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The transcription factor LaMYC4 from lavender regulates volatile Terpenoid biosynthesis
No full textBackground The basic helix-loop-helix (bHLH) transcription factors (TFs), as one of the largest families of TFs, are essential regulators of plant terpenoid biosynthesis and response to stresses. Lavender has more than 75 volatile terpenoids, yet few TFs have been identified to be involved in the terpenoid biosynthesis. Results Based on RNA-Seq, reverse transcription-quantitative polymerase chain reaction, and transgenic technology, this study characterized the stress-responsive transcription factor LaMYC4 regulates terpenoid biosynthesis. Methyl jasmonate (MeJA) treatment increased volatile terpenoid emission, and the differentially expressed gene LaMYC4 was isolated. LaMYC4 expression level was higher in leaf than in other tissues. The expression of LaMYC4 decreased during flower development. The promoter of LaMYC4 contained hormone and stress-responsive regulatory elements and was responsive to various treatments, including UV, MeJA treatment, drought, low temperature, Pseudomonas syringae infection, and NaCl treatment. LaMYC4 overexpression increased the levels of sesquiterpenoids, including caryophyllenes, in Arabidopsis and tobacco plants. Furthermore, the expression of crucial node genes involved in terpenoid biosynthesis and glandular trichome number and size increased in transgenic tobacco. Conclusions We have shown that the stress-responsive MYC TF LaMYC4 from 'Jingxun 2' lavender regulates volatile terpenoid synthesis. This study is the first to describe the cloning of LaMYC4, and the results help understand the role of LaMYC4 in terpenoid biosynthesis
Disentangling the effects of nitrogen availability and soil acidification on microbial taxa and soil carbon dynamics in natural grasslands
No full textAlthough nitrogen (N) enrichment enhances both soil N availability and soil acidification, it is difficult to isolate their effects on microbial taxa that drive the soil carbon (C) dynamics under different microbial C limitation conditions in natural ecosystems. Based on long-term field N addition, field acid addition, and laboratory incubation experiments in the Inner Mongolian grassland, we disentangled the effects of increased N availability and soil acidification on relative abundance of bacterial and fungal taxa under the mild (soil incubation for 28 days) and strong microbial C limitations (soil incubation for 191 days). Bacterial and fungal taxa are grouped into four ecological categories (N sensitive, acid sensitive, N and acid sensitive, N and acid insensitive) with multiple levels of N addition. In the context of the mild microbial C limitation, increased N availability promoted the relative abundance of the fungal class Eurotiomycetes (N positive sensitivity) under the low-medium levels of N addition, with an associated decrease in soil labile carbonyl C content. Conversely, increased N availability reduced the relative abundance of fungal class Sordariomycetes (N negative sensitivity) and bacterial gene copies (N and acid negative sensitivity) under the high levels of N addition, with associated increases in labile O-alkyl C and di-O-alkyl C content, making soil C more labile. In the context of the strong microbial C limitation, increased soil acidification promoted the abundance of acidophilous fungal classes Sordariomycetes and Eurotiomycetes under the low-medium levels of N addition, with an associated decrease in soil labile carbonyl C content. However, increased N availability promoted the relative abundance of the bacterial phylum Thaumarchaeota (N positive sensitivity equal to acid negative sensitivity), with associated low labile O-alkyl C and di-O-alkyl C content, leaving C chemistry more resistant. By applying the ecological category concept to soil microbes, our findings highlight that the N enrichment-induced shifts in abundance of N- and/or acid-sensitive categories are tightly associated with the changes in soil organic carbon (SOC) chemical composition, and the relationship between microbial function groups and SOC chemistry varied substantially under the mild versus strong microbial C limitations
Nitrogen Deposition Drives Response and Recovery in the Context of Precipitation Change and Its Reversal in an Arid Ecosystem
No full textClimatic change profoundly impacts terrestrial ecosystem function and structure. However, it remains unclear how an entire ecosystem responds to precipitation fluctuations in relation to nitrogen (N) deposition, especially in arid ecosystems. A field experiment was conducted in a desert steppe over the course of 4 years to determine plant community and belowground responses to precipitation alteration and a subsequent precipitation regime reversal treatment under increased N addition, with an initial 3-year precipitation regime manipulation period followed by a fourth-year reversal. The aboveground net primary production (ANPP) significantly increased with increased precipitation, particularly at high N levels. However, the precipitation regime reversal treatment in the final year reversed the ANPP effects induced by the previous precipitation alteration. Soil microbial carbon and N content significantly increased with increasing precipitation, whereas the precipitation reversal in the final year partly eliminated the soil microbial effects produced by this previous precipitation alteration. Plant community composition shifted under both the precipitation and N treatments, with a few critical species playing crucial roles. The response ratio (initial treatment vs. control) of ANPP increased with increased precipitation during the first 3 years. Both the resilience (precipitation regime reversal treatment vs. control) and the limitation or promotion index (LPI, precipitation reversal treatment vs. initial treatment) of NPP were relatively high under the initial low precipitation and the final high precipitation regimes. Structural equation modeling in particular illustrated that the precipitation alteration treatments made greater contributions to the response ratio, resilience and LPI of the NPP than did N deposition via either the soil microbial levels or the plant diversity index. We should therefore consider both vegetation productivity and its compositional shift, as well as the associations with soil microbes under contrasting environmental changes, to accurately assess and predict the responses of terrestrial ecosystems to climate change
A reference-guided TILLING by amplicon-sequencing platform supports forward and reverse genetics in barley
No full textBarley is a diploid species with a genome smaller than those of other members of the Triticeae tribe, making it an attractive model for genetic studies in Triticeae crops. The recent development of barley genomics has created a need for a high-throughput platform to identify genetically uniform mutants for gene function investigations. In this study, we report an ethyl methanesulfonate (EMS)-mutagenized population consisting of 8525M3 lines in the barley landrace Hatiexi'' (HTX), which we complement with a high-quality de novo assembly of a reference genome for this genotype. The mutation rate within the population ranged from 1.51 to 4.09 mutations per megabase, depending on the treatment dosage of EMS and the mutation discrimination platform used for genotype analysis. We implemented a three-dimensional DNA pooling strategy combined with multiplexed amplicon sequencing to create a highly efficient and cost-effective TILLING (targeting induced locus lesion in genomes) platform in barley. Mutations were successfully identified from 72 mixed amplicons within a DNA pool containing 64 individual mutants and from 56 mixed amplicons within a pool containing 144 individuals. We discovered abundant allelic mutants for dozens of genes, including the barley Green Revolution contributor gene Brassinosteroid insensitive 1 (BRI1). As a proof of concept, we rapidly determined the causal gene responsible for a chlorotic mutant by following the MutMap strategy, demonstrating the value of this resource to support forward and reverse genetic studies in barley
A novel entropy-based method to quantify forest canopy structural complexity from multiplatform lidar point clouds
No full textForest canopy structural complexity (CSC) describes the three-dimensional (3D) arrangement of canopy ele-ments, and has become an emergent forest attribute mediating forest ecosystem functioning along with species diversity. Light detection and ranging (lidar), especially the emerging near-surface lidar platforms (e.g., terrestrial laser scanning/TLS, backpack laser scanning/BLS, unmanned aerial vehicle laser scanning/ULS), can depict 3D canopy information with high efficiency and accuracy, providing an ideal data source for forest CSC quantification. However, current existing lidar-based CSC quantification indices may share common limitations of getting saturated in structurally complex forest stands and not fully capturing within-canopy structural var-iations. In this study, we introduced the concept of entropy into forest CSC quantification, and proposed a new forest CSC index, namely canopy entropy (CE). Two major bottlenecks were addressed in the CE calculation procedure, including (1) using a Mann-Kendall (MK) test-based resampling strategy to address the issue of incongruent sampling chances of canopy elements at different locations from different lidar systems, and (2) using a kernel density estimation (KDE)-based method to reduce its dependence on point density. The effec-tiveness and generality of CE were evaluated by simulating TLS and ULS point clouds from nine forest stands and collecting TLS, BLS, and ULS point clouds from 110 field plots distributed in five forest sites, covering a large variety of forest types and forest CSC conditions. The results showed that CE was an effective forest CSC quantification index that successfully captured CSC variations caused by both tree density and the number of vertical canopy layers. It had significant positive correlations with four widely used CSC indices (i.e., canopy cover, foliage height diversity, canopy top rugosity, and fractal dimension; R2: 0.32 to 0.67), but outperformed them by overcoming their common limitations. CE estimates from multiplatform lidar point clouds agreed well with each other (R2 >= 0.70, RMSE <= 0.10), indicating it has generality in cross-platform forest CSC quantification practices. We believe the proposed CE index has great potential to help us unravel the correlations among forest CSC, species diversity, and forest ecosystem functions, and therefore improve our understanding on forest ecosystem processes
The ecological adaptation of the unparalleled plastome character evolution in slipper orchids
No full textPlastomes may have undergone adaptive evolution in the process of plant adaptation to diverse environments, whereby species may differ in plastome characters. Cypripedioideae successfully colonized distinct environments and could be an ideal group for studying the interspecific variation and adaptive evolution of plastomes. Comparative study of plastomes, ancestral state reconstruction, phylogenetic-based analysis, ecological niche modelling, and selective pressure analysis were conducted to reveal the evolutionary patterns of plastomes in Cypripedioideae and their relationship with environmental factors. The plastomes of the three evolved genera had reduced plastome size, increased GC content, and compacted gene content compared to the basal group. Variations in plastome size and GC content are proved to have clear relationships with climate regions. Furthermore, ecological niche modelling revealed that temperature and water factors are important climatic factors contributing to the distributional difference which is directly correlated with the climate regions. The temperature-sensitive genes ndh genes, infA, and rpl20 were found to be either lost/pseudogenized or under positive selection in the evolved groups. Unparalleled plastome character variations were discovered in slipper orchids. Our study indicates that variations in plastome characters have adaptive consequences and that temperature and water factors are important climatic factors that affect plastome evolution. This research highlights the expectation that plants can facilitate adaptation to different environmental conditions with the changes in plastome and has added critical insight for understanding the process of plastome evolution in plants
A Ca2+-binding motif underlies the unusual properties of certain photosynthetic bacterial core light-harvesting complexes
No full textThe mildly thermophilic purple phototrophic bacterium Allochromatium tepidum provides a unique model for investigating various intermediate phenotypes observed between those of thermophilic and mesophilic counterparts. The core light-harvesting (LH1) complex from A. tepidum exhibits an absorption maximum at 890 nm and mildly enhanced thermostability, both of which are Ca2+-dependent. However, it is unknown what structural determinants might contribute to these properties. Here, we present a cryo-EM structure of the reaction center-associated LH1 complex at 2.81 angstrom resolution, in which we identify multiple pigment-binding alpha- and beta-polypeptides within an LH1 ring. Of the 16 alpha-polypeptides, we show that six (alpha 1) bind Ca2+ along with beta 1- or beta 3-polypeptides to form the Ca-2-binding sites. This structure differs from that of fully Ca2+-bound LH1 from Thermochromatium tepidum, enabling determination of the minimum structural requirements for Ca2+-binding. We also identified three amino acids (Trp44, Asp47, and le49) in the C-terminal region of the A. tepidum alpha 1-polypeptide that ligate each Ca ion, forming a Ca2+-binding WxxDxl motif that is conserved in all Ca2+ bound LH1 alpha-polypeptides from other species with reported structures. The partial Ca-2-bound structure further explains the unusual phenotypic properties observed for this bacterium in terms of its Ca2+-requirements for thermostability, spectroscopy, and phototrophic growth, and supports the hypothesis that A. tepidum may represent a transitional species between mesophilic and thermophilic purple sulfur bacteria. The characteristic arrangement of multiple appolypeptides also suggests a mechanism of molecular recognition in the expression and/or assembly of the LH1 complex that could be regulated through interactions with reaction center subunits
Molecular evolution and functional characterization of chitinase gene family in Populus trichocarpa
No full textChitinases, the chitin-degrading enzymes, have been shown to play important role in defense against the chitincontaining fungal pathogens. In this study, we identified 48 chitinase-coding genes from the woody model plant Populus trichocarpa. Based on phylogenetic analysis, the Populus chitinases were classified into seven groups. Different gene structures and protein domain architectures were found among the seven Populus chitinase groups. Selection pressure analysis indicated that all the seven groups are under purifying selection. Phylogenetic analysis combined with chromosome location analysis showed that Populus chitinase gene family mainly expanded through tandem duplication. The Populus chitinase gene family underwent marked expression divergence and is inducibly expressed in response to treatments, such as chitosan, chitin, salicylic acid and methyl jasmonate. Protein enzymatic activity analysis showed that Populus chitinases had activity towards both chitin and chitosan. By integrating sequence characteristic, phylogenetic, selection pressure, gene expression and protein activity analysis, this study shed light on the evolution and function of chitinase family in poplar
Two independent allohexaploidizations and genomic fractionation in Solanales
No full textSolanales, an order of flowering plants, contains the most economically important vegetables among all plant orders. To date, many Solanales genomes have been sequenced. However, the evolutionary processes of polyploidization events in Solanales and the impact of polyploidy on species diversity remain poorly understood. We compared two representative Solanales genomes (Solanum lycopersicum L. and Ipomoea triloba L.) and the Vitis vinifera L. genome and confirmed two independent polyploidization events. Solanaceae common hexaploidization (SCH) and Convolvulaceae common hexaploidization (CCH) occurred similar to 43-49 and similar to 40-46 million years ago (Mya), respectively. Moreover, we identified homologous genes related to polyploidization and speciation and constructed multiple genomic alignments with V. vinifera genome, providing a genomic homology framework for future Solanales research. Notably, the three polyploidization-produced subgenomes in both S. lycopersicum and I. triloba showed significant genomic fractionation bias, suggesting the allohexaploid nature of the SCH and CCH events. However, we found that the higher genomic fractionation bias of polyploidization-produced subgenomes in Solanaceae was likely responsible for their more abundant species diversity than that in Convolvulaceae. Furthermore, through genomic fractionation and chromosomal structural variation comparisons, we revealed the allohexaploid natures of SCH and CCH, both of which were formed by two-step duplications. In addition, we found that the second step of two paleohexaploidization events promoted the expansion and diversity of beta-amylase (BMY) genes in Solanales. These current efforts provide a solid foundation for future genomic and functional exploration of Solanales
Tolerant mechanism of model legume plant Medicago truncatula to drought, salt, and cold stresses
No full textLegume plants produce one-third of the total yield of primary crops and are important food sources for both humans and animals worldwide. Frequent exposure to abiotic stresses, such as drought, salt, and cold, greatly limits the production of legume crops. Several morphological, physiological, and molecular studies have been conducted to characterize the response and adaptation mechanism to abiotic stresses. The tolerant mechanisms of the model legume plant Medicago truncatula to abiotic stresses have been extensively studied. Although many potential genes and integrated networks underlying the M. truncatula in responding to abiotic stresses have been identified and described, a comprehensive summary of the tolerant mechanism is lacking. In this review, we provide a comprehensive summary of the adaptive mechanism by which M. truncatula responds to drought, salt, and cold stress. We also discuss future research that need to be explored to improve the abiotic tolerance of legume plants