Search

The chloroplast genomes of angiosperms usually have a stable circular quadripartite structure that exhibits high consistency in genome size and gene order. As one of the most diverse genera of angiosperms, Carex is of great value for the study of evolutionary relationships and speciation within its genus, but the study of the structure of its chloroplast genome is limited due to its highly expanded and restructured genome with a large number of repeats. In this study, we provided a more detailed account of the chloroplast genomes of Carex using a hybrid assembly of second- and third-generation sequencing and examined structural variation within this genus. The study revealed that chloroplast genomes of four Carex species are significantly longer than that of most angiosperms and are characterized by high sequence rearrangement rates, low GC content and gene density, and increased repetitive sequences. The location of chloroplast genome structural variation in the species of Carex studied is closely related to the positions of long repeat sequences; this genus provides a typical example of chloroplast structural variation and expansion caused by long repeats. Phylogenetic relationships constructed based on the chloroplast protein-coding genes support the latest taxonomic system of Carex, while revealing that structural variation in the chloroplast genome of Carex may have some phylogenetic significance. Moreover, this study demonstrated a hybrid assembly approach based on long and short reads to analyze complex chloroplast genome assembly and also provided an important reference for the analysis of structural rearrangements of chloroplast genomes in other taxa.

Interactions between weeds and crops often occur by resource competition or allelopathy. However, it is still unknown how local weed species influence artificially introduced switchgrass. In this study, four experiments were conducted to evaluate the inhibitory effects of redroot pigweed (Amaranthus retroflexus) and crabgrass (Digitaria sanguinalis) on germination and growth of the lowland tetraploid switchgrass cultivar ‘Alamo’ (Panicum virgatum cv. Alamo). Switchgrass germination was significantly inhibited in Petri dishes, with 48.1% and 33.9% inhibitions on germination rate by redroot pigweed and crabgrass root aqueous extracts, respectively, at 0.1 g mL−1 concentration. Significant inhibitory effects on switchgrass seedling biomass were observed at 5:5 ratio with redroot pigweed and crabgrass in glass jars, with 61.6% and 53.4% inhibitions on plant biomass, respectively. Under the same root segregation, redroot pigweed had a stronger inhibitory effect on switchgrass seedling growth than crabgrass. Growth of transplanted switchgrass seedlings was significantly inhibited by local weeds in the field, with 46.2% and 11.7% inhibitions on shoot biomass during the first and second growing seasons, respectively. However, no significant growth reduction in switchgrass was detected in the third growing season. These findings further our understanding of weed–crop interactions and could help develop weeds management strategies with ecological security.

The bioenergy crop switchgrass (Panicum virgatum L.) has been recognized as friendly to the soil of cultivated land depending on the previous land use types and management practices. However, the effects of switchgrass establishment on soil properties at a broader depth when it is harvested annually without any fertilization in northern China largely remain unknown. To explore the impacts of unfertilized switchgrass on soil physical and chemical properties, 0–100 cm soil samples were collected from 7-year cropland-to-switchgrass conversion and the bare land (control). The results showed that switchgrass establishment increased soil total and capillary porosity, CFU numbers of the microbial communities (fungi, bacteria, and actinomycetes), contents of microbial biomass (carbon, nitrogen, and phosphorus), and water-soluble organic carbon, and decreased soil bulk density, mostly at 0–60 cm depths, compared to the control values. Notably, the annual harvest of switchgrass insignificantly increased soil total and available nitrogen contents and slightly reduced available phosphorus and potassium contents. In conclusion, long-term cropland conversion to unfertilized switchgrass could ameliorate soil properties and does not cause soil depletion. The output of this study could inspire governments and farmers to make large-scale use of switchgrass in the ecological restoration of abandoned cropland in north China.

Background Zoysia japonica is an important warm-season turfgrass used worldwide. Although the draft genome sequence and a vast amount of next-generation sequencing data have been published, the current genome annotation and complete mRNA structure remain incomplete. Therefore, to analyze the full-length transcriptome of Z. japonica, we used the PacBio single-molecule long-read sequencing method in this study. Results First, we generated 37,056 high-confidence non-redundant transcripts from 16,005 gene loci. Next, 32,948 novel transcripts, 913 novel gene loci, 8035 transcription factors, 89 long non-coding RNAs, and 254 fusion transcripts were identified. Furthermore, 15,675 alternative splicing events and 5325 alternative polyadenylation sites were detected. In addition, using bioinformatics analysis, the underlying transcriptional mechanism of senescence was explored based on the revised reference transcriptome. Conclusion This study provides a full-length reference transcriptome of Z. japonica using PacBio single-molecule long-read sequencing for the first time. These results contribute to our knowledge of the transcriptome and improve the knowledge of the reference genome of Z. japonica. This will also facilitate genetic engineering projects using Z. japonica.

The turfgrass species Carex rigescens has broad development and utilization prospects in landscaping construction. However, seed dormancy and a low germination rate have inhibited its application. Furthermore, the molecular mechanisms of seed germination in C. rigescens have not been thoroughly studied. Therefore, in the present study, PacBio full-length transcriptome sequencing combined with Illumina sequencing was employed to elucidate the germination mechanism of C. rigescens seeds under variable temperatures. In general, 156,750 full-length non-chimeric sequences, including those for 62,086 high-quality transcripts, were obtained using single-molecule long read sequencing. In total, 40,810 high-quality non-redundant, 1,675 alternative splicing, 28,393 putative coding sequences, and 1,052 long non-coding RNAs were generated. Based on the newly constructed full-length reference transcriptome, 23,147 differentially expressed genes were identified. We screened four hub genes participating in seed germination using weighted gene co-expression network analysis. Combining these results with the physiological observations, the important roles of sucrose and starch metabolic pathways in germination are further discussed. In conclusion, we report the first full-length transcriptome of C. rigescens, and investigated the physiological and transcriptional mechanisms of seed germination under variable temperatures. Our results provide valuable information for future transcriptional analyses and gene function studies of C. rigescens.

Pheophytinase (PPH), the phytol hydrolase, plays important roles in chlorophyll degradation. Nevertheless, little attention has been paid to the PPHs in warm-season grass species; neither its detailed function in photosynthesis has been systematically explored to date. In this study, we isolated ZjPPH from Zoysia japonica, an excellent warm-season turfgrass species. Quantitative real-time PCR analysis and promoter activity characterization revealed that the expression of ZjPPH could be induced by senescence, ABA, and dark induction. Subcellular localization observation proved that ZjPPH was localized in the chloroplasts. Overexpression of ZjPPH accelerated the chlorophyll degradation and rescued the stay-green phenotype of the Arabidopsis pph mutant. Moreover, ZjPPH promoted senescence with the accumulation of ABA and soluble sugar contents, as well as the increased transcriptional level of SAG12 and SAG14. Transmission electron microscopy investigation revealed that ZjPPH caused the decomposition of chloroplasts ultrastructure in stable transformed Arabidopsis. Furthermore, chlorophyll a fluorescence transient measurement analysis suggested that ZjPPH suppressed photosynthesis efficiency by mainly suppressing both photosystem II (PSII) and photosystem I (PSI). In conclusion, ZjPPH plays an important role in chlorophyll degradation and senescence. It could be a valuable target for genetic editing to cultivate new germplasms with stay-green performance and improved photosynthetic efficiency.

Pheophytinase (PPH), the phytol hydrolase, plays important roles in chlorophyll degradation. Nevertheless, little attention has been paid to the PPHs in warm-season grass species; neither its detailed function in photosynthesis has been systematically explored to date. In this study, we isolated ZjPPH from Zoysia japonica, an excellent warm-season turfgrass species. Quantitative real-time PCR analysis and promoter activity characterization revealed that the expression of ZjPPH could be induced by senescence, ABA, and dark induction. Subcellular localization observation proved that ZjPPH was localized in the chloroplasts. Overexpression of ZjPPH accelerated the chlorophyll degradation and rescued the stay-green phenotype of the Arabidopsis pph mutant. Moreover, ZjPPH promoted senescence with the accumulation of ABA and soluble sugar contents, as well as the increased transcriptional level of SAG12 and SAG14. Transmission electron microscopy investigation revealed that ZjPPH caused the decomposition of chloroplasts ultrastructure in stable transformed Arabidopsis. Furthermore, chlorophyll a fluorescence transient measurement analysis suggested that ZjPPH suppressed photosynthesis efficiency by mainly suppressing both photosystem II (PSII) and photosystem I (PSI). In conclusion, ZjPPH plays an important role in chlorophyll degradation and senescence. It could be a valuable target for genetic editing to cultivate new germplasms with stay-green performance and improved photosynthetic efficiency.

Buffalograss [Buchloe dactyloides (Nutt.) Engelm.] has become the most widely cultivated warm-season turfgrass in northern China because of its low-maintenance requirements. Nitrogen (N) can be applied to plants in a range of formulations. However, preference of nitrogen uptake and the effects of N form on plant growth and nitrogen accumulation has not been established in buffalograss. In this study, we evaluated the effects of different inorganic nitrogen forms (NO3−-N, NH4+-N, and NO3−-N: NH4+-N = 1:1) on growth and nitrogen accumulation in buffalograss seedlings. Results showed that supply of three N forms significantly increased buffalograss seedlings growth, biomass, and N contents of all plant organs compared with the seedlings receiving free nitrogen. Plants achieved better growth performance when they received nitrate as the sole N source, which stimulated stolon growth and increased the biomass of ramets, spacers, and aboveground and total plant biomass, and also allocated more biomass to ramets and more N to spacers. Meanwhile, those plants supplied with the treatment +NH4NO3 displayed a significantly greater N content in the ramet, 15N abundance, and 15N accumulation amount in all organs. These data suggest NO3−-N supplied either singly or in mixture increased vegetative propagation and thus facilitates buffalograss establishment. However, applications of ammonium caused detrimental effects on buffalograss seedlings growth, but +NO3− could alleviate NH4+-induced morphological disorders. Thus, recommendations to increase vegetative propagation and biomass accumulation in buffalograss seedlings should consider increasing NO3−-N in a fertility program and avoiding applications of nitrogen as NH4+-N.

Growing evidence indicates that some grass species are more tolerant to various abiotic and biotic stresses than many crops. Zinc finger proteins play important roles in plant abiotic and biotic stresses. Although genes coding for these proteins have been cloned and identified in various plants, their function and underlying transcriptional mechanisms in the halophyte Zoysia japonica are barely known. In the present study, ZjZFN1 was isolated from Z. japonica using RACE method. Quantitative real time PCR results revealed that the expression of ZjZFN1 was much higher in leaf than in root and stem tissues, and induced by salt, cold or ABA treatment. The subcellular localization assay demonstrated that ZjZFN1 was localized to the nucleus. Expression of the ZjZFN1 in Arabidopsis thaliana improved seed germination and enhanced plant adaption to salinity stress with improved percentage of green cotyledons and growth status under salinity stress. Physiological and transcriptional analyses suggested that ZjZFN1 might, at least in part, influence reactive oxygen species accumulation and regulate the transcription of salinity responsive genes. Furthermore, RNA-sequencing analysis of ZjZFN1-overexpressing plants revealed that ZjZFN1 may serve as a transcriptional activator in the regulation of stress responsive pathways, including phenylalanine metabolism, α-linolenic acid metabolism and phenylpropanoid biosynthesis pathways. Taken together, these results provide evidence that ZjZFN1 is a potential key player in plants' tolerance to salt stress, and it could be a valuable gene in Z. japonica breeding projects.

Growing evidence indicates that some grass species are more tolerant to various abiotic and biotic stresses than many crops. Zinc finger proteins play important roles in plant abiotic and biotic stresses. Although genes coding for these proteins have been cloned and identified in various plants, their function and underlying transcriptional mechanisms in the halophyte Zoysia japonica are barely known. In the present study, ZjZFN1 was isolated from Z. japonica using RACE method. Quantitative real time PCR results revealed that the expression of ZjZFN1 was much higher in leaf than in root and stem tissues, and induced by salt, cold or ABA treatment. The subcellular localization assay demonstrated that ZjZFN1 was localized to the nucleus. Expression of the ZjZFN1 in Arabidopsis thaliana improved seed germination and enhanced plant adaption to salinity stress with improved percentage of green cotyledons and growth status under salinity stress. Physiological and transcriptional analyses suggested that ZjZFN1 might, at least in part, influence reactive oxygen species accumulation and regulate the transcription of salinity responsive genes. Furthermore, RNA-sequencing analysis of ZjZFN1-overexpressing plants revealed that ZjZFN1 may serve as a transcriptional activator in the regulation of stress responsive pathways, including phenylalanine metabolism, α-linolenic acid metabolism and phenylpropanoid biosynthesis pathways. Taken together, these results provide evidence that ZjZFN1 is a potential key player in plants’ tolerance to salt stress, and it could be a valuable gene in Z. japonica breeding projects.

Switchgrass is a photoperiod-sensitive energy grass suitable for growing in the marginal lands of China. We explored the effects of extended photoperiods of low-irradiance light (7 μmol·m-2·s-1, no effective photosynthesis) on the growth, the biomass dry weight, the biomass allocation, and, especially, the stem digestibility and cell wall characteristics of switchgrass. Two extended photoperiods (i.e., 18 and 24 h) were applied over Alamo. Extended light exposure (18 and 24 h) resulted in delayed heading and higher dry weights of vegetative organs (by 32.87 and 35.94%, respectively) at the expense of reducing the amount of sexual organs (by 40.05 and 50.87%, respectively). Compared to the control group (i.e., natural photoperiod), the yield of hexoses (% dry matter) in the stems after a direct enzymatic hydrolysis (DEH) treatment significantly increased (by 44.02 and 46.10%) for those groups irradiated during 18 and 24 h, respectively. Moreover, the yield of hexoses obtained via enzymatic hydrolysis increased after both basic (1% NaOH) and acid (1% H2SO4) pretreatments for the groups irradiated during 18 and 24 h. Additionally, low-irradiance light extension (LILE) significantly increased the content of non-structural carbohydrates (NSCs) while notably reducing the lignin content and the syringyl to guaiacyl (S/G) ratio. These structural changes were in part responsible for the observed improved stem digestibility. Remarkably, LILE significantly decreased the cellulose crystallinity index (CrI) of switchgrass by significantly increasing both the arabinose substitution degree in xylan and the content of ammonium oxalate-extractable uronic acids, both favoring cellulose digestibility. Despite this LILE technology is not applied to the cultivation of switchgrass on a large scale yet, we believe that the present work is important in that it reveals important relationships between extended day length irradiations and biomass production and quality. Additionally, this study paves the way for improving biomass production and digestibility via genetic modification of day length sensitive transcription factors or key structural genes in switchgrass leaves.

Bacillus thuringiensis (Bt) cotton is grown worldwide, including in saline soils, but the effect of salinity on ion fluxes of Bt cotton remains unknown. Responses of two transgenic Bt cotton genotypes (SGK321 and 29317) and their corresponding receptors, Shiyuan 321 (SY321) and Jihe 321 (J321), to 150 mmol L −1 NaCl stress were studied in a growth chamber. The root dry weight of SGK321 and 29317 under NaCl treatment was decreased by 30 and 31%, respectively. However, their corresponding receptor cultivars SY321 and J321 were less affected (19 and 24%, respectively). The root length and surface area of the Bt cultivars were significantly decreased relative to their receptors under salt stress. NaCl treatment significantly increased Cry1Ac mRNA transcript levels in SGK321 and 29317 but did not affect Bt protein content in leaves or roots of either cultivar at 1 and 7 d after NaCl treatment. Fluxes of Na + , K + , and H + in roots were investigated using the scanning ion-selective electrode technique. Both mean K+ efflux rate and transient K + efflux of the Bt cultivars increased four-fold compared to their corresponding receptors when exposed to salinity stress. There were no significant differences in Na + efflux between Bt and non-Bt cottons. Furthermore, the Na + contents in roots and leaves of all genotypes dramatically increased under salt stress, whereas K + contents decreased. Our results suggested that Bt cotton cultivars are more sensitive to salt stress than their receptor genotypes.

Abscisic acid (ABA) is a key component of the signaling system that integrates plant adaptive responses to abiotic stress. Overexpression of Arabidopsis molybdenum cofactor sulfurase gene (LOS5) in maize markedly enhanced the expression of ZmAO and aldehyde oxidase (AO) activity, leading to ABA accumulation and increased drought tolerance. Transgenic maize (Zea mays L.) exhibited the expected reductions in stomatal aperture, which led to decreased water loss and maintenance of higher relative water content (RWC) and leaf water potential. Also, transgenic maize subjected to drought treatment exhibited lower leaf wilting, electrolyte leakage, malondialdehyde (MDA) and H(2)O(2) content, and higher activities of antioxidative enzymes and proline content compared to wild-type (WT) maize. Moreover, overexpression of LOS5 enhanced the expression of stress-regulated genes such as Rad 17, NCED1, CAT1, and ZmP5CS1 under drought stress conditions, and increased root system development and biomass yield after re-watering. The increased drought tolerance in transgenic plants was associated with ABA accumulation via activated AO and expression of stress-related gene via ABA induction, which sequentially induced a set of favorable stress-related physiological and biochemical responses.

Drought is a major environmental stress factor that affects growth and development of plants. Abscisic acid (ABA), osmotically active compounds, and synthesis of specific proteins, such as proteins that scavenge oxygen radicals, are crucial for plants to adapt to water deficit. LOS5/ABA3 (LOS5) encodes molybdenum-cofactor sulfurase, which is a key regulator of ABA biosynthesis. We overexpressed LOS5 in tobacco using Agrobacterium-mediated transformation. Detached leaves of LOS5-overexpressing seedlings showed lower transpirational water loss than that of nontransgenic seedlings in the same period under normal conditions. When subjected to water-deficit stress, transgenic plants showed less wilting, maintained higher water content and better cellular membrane integrity, accumulated higher quantities of ABA and proline, and exhibited higher activities of antioxidant enzymes, i.e., superoxide dismutase, catalase, peroxidase and ascorbate peroxidase, as compared with control plants. Furthermore, LOS5-overexpressing plants treated with 30% polyethylene glycol showed similar performance in cellular membrane protection, ABA and proline accumulation, and activities of catalase and peroxidase to those under drought stress. Thus, overexpression of LOS5 in transgenic tobacco can enhance drought tolerance.