural protein motif that most frequently interacts with the SKP1 protein, the core of the SCFs (SKP1-CULLIN-F-box protein ligase) E3 ubiquitin protein ligases. As part of the SCF complexes, the various F-box proteins recruit substrates for degradation through ubiquitination. In this study, we functionally characterized an F-box gene (MtF-box) identified earlier in a population of Tnt1 retrotransposon-tagged mutants of Medicago truncatula and its Arabidopsis thaliana homolog (AtF-box) using gain- and loss-of-function plants. We highlighted the importance of MtF-box in leaf development of M. truncatula. Protein-protein interaction analyses revealed the 2-isopropylmalate synthase (IPMS) protein as a common interactor partner of MtF-box and AtF-box, being a key enzyme in the biosynthesis pathway of the branched-chain amino acid leucine. For further detailed analysis, we focused on AtF-box and its role during the cell division cycle. Based on this work, we suggest a mechanism for the role of the studied F-box gene in regulation of leucine homeostasis, which is important for growth.

Functional Innovation through Gene Duplication Followed by Frameshift Mutation

In his influential book “Evolution by Gene Duplication”, Ohno postulated that frameshift mutation could lead to a new function after duplication, but frameshift mutation is generally thought to be deleterious, and thus drew little attention in functional innovation in duplicate evolution. To this end, we here report an exhaustive survey of the genomes of human, mouse, zebrafish, and fruit fly. We identified 80 duplicate genes that involved frameshift mutations after duplication. The frameshift mutation preferentially located close to the C-terminus in most cases (55/88), which indicated that a frameshift mutation that changed the reading frame in a small part at the end of a duplicate may likely have contributed to adaptive evolution (e.g., human genes NOTCH2NL and ARHGAP11B) otherwise too deleterious to survive. A few cases (11/80) involved multiple frameshift mutations, exhibiting various patterns of modifications of the reading frame. Functionality of duplicate genes involving frameshift mutations was confirmed by sequence characteristics and expression profile, suggesting a potential role of frameshift mutation in creating functional novelty. We thus showed that genomes have non-negligible numbers of genes that have experienced frameshift mutations following gene duplication. Our results demonstrated the potential importance of frameshift mutations in molecular evolution, as Ohno verbally argued 50 years ago.

Genetic Divergence of Lineage-Specific Tandemly Duplicated Gene Clusters in Four Diploid Potato Genotypes

Potato (Solanum tuberosum L.) is the most important non-grain food crop. Tandem duplication significantly contributes to genome evolution. The objectives of this study were to (i) identify tandemly duplicated genes and compare their genomic distributions across potato genotypes, (ii) investigate the bias in functional specificities, (iii) explore the relationships among coding sequence, promoter and expression divergences associated with tandemly duplicated genes, (iv) examine the role of tandem duplication in generating and expanding lineage-specific gene families, (v) investigate the evolutionary forces affecting tandemly duplicated genes, and (vi) assess the similarities and differences with respect to above mentioned aspects between cultivated genotypes and their wild-relative. In this study, we used well-annotated and chromosome-scale de novo genome assemblies of multiple potato genotypes. Our results showed that tandemly duplicated genes are abundant and dispersed through the genome. We found that several functional specificities, such as disease resistance, stress-tolerance, and biosynthetic pathways of tandemly duplicated genes were differentially enriched across multiple potato genomes. Our results indicated the existence of a significant correlation among expression, promoter, and protein divergences in tandemly duplicated genes. We found about one fourth of tandemly duplicated gene clusters as lineage-specific among multiple potato genomes, and these tended to localize toward centromeres and revealed distinct selection signatures and expression patterns. Furthermore, our results showed that a majority of duplicated genes were retained through sub-functionalization followed by genetic redundancy, while only a small fraction of duplicated genes was retained though neo-functionalization. The lineage-specific expansion of gene families by tandem duplication coupled with functional bias might have significantly contributed to potato's genotypic diversity, and, thus, to adaption to environmental stimuli.

The reference genome and full-length transcriptome of pakchoi provide insights into cuticle formation and heat adaption

Brassica rapa includes various vegetables with high economic value. Among them, green petiole type pakchoi (B. rapa ssp. chinensis) is one of the major vegetables grown in southern China. Compared with other B. rapa varieties, green petiole type pakchoi shows a higher level of heat resistance, which is partially derived from the rich epicuticular wax. Here we sequence a high-quality genome of green petiole type pakchoi, which has been widely used as the parent in breeding. Our results reveal that long terminal repeat retrotransposon insertion plays critical roles in promoting the genome expansion and transcriptional diversity of pakchoi genes through preferential insertions, particularly in cuticle biosynthetic genes. After whole-genome triplication, over-retained pakchoi genes escape stringent selection pressure, and among them a set of cuticle-related genes are retained. Using bulked-segregant analysis of a heat-resistant pakchoi cultivar, we identify a frame-shift deletion across the third exon and the subsequent intron of BrcCER1 in candidate regions. Using Nanopore long-read sequencing, we analyze the full-length transcriptome of two pakchoi cultivars with opposite sensitivity to high temperature. We find that the heat-resistant pakchoi cultivar can mitigate heat-caused leaf damage by activating an unfolded protein response, as well as by inhibiting chloroplast development and energy metabolism, which are presumably mediated by both transcriptional regulation and splicing factors. Our study provides valuable resources for Brassica functional genomics and breeding research, and deepens our understanding of plant stress resistance.

Genome-wide characterization, evolution, structure, and expression analysis of the F-box genes in Caenorhabditis

BACKGROUND

F-box proteins represent a diverse class of adaptor proteins of the ubiquitin-proteasome system (UPS) that play critical roles in the cell cycle, signal transduction, and immune response by removing or modifying cellular regulators. Among closely related organisms of the Caenorhabditis genus, remarkable divergence in F-box gene copy numbers was caused by sizeable species-specific expansion and contraction. Although F-box gene number expansion plays a vital role in shaping genomic diversity, little is known about molecular evolutionary mechanisms responsible for substantial differences in gene number of F-box genes and their functional diversification in Caenorhabditis. Here, we performed a comprehensive evolution and underlying mechanism analysis of F-box genes in five species of Caenorhabditis genus, including C. brenneri, C. briggsae, C. elegans, C. japonica, and C. remanei.

RESULTS

Herein, we identified and characterized 594, 192, 377, 39, 1426 F-box homologs encoding putative F-box proteins in the genome of C. brenneri, C. briggsae, C. elegans, C. japonica, and C. remanei, respectively. Our work suggested that extensive species-specific tandem duplication followed by a small amount of gene loss was the primary mechanism responsible for F-box gene number divergence in Caenorhabditis genus. After F-box gene duplication events occurred, multiple mechanisms have contributed to gene structure divergence, including exon/intron gain/loss, exonization/pseudoexonization, exon/intron boundaries alteration, exon splits, and intron elongation by tandem repeats. Based on high-throughput RNA sequencing data analysis, we proposed that F-box gene functions have diversified by sub-functionalization through highly divergent stage-specific expression patterns in Caenorhabditis species.

CONCLUSIONS

Massive species-specific tandem duplications and occasional gene loss drove the rapid evolution of the F-box gene family in Caenorhabditis, leading to complex gene structural variation and diversified functions affecting growth and development within and among Caenorhabditis species. In summary, our findings outline the evolution of F-box genes in the Caenorhabditis genome and lay the foundation for future functional studies.

The jojoba genome reveals wide divergence of the sex chromosomes in a dioecious plant

Most flowering plants are hermaphrodites, but around 6% of species are dioecious, having separate male and female plants. Sex chromosomes and some sex-specific genes have been reported in plants, but the genome sequences have not been compared. We now report the genome sequence of male and female jojoba (Simmondsia chinensis) plants, revealing a very large difference in the sex chromosomes. The male genome assembly was 832 Mb and the female 822 Mb. This was explained by the large size differences in the Y chromosome (37.6 Mb) compared with the X chromosome (26.9 Mb). Relative to the X chromosome, the Y chromosome had two large insertions each of more than 5 Mb containing more than 400 genes. Many of the genes in the chromosome-specific regions were novel. These male-specific regions included many flowering-related and stress response genes. Smaller insertions found only in the X chromosome totalled 877 kb. The wide divergence of the sex chromosomes suggests a long period of adaptation to diverging sex-specific roles. Male and female plants may have evolved to accommodate factors such as differing reproductive resource allocation requirements under the stress of the desert environment in which the plants are found. The sex-determining regions accumulate genes beneficial to each sex. This has required the evolution of many more novel sex-specific genes than has been reported for other organisms. This suggest that dioecious plants provide a novel source of genes for manipulation of reproductive performance and environmental adaptation in crops.

Loss-of-function of ARABIDOPSIS F-BOX PROTEIN HYPERSENSITIVE TO ABA 1 enhances drought tolerance and delays germination

ABA is a phytohormone involved in diverse plant events such as seed germination and drought response. An F-box protein functions as a substrate receptor of the SCF complex and is responsible for ubiquitination of target proteins, triggering their subsequent degradation mediated by ubiquitin proteasome system. Here, we have isolated a gene named ARABIDOPSIS F-BOX PROTEIN HYPERSENSITIVE TO ABA 1 (AFA1) that was upregulated by ABA. AFA1 interacted with adaptor proteins of the SCF complex, implying its role as a substrate receptor of the complex. Its loss of function mutants, afa1 seedlings, exhibited ABA-hypersensitivity, including delayed germination in the presence of ABA. Moreover, loss of AFA1 led to increased drought tolerance in adult plants. Microarray data with ABA treatments indicated that 129 and 219 genes were upregulated or downregulated, respectively, by more than three times in afa1 relative to the wild type. Among the upregulated genes in afa1, the expression of 28.7% was induced by more than three times in the presence of ABA, while only 9.3% was repressed to the same extent. These data indicate that AFA1 is involved in the downregulation of many ABA-inducible genes, in accordance with the ABA-hypersensitive phenotype of afa1. Epistasis analysis showed that AFA1 could play a role upstream of ABI4 and ABI5 in the ABA signaling for germination inhibition. Collectively, our findings suggest that AFA1 is a novel F-box protein that negatively regulates ABA signaling.

Tomato chlorosis virus-encoded p22 suppresses auxin signalling to promote infection via interference with SKP1-Cullin-F-boxTIR1 complex assembly

Phytohormone auxin plays a fundamental role in plant growth and defense against pathogens. However, how auxin signalling is regulated during virus infection in plants remains largely unknown. Auxin/indole-3-acetic acid (Aux/IAA) is the repressor of auxin signalling and can be recognized by an F-box protein transport inhibitor response 1 (TIR1). Ubiquitination and degradation of Aux/IAA by SKP1-Cullin-F-boxTIR1 (SCFTIR1 ) complex can trigger auxin signalling. Here, with an emerging important plant virus worldwide, we showed that tomato chlorosis virus (ToCV) infection or stable transgenic overexpression of its p22 protein does not alter auxin accumulation level but significantly decreases the expression of auxin signalling-responsive genes, suggesting that p22 can attenuate host auxin signalling. Further, p22 could bind the C-terminal of SKP1.1 and compete with TIR1 to interfere with the SCFTIR1 complex assembly, leading to a suppression of Aux/IAA degradation. Silencing and over-expression assays suggested that both NbSKP1.1 and NbTIR1 suppress ToCV accumulation and disease symptoms. Altogether, ToCV p22 disrupts the auxin signalling through destabilizing SCFTIR1 by interacting with the C-terminal of NbSKP1.1 to promote ToCV infection. Our findings uncovered a previously unknown molecular mechanism employed by a plant virus to manipulate SCF complex-mediated ubiquitin pathway and to reprogram auxin signalling for efficient infection.

Conservation lost: host-pathogen battles drive diversification and expansion of gene families

One of the strongest drivers in evolution is the struggle to survive a host-pathogen battle. This pressure selects for diversity among the factors directly involved in this battle, including virulence factors deployed by pathogens, their corresponding host targets, and host immune factors. A logical outcome of this diversification is that over time, the sequence of many immune factors will not be evolutionarily conserved across a broad range of species. Thus, while universal sequence conservation is often hailed as the hallmark of the importance of a particular gene, the immune system does not necessarily play by these rules when defending against co-evolving pathogens. This loss of sequence conservation is in contrast to many signaling pathways in development and basic cell biology that are not targeted by pathogens. In addition to diversification, another consequence of host-pathogen battles can be an amplification in gene number, thus leading to large gene families that have sequence relatively specific to a particular strain, species, or clade. Here we highlight this general theme across a variety of pathogen virulence factors and host immune factors. We summarize the wide range and number across species of these expanded, lineage-specific host-pathogen factors including ubiquitin ligases, nucleotide-binding leucine-rich repeat receptors, GTPases, and proteins without obvious biochemical function but that nonetheless play key roles in immunity.

RNase-based self-incompatibility in cacti

Approximately one-half of all flowering plants express genetically based physiological mechanisms that prevent self-fertilisation. One such mechanism, termed RNase-based self-incompatibility, employs ribonucleases as the pistil component. Although it is widespread, it has only been characterised in a handful of distantly related families, partly due to the difficulties presented by life history traits of many plants, which complicate genetic research. Many species in the cactus family are known to express self-incompatibility but the underlying mechanisms remain unknown. We demonstrate the utility of a candidate-based RNA-seq approach, combined with some unusual features of self-incompatibility-causing genes, which we use to uncover the genetic basis of the underlying mechanisms. Specifically, we assembled transcriptomes from Schlumbergera truncata (crab cactus or false Christmas cactus), and interrogated them for tissue-specific expression of candidate genes, structural characteristics, correlation with expressed phenotype(s), and phylogenetic placement. The results were consistent with operation of the RNase-based self-incompatibility mechanism in Cactaceae. The finding yields additional evidence that the ancestor of nearly all eudicots possessed RNase-based self-incompatibility, as well as a clear path to better conservation practices for one of the most charismatic plant families.

The regulatory activities of microRNAs in non-vascular plants: a mini review

MicroRNA-mediated gene regulation in non-vascular plants is potentially involved in several unique biological functions, including biosynthesis of several highly valuable exclusive bioactive compounds, and those small RNAs could be manipulated for the overproduction of essential bioactive compounds in the future. MicroRNAs (miRNAs) are a class of endogenous, small (20-24 nucleotides), non-coding RNA molecules that regulate gene expression through the miRNA-mediated mechanisms of either translational inhibition or messenger RNA (mRNA) cleavage. In the past years, studies have mainly focused on elucidating the roles of miRNAs in vascular plants as compared to non-vascular plants. However, non-vascular plant miRNAs have been predicted to be involved in a wide variety of specific biological mechanisms; nevertheless, some of them have been demonstrated explicitly, thus showing that the research field of this plant group owns a noteworthy potential to develop novel investigations oriented towards the functional characterization of these miRNAs. Furthermore, the insights into the roles of miRNAs in non-vascular plants might be of great importance for designing the miRNA-based genetically modified plants for valuable secondary metabolites, active compounds, and biofuels in the future. Therefore, in this current review, we provide an overview of the potential roles of miRNAs in different groups of non-vascular plants such as algae and bryophytes.

Regulation of Glycosylphosphatidylinositol-Anchored Protein (GPI-AP) Expression by F-Box/LRR-Repeat (FBXL) Protein in Wheat (Triticum aestivum L.)

F-box proteins are substrate recognition components of the Skp1-Cullin-F-box (SCF) complex, which performs many important biological functions including the degradation of numerous proteins via the ubiquitin–26S proteasome system. In this study, we isolated the gene encoding the F-box/LRR-repeat (FBXL) protein from wheat (Triticum aestivum L.) seedlings and validated that the TaFBXL protein is a component of the SCF complex. Yeast two-hybrid assays revealed that TaFBXL interacts with the wheat glycosylphosphatidylinositol-anchored protein (TaGPI-AP). The green fluorescent protein (GFP) fusion protein of TaFBXL was detected in the nucleus and plasma membrane, whereas that of TaGPI-AP was observed in the cytosol and probably also plasma membrane. yeast two-hybrid and bimolecular fluorescence complementation (BiFC) assays revealed that TaFBXL specifically interacts with TaGPI-AP in the nucleus and plasma membrane, and TaGPI-AP is targeted by TaFBXL for degradation via the 26S proteasome system. In addition, TaFBXL and TaGPI-AP showed antagonistic expression patterns upon treatment with indole-3-acetic acid (IAA), and the level of TaGPI-AP was higher in tobacco leaves treated with both MG132 (proteasome inhibitor) and IAA than in leaves treated with either MG132 or IAA. Taken together, our data suggest that TaFBXL regulates the TaGPI-AP protein level in response to exogenous auxin application.

Genome-wide survey of the F-box/Kelch (FBK) members and molecular identification of a novel FBK gene TaAFR in wheat

F-box proteins play critical roles in plant responses to biotic/abiotic stresses. In the present study, a total of 68 wheat F-box/Kelch (TaFBK) genes, unevenly distributed across 21 chromosomes and encoding 74 proteins, were identified in EnsemblPlants. Protein sequences were compared with those of Arabidopsis and three cereal species by phylogenetic and domain analyses, where the wheat sequences were resolved into 6 clades. In silico analysis of a digital PCR dataset revealed that TaFBKs were expressed at multiple developmental stages and tissues, and in response to drought and/or heat stresses. The TaFBK19 gene, a homolog of the Attenuated Far-Red Response (AFR) genes in other plant species, and hence named TaAFR, was selected for further analysis. Reverse-transcription quantitative real-time PCR (RT-qPCR) was carried out to determine tissue-specific, hormone and stress (abiotic/biotic) responsive expression patterns. Of interest, TaAFR was expressed most abundantly in the leaves, and its expression in response to leaf rust variants suggests a potential role in compatible vs incompatible rust responses. The protein was predicted to localize in cytosol, but it was shown experimentally to localize in both the cytosol and the nucleus of tobacco. A series of protein interaction studies, starting with a yeast-2-hybrid (Y2H) library screen (wheat leaf infected with incompatible leaf rust pathogens), led to the identification of three TaAFR interacting proteins. Skp1/ASK1-like protein (Skp1) was found to interact with the F-box domain of TaAFR, while ADP-ribosylation factor 2-like isoform X1 (ARL2) and phenylalanine ammonia-lyase (PAL) were shown to interact with its Kelch domain. The data presented herein provides a solid foundation from which the function and metabolic network of TaAFR and other wheat FBKs can be further explored.

SmKFB5 protein regulates phenolic acid biosynthesis by controlling the degradation of phenylalanine ammonia-lyase in Salvia miltiorrhiza

Phenolic acids are the major secondary metabolites and significant bioactive constituents of the medicinal plant Salvia miltiorrhiza. Many enzyme-encoding genes and transcription factors involved in the biosynthesis of phenolic acids have been identified, but the underlying post-translational regulatory mechanisms are poorly understood. Here, we demonstrate that the S. miltiorrhiza Kelch repeat F-box protein SmKFB5 physically interacts with three phenylalanine ammonia-lyase (PAL) isozymes and mediates their proteolytic turnover via the ubiquitin-26S proteasome pathway. Disturbing the expression of SmKFB5 reciprocally affected the abundance of SmPAL protein and the accumulation of phenolic acids, suggesting that SmKFB5 is a post-translational regulator responsible for the turnover of PAL and negatively controlling phenolic acids. Furthermore, we discovered that treatment of the hairy root of S. miltiorrhiza with methyl jasmonate suppressed the expression of SmKFB5 while inducing the transcription of SmPAL1 and SmPAL3. These data suggested that methyl jasmonate consolidated both transcriptional and post-translational regulation mechanisms to enhance phenolic acid biosynthesis. Taken together, our results provide insights into the molecular mechanisms by which SmKFB5 mediates the regulation of phenolic acid biosynthesis by jasmonic acid, and suggest valuable targets for plant breeders in tailoring new cultivars.

A Machine Learning Approach to Prioritizing Functionally Active F-box Members in Arabidopsis thaliana

Protein degradation through the Ubiquitin (Ub)-26S Proteasome System (UPS) is a major gene expression regulatory pathway in plants. In this pathway, the 76-amino acid Ub proteins are covalently linked onto a large array of UPS substrates with the help of three enzymes (E1 activating, E2 conjugating, and E3 ligating enzymes) and direct them for turnover in the 26S proteasome complex. The S-phase Kinase-associated Protein 1 (Skp1), CUL1, F-box (FBX) protein (SCF) complexes have been identified as the largest E3 ligase group in plants due to the dramatic number expansion of the FBX genes in plant genomes. Since it is the FBX proteins that recognize and determine the specificity of SCF substrates, much effort has been done to characterize their genomic, physiological, and biochemical roles in the past two decades of functional genomic studies. However, the sheer size and high sequence diversity of the FBX gene family demands new approaches to uncover unknown functions. In this work, we first identified 82 known FBX members that have been functionally characterized up to date in Arabidopsis thaliana. Through comparing the genomic structure, evolutionary selection, expression patterns, domain compositions, and functional activities between known and unknown FBX gene members, we developed a neural network machine learning approach to predict whether an unknown FBX member is likely functionally active in Arabidopsis, thereby facilitating its future functional characterization.