Transcriptome analysis reveals common and distinct mechanisms for sheepgrass (Leymus chinensis) responses to defoliation compared to mechanical wounding

Transcriptional Memory in Taraxacum mongolicum in Response to Long-Term Different Grazing Intensities

Grazing, as an important land use method in grassland, has a significant impact on the morphological and physiological traits of plants. However, little is known about how the molecular mechanism of plant responds to different grazing intensities. Here, we investigated the response of Taraxacum mongolicum to light grazing and heavy grazing intensities in comparison with a non-grazing control. Using de novo transcriptome assembly, T. mongolicum leaves were compared for the expression of the different genes under different grazing intensities in natural grassland. In total, 194,253 transcripts were de novo assembled and comprised in nine leaf tissues. Among them, 11,134 and 9058 genes were differentially expressed in light grazing and heavy grazing grassland separately, with 5867 genes that were identified as co-expression genes in two grazing treatments. The Nr, SwissProt, String, GO, KEGG, and COG analyses by BLASTx searches were performed to determine and further understand the biological functions of those differentially expressed genes (DEGs). Analysis of the expression patterns of 10 DEGs by quantitative real-time RT-PCR (qRT-PCR) confirmed the accuracy of the RNA-Seq results. Based on a comparative transcriptome analysis, the most significant transcriptomic changes that were observed under grazing intensity were related to plant hormone and signal transduction pathways, carbohydrate and secondary metabolism, and photosynthesis. In addition, heavy grazing resulted in a stronger transcriptomic response compared with light grazing through increasing the of the secondary metabolism- and photosynthesis-related genes. These changes in key pathways and related genes suggest that they may synergistically respond to grazing to increase the resilience and stress tolerance of T. mongolicum. Our findings provide important clues for improving grassland use and protection and understanding the molecular mechanisms of plant response to grazing.

Systemic Expression of Genes Involved in the Plant Defense Response Induced by Wounding in Senna tora

Wounds in tissues provide a pathway of entry for pathogenic fungi and bacteria in plants. Plants respond to wounding by regulating the expression of genes involved in their defense mechanisms. To analyze this response, we investigated the defense-related genes induced by wounding in the leaves of Senna tora using RNA sequencing. The genes involved in jasmonate and ethylene biosynthesis were strongly induced by wounding, as were a large number of genes encoding transcription factors such as ERFs, WRKYs, MYBs, bHLHs, and NACs. Wounding induced the expression of genes encoding pathogenesis-related (PR) proteins, such as PR-1, chitinase, thaumatin-like protein, cysteine proteinase inhibitor, PR-10, and plant defensin. Furthermore, wounding led to the induction of genes involved in flavonoid biosynthesis and the accumulation of kaempferol and quercetin in S. tora leaves. All these genes were expressed systemically in leaves distant from the wound site. These results demonstrate that mechanical wounding can lead to a systemic defense response in the Caesalpinioideae, a subfamily of the Leguminosae. In addition, a co-expression analysis of genes induced by wounding provides important information about the interactions between genes involved in plant defense responses.

Integrated Analysis of the Transcriptome and Metabolome Revealed Candidate Genes Involved in GA3-Induced Dormancy Release in Leymus chinensis Seeds

Leymus chinensis is a perennial forage grass that has good palatability, high yield and high feed value, but seed dormancy is a major problem limiting the widespread cultivation of L. chinensis. Here, we performed transcriptomic and metabolomic analysis of hulled and de-hulled seeds of L. chinensis treated with or without GA₃ to investigate the changes in gene and metabolites associated with dormancy release induced by GA₃. The germination test revealed that the optimum concentration of GA₃ for disruption of L. chinensis seed dormancy was 577 μM. A total of 4327 and 11,919 differentially expressed genes (DEGs) and 871 and 650 differentially abundant metabolites were identified in de-hulled and hulled seeds treated with GA₃, respectively, compared with seeds soaked in sterile water. Most of the DEGs were associated with starch and sucrose metabolism, protein processing in the endoplasmic reticulum, endocytosis and ribosomes. Furthermore, isoquinoline alkaloid biosynthesis, tyrosine metabolism, starch and sucrose metabolism, arginine and proline metabolism, and amino sugar and nucleotide sugar metabolism were significantly enriched pathways. Integrative analysis of the transcriptomic and metabolomic data revealed that starch and sucrose metabolism is one of the most important pathways that may play a key role in providing carbon skeletons and energy supply for the transition of L. chinensis seeds from a dormant state to germination by suppressing the expression of Cel61a, egID, cel1, tpsA, SPAC2E11.16c and TPP2, enhancing the expression of AMY1.1, AMY1.2, AMY1.6 and GLIP5, and inhibiting the synthesis of cellobiose, cellodextrin, and trehalose while promoting the hydrolysis of sucrose, starch, cellobiose, cellodextrin, and trehalose to glucose. This study identified several key genes and provided new insights into the molecular mechanism of seed dormancy release induced by GA₃ in L. chinensis. These putative genes will be valuable resources for improving the seed germination rate in future breeding studies.

De novo assembly, annotation, marker discovery, and genetic diversity of the Stipa breviflora Griseb. (Poaceae) response to grazing

Grassland is one of the most widely-distributed ecosystems on Earth and provides a variety of ecosystem services. Grasslands, however, currently suffer from severe degradation induced by human activities, overgrazing pressure and climate change. In the present study, we explored the transcriptome response of Stipa breviflora, a dominant species in the desert steppe, to grazing through transcriptome sequencing, the development of simple sequence repeat (SSR) markers, and analysis of genetic diversity. De novo assembly produced 111,018 unigenes, of which 88,164 (79.41%) unigenes were annotated. A total of 686 unigenes showed significantly different expression under grazing, including 304 and 382 that were upregulated and downregulated, respectively. These differentially expressed genes (DEGs) were significantly enriched in the “alpha-linolenic acid metabolism” and “plant-pathogen interaction” pathways. Based on transcriptome sequencing data, we developed eight SSR molecular markers and investigated the genetic diversity of S. breviflora in grazed and ungrazed sites. We found that a relatively high level of S. breviflora genetic diversity occurred under grazing. The findings of genes that improve resistance to grazing are helpful for the restoration, conservation, and management of desert steppe.

A Leymus chinensis histidine-rich Ca2+-binding protein binds Ca2+/Zn2+ and suppresses abscisic acid signaling in Arabidopsis

Intracellular Ca²⁺ plays an essential role in plant cellular sensing of various environmental stress signals by modulating the activity of Ca²⁺-binding proteins. Leymus chinensis is a dominant forage grass widely distributed in the Eurasian Steppe that is well adapted to drought and salty soils common in the region. Through transcript profiling of L. chinensis roots, we identified a transcript predicted to encode histidine-rich calcium-binding protein (HRC), a protein recently characterized in wheat. L. chinensis HRC (LcH RC) localized in the nucleus, as demonstrated using a transient gene expression method that we developed for this species. Different regions of LcHRC showed affinity for either Ca²⁺ or Zn²⁺, but not Mg²⁺ and Mn²⁺. Arabidopsis thaliana seedlings heterologously overexpressing LcHRC showed greater sensitivity to abscisic acid (ABA), along with decreased expression of some ABA-induced marker genes, but no increase in ABA content. Screening a Arabidopsis cDNA yeast library identified a Tudor/PWWP/MBT-domain-containing protein (AtPWWP3) that interacts with LcHRC. AtPWWP3 also localized in the nucleus and is predicted to mediate gene expression by modifying histone deacetylation. Based on these results, we propose a functional model of LcHRC action.

Physiological and transcriptome analysis of Poa pratensis var. anceps cv. Qinghai in response to cold stress

BACKGROUND

Low temperature limits the growth and development and geographical distribution of plants. Poa pratensis is a cool-season turfgrass mainly grown in urban areas. However, low winter temperature or cold events in spring and autumn may cause P.pratensis mortality, affecting the appearance of lawns. P.pratensis var. anceps cv. Qinghai (PQ) is widely distributed in the Qinghai-Tibet Plateau above 3000 m. PQ has greater cold tolerance than the commercially cultivated P.pratensis varieties. However, existing studies on the response mechanism of PQ to low temperatures have mainly focused on physiological and biochemical perspectives, while changes in the PQ transcriptome during the response to cold stress have not been reported.

RESULTS

To investigate the molecular mechanism of the PQ cold response and identify genes to improve the low-temperature tolerance of P.pratensis, we analyzed and compared the transcriptomes of PQ and the cold-sensitive P.pratensis cv. 'Baron' (PB) under cold stress using RNA sequencing. We identified 5996 and 3285 differentially expressed genes (DEGs) between the treatment vs control comparison of PQ and PB, respectively, with 5612 DEGs specific to PQ. Based on the DEGs, important Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, such as "starch and sucrose metabolism", "protein processing in endoplasmic reticulum", "phenylalanine metabolism" and "glycolysis/gluconeogenesis" were significantly enriched in PQ, and "starch and sucrose metabolism", "phenylpropanoid biosynthesis", "galactose metabolism" and "glutathione metabolism" were significantly enriched in PB. In addition, the "glycolysis" and "citrate cycle (TCA cycle)" pathways were identified as involved in cold tolerance of P.pratensis.

CONCLUSIONS

As we know, this is the first study to explore the transcriptome of P.pratensis var. anceps cv. Qinghai. Our study not noly provides important insights into the molecular mechanisms of P.pratensis var. anceps cv. Qinghai responds to cold stress, but also systematically reveals the changes of key genes and products of glycolysis and TCA cycle in response to cold stress, which is conductive to the breeding of cold-tolerance P.pratensis genotype.

Transcriptome Analysis of Wounding in the Model Grass Lolium temulentum

For forage and turf grasses, wounding is a predominant stress that often results in extensive loss of vegetative tissues followed by rapid regrowth. Currently, little is known concerning the perception, signaling, or molecular responses associated with wound stress in forage- and turf-related grasses. A transcriptome analysis of Lolium temulentum plants subjected to severe wounding revealed 9413 upregulated and 7704 downregulated, distinct, differentially expressed genes (DEGs). Categories related to signaling, transcription, and response to stimuli were enriched in the upregulated DEGs. Specifically, sequences annotated as enzymes involved in hormone biosynthesis/action and cell wall modifications, mitogen-activated protein kinases, WRKY transcription factors, proteinase inhibitors, and pathogen defense-related DEGs were identified. Surprisingly, DEGs related to heat shock and chaperones were more prevalent in the downregulated DEGs when compared with the upregulated DEGs. This wound transcriptome analysis is the first step in identifying the molecular components and pathways used by grasses in response to wounding. The information gained from the analysis will provide a valuable molecular resource that will be used to develop approaches that can improve the recovery, regrowth, and long-term fitness of forage and turf grasses before/after cutting or grazing.

Interactive effects of exogenous melatonin and Rhizophagus intraradices on saline-alkaline stress tolerance in Leymus chinensis

Melatonin, a ubiquitous molecule found in almost all organisms, is considered an important regulator in plant growth. However, little is known about the interactive effect of melatonin and arbuscular mycorrhizal (AM) fungi on plant resistance against soil salinity and alkalinity. To fill in such a gap in knowledge, we conducted three experiments to explore (1) whether exogenous melatonin and an AM fungus had interactive effects on plant response to saline-alkaline stress, (2) whether the influence of melatonin on mycorrhizal plant stress tolerance was attributable to effect on the AM fungus, and (3) whether the effect of melatonin application was due to changes in soil salinity and alkalinity. We found interactive effects between melatonin and the AM fungus on alleviating ROS burst, decreasing malondialdehyde content and protecting Leymus chinensis photosynthetic activity through activation of antioxidant enzyme and gene expression (superoxide dismutase, catalase, ascorbate peroxidase, and glutathione reductase) in plant shoots and roots. Our results showed that exogenous melatonin promoted spore germination and hyphal length of the AM fungus under Petri-dish conditions. However, exogenous melatonin application did not exhibit significant effects on soil salinity and alkalinity. This study provides an insight into the beneficial effects of exogenous melatonin on saline-alkaline stress tolerance in mycorrhizal L. chinensis through regulating antioxidant systems, protecting photosynthetic activity, and promoting associated AM fungal growth without changing soil salinity and alkalinity. It also reveals potential applications of exogenous melatonin and AM fungi for the restoration of saline-alkaline degraded grassland.

Transcriptome analysis of the model grass Lolium temulentum exposed to green leaf volatiles

BACKGROUND

Forage and turf grasses are routinely cut and grazed upon throughout their lifecycle. When grasses are cut or damaged, they rapidly release a volatile chemical cocktail called green leaf volatiles (GLV). Previously we have shown that mechanical wounding or exposure to GLV released from cut grass, activated a Lt 46 kDa mitogen-activated protein kinase (MAPK) within 3 min and a 44 kDa MAPK within 15-20 min in the model grass species Lolium temulentum (Lt). Currently very little is known concerning the perception, signaling or molecular responses associated with wound stress in grasses. Since GLV are released during wounding, we wanted to investigate what genes and signaling pathways would be induced in undamaged plants exposed to GLV.

RESULTS

RNA-Seq generated transcriptome of Lolium plants exposed to GLV identified 4308 up- and 2794 down-regulated distinct differentially-expressed sequences (DES). Gene Ontology analysis revealed a strong emphasis on signaling, response to stimulus and stress related categories. Transcription factors and kinases comprise over 13% of the total DES found in the up-regulated dataset. The analysis showed a strong initial burst within the first hour of GLV exposure with over 60% of the up-regulated DES being induced. Specifically sequences annotated for enzymes involved in the biosynthesis of jasmonic acid and other plant hormones, mitogen-activated protein kinases and WRKY transcription factors were identified. Interestingly, eleven DES for ferric reductase oxidase, an enzyme involved in iron uptake and transport, were exclusively found in the down-regulated dataset. Twelve DES of interest were selected for qRT-PCR analysis; all displayed a rapid induction one hour after GLV exposure and were also strongly induced by mechanical wounding.

CONCLUSION

The information gained from the analysis of this transcriptome and previous studies suggests that GLV released from cut grasses transiently primes an undamaged plant's wound stress pathways for potential oncoming damage, and may have a dual role for inter- as well as intra-plant signaling.

Potential molecular mechanisms of overgrazing-induced dwarfism in sheepgrass (Leymus chinensis) analyzed using proteomic data

BACKGROUND

This study was designed to reveal potential molecular mechanisms of long-term overgrazing-induced dwarfism in sheepgrass (Leymus chinensis).

METHODS

An electrospray ionisation mass spectrometry system was used to generate proteomic data of dwarf sheepgrass from a long-term overgrazed rangeland and normal sheepgrass from a long-term enclosed rangeland. Differentially expressed proteins (DEPs) between dwarf and normal sheepgrass were identified, after which their potential functions and interactions with each other were predicted. The expression of key DEPs was confirmed by high-performance liquid chromatography mass spectrometry (HPLC-MS) using a multiple reaction monitoring method.

RESULTS

Compared with normal sheepgrass, a total of 51 upregulated and 53 downregulated proteins were identified in dwarf sheepgrass. The amino acids biosynthesis pathway was differentially enriched between the two conditions presenting DEPs, such as SAT5_ARATH and DAPA_MAIZE. The protein-protein interaction (PPI) network revealed a possible interaction between RPOB2_LEPTE, A0A023H9M8_9STRA, ATPB_DIOEL, RBL_AMOTI and DNAK_GRATL. Four modules were also extracted from the PPI network. The HPLC-MS analysis confirmed the upregulation and downregulation of ATPB_DIOEL and DNAK_GRATL, respectively in dwarf samples compared with in the controls.

CONCLUSIONS

The upregulated ATPB_DIOEL and downregulated DNAK_GRATL as well as proteins that interact with them, such as RPOB2_LEPTE, A0A023H9M8_9STRA and RBL_AMOTI, may be associated with the long-term overgrazing-induced dwarfism in sheepgrass.

Plant sizes mediate mowing-induced changes in nutrient stoichiometry and allocation of a perennial grass in semi-arid grassland

While mowing‐induced changes in plant traits and their effects on ecosystem functioning in semi‐arid grassland are well studied, the relations between plant size and nutrient strategies are largely unknown. Mowing may drive the shifts of plant nutrient limitation and allocation. Here, we evaluated the changes in nutrient stoichiometry and allocation with variations in sizes of Leymus chinensis, the dominant plant species in Inner Mongolia grassland, to various mowing frequencies in a 17‐yr controlled experiment. Affected by mowing, the concentrations of nitrogen (N), phosphorus (P), and carbon (C) in leaves and stems were significantly increased, negatively correlating with plant sizes. Moreover, we found significant trade‐offs between the concentrations and accumulation of N, P, and C in plant tissues. The N:P ratios of L. chinensis aboveground biomass, linearly correlating with plant size, significantly decreased with increased mowing frequencies. The ratios of C:N and C:P of L. chinensis individuals were positively correlated with plant size, showing an exponential pattern. With increased mowing frequencies, L. chinensis size was correlated with the allocation ratios of leaves to stems of N, P, and C by the tendencies of negative parabola, positive, and negative linear. The results of structure equation modeling showed that the N, P, and C allocations were co‐regulated by biomass allocation and nutrient concentration ratios of leaves to stems. In summary, we found a significant decoupling effect between plant traits and nutrient strategies along mowing frequencies. Our results reveal a mechanism for how long‐term mowing‐induced changes in concentrations, accumulations, ecological stoichiometry, and allocations of key elements are mediated by the variations in plant sizes of perennial rhizome grass.

Gibberellin stimulates regrowth after defoliation of sheepgrass (Leymus chinensis) by regulating expression of fructan-related genes

Gibberellins (GAs) affect forage growth and development; however, it is largely unknown how GAs regulate the metabolism of fructan (an important polysaccharide reserve in many cereals) and the regrowth of forage plants after defoliation. To explore the mechanism of the responses of defoliated sheepgrass [Leymus chinensis (Trin.) Tzvel] to GA, we sprayed defoliated sheepgrass with GA3 and/or paclobutrazol (PAC; an inhibitor of GA biosynthesis) and analyzed the growth characteristics, carbohydrate contents, and transcript levels of genes related to GA metabolism, GA signal transduction, and fructan metabolism. The results showed that spraying exogenous GA3 onto defoliated sheepgrass promoted leaf and internode elongation, while spraying with PAC inhibited leaf and internode elongation, compared with the control. Spraying GA3 onto defoliated sheepgrass also altered the fructan content by extending the period of fructan utilization. At the transcriptional level, exogenous GA3 increased the transcript levels of genes related to GA metabolism in the sheath. Taken together, our results suggest that exogenous GA3 stimulates the regrowth of defoliated sheepgrass regrowth by regulating GA and fructan-related genes, and by promoting endogenous GA synthesis, fructan metabolism, and signaling.

New Insights on Drought Stress Response by Global Investigation of Gene Expression Changes in Sheepgrass (Leymus chinensis)

Water is a critical environmental factor that restricts the geographic distribution of plants. Sheepgrass [Leymus chinensis, (Trin.) Tzvel] is an important forage grass in the Eurasia Steppe and a close germplasm for wheat and barley. This native grass adapts well to adverse environments such as cold, salinity, alkalinity and drought, and it can survive when the soil moisture may be less than 6% in dry seasons. However, little is known about how sheepgrass tolerates water stress at the molecular level. Here, drought stress experiment and RNA-sequencing (RNA-seq) was performed in three pools of RNA samples (control, drought stress, and rewatering). We found that sheepgrass seedlings could still survive when the soil water content (SWC) was reduced to 14.09%. Differentially expressed genes (DEGs) analysis showed that 7320 genes exhibited significant responses to drought stress. Of these DEGs, 2671 presented opposite expression trends before and after rewatering. Furthermore, ~680 putative sheepgrass-specific water responsive genes were revealed that can be studied deeply. Gene ontology (GO) annotation revealed that stress-associated genes were activated extensively by drought treatment. Interestingly, cold stress-related genes were up-regulated greatly after drought stress. The DEGs of MAPK and calcium signal pathways, plant hormone ABA, jasmonate, ethylene, brassinosteroid signal pathways, cold response CBF pathway participated coordinatively in sheepgrass drought stress response. In addition, we identified 288 putative transcription factors (TFs) involved in drought response, among them, the WRKY, NAC, AP2/ERF, bHLH, bZIP, and MYB families were enriched, and might play crucial and significant roles in drought stress response of sheepgrass. Our research provided new and valuable information for understanding the mechanism of drought tolerance in sheepgrass. Moreover, the identification of genes involved in drought response can facilitate the genetic improvement of crops by molecular breeding.

Transcriptome Sequencing and Analysis for Culm Elongation of the World's Largest Bamboo (Dendrocalamus sinicus)

Dendrocalamus sinicus is the world’s largest bamboo species with strong woody culms, and known for its fast-growing culms. As an economic bamboo species, it was popularized for multi-functional applications including furniture, construction, and industrial paper pulp. To comprehensively elucidate the molecular processes involved in its culm elongation, Illumina paired-end sequencing was conducted. About 65.08 million high-quality reads were produced, and assembled into 81,744 unigenes with an average length of 723 bp. A total of 64,338 (79%) unigenes were annotated for their functions, of which, 56,587 were annotated in the NCBI non-redundant protein database and 35,262 were annotated in the Swiss-Prot database. Also, 42,508 and 21,009 annotated unigenes were allocated to gene ontology (GO) categories and clusters of orthologous groups (COG), respectively. By searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG), 33,920 unigenes were assigned to 128 KEGG pathways. Meanwhile, 8,553 simple sequence repeats (SSRs) and 81,534 single-nucleotide polymorphism (SNPs) were identified, respectively. Additionally, 388 transcripts encoding lignin biosynthesis were detected, among which, 27 transcripts encoding Shikimate O-hydroxycinnamoyltransferase (HCT) specifically expressed in D. sinicus when compared to other bamboo species and rice. The phylogenetic relationship between D. sinicus and other plants was analyzed, suggesting functional diversity of HCT unigenes in D. sinicus. We conjectured that HCT might lead to the high lignin content and giant culm. Given that the leaves are not yet formed and culm is covered with sheaths during culm elongation, the existence of photosynthesis of bamboo culm is usually neglected. Surprisedly, 109 transcripts encoding photosynthesis were identified, including photosystem I and II, cytochrome b6/f complex, photosynthetic electron transport and F-type ATPase, and 24 transcripts were characterized as antenna proteins that regarded as the main tool for capturing light of plants, implying stem photosynthesis plays a key role during culm elongation due to the unavailability of its leaf. By real-time quantitative PCR, the expression level of 6 unigenes was detected. The results showed the expression level of all genes accorded with the transcriptome data, which confirm the reliability of the transcriptome data. As we know, this is the first study underline the D. sinicus transcriptome, which will deepen the understanding of the molecular mechanisms of culm development. The results may help variety improvement and resource utilization of bamboos.

Global transcriptome profiling analysis reveals insight into saliva-responsive genes in alfalfa

We studied the genome-wide multiple time-course transcriptome dynamics after saliva deposition in alfalfa and demonstrate that saliva deposition functions as a stress that negatively affects the regrowth of alfalfa. Saliva deposition is one of the key factors influencing plant-herbivore interactions during grazing. Although many studies have focused on the effects of saliva deposition on plant regrowth, no consistent conclusions have been reached. Alfalfa is the most extensively cultivated forage legume, yet most alfalfa cultivars, thus far, are not grazing-tolerant. To better understand the underlying mechanism, we undertook a study to evaluate the global changes in the transcriptome of alfalfa after cow saliva deposition treatment. In this study, cDNA libraries from alfalfa seedlings at 0, 4, 8, and 24 h after cow saliva deposition were constructed and sequenced, resulting in the identification of 53,195 annotated unigenes, from which 4,814 unigenes were significantly differentially expressed. A metabolic pathway enrichment analysis demonstrated that saliva deposition functions as a stress that negatively affects the regrowth of alfalfa by modifying jasmonic acid synthesis, enhancing the susceptibility to pathogens and reducing the expression levels of ribosomal protein genes. In the present study, we demonstrate the potential effects of saliva deposition on alfalfa regrowth at the transcriptome level. These fundamental and important findings could facilitate further investigations into the molecular mechanisms underlying the responses of alfalfa and other related species to herbivore grazing.

Transcriptome profiling and digital gene expression by deep sequencing in early somatic embryogenesis of endangered medicinal Eleutherococcus senticosus Maxim

Somatic embryogenesis (SE) has been studied as a model system to understand molecular events in physiology, biochemistry, and cytology during plant embryo development. In particular, it is exceedingly difficult to access the morphological and early regulatory events in zygotic embryos. To understand the molecular mechanisms regulating early SE in Eleutherococcus senticosus Maxim., we used high-throughput RNA-Seq technology to investigate its transcriptome. We obtained 58,327,688 reads, which were assembled into 75,803 unique unigenes. To better understand their functions, the unigenes were annotated using the Clusters of Orthologous Groups, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes databases. Digital gene expression libraries revealed differences in gene expression profiles at different developmental stages (embryogenic callus, yellow embryogenic callus, global embryo). We obtained a sequencing depth of >5.6 million tags per sample and identified many differentially expressed genes at various stages of SE. The initiation of SE affected gene expression in many KEGG pathways, but predominantly that in metabolic pathways, biosynthesis of secondary metabolites, and plant hormone signal transduction. This information on the changes in the multiple pathways related to SE induction in E. senticosus Maxim. embryogenic tissue will contribute to a more comprehensive understanding of the mechanisms involved in early SE. Additionally, the differentially expressed genes may act as molecular markers and could play very important roles in the early stage of SE. The results are a comprehensive molecular biology resource for investigating SE of E. senticosus Maxim.

Contrasting Effects of Long-Term Grazing and Clipping on Plant Morphological Plasticity: Evidence from a Rhizomatous Grass

Understanding the mechanism of plant morphological plasticity in response to grazing and clipping of semiarid grassland can provide insight into the process of disturbance-induced decline in grassland productivity. In recent studies there has been controversy regarding two hypotheses: 1) grazing avoidance; and 2) growth limiting mechanisms of morphological plasticity in response to defoliation. However, the experimental evidence presented for the memory response to grazing and clipping of plants has been poorly reported. This paper reports on two experiments that tested these hypotheses in field and in a controlled environment, respectively. We examined the effects of long-term clipping and grazing on the functional traits and their plasticity for Leymus chinensis (Trin.) Tzvelev (the dominate species) in the typical-steppe grassland of Inner Mongolia, China. There were four main findings from these experiments. (i) The majority of phenotypic traits of L. chinensis tended to significantly miniaturize in response to long-term field clipping and grazing. (ii) The significant response of morphological plasticity with and without grazing was maintained in a hydroponic experiment designed to remove environmental variability, but there was no significant difference in L. chinensis individual size traits for the clipping comparison. (iii) Plasticity indexes of L. chinensis traits in a controlled environment were significantly lower than under field conditions indicating that plants had partial and slight memory effect to long-term grazing. (iv) The allometry of various phenotypic traits, indicated significant trade-offs between leaf and stem allocation with variations in plant size induced by defoliation, which were maintained only under grazing in the hydroponic controlled environment experiment. Taken together, our findings suggest that the morphological plasticity of L. chinensis induced by artificial clipping was different with that by livestock grazing. The miniaturization of plant size in long-term grazed grassland may reflect retained characteristics of dwarf memory for adaptation to long-term grazing by large herbivores.

Prediction of Leymus arenarius (L.) antimicrobial peptides based on de novo transcriptome assembly

Leymus arenarius is a unique wild growing Poaceae plant exhibiting extreme tolerance to environmental conditions. In this study we for the first time performed whole-transcriptome sequencing of lymegrass seedlings using Illumina platform followed by de novo transcriptome assembly and functional annotation. Our goal was to identify transcripts encoding antimicrobial peptides (AMPs), one of the key components of plant innate immunity. Using the custom software developed for this study that predicted AMPs and classified them into families, we revealed more than 160 putative AMPs in lymegrass seedlings. We classified them into 7 families based on their cysteine motifs and sequence similarity. The families included defensins, thionins, hevein-like peptides, snakins, cyclotide, alfa-hairpinins and LTPs. This is the first communication about the presence of almost all known AMP families in trascriptomic data of a single plant species. Additionally, cysteine-rich peptides that potentially represent novel families of AMPs were revealed. We have confirmed by RT-PCR validation the presence of 30 transcripts encoding selected AMPs in lymegrass seedlings. In summary, the presented method of pAMP prediction developed by us can be applied for relatively fast and simple screening of novel components of plant immunity system and is well suited for whole-transcriptome or genome analysis of uncharacterized plants.

De novo assembly and transcriptomic profiling of the grazing response in Stipa grandis

Background

Stipa grandis (Poaceae) is one of the dominant species in a typical steppe of the Inner Mongolian Plateau. However, primarily due to heavy grazing, the grasslands have become seriously degraded, and S. grandis has developed a special growth-inhibition phenotype against the stressful habitat. Because of the lack of transcriptomic and genomic information, the understanding of the molecular mechanisms underlying the grazing response of S. grandis has been prohibited.

Results

Using the Illumina HiSeq 2000 platform, two libraries prepared from non-grazing (FS) and overgrazing samples (OS) were sequenced. De novo assembly produced 94,674 unigenes, of which 65,047 unigenes had BLAST hits in the National Center for Biotechnology Information (NCBI) non-redundant (nr) database (E-value < 10^-5). In total, 47,747, 26,156 and 40,842 unigenes were assigned to the Gene Ontology (GO), Clusters of Orthologous Group (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, respectively. A total of 13,221 unigenes showed significant differences in expression under the overgrazing condition, with a threshold false discovery rate ≤ 0.001 and an absolute value of log₂Ratio ≥ 1. These differentially expressed genes (DEGs) were assigned to 43,257 GO terms and were significantly enriched in 32 KEGG pathways (q-value ≤ 0.05). The alterations in the wound-, drought- and defense-related genes indicate that stressors have an additive effect on the growth inhibition of this species.

Conclusions

This first large-scale transcriptome study will provide important information for further gene expression and functional genomics studies, and it facilitated our investigation of the molecular mechanisms of the S. grandis grazing response and the associated morphological and physiological characteristics.

Bovine serum albumin in saliva mediates grazing response in Leymus chinensis revealed by RNA sequencing

Background

Sheepgrass (Leymus chinensis) is an important perennial forage grass across the Eurasian Steppe and is adaptable to various environmental conditions, but little is known about its molecular mechanism responding to grazing and BSA deposition. Because it has a large genome, RNA sequencing is expensive and impractical except for the next-generation sequencing (NGS) technology.

Results

In this study, NGS technology was employed to characterize de novo the transcriptome of sheepgrass after defoliation and grazing treatments and to identify differentially expressed genes (DEGs) responding to grazing and BSA deposition. We assembled more than 47 M high-quality reads into 120,426 contigs from seven sequenced libraries. Based on the assembled transcriptome, we detected 2,002 DEGs responding to BSA deposition during grazing. Enrichment analysis of Gene ontology (GO), EuKaryotic Orthologous Groups (KOG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways revealed that the effects of grazing and BSA deposition involved more apoptosis and cell oxidative changes compared to defoliation. Analysis of DNA fragments, cell oxidative factors and the lengths of leaf scars after grazing provided physiological and morphological evidence that BSA deposition during grazing alters the oxidative and apoptotic status of cells.

Conclusions

This research greatly enriches sheepgrass transcriptome resources and grazing-stress-related genes, helping us to better understand the molecular mechanism of grazing in sheepgrass. The grazing-stress-related genes and pathways will be a valuable resource for further gene-phenotype studies.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1126) contains supplementary material, which is available to authorized users.

Ragweed (Ambrosia artemisiifolia) pollen allergenicity: SuperSAGE transcriptomic analysis upon elevated CO2 and drought stress

BACKGROUND

Pollen of common ragweed (Ambrosia artemisiifolia) is a main cause of allergic diseases in Northern America. The weed has recently become spreading as a neophyte in Europe, while climate change may also affect the growth of the plant and additionally may also influence pollen allergenicity. To gain better insight in the molecular mechanisms in the development of ragweed pollen and its allergenic proteins under global change scenarios, we generated SuperSAGE libraries to identify differentially expressed transcripts.

RESULTS

Ragweed plants were grown in a greenhouse under 380 ppm CO2 and under elevated level of CO2 (700 ppm). In addition, drought experiments under both CO2 concentrations were performed. The pollen viability was not altered under elevated CO2, whereas drought stress decreased its viability. Increased levels of individual flavonoid metabolites were found under elevated CO2 and/or drought. Total RNA was isolated from ragweed pollen, exposed to the four mentioned scenarios and four SuperSAGE libraries were constructed. The library dataset included 236,942 unique sequences, showing overlapping as well as clear differently expressed sequence tags (ESTs). The analysis targeted ESTs known in Ambrosia, as well as in pollen of other plants. Among the identified ESTs, those encoding allergenic ragweed proteins (Amb a) increased under elevated CO2 and drought stress. In addition, ESTs encoding allergenic proteins in other plants were also identified.

CONCLUSIONS

The analysis of changes in the transcriptome of ragweed pollen upon CO2 and drought stress using SuperSAGE indicates that under global change scenarios the pollen transcriptome was altered, and impacts the allergenic potential of ragweed pollen.