Search

Background: LncRNAs are extensively involved in plant biological processes. However, the lack of a comprehensive lncRNA landscape in moso bamboo has hindered the molecular study of lncRNAs. Moreover, the role of lncRNAs in secondary cell wall (SCW) biosynthesis of moso bamboo is elusive. Results: For comprehensively identifying lncRNA throughout moso bamboo genome, we collected 231 RNA-Seq datasets, 1 Iso-Seq dataset, and 1 full-length cDNA dataset. We used a machine learning approach to improve the pipeline of lncRNA identification and functional annotation based on previous studies and identified 37,009 lncRNAs in moso bamboo. Then, we established a network of potential lncRNA-coding gene for SCW biosynthesis and identified SCW-related lncRNAs. We also proposed that a mechanism exists in bamboo to direct phenylpropanoid intermediates to lignin or flavonoids biosynthesis through the PAL/4CL/C4H genes. In addition, we identified 4 flavonoids and 1 lignin-preferred genes in the PAL/4CL/C4H gene families, which gained implications in molecular breeding. Conclusions: We provided a comprehensive landscape of lncRNAs in moso bamboo. Through analyses, we identified SCW-related lncRNAs and improved our understanding of lignin and flavonoids biosynthesis. [ABSTRACT FROM AUTHOR]

Background: The subfamily Bambusoideae belongs to the grass family Poaceae and has significant roles in culture, economy, and ecology. However, the phylogenetic relationships based on large-scale chloroplast genomes (CpGenomes) were elusive. Moreover, most of the chloroplast DNA sequencing methods cannot meet the requirements of large-scale CpGenome sequencing, which greatly limits and impedes the in-depth research of plant genetics and evolution. Results: To develop a set of bamboo probes, we used 99 high-quality CpGenomes with 6 bamboo CpGenomes as representative species for the probe design, and assembled 15 M unique sequences as the final pan-chloroplast genome. A total of 180,519 probes for chloroplast DNA fragments were designed and synthesized by a novel hybridization-based targeted enrichment approach. Another 468 CpGenomes were selected as test data to verify the quality of the newly synthesized probes and the efficiency of the probes for chloroplast capture. We then successfully applied the probes to synthesize, enrich, and assemble 358 non-redundant CpGenomes of woody bamboo in China. Evaluation analysis showed the probes may be applicable to chloroplasts in Magnoliales, Pinales, Poales et al. Moreover, we reconstructed a phylogenetic tree of 412 bamboos (358 in-house and 54 published), supporting a non-monophyletic lineage of the genus Phyllostachys. Additionally, we shared our data by uploading a dataset of bamboo CpGenome into CNGB (https://db.cngb.org/search/project/CNP0000502/) to enrich resources and promote the development of bamboo phylogenetics. Conclusions: The development of the CpGenome enrichment pipeline and its performance on bamboos recommended an inexpensive, high-throughput, time-saving and efficient CpGenome sequencing strategy, which can be applied to facilitate the phylogenetics analysis of most green plants. [ABSTRACT FROM AUTHOR]

A underwater wireless optical communication (UWOC) system using a multi-pixel photon counter (MPPC) as the receiver and orthogonal frequency division multiplexing (OFDM) was proposed and experimentally investigated. The MPPC with high sensitivity combined with quadrature amplitude modulation (QAM) OFDM with high spectral efficiency can potentially support a data rate of hundreds of Mbps under a relatively long underwater transmission distance. Although the photoelectric response of each individual pixel in the MPPC is nonlinear due to its intrinsic dead time, the MPPC consisting of thousands of pixels can be operated like a linear photodetector due to the statistical effect. A net data rate of 312.03 Mbps, with a bit error rate (BER) below the forward error correction (FEC) limit, was successfully achieved over a 21-m underwater channel exploiting 32-QAM OFDM modulation. [ABSTRACT FROM AUTHOR]

Abstract Presently, most of the long-reach underwater wireless optical communication (UWOC) systems employ laser diodes rather than light-emitting diodes (LEDs) as the transmitters. Due to lasers' smaller divergence angles, those UWOC systems could realize longer communication links. Although LED-based long-reach UWOC has distinguished advantages, it suffers from very low received optical power. Fortunately, highly sensitive multi-pixel photon counter (MPPC) and energy efficient pulse position modulation (PPM) pave a way towards LED-based long-reach UWOC. In this paper, we investigated the underlying working principle of an MPPC and proposed a UWOC system based on single LED as well as a lens-free MPPC with digital output. The relationship between the MPPC p.e. threshold and its received optical power was theoretically studied and further proved by experimental results. Single 2.3-MHz, 3-W blue LED was used as the transmitter to generate 8-PPM to 64-PPM signals with a 5-MHz slot frequency. After a 46-m underwater transmission, the measured BERs were all below the forward error correction (FEC) limit, which were achieved with less than 100 incident photons during each pulse slot. [ABSTRACT FROM AUTHOR]

Background: Recently, the conversion therapies of FOLFOX-HAIC for patients with unresectable hepatocellular carcinoma (uHCC) have dramatically increased the tumor responses and conversion rate; thus, the prognosis of uHCC patients was expected to be prolonged. However, the postoperative recurrence of uHCC patients who successfully underwent conversion therapies stayed high. The present study evaluated the efficacy and safety of postoperatively adjuvant therapy in treating uHCC patients who received FOLFOX-HAIC-based conversion therapy. Methods: In this real-world retrospective study, uHCC patients who received FOLFOX-HAIC-based conversion therapy were included. The recurrence-free survival (RFS), as primary outcomes, was compared between patients who received adjuvant therapy (AT group) or non-adjuvant therapy (nAT group) using survival analysis and Cox regression. Imbalances in baseline clinical features between the two groups were adjusted through propensity score matching (PSM) and inverse probability of treatment weighting (IPTW). Results: Between January 2016 and December 2022, 204 uHCC patients who received FOLFOX-HAIC-based conversion therapy were included and assigned into AT group (n = 47) and nAT group (n = 157), respectively. The median RFS was significantly longer in the AT group than the nAT group before adjustment [19.2 vs. 10.8 months; hazard ratio (HR), 0.584; 95% CI, 0.383–0.892; P = 0.028], after PSM and after IPTW. Subsequent subgroup analyses revealed the RFS of adjuvant therapy was best in uHCC patients with younger than 60 years, macrovascular invasion, and positive hepatitis B surface antigen. Conclusion: Postoperatively, adjuvant therapy was associated with improved survival outcomes compared with non-adjuvant therapy after FOLFOX-HAIC-based conversion therapy among uHCC patients, especially for patients with macrovascular invasion and positive hepatitis B surface antigen. [ABSTRACT FROM AUTHOR]

Background: Pyroptosis is closely associated with chemotherapeutic drugs and immune response. Here, we investigated whether oxaliplatin, a key drug in FOLFOX-hepatic artery infusion chemotherapy (FOLFOX-HAIC), induces pyroptosis in hepatoma cells and enhances antitumor immunity after tumor cell death. Methods: Hepatoma cells were treated with oxaliplatin. Pyroptosis and immunoreactivity were evaluated in vitro and in vivo. Results: Oxaliplatin activated caspase-3-mediated gasdermin E (GSDME) cleavage and induced pyroptosis in Hep G2 and SK-Hep-1 cells in vitro. Liver cancer cells with high levels of GSDME expression are prone to pyroptosis. Bioinformatic analysis revealed that pyrolysis-related genes are closely related to immunity. In vivo experiments revealed that oxaliplatin exhibited superior antitumor efficacy in mice with normal immune function and more pronounced inhibitory effect on hepatocellular carcinoma with high GSDME levels. Higher levels of cytokines and greater CD8+ T cell infiltration were observed in tumor tissues with better efficacy. Furthermore, an in vitro coculture assay confirmed that oxaliplatin-induced pyroptosis in Hep G2 cells overexpressing GSDME and activated the p38/MAPK signaling pathway to improve the cytotoxicity of CD8+ T cells. Analysis of clinical samples of HCC suggested that the efficacy of FOLFOX-HAIC in patients with high GSDME expression was better than that in patients with low GSDME expression. Conclusions: Oxaliplatin induced pyroptosis in hepatoma cells by activating caspase-3-mediated cleavage of GSDME, which enhanced the cytotoxicity of CD8+ T cells by regulating the p38/MAPK signaling pathway. These results suggest that GSDME level may be used as a marker to predict the efficacy of FOLFOX-HAIC. [ABSTRACT FROM AUTHOR]

Background: The rattan is a valuable plant resource with multiple applications in tropical forests. Calamus simplicifolius and Daemonorops jenkinsiana are the two most representative rattan species, supplying over 95% of the raw materials for the rattan industry. Hence, the wood properties of both rattans have always attracted researchers' attention. Results: We re-annotated the genomes, obtained 81 RNA-Seq datasets, and developed an improved pipeline to increase the reliability of co-expression networks of both rattans. Based on the data and pipeline, co-expression relationships were detected in 11 NACs, 49 MYBs, and 86 lignin biosynthesis genes in C. simplicifolius and four NACs, 59 MYBs, and 76 lignin biosynthesis genes in D. jenkinsiana, respectively. Among these co-expression pairs, several genes had a close relationship to the development of wood properties. Additionally, we detected the enzyme gene on the lignin biosynthesis pathway was regulated by either NAC or MYB, while LACCASES was regulated by both NAC and MYB. For D. jenkinsiana, the lignin biosynthesis regulatory network was characterized by positive regulation, and MYB possible negatively regulate non-expressed lignin biosynthesis genes in stem tissues. For C. simplicifolius, NAC may positively regulate highly expressed genes and negatively regulate non-expressed lignin biosynthesis genes in stem tissues. Furthermore, we established core regulatory networks of NAC and MYB for both rattans. Conclusions: This work improved the accuracy of rattan gene annotation by integrating an efficient co-expression network analysis pipeline, enhancing gene coverage and accuracy of the constructed network, and facilitating an understanding of co-expression relationships among NAC, MYB, and lignin biosynthesis genes in rattan and other plants. [ABSTRACT FROM AUTHOR]

Background: Xylan is one of the most abundant hemicelluloses and can crosslink cellulose and lignin to increase the stability of cell walls. A number of genes encoding glycosyltransferases play vital roles in xylan biosynthesis in plants, such as those of the GT43 family. However, little is known about glycosyltransferases in bamboo, especially woody bamboo which is a good substitute for timber. Results: A total of 17 GT43 genes (PeGT43–1 ~ PeGT43–17) were identified in the genome of moso bamboo (Phyllostachys edulis), which belong to three subfamilies with specific motifs. The phylogenetic and collinearity analyses showed that PeGT43s may have undergone gene duplication, as a result of collinearity found in 12 pairs of PeGT43s, and between 17 PeGT43s and 10 OsGT43s. A set of cis-acting elements such as hormones, abiotic stress response and MYB binding elements were found in the promoter of PeGT43s. PeGT43s were expressed differently in 26 tissues, among which the highest expression level was found in the shoots, especially in the rapid elongation zone and nodes. The genes coexpressed with PeGT43s were annotated as associated with polysaccharide metabolism and cell wall biosynthesis. qRT–PCR results showed that the coexpressed genes had similar expression patterns with a significant increase in 4.0 m shoots and a peak in 6.0 m shoots during fast growth. In addition, the xylan content and structural polysaccharide staining intensity in bamboo shoots showed a strong positive correlation with the expression of PeGT43s. Yeast one-hybrid assays demonstrated that PeMYB35 could recognize the 5′ UTR/promoter of PeGT43–5 by binding to the SMRE cis-elements. Conclusions: PeGT43s were found to be adapted to the requirement of xylan biosynthesis during rapid cell elongation and cell wall accumulation, as evidenced by the expression profile of PeGT43s and the rate of xylan accumulation in bamboo shoots. Yeast one-hybrid analysis suggested that PeMYB35 might be involved in xylan biosynthesis by regulating the expression of PeGT43–5 by binding to its 5′ UTR/promoter. Our study provides a comprehensive understanding of PeGT43s in moso bamboo and lays a foundation for further functional analysis of PeGT43s for xylan biosynthesis during rapid growth. [ABSTRACT FROM AUTHOR]

Moso bamboo (Phyllostachys edulis) is a valuable nontimber forestry product with a biennial cycle, producing abundant bamboo shoots within one year (on-year) and few shoots within the following year (off-year). Moso bamboo plants undergo clonal reproduction, resulting in similar genetic backgrounds. However, the number of moso bamboo shoots produced each year varies. Despite this variation, the impact of soil nutrients and the root microbiome on the biennial bearing of moso bamboo is poorly understood. We collected 139 soil samples and determined 14 major physicochemical properties of the rhizosphere, rhizoplane, and bulk soil in different seasons (i.e., the growing and deciduous seasons) and different years (i.e., on- and off-years). Based on 16S rRNA and metagenomic sequencing, major variations were found in the rhizospheric microbial composition during different seasons and years in the moso bamboo forest. Environmental driver analysis revealed that essential nutrients (i.e., SOC, TOC, TN, P, and NH 4 +) were the main drivers of the soil microbial community composition and were correlated with the on- and off-year cycles. Moreover, 19 MAGs were identified as important biomarkers that could distinguish on- and off-years. We found that both season and year influenced both the microbial community structure and functional pathways through the biosynthesis of nutrients that potentially interact with the moso bamboo growth rhythm, especially the on-year root-associated microbiome, which had a greater abundance of specific nutrients such as gibberellins and vitamin B 6. This work provides a dynamic perspective of the differential responses of various on- and off-year microbial communities and enhances our understanding of bamboo soil microbiome biodiversity and stability. [Display omitted] • There are dynamic changes in the microbial community composition of the biennial bearing of moso bamboo in different seasons. • Essential nutrients (SOC, TOC, TN, P, and NH 4 +) were identified as the primary drivers of soil microbial community composition, correlating with on- and off-year cycles. • The major differential species Dormibacterota abundance in on- and off-year is driven by nutrients and is the central species in the microbial co-occurrence networks. • The metabolic function of Dormibacterota provides insights to explain the biennial bearing of moso bamboo. [ABSTRACT FROM AUTHOR]

Background Calamus simplicifolius and Daemonorops jenkinsiana are two representative rattans, the most significant material sources for the rattan industry. However, the lack of reference genome sequences is a major obstacle for basic and applied biology on rattan. Findings We produced two chromosome-level genome assemblies of C. simplicifolius and D. jenkinsiana using Illumina, Pacific Biosciences, and Hi-C sequencing data. A total of ∼730 Gb and ∼682 Gb of raw data covered the predicted genome lengths (∼1.98 Gb of C. simplicifolius and ∼1.61 Gb of D. jenkinsiana) to ∼372 × and ∼426 × read depths, respectively. The two de novo genome assemblies, ∼1.94 Gb and ∼1.58 Gb, were generated with scaffold N50s of ∼160 Mb and ∼119 Mb in C. simplicifolius and D. jenkinsiana, respectively. The C. simplicifolius and D. jenkinsiana genomes were predicted to harbor  51,235 and  53,342 intact protein-coding gene models, respectively. Benchmarking Universal Single-Copy Orthologs evaluation demonstrated that genome completeness reached 96.4% and 91.3% in the C. simplicifolius and D. jenkinsiana genomes, respectively. Genome evolution showed that four Arecaceae plants clustered together, and the divergence time between the two rattans was ∼19.3 million years ago. Additionally, we identified 193 and 172 genes involved in the lignin biosynthesis pathway in the C. simplicifolius and D. jenkinsiana genomes, respectively. Conclusions We present the first de novo assemblies of two rattan genomes (C. simplicifolius and D. jenkinsiana). These data will not only provide a fundamental resource for functional genomics, particularly in promoting germplasm utilization for breeding, but also serve as reference genomes for comparative studies between and among different species. [ABSTRACT FROM AUTHOR]

Background Bamboo is one of the most important nontimber forestry products worldwide. However, a chromosome-level reference genome is lacking, and an evolutionary view of alternative splicing (AS) in bamboo remains unclear despite emerging omics data and improved technologies. Results Here, we provide a chromosome-level de novo genome assembly of moso bamboo (Phyllostachys edulis) using additional abundance sequencing data and a Hi-C scaffolding strategy. The significantly improved genome is a scaffold N50 of 79.90 Mb, approximately 243 times longer than the previous version. A total of 51,074 high-quality protein-coding loci with intact structures were identified using single-molecule real-time sequencing and manual verification. Moreover, we provide a comprehensive AS profile based on the identification of 266,711 unique AS events in 25,225 AS genes by large-scale transcriptomic sequencing of 26 representative bamboo tissues using both the Illumina and Pacific Biosciences sequencing platforms. Through comparisons with orthologous genes in related plant species, we observed that the AS genes are concentrated among more conserved genes that tend to accumulate higher transcript levels and share less tissue specificity. Furthermore, gene family expansion, abundant AS, and positive selection were identified in crucial genes involved in the lignin biosynthetic pathway of moso bamboo. Conclusions These fundamental studies provide useful information for future in-depth analyses of comparative genome and AS features. Additionally, our results highlight a global perspective of AS during evolution and diversification in bamboo. [ABSTRACT FROM AUTHOR]