of Botany,Chinese Academy Of Sciences
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Genomes of leafy and leafless Platanthera orchids illuminate the evolution of mycoheterotrophy
No full textAnalyses of the genome sequences and expression data for two closely related mycoheterotrophic orchid species provide insights into the genomic basis underlying the evolution of mycoheterotrophy. To improve our understanding of the origin and evolution of mycoheterotrophic plants, we here present the chromosome-scale genome assemblies of two sibling orchid species: partially mycoheterotrophic Platanthera zijinensis and holomycoheterotrophic Platanthera guangdongensis. Comparative analysis shows that mycoheterotrophy is associated with increased substitution rates and gene loss, and the deletion of most photoreceptor genes and auxin transporter genes might be linked to the unique phenotypes of fully mycoheterotrophic orchids. Conversely, trehalase genes that catalyse the conversion of trehalose into glucose have expanded in most sequenced orchids, in line with the fact that the germination of orchid non-endosperm seeds needs carbohydrates from fungi during the protocorm stage. We further show that the mature plant of P. guangdongensis, different from photosynthetic orchids, keeps expressing trehalase genes to hijack trehalose from fungi. Therefore, we propose that mycoheterotrophy in mature orchids is a continuation of the protocorm stage by sustaining the expression of trehalase genes. Our results shed light on the molecular mechanism underlying initial, partial and full mycoheterotrophy
Functional Genomic Analysis of the SPL9 Gene in Arabidopsis thaliana under Low Phosphate Conditions
No full textInorganic phosphate (Pi) is an essential nutrient, which is often served as a limiting factor in plant growth. It has been reported that SPL family members, such as SPL3, regulate Pi deficiency responses by controlling the expression of Pi deficiency responsive genes. To elucidate whether SPL9 respond to low phosphorus stress, we investigated the phenotypes and conducted RNA sequencing analysis in transgenic Arabidopsis thaliana with overexpressing rSPL9 (R9) under conditions of both normal and low Pi availability. Compared with wild-type plants, R9 showed decreased anthocyanin accumulation and increased Pi contents in shoots under Pi deficiency. Through RNA-seq analysis compared with wild-type plants, we detected 217 genes significantly differentially expressed in conditions of Pi sufficiency, and 121 genes differentially expressed in conditions of Pi deficiency in R9 plants. Under Pi deficiency, MYB62 and ZAT6 are two important differentially expressed genes (DEGs) that both regulate the Pi uptake processes. In addition, these DEGs included multiple protein kinases, jasmonic acid response genes and genes related to salt stress responses. Genes associated with hydrolase and transferase activity were also differentially regulated by Pi deficiency, such as cytochrome P450 monooxygenases. Of particular note, the transcription factor AP2-EREBP and members of the bHLH family were among the most significantly differentially regulated genes identified under both Pi sufficient and Pi deficient conditions. In conclusion, our analysis of the R9 transcriptome highlights the importance of SPL9 under conditions of Pi-deficiency. Except for stress and defense response genes, the R9 transcriptome also characterized the induction of ethylene or jasmonic acid signaling under Pi deficiency
Cellular localization of Arabidopsis EARLY FLOWERING3 is responsive to light quality
No full textCircadian clocks facilitate the coordination of physiological and developmental processes to changing daily and seasonal cycles. A hub for environmental signaling pathways in the Arabidopsis (Arabidopsis thaliana) circadian clock is the evening complex (EC), a protein complex composed of EARLY FLOWERING3 (ELF3), ELF4, and LUX ARRYTHMO (LUX). Formation of the EC depends on ELF3, a scaffold protein that recruits the other components of the EC and chromatin remodeling enzymes to repress gene expression. Regulating the cellular distribution of ELF3 is thus an important mechanism in controlling its activity. Here, we determined that the cellular and sub-nuclear localization of ELF3 is responsive to red (RL) and blue light and that these two wavelengths have apparently competitive effects on where in the cell ELF3 localizes. We further characterized the RL response, revealing that at least two RL pathways influence the cellular localization of ELF3. One of these depends on the RL photoreceptor phytochrome B (phyB), while the second is at least partially independent of phyB activity. Finally, we investigated how changes in the cellular localization of ELF3 are associated with repression of EC target-gene expression. Our analyses revealed a complex effect whereby ELF3 is required for controlling RL sensitivity of morning-phased genes, but not evening-phased genes. Together, our findings establish a previously unknown mechanism through which light signaling influences ELF3 activity. Light signaling pathways converge on the evening complex scaffold protein EARLY FLOWERING3 by controlling its cellular and sub-cellular localization and regulating circadian clock gene expression
Divergence of active site motifs among different classes of Populus glutaredoxins results in substrate switches
No full textEnzymes are essential components of all biological systems. The key characteristics of proteins functioning as enzymes are their substrate specificities and catalytic efficiencies. In plants, most genes encoding enzymes are members of large gene families. Within such families, the contributions of active site motifs to the functional divergence of duplicate genes have not been well elucidated. In this study, we identified 41 glutaredoxin (GRX) genes in the Populus trichocarpa genome. GRXs are ubiquitous enzymes in plants that play important roles in developmental and stress tolerance processes. In poplar, GRX genes were divided into four classes based on clear differences in gene structure and expression pattern, subcellular localization, enzymatic activity, and substrate specificity of the encoded proteins. Using site-directed mutagenesis, this study revealed that the divergence of the active site motif among different classes of GRX proteins resulted in substrate switches and thus provided new insights into the molecular evolution of these important plant enzymes
PtoMPO1, a negative mediator, functions in poplar drought tolerance
No full textDrought, as one of the most severe abiotic stresses in nature, adversely affects plant growth and development. Poplar is a woody plant which is prone to water-deficit sensitivity. Therefore, it is important to improve our understanding of how poplar responds to drought stress. Here, we cloned a gene from Populus tomentosa, namely PtoMPO1. PtoMPO1 encodes a DUF962 domain protein that is a homolog of yeast dioxygenase Mpo1 and Ara-bidopsis MHP1. The transcripts of PtoMPO1 were repressed by drought stress and ABA. Atmhp1-1 was a T-DNA insertion mutant lacking AtMHP1, and heteroexpression of PtoMPO1 in Atmhp1-1 significantly alleviated the sensitivity of Atmhp1-1 to ABA and NaCl, implying the functional replacement of PtoMPO1 to AtMHP1. PtoMPO1 overexpression decreased but PtoMPO1 mutation enhanced poplar drought tolerance. Furthermore, the expres-sion of drought-related gene PtoRD26 is markedly lower in PtoMPO1-overexpressing plants and notably higher in Ptompo1 mutants compared to that in the wild type. Overall, these results suggested that PtoMPO1 functions as a novel negative mediator for drought tolerance in poplar
Ancestral function but divergent epigenetic regulation of HAIKU2 reveals routes of seed developmental evolution
No full textEvolution is driven by various mechanisms. A directional increase in the embryo to endosperm ratio is an evolutionary trend within the angiosperms. The endosperm constitutes a major portion of the seed volume in Poales and some dicots. However, in other dicots such as Arabidopsis and soybean, the endosperm pro-liferates early, followed by embryo growth to replace the endosperm. The Arabidopsis leucine-rich repeat receptor protein kinase AtHAIKU2 (AtIKU2) is a key regulator of early endosperm proliferation. In this study, we found that IKU2s from Brachypodium, rice, and soybean can complement the abnormal seed develop-mental phenotype of Atiku2, while AtIKU2 also rescues the defective endosperm proliferation in the Bra-chypodium BdIKU2 knockout mutant seeds. AtIKU2 and soybean GmIKU2 are actively expressed a few days after fertilization. Thereafter, expression of AtIKU2 is suppressed by the FIS-PRC2 complex-mediated H3K27me3. The soybean GmIKU2 locus is also enriched with H3K27me3 marks. The histone methyltrans-ferase AtMEA is unique to Brassicaceae, but one GmSWN in soybean plays a similar role in seed develop-ment as AtMEA. By contrast, the BdIKU2 and rice OsIKU2 loci are continuously expressed and are devoid of H3K27me3 marks. Taken together, these results suggest that IKU2 genes retain an ancestral function, but the duration of their expression that is controlled by PRC2-mediated epigenetic silencing contributes to silenced or persistent endosperm proliferation in different species. Our study reveals an epigenetic mech-anism that drives the development of vastly different seed ontogenies
Too much of a good thing? Inorganic nitrogen (N) inhibits moss-associated N2 fixation but organic N can promote it
No full textMoss-associated nitrogen (N-2) fixation is one of the main inputs of new N in pristine ecosystems that are characterized by low N availability. Previous studies have shown that N-2 fixation is inhibited by inorganic N (IN) inputs, but if N-2 fixation in mosses is similarly affected by organic N (ON) remains unknown. Here, we assessed N-2 fixation in two dominant mosses in boreal forests (Pleurozium schreberi and Sphagnum capillifolium) in response to different levels of N, simulating realistic (up to 4 kg N ha(-1) year(-1)) and extreme N addition rates in pristine ecosystems (up to 20 kg N ha(-1) year(-1)) of IN (ammonium nitrate) and ON (alanine and urea). We also assessed if N-2 fixation can recover from the N additions. In the realistic scenario, N-2 fixation was inhibited by increasing NH4NO3 additions in P. schreberi but not in S. capillifolium, and alanine and urea stimulated N-2 fixation in both moss species. In contrast, in the extreme N additions, increasing N inputs inhibited N-2 fixation in both moss species and all N forms. Nitrogen fixation was more sensitive to N inputs in P. schreberi than in S. capillifolium and was higher in the recovery phase after the realistic compared to the extreme N additions. These results demonstrate that N-2 fixation in mosses is less sensitive to organic than inorganic N inputs and highlight the importance of considering different N forms and species-specific responses when estimating the impact of N inputs on ecosystem functions such as moss-associated N-2 fixation
A lineage-specific arginine in POS1 is required for fruit size control in Physaleae (Solanaceae) via gene co-option
No full textSolanaceae have important economic value mainly due to their edible fruits. Physalis organ size 1/cytokinin response factor 3 (POS1/CRF3), a unique gene in Solanaceae, is involved in fruit size variation in Physalis but not in Solanum. However, the underlying mechanisms remain elusive. Here, we found that POS1/CRF3 was likely created via the fusion of CRF7 and CRF8 duplicates. Multiple genetic manipulations revealed that only POS1 and Capsicum POS1 (CaPOS1) functioned in fruit size control via the positive regulation of cell expansion. Comparative studies in a phylogenetic framework showed the directional enhancement of POS1-like expression in the flowers and fruits of Physaleae and the specific gain of certain interacting proteins associated with cell expansion by POS1 and CaPOS1. A lineage-specific single nucleotide polymorphism (SNP) caused the 68th amino acid histidine in the POS1 orthologs of non-Physaleae (Nicotiana and Solanum) to change to arginine in Physaleae (Physalis and Capsicum). Substituting the arginine in Physaleae POS1-like by histidine completely abolished their function in the fruits and the protein-protein interaction (PPI) with calreticulin-3. Transcriptomic comparison revealed the potential downstream pathways of POS1, including the brassinosteroid biosynthesis pathway. However, POS1-like may have functioned ancestrally in abiotic stress within Solanaceae. Our work demonstrated that heterometric expression and a SNP caused a single amino acid change to establish new PPIs, which contributed to the co-option of POS1 in multiple regulatory pathways to regulate cell expansion and thus fruit size in Physaleae. These results provide new insights into fruit morphological evolution and fruit yield control
The expression of demographic costs of reproduction varies among coexisting plants with different life history traits
No full textDemographic costs of reproduction in flowering plants should depend on life history and reproductive efforts, but how the expression of costs varies with life-history traits is poorly understood. We experimentally increased and reduced reproductive effort (fruit production) to quantify demographic costs of reproduction in four coexisting species with contrasting growth forms (clonal vs. non-clonal) and flower production (single- vs. multi-flowered). We repeated the experiment for 3 years and measured the demographic rates the year after the treatment. In 2 years, we also quantified the costs of flower maintenance by contrasting the performance of non-fruiting plants with intact flowers and plants with their flowers removed. Costs varied among species, in both magnitude and demographic rate affected. Costs of natural reproduction were expressed as reductions in size and fecundity next year, whereas increased reproduction additionally reduced sprouting probability. The magnitude of demographic costs of both reproduction and flower maintenance was highest in the non-clonal, multi-flowered species, and costs were more frequently detected in the two multi-flowered species than in the single-flowered ones. This may be explained by higher biomass allocation to reproductive parts and a longer flowering period in the former. Demographic costs of reproduction did not depend on clone size. Synthesis. These results document that demographic costs vary among coexisting species sharing similar niches and are associated with divergence in life-history traits. Such trait-dependent variation in costs may reduce competition among coexisting species and facilitate diversity
Species richness, functional traits and climate interactively affect tree survival in a large forest biodiversity experiment
No full textTree survival affects forest biodiversity, structure and functioning. However, little is known about feedback effects of biodiversity on survival and its dependence on functional traits and interannual climatic variability. With an individual-based dataset from a large subtropical forest biodiversity experiment, we evaluated how species richness, functional traits and time-dependent covariates affected annual tree survival rates from age 3-12 (years) after planting 39 species across a diversity gradient from 1 to 2, 4, 8 and 16 tree species. We found that overall survival rates marginally increased with diversity at the plot level, with large variation among plots within diversity levels. Significant variation among species in survival responses to diversity and changes in these responses with age were related to species functional traits and climatic conditions. Generally, survival rates of conservative species (evergreen, late-successional species with thick leaves and high carbon to nitrogen ratio but low specific leaf area, leaf phosphorus and hydraulic conductivity) increased with diversity, age and yearly precipitation, whereas acquisitive species showed opposite responses. Synthesis. Our results indicate that interactions between diversity, species functional traits and yearly climatic conditions can balance survival among species in diverse forests. Planting mixtures of species that differ in functional traits in afforestation projects may lead to a positive feedback loop where biodiversity maintains biodiversity, together with its previously reported beneficial effects on ecosystem functioning