BackgroundBamboo 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.ResultsHere, 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.ConclusionsThese 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.

SUMMARY The recent discovery of the positive-sense ssRNA Orsay virus (OV) as a natural pathogen of the nematode, Caenorhabditis elegans, has stimulated interest in exploring virus-nematode interactions. However, OV infection is restricted to a small number of intestinal cells, even in nematodes defective in their antiviral RNA interference (RNAi) response, and is neither lethal nor vertically transmitted. Using a fluorescent reporter strain of the negative-sense ssRNA vesicular stomatitis virus (VSV), we show that microinjection of VSV particles leads to a dose-dependent, muscle tissue-tropic, lethal infection in C. elegans. Furthermore, we find nematodes deficient for components of the antiviral RNAi pathway, such as Dicer-related helicase 1 (DRH-1), to display hypersusceptibility to VSV infection as evidenced by elevated infection rates, virus replication in multiple tissue types, and earlier mortality. Strikingly, infection of oocytes and embryos could also be observed in drh-1 mutants. Our results suggest that the antiviral RNAi response not only inhibits vertical VSV transmission but also promotes transgenerational inheritance of antiviral immunity. Our study introduces a new, in vivo virus-host model system for exploring arbovirus pathogenesis and provides the first evidence for vertical pathogen transmission in C. elegans.

Aquaporins (AQPs) are known to play a major role in maintaining water and hydraulic conductivity balance in the plant system. Numerous studies have showed AQPs execute multi-function throughout plant growth and development, including water transport, nitrogen, carbon, and micronutrient acquisition etc. However, little information on AQPs is known in bamboo. In this study, we present the first genome-wide identification and characterization of AQP genes in moso bamboo (Phyllostachys edulis) using bioinformatics. In total, 26 AQP genes were identified by homologous analysis, which were divided into four groups (PIPs, TIPs, NIPs, and SIPs) based on the phylogenetic analysis. All the genes were located on 26 different scaffolds respectively on basis of the gene mapped to bamboo genome. Evolutionary analysis indicated that Ph. edulis was more close to Oryza sativa than Zea mays in the genetic relationship. Besides, qRT-PCR was used to analyze gene expression profiles, which revealed that AQP genes were expressed constitutively in all the detected tissues, and were all responsive to the environmental cues such as drought, water, and NaCl stresses. This data suggested that AQPs may play fundamental roles in maintaining normal growth and development of bamboo, which would contribute to better understanding for the complex regulation mechanism involved in the fast-growing process of bamboo. Furthermore, the result could provide valuable information for further research on bamboo functional genomics.

Supporting InformationThe Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.analchem.9b04505. Detailed experimental procedures for Western blot, bisulfite sequencing, Northern blot, structure-based docking, and electrophoretic mobility shift assay; LC-MS/MS quantification data; and Western blot images (PDF) A list of proteins with relative binding ratios toward m 5 C-over C-containing RNA identified from SILAC-based affinity screening experiments with the use of lysate of HeLa cells (XLSX) A list of proteins with relative binding ratios toward m 5 C-over C-containing RNA identified from SILAC-based affinity screening experiments with the use of lysate of HEK293T cells (XLSX) A list of m 5 C sites in HEK293T cells and the isogenic YTHDF2 knockout cells, as obtained from bisulfite sequencing analysis (XLSX) A list of m 5 C sites that are commonly identified from the current bisulfite sequencing experiment and from previously published miCLIP analysis (XLSX)

BackgroundPhotosynthesis plays a vital role as an energy source for plant metabolism, and its efficiency may be drastically reduced owing to abiotic stresses. Moso bamboo (Phyllostachys edulis), is a renewable and versatile resource with significant ecological and economic value, which encounters high light stress with large amplitude in natural environment. However, the gene expression profiles in response to high light were elusive in bamboo.ResultsWe firstly performed physiological experiments on moso bamboo leaves treated with high light (1200 μmol · m−2 · s−1). Based on the physiological results, three samples of leaves treated with high light for 0 h (CK), 0.5 h (0.5H), and 8 h (8H) were selected to perform further high-throughput RNA sequencing (RNA-Seq), respectively. Then, the transcriptomic result demonstrated that the most genes were expressed at a statistically significant value (FPKM ≥ 1) and the RNA-Seq data were validated via quantitative real time PCR. Moreover, some significant gene expression changes were detected. For instance, 154 differentially expressed genes were detected in 0.5H vs. CK, those in 8H vs. CK were 710, and 429 differentially expressed genes were also identified in 0.5H vs.8 H. Besides, 47 gene annotations closely related to photosynthesis were refined, including 35 genes annotated as light-harvesting chlorophyll a/b-binding (LHC) proteins, 9 LHC-like proteins and 3 PsbSs. Furthermore, the pathway of reactive oxygen species (ROS) in photosynthesis was further analyzed. A total of 171 genes associated with ROS-scavenging were identified. Some up-regulated transcript factors, such as NAC, WRKY, AR2/ERF, and bHLH, mainly concentrated in short-term response, while C2H2, HSF, bZIP, and MYB were largely involved in short and middle terms response to high light.ConclusionBased on the gene expression analysis of moso bamboo in response to high light, we thus identified the global gene expression patterns, refined the annotations of LHC protein, LHC-like protein and PsbS, detected the pathway of ROS as well as identified ROS-scavenging genes and transcription factors in the regulation of photosynthetic and related metabolisms. These findings maybe provide a starting point to interpret the molecular mechanism of photosynthesis in moso bamboo under high light stress.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0720-9) contains supplementary material, which is available to authorized users.

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PeTIP4;1-1, an aquaporin gene involved in bamboo shoot growth, is regulated by abiotic stresses. Overexpression of PeTIP4;1-1 confers drought and salinity tolerance in transgenic Arabidopsis. Aquaporins play a central role in numerous physiological processes throughout plant growth and development. PeTIP4;1-1, an aquaporin gene isolated from moso bamboo (Phyllostachys edulis), comprises an open reading frame (ORF) of 756 bp encoding a peptide of 251 amino acids. The genomic sequence corresponding to the ORF of PeTIP4;1-1 was 1777 bp and contained three exons separated by two introns. PeTIP4;1-1 was constitutively expressed at the highest level in culms, and the expression level was elevated with increasing height of the bamboo shoot. PeTIP4;1-1 was significantly up-regulated in response to drought and salinity stresses in bamboo roots and leaves. To investigate the role of PeTIP4;1-1 in response to drought and salinity stresses, transgenic Arabidopsis plants overexpressing PeTIP4;1-1 under the control of CaMV 35S promoter were generated and subjected to morphological and physiological assays. Compared with Col-0, the transgenic plants showed enhanced tolerance to drought and salinity stresses and produced longer taproots, which had more green leaves, higher F /F and NPQ values, higher activities of SOD, POD and CAT, lower MDA concentration and higher water content. Transcript levels of three stress-related genes (AtP5CS, AtNHX1 and AtLEA) were enhanced. These results indicated that PeTIP4;1-1 might play an important function in response to drought and salinity stresses, and is a candidate gene for breeding of stress tolerance in other crops through genetic engineering.

As an important member in homologous recombination repair, RAD52 plays a crucial part in maintaining genomic stability and prevent carcinogenesis. Several cancer susceptibility RAD52 single nucleotide polymorphisms (SNPs) have been identified previously. However, little or nothing has been known about the RAD52 SNPs and their functional significance in hepatitis B viruses (HBV)-related hepatocellular carcinoma (HCC). Therefore, we investigated the association between five RAD52 SNPs (rs1051669, rs10774474, rs11571378, rs7963551, and rs6489769) and HBV-related HCC risk as well as its biological function in vivo. Genotypes were determined in two independent case-control sets from two regions of China. Odds ratios (ORs) and 95% confidence intervals (CIs) were estimated by logistic regression. The allele-specific regulation on RAD52 expression by the functional genetic variant was examined with normal liver tissues. We found that only the RAD52 rs7963551 SNP was significantly associated with HCC risk, with the odds of having the rs7963551 CC genotype in patients was 0.59 (95% CI = 0.45-0.78, P = 1.5 × 10(-4), HCC cases versus chronic HBV carriers) or 0.65 (95% CI = 0.52-0.81, P = 1.1 × 10(-4), HCC cases versus healthy controls) compared with the AA genotype. In the genotype-phenotype correlation analyses of 44 human liver tissue samples, rs7963551 CC or AC was associated with a statistically significant increase of RAD52 mRNA expression, which are consistent to functional relevance of allelic regulation of RAD52 expression by rs7963551 SNP and miRNA let-7 in cancer cells. Our data demonstrated that RAD52 functional rs7963551 SNP contributes to susceptibility to developing HCC.