Overexpression of PvSVP1, an SVP-like gene of bamboo, causes early flowering and abnormal floral organs in Arabidopsis and rice.

Bamboo is a nontimber woody plant featuring a long vegetative stage and uncertain flowering time. Therefore, the genes belonging to flowering repressors might be essential in regulating the transition from the vegetative to reproductive stage in bamboo. The Short Vegetative Phase ( SVP) gene plays a pivotal role in floral transition and development. However, little is known about the bamboo SVP homologues. In this study, Phyllostachys violascens PvSVP1 is isolated by analysis of the P. edulis transcriptome database. Phylogenetic analysis shows that PvSVP1 is closely related to OsMADS55 (rice SVP homolog). PvSVP1 is ubiquitously expressed in various tissues, predominantly in vegetative tissues. To investigate the function of PvSVP1, PvSVP1 is overexpressed in Arabidopsis and rice under the influence of the 35S promoter. Overexpression of PvSVP1 in Arabidopsis causes early flowering and produces abnormal petals and sepals. Quantitative real-time PCR reveals that overexpression in Arabidopsis produces an early flowering phenotype by downregulating FLC and upregulating FT and produces abnormal floral organs by upregulating AP1, AP3 and PI expressions. Simultaneously, overexpression of PvSVP1 in rice alters the expressions of flowering-related genes such as Hd3a, RFT1, OsMADS56 and Ghd7 and promotes flowering under field conditions. In addition, PvSVP1 may be a nuclear protein which interacts with PvVRN1 and PvMADS56 on the yeast two-hybrid and BiFC systems. Our study suggests that PvSVP1 may play a vital role in flowering time and development by interacting with PvVRN1 and PvMADS56 in the nucleus. Furthermore, this study paves the way toward understanding the complex flowering process of bamboo.

Entailing the Next-Generation Sequencing and Metabolome for Sustainable Agriculture by Improving Plant Tolerance.

Crop production is a serious challenge to provide food for the 10 billion individuals forecasted to live across the globe in 2050. The scientists' emphasize establishing an equilibrium among diversity and quality of crops by enhancing yield to fulfill the increasing demand for food supply sustainably. The exploitation of genetic resources using genomics and metabolomics strategies can help generate resilient plants against stressors in the future. The innovation of the next-generation sequencing (NGS) strategies laid the foundation to unveil various plants' genetic potential and help us to understand the domestication process to unmask the genetic potential among wild-type plants to utilize for crop improvement. Nowadays, NGS is generating massive genomic resources using wild-type and domesticated plants grown under normal and harsh environments to explore the stress regulatory factors and determine the key metabolites. Improved food nutritional value is also the key to eradicating malnutrition problems around the globe, which could be attained by employing the knowledge gained through NGS and metabolomics to achieve suitability in crop yield. Advanced technologies can further enhance our understanding in defining the strategy to obtain a specific phenotype of a crop. Integration among bioinformatic tools and molecular techniques, such as marker-assisted, QTLs mapping, creation of reference genome, de novo genome assembly, pan- and/or super-pan-genomes, etc., will boost breeding programs. The current article provides sequential progress in NGS technologies, a broad application of NGS, enhancement of genetic manipulation resources, and understanding the crop response to stress by producing plant metabolites. The NGS and metabolomics utilization in generating stress-tolerant plants/crops without deteriorating a natural ecosystem is considered a sustainable way to improve agriculture production. This highlighted knowledge also provides useful research that explores the suitable resources for agriculture sustainability.

MicroRNAs play important roles in regulating the rapid growth of the Phyllostachys edulis culm internode.

Moso bamboo (Phyllostachys edulis) is a fast-growing species with uneven growth and lignification from lower to upper segments within one internode. MicroRNAs (miRNAs) play a vital role in post-transcriptional regulation in plants. However, how miRNAs regulate fast growth in bamboo internodes is poorly understood. In this study, one moso bamboo internode was divided during early rapid growth into four segments called F4 (bottom) to F1 (upper) and these were then analysed for transcriptomes, miRNAs and degradomes. The F4 segment had a higher number of actively dividing cells as well as a higher content of auxin (IAA), cytokinin (CK) and gibberellin (GA) compared with the F1 segment. RNA-seq analysis showed DNA replication and cell division-associated genes highly expressed in F4 rather than in F1. In total, 63 miRNAs (DEMs) were identified as differentially expressed between F4 and F1. The degradome and the transcriptome indicated that many downstream transcription factors and hormonal responses genes were modulated by DEMs. Several miR-target interactions were further validated by tobacco co-infiltration. Our findings give new insights into miRNA-mediated regulatory pathways in bamboo, and will contribute to a comprehensive understanding of the molecular mechanisms governing rapid growth.

Comprehensive Analysis of Five Phyllostachys edulis SQUA-like Genes and Their Potential Functions in Flower Development.

Bamboo is one of the most important non-timber forest resources worldwide. It has considerable economic value and unique flowering characteristics. The long juvenile phase in bamboo and unpredictable flowering time limit breeding and genetic improvement and seriously affect the productivity and application of bamboo forests. Members of SQUA-like subfamily genes play an essential role in controlling flowering time and floral organ identity. A comprehensive study was conducted to explain the functions of five SQUA-like subfamily genes in Phyllostachys edulis. Expression analysis revealed that all PeSQUAs have higher transcript levels in the reproductive period than in the juvenile phase. However, PeSQUAs showed divergent expression patterns during inflorescence development. The protein-protein interaction (PPI) patterns among PeSQUAs and other MADS-box members were analyzed by yeast two-hybrid (Y2H) experiments. Consistent with amino acid sequence similarity and phylogenetic analysis, the PPI patterns clustered into two groups. PeMADS2, 13, and 41 interacted with multiple PeMADS proteins, whereas PeMADS3 and 28 hardly interacted with other proteins. Based on our results, PeSQUA might possess different functions by forming protein complexes with other MADS-box proteins at different flowering stages. Furthermore, we chose PeMADS2 for functional analysis. Ectopic expression of PeMADS2 in Arabidopsis and rice caused early flowering, and abnormal phenotype was observed in transgenic Arabidopsis lines. RNA-seq analysis indicated that PeMADS2 integrated multiple pathways regulating floral transition to trigger early flowering time in rice. This function might be due to the interaction between PeMADS2 and homologous in rice. Therefore, we concluded that the five SQUA-like genes showed functional conservation and divergence based on sequence differences and were involved in floral transitions by forming protein complexes in P. edulis. The MADS-box protein complex model obtained in the current study will provide crucial insights into the molecular mechanisms of bamboo's unique flowering characteristics.

Homo- and Hetero-Dimers of CAD Enzymes Regulate Lignification and Abiotic Stress Response in Moso Bamboo.

Lignin biosynthesis enzymes form complexes for metabolic channelling during lignification and these enzymes also play an essential role in biotic and abiotic stress response. Cinnamyl alcohol dehydrogenase (CAD) is a vital enzyme that catalyses the reduction of aldehydes to alcohols, which is the final step in the lignin biosynthesis pathway. In the present study, we identified 49 CAD enzymes in five Bambusoideae species and analysed their phylogenetic relationships and conserved domains. Expression analysis of Moso bamboo PheCAD genes in several developmental tissues and stages revealed that among the PheCAD genes, PheCAD2 has the highest expression level and is expressed in many tissues and PheCAD1, PheCAD6, PheCAD8 and PheCAD12 were also expressed in most of the tissues studied. Co-expression analysis identified that the PheCAD2 positively correlates with most lignin biosynthesis enzymes, indicating that PheCAD2 might be the key enzyme involved in lignin biosynthesis. Further, more than 35% of the co-expressed genes with PheCADs were involved in biotic or abiotic stress responses. Abiotic stress transcriptomic data (SA, ABA, drought, and salt) analysis identified that PheCAD2, PheCAD3 and PheCAD5 genes were highly upregulated, confirming their involvement in abiotic stress response. Through yeast two-hybrid analysis, we found that PheCAD1, PheCAD2 and PheCAD8 form homo-dimers. Interestingly, BiFC and pull-down experiments identified that these enzymes form both homo- and hetero- dimers. These data suggest that PheCAD genes are involved in abiotic stress response and PheCAD2 might be a key lignin biosynthesis pathway enzyme. Moreover, this is the first report to show that three PheCAD enzymes form complexes and that the formation of PheCAD homo- and hetero- dimers might be tissue specific.

Comparative transcriptomic analysis of the flower induction and development of the Lei bamboo (Phyllostachys violascens).

BACKGROUND: Bamboo is a very important forest resource. However, the prolonged vegetative stages and uncertainty of flowering brings difficulties in bamboo flowers sampling. Until now, the flowering mechanism of bamboo is still unclear. RESULTS: In this study, three successive stages of flowering buds and the corresponding vegetative buds (non-flowering stage) from Lei bamboo (Phyllostachys violascens) were collected for transcriptome analysis using Illumina RNA-Seq method. We generated about 442 million clean reads from the above samples, and 132,678 unigenes were acquired with N50 of 1080 bp. A total of 7266 differentially expressed genes (DEGs) were determined. According to expression profile and gene function analysis, some environmental stress responsive and plant hormone-related DEGs were highly expressed in the inflorescence meristem formation stage (TF_1) while some floral organ development related genes were up-regulated significantly in floral organs determination stage (TF_2) and floral organs maturation (TF_3) stage, implying the essential roles of these DEGs in flower induction and maturation of Lei bamboo. Additionally, a total of 25 MADS-box unigenes were identified. Based on the expression profile, B, C/D and E clade genes were more related to floral organs development compared with A clade genes in Lei bamboo. CONCLUSIONS: This transcriptome data presents fundamental information about the genes and pathways involved in flower induction and development of Lei bamboo. Moreover, a critical sampling method is provided which could be benefit for bamboo flowering mechanism study.

Effects of epigallocatechin-3-gallate on the HMGB1/RAGE pathway in PM2.5-exposed asthmatic rats.

Current studies have shown that long-term exposure to fine particulate matter (PM2.5) can aggravate lung injury in asthmatic children. The HMGB1/RAGE pathway may play an important role, but few studies on the HMGB1/RAGE signaling pathway in PM2.5-induced asthma have been performed. Epigallocatechin-3-gallate (EGCG), which has antioxidant, anti-inflammatory and immunomodulatory effects, has not been examined in studies at home and abroad. In this study, we established an animal model of asthma and observed that the lung tissue was damaged, inflammatory cells infiltrated, bronchial wall thickness (WTt) and bronchial smooth muscle thickness (WTm) increased and the HMGB1 and RAGE mRNA and protein expression increased. The asthmatic rats exposed to PM2.5 showed significantly increased lung injury and inflammatory cell infiltration, WTt and WTm further increased, and HMGB1 and RAGE mRNA and protein levels were higher than those in the asthma group. The asthmatic rats exposed to PM2.5 were treated with EGCG, which alleviated the lung injury, reduced the number of inflammatory cells, decreased WTt and WTm, and reduced the expression of HMGB1 and RAGE mRNA and protein. The high-dose group showed more significant effects than the other groups. In conclusion, our results suggest that HMGB1 and RAGE are involved in the pathogenesis of asthma. PM2.5 exposure significantly aggravated airway inflammation injury in asthmatic rats. EGCG can reduce lung injury and airway remodeling in PM2.5-exposed asthmatic rats and has lung protective effects. The mechanism may be related to regulation of the HMGB1/RAGE signaling pathway. Our results may provide new ideas and methods for the prevention and treatment of PM2.5-induced asthma.

Genome-wide identification of MADS-box family genes in moso bamboo (Phyllostachys edulis) and a functional analysis of PeMADS5 in flowering.

BACKGROUND: MADS-box genes encode a large family of transcription factors that play significant roles in plant growth and development. Bamboo is an important non-timber forest product worldwide, but previous studies on the moso bamboo (Phyllostachys edulis) MADS-box gene family were not accurate nor sufficiently detailed. RESULTS: Here, a complete genome-wide identification and characterization of the MADS-box genes in moso bamboo was conducted. There was an unusual lack of type-I MADS-box genes in the bamboo genome database ( http://202.127.18.221/bamboo/index.php ), and some of the PeMADS sequences are fragmented and/or inaccurate. We performed several bioinformatics techniques to obtain more precise sequences using transcriptome assembly. In total, 42 MADS-box genes, including six new type-I MADS-box genes, were identified in bamboo, and their structures, phylogenetic relationships, predicted conserved motifs and promoter cis-elements were systematically investigated. An expression analysis of the bamboo MADS-box genes in floral organs and leaves revealed that several key members are involved in bamboo inflorescence development, like their orthologous genes in Oryza. The ectopic overexpression of one MADS-box gene, PeMADS5, in Arabidopsis triggered an earlier flowering time and the development of an aberrant flower phenotype, suggesting that PeMADS5 acts as a floral activator and is involved in bamboo flowering. CONCLUSION: We produced the most comprehensive information on MADS-box genes in moso bamboo. Additionally, a critical PeMADS gene (PeMADS5) responsible for the transition from vegetative to reproductive growth was identified and shown to be related to bamboo floral development.

Rice Sucrose Partitioning Mediated by a Putative Pectin Methyltransferase and Homogalacturonan Methylesterification.

Homogalacturonan (HG) is the main component of pectins. HG methylesterification has recently emerged as a key determinant controlling cell attachment, organ formation, and phyllotaxy. However, whether and how HG methylesterification affects intercellular metabolite transport has rarely been reported. Here, we identified and characterized knockout mutants of the rice (Oryza sativa) OsQUA2 gene encoding a putative pectin methyltransferase. Osqua2 mutants exhibit a remarkable decrease in the degree of methylesterification of HG in the culm-sieve element cell wall and a markedly reduced grain yield. The culm of Osqua2 mutant plants contains excessive sucrose (Suc), and a 13CO2 feeding experiment showed that the Suc overaccumulation in the culm was caused by blocked Suc translocation. These and other findings demonstrate that OsQUA2 is essential for maintaining a high degree of methylesterification of HG in the rice culm-sieve element cell wall, which may be critical for efficient Suc partitioning and grain filling. In addition, our results suggest that the apoplastic pathway is involved in long-distance Suc transport in rice. The identification and characterization of the OsQUA2 gene and its functionality revealed a previously unknown contribution of HG methylesterification and provided insight into how modification of the cell wall regulates intercellular transport in plants.

Kinin B1 receptor blockade and ACE inhibition attenuate cardiac postinfarction remodeling and heart failure in rats.

INTRODUCTION: The aim of the present study was to evaluate the effects of the novel kinin B1 receptor antagonist BI113823 on postinfarction cardiac remodeling and heart failure, and to determine whether B1 receptor blockade alters the cardiovascular effects of an angiotensin 1 converting enzyme (ACE) inhibitor in rats. METHODS AND RESULTS: Sprague Dawley rats were subjected to permanent occlusion of the left coronary artery. Cardiovascular function was determined at 6weeks postinfarction. Treatment with either B1 receptor antagonist (BI113823) or an ACE inhibitor (lisinopril) alone or in combination significantly reduced the heart weight-to-body weight and lung weight-to-body weight ratios, and improved postinfarction cardiac function as evidenced by greater cardiac output, the maximum rate of left ventricular pressure rise (±dP/dtmax), left ventricle ejection fraction, fractional shorting, better wall motion, and attenuation of elevated left ventricular end diastolic pressure (LVEDP). Furthermore, all three treatment groups exhibited significant reduction in cardiac interstitial fibrosis, collagen deposition, CD68 positive macrophages, neutrophils, and proinflammatory cytokine production (TNF-α and IL-1ß), compared to vehicle controls. CONCLUSION: The present study shows that treatment with the novel kinin B1 receptor antagonist, BI113823, reduces postinfarction cardiac remodeling and heart failure, and does not influence the cardiovascular effects of the ACE inhibitor.

Interaction of sodium bicarbonate and Na+/H+ exchanger inhibition in the treatment of acute metabolic acidosis in pigs.

OBJECTIVE: Administration of NaHCO3 does not improve cellular function or reduce the mortality of acute lactic acidosis. This might be related to aggravation of intracellular acidosis, but it could also be due to activation of Na+/H+ exchanger with a deleterious increment in intracellular calcium ([Ca2+]i). This study examined the impact of coadministration of NaHCO3 and a selective inhibitor of Na+/H+ exchanger, sabiporide on cardiovascular function, changes in proinflammatory cytokines, and organ function in a model of acute lactic acidosis produced by hemorrhagic hypotension followed by infusion of lactic acid. DESIGN: Experimental, prospective study. SETTING: Medical Center research laboratory. SUBJECTS: Male Yorkshire pigs. INTERVENTIONS: Anesthetized pigs were subjected to hypovolemia for 30 minutes and followed by DL-lactic acid infusion, and then either saline or sodium bicarbonate was infused. MEASUREMENTS AND MAIN RESULTS: Hypovolemia followed by a DL-lactic acid infusion resulted in severe acidemia with a blood pH~6.8. Administration of NaHCO3 did not improve cardiovascular performance or decrease the levels of proinflammatory responses, whereas administration of sabiporide prior to acid or NaHCO3 infusion improved cardiopulmonary performance and blood oxygenation, reduced nuclear factor-κB activation, neutrophil accumulation, and proinflammatory cytokine production, and attenuated organ injury. Exposure of rat cardiac myocytes to a pH of 7.2 led to a marked increase of [Ca2+]i, and release of lactate dehydrogenase from cells which were further augmented after increase in external pH by addition of NaHCO3. Both the increase in [Ca2+]i and release of lactate dehydrogenase were attenuated in the presence of sabiporide. CONCLUSIONS: Coadministration of Na/H exchanger inhibitor with sodium bicarbonate improves cardiovascular performances, reduces proinflammatory responses, and attenuates organ injury. This improvement in these variables appears to be related to prevention of a rise in intracellular calcium occurring after both exposures to acid and bicarbonate.

Coadministration of a Na+-H+ exchange inhibitor and sodium bicarbonate for the treatment of asphyxia-induced cardiac arrest in piglets.

BACKGROUND: The present study tested the hypothesis that addition of an inhibitor of Na(+)/H(+) exchanger (NHE1) to sodium bicarbonate might improve the response to base therapy from prolonged asphyxial cardiac arrest in piglets. METHODS: Asphyxial cardiac arrest was induced by endotracheal tube clamping. Animals were randomly assigned to four study groups: (i) vehicle control, (ii) administration of sabiporide (NHE1 inhibitor), (iii) administration of sodium bicarbonate, and (iv) administration of sabiporide and sodium bicarbonate. RESULTS: Administration of sodium bicarbonate alone did not affect survival, hemodynamic measures, and regional blood flow to critical tissues such as brain, heart, kidney, liver, and spleen. In contrast, sabiporide given alone or combined with sodium bicarbonate improved these. Furthermore, treatment with sabiporide reduced accumulation of neutrophils, reduced cytokine production in the lung, and reduced plasma levels of cardiac troponin-I, alanine aminotransferase, aspartate aminotransferase, and urea. In addition, the combined use of sabiporide and sodium bicarbonate had more profound reduction in interleukin (IL)-6 and IL-10, compared to sabiporide alone. CONCLUSION: These results suggest that addition of sabiporide to the administration of sodium bicarbonate might improve hemodynamic response and dampen the inflammatory cascade noted with cardiac arrest, and therefore being an attractive option in the treatment of cardiac arrest.

Sabiporide improves cardiovascular function and attenuates organ injury from severe sepsis.

BACKGROUND: The aim of the present study was to evaluate the efficacy of orally administered sabiporide, a selective Na(+)/H(+) exchanger inhibitor on whole body protection from severe sepsis in rats. METHODS: Series 1: Sepsis was induced by cecal ligation and puncture (CLP). Animals received treatment of vehicle or sabiporide (10 mg/kg, p.o.). The experiment was terminated 20 h after CLP. Series 2: At 20 h after CLP, the necrotic cecum was excised and the abdominal cavity was washed. The animals were then returned to their cages. The experiment was terminated 7 d after CLP. RESULTS: Series 1: Compared with vehicle treatment, administration of sabiporide prevented hemodynamic derangement and improved cardiac function as evidenced by improved arterial pressure, left ventricle systolic pressure, ±dp/dt max, ejection fraction and fractional shorting, attenuated left ventricle end-diastolic pressure elevation, and wall motion abnormality. Furthermore, administration of sabiporide attenuated intestinal mucosal hyperpermeability and reduced accumulation of abdominal ascites. In addition, treatment with sabiporide also reduced plasma levels of tumor necrosis factor-α, interleukin 6, interleukin 10, cardiac troponin, aspartate aminotransferase, alanine aminotransferase, urea, and lactate, and attenuated neutrophil infiltration in the liver and gut. Series 2: Administration of sabiporide improved the 7-day survival rate after CLP in rats (42% in vehicle group versus 75% in sabiporide group). CONCLUSIONS: Administration of sabiporide improved cardiovascular performance, lessened the inflammatory response, tissue hypoperfusion and multiorgan injury, and most importantly reduced mortality.

The CONSTANS-LIKE gene PeCOL13 regulates flowering through intron-retained alternative splicing in Phyllostachys edulis.

Woody bamboo exhibits a unique flowering characteristic with a lengthy flowering cycle, often followed by death. In many plant species, alternative splicing (AS) is a common phenomenon involved in controlling flowering. In this study, a PeCOL13 gene in moso bamboo (Phyllostachys edulis) was characterized. It produced two isoforms: PeCOL13α and PeCOL13ß, due to an intron-retained AS. The PeCOL13α expressed in the vegetative phase and the reproductive phase, but the PeCOL13ß didn't express during the vegetative phase and showed only a weak expression from F1 to F3 during the reproductive phase. Overexpression of PeCOL13α in rice (Oryza sativa) resulted in a delayed heading time through inhibiting the expressions of Hd3a, OsFTL1, and Ehd1 and activating the expressions of Ghd7 and RCN1. However, the PeCOL13ß-overexpressed rice didn't show any significant differences in flowering compared with wild-type (WT), and the expressions of downstream flowering genes had no notable changes. Further analysis revealed that both PeCOL13α and PeCOL13ß can bind to the PeFT promoter. Meanwhile, PeCOL13α can inhibit the transcription of PeFT, but PeCOL13ß showed no effect. When PeCOL13α and PeCOL13ß coexist, the inhibitory effect of PeCOL13α on PeFT transcription was weakened by PeCOL13ß. This study provides new insights into the mechanism of bamboo flowering research.

Molecular identification of Bambusa changningensis is the natural bamboo hybrid of B. rigida × Dendrocalamus farinosus.

Bamboo is one of the fastest-growing plants commonly used in food, fibre, paper, biofuel, ornamental and medicinal industries. Natural hybridization in bamboo is rare due to its long vegetative period followed by gregarious flowering and death of the entire population. In the current study, a new bamboo species, Bambusa changningensis, shows intermediate characteristics of Dendrocalamus farinosus and B. rigida morphologically, but it is unknown whether B. changningensis is a natural hybrid. Moreover, B. changningensis has been identified as a superior variety of Sichuan Province with high pulping yield, fibre length and width. Therefore, we analyzed the morphological characteristics, DNA markers, DNA barcoding and chloroplast genomes to identify the hybrid origin of B. changningensis and possible maternal parent. We have developed the transcriptomic data for B. changningensis and mined the SSR loci. The putative parental lines and hybrid were screened for 64 SSR makers and identified that SSR14, SSR28, SSR31 and SSR34 markers showed both alleles of the parental species in B. changningensis, proving heterozygosity. Sequencing nuclear gene GBSSI partial regions and phylogenetic analysis also confirm the hybrid nature of B. changningensis. Further, we have generated the complete chloroplast genome sequence (139505 bp) of B. changningensis. By analyzing the cp genomes of both parents and B. changningensis, we identified that B. rigida might be the female parent. In conclusion, our study identified that B. changningensis is a natural hybrid, providing evidence for bamboo's natural hybridization. This is the first report on confirming a natural bamboo hybrid and its parents through SSR and chloroplast genome sequence.

Role of HMGB1 in apoptosis-mediated sepsis lethality.

Severe sepsis, a lethal syndrome after infection or injury, is the third leading cause of mortality in the United States. The pathogenesis of severe sepsis is characterized by organ damage and accumulation of apoptotic lymphocytes in the spleen, thymus, and other organs. To examine the potential causal relationships of apoptosis to organ damage, we administered Z-VAD-FMK, a broad-spectrum caspase inhibitor, to mice with sepsis. We found that Z-VAD-FMK-treated septic mice had decreased levels of high mobility group box 1 (HMGB1), a critical cytokine mediator of organ damage in severe sepsis, and suppressed apoptosis in the spleen and thymus. In vitro, apoptotic cells activate macrophages to release HMGB1. Monoclonal antibodies against HMGB1 conferred protection against organ damage but did not prevent the accumulation of apoptotic cells in the spleen. Thus, our data indicate that HMGB1 production is downstream of apoptosis on the final common pathway to organ damage in severe sepsis.

Genome-wide identification and evolution of WNK kinases in Bambusoideae and transcriptional profiling during abiotic stress in Phyllostachys edulis.

With-no-lysine (WNK) kinases play vital roles in abiotic stress response, circadian rhythms, and regulation of flowering time in rice, Arabidopsis, and Glycine max. However, there are no previous reports of WNKs in the Bambusoideae, although genome sequences are available for diploid, tetraploid, and hexaploid bamboo species. In the present study, we identified 41 WNK genes in five bamboo species and analysed gene evolution, phylogenetic relationship, physical and chemical properties, cis-elements, and conserved motifs. We predicted the structure of PeWNK proteins of moso bamboo and determined the exposed, buried, structural and functional amino acids. Real-time qPCR analysis revealed that PeWNK5, PeWNK7, PeWNK8, and PeWNK11 genes are involved in circadian rhythms. Analysis of gene expression of different organs at different developmental stages revealed that PeWNK genes are tissue-specific. Analysis of various abiotic stress transcriptome data (drought, salt, SA, and ABA) revealed significant gene expression levels in all PeWNKs except PeWNK11. In particular, PeWNK8 and PeWNK9 were significantly down- and up-regulated, respectively, after abiotic stress treatment. A co-expression network of PeWNK genes also showed that PeWNK2, PeWNK4, PeWNK7, and PeWNK8 were co-expressed with transcriptional regulators related to abiotic stress. In conclusion, our study identified the PeWNKs of moso bamboo involved in circadian rhythms and abiotic stress response. In addition, this study serves as a guide for future functional genomic studies of the WNK genes of the Bambusoideae.

Combined intensive management of fertilization, tillage, and organic material mulching regulate soil bacterial communities and functional capacities by altering soil potassium and pH in a Moso bamboo forest.

Intensive management is a common practice in agricultural and forestry ecosystems to improve soil quality and crop yield by influencing nutrient supply and soil microbiota; however, the linkage between soil nutrients and bacterial community and functional capacities in intensively managed economic forests has not been well studied. In this study, we investigated the soil properties such as available potassium (AK), available nitrogen (AN), available phosphorus (AP), ammonium (NH 4 + ), nitrate (NO 3 - ), organic matter (OM), total nitrogen (TN), total phosphorus (TP), bacterial diversity and community composition, potential functions of rhizome roots, and soil microbiota across a chronosequence of intensively managed Moso bamboo (Phyllostachys edulis) forests. Our results demonstrated that the combined intensive management (deep tillage, fertilization, and organic material mulching) in this study caused a significant increase in the concentrations of AK, AN, AP, NH 4 + , NO 3 - , OM, TN, and TP (P < 0.05). However, they led to a remarkable decrease in pH (P < 0.05). Such changes lowered the Shannon diversity of the soil and rhizome root microbiota but did not significantly affect the community composition and functional capacity. Soil bacterial community variation was predominantly mediated by soil total potassium (TK) (15.02%), followed by pH (11.29%) and AK (11.13%). We further observed that Nitrospirae accounted for approximately 50% of the variation in soil pH, NO 3 - , NH 4 + , and AK, indicating its importance in soil nutrient cycling, especially nitrogen cycling. Accordingly, we propose that the management-induced changes in soil parameters reshaped the bacterial community structure and keystone bacterial assemblage, leading to the differentiation of microbial functions.

Complete Chloroplast Genome Features of Dendrocalamusfarinosus and Its Comparison and Evolutionary Analysis with Other Bambusoideae Species.

Dendrocalamus farinosus is one of the essential bamboo species mainly used for food and timber in the southwestern region of China. In this study, the complete chloroplast (cp) genome of D. farinosus is sequenced, assembled, and the phylogenetic relationship analyzed. The cp genome has a circular and quadripartite structure, has a total length of 139,499 bp and contains 132 genes: 89 protein-coding genes, eight rRNAs and 35 tRNAs. The repeat analyses showed that three types of repeats (palindromic, forward and reverse) are present in the genome. A total of 51 simple sequence repeats are identified in the cp genome. The comparative analysis between different species belonging to Dendrocalamus revealed that although the cp genomes are conserved, many differences exist between the genomes. The analysis shows that the non-coding regions were more divergent than the coding regions, and the inverted repeat regions are more conserved than the single-copy regions. Moreover, these results also indicate that rpoC2 may be used to distinguish between different bamboo species. Phylogenetic analysis results supported that D. farinosus was closely related to D. latiflorus. Furthermore, these bamboo species' geographical distribution and rhizome types indicate two evolutionary pathways: one is from the tropics to the alpine zone, and the other is from the tropics to the warm temperate zone. Our study will be helpful in the determination of the cp genome sequences of D. farinosus, and provides new molecular data to understand the Bambusoideae evolution.

Integrative transcriptomic and metabolomic data provide insights into gene networks associated with lignification in postharvest Lei bamboo shoots under low temperature.

Lei bamboo (Phyllostachys violascens) shoots are delicious food in Asia. Here, the molecular basis of lignification in postharvest Lei bamboo shoots under low temperature (LT) is revealed by transcriptomic and metabolomics analyses for the first time. We identified substantial accumulations of jasmonates (JAs) and major lignin biosynthesis precursors (coumarin, trans-4-coumaric acid, trans-ferulic acid and L-phenylalanine). Transcriptome analysis indicated that some regulatory genes were significantly differentially expressed, and the expression patterns of them were highly consistent with the changes in the key lignin precursors or JA profiles. Co-expression analysis showed that the LT responsive genes PvCRPK-4/-5, PvICE2-1/2, PvDREB2B might form a network module with the lignin (PvC3H-2/3, PvC4H-2/4, PvCAD-1/2/3/4, etc.) or JA biosynthesis genes (PvOPR2, PvJAZ-4 and PvPEX5, etc.), indicating a LT-lignification or LT-JA-lignification regulatory pathway in Lei bamboo shoots. Above all, our findings provide new an insight into the LT-associated lignification in postharvest bamboo shoots.