Comprehensive profiling of epigenetic modifications in fast-growing Moso bamboo shoots

Comparative analysis of different Phyllostachys species on gut microbiome and fecal metabolome in giant pandas (Ailuropoda melanoleuca)

The influences of different bamboo species on the microbiome and metabolome of giant pandas (Ailuropoda melanoleuca) remain understudied. The aim of this study was to investigate the effects of different Phyllostachys species on the gut microbial communities and fecal metabolite profiles in giant pandas. Metagenome and metabolome were performed on the feces of giant pandas fed with different Phyllostachys species (P. edulis, P. iridescens, P. glauca, and P. violascens). The results of metagenome showed that dietary with P. glauca could notably decrease the microbial Shannon index. The relative abundances of both Cellulosilyticum and Pseudomonas were enhanced after dietary with P. iridescens, suggesting P. iridescens could enhance the cellulose-degrading function in giant pandas. However, dietary with P. glauca or P. violascens could increase the relative abundances of certain pathogenic bacteria (Escherichia, Shigella, and Klebsiella). Metabolomics analysis further revealed that all experimental groups exhibited notably elevated levels of fecal flavonoids and fatty acids. In addition, the correlation analysis showed that certain nutrients of bamboo leaves (mainly crude protein and Cu) were significantly correlated with several differential gut bacteria and fecal metabolites. Based on the present results, P. iridescens might be a substitute for the routinely used Phyllostachys species (P. edulis) in the captive management of giant pandas. The results have revealed that bamboo species is an important factor affecting the gut microbiota and fecal metabolites in giant pandas. Our results could provide important information about bamboo species-induced alterations on the microbiome and metabolome in giant pandas.

Advances in bamboo genomics: Growth and development, stress tolerance, and genetic engineering

Bamboo is a fast-growing and ecologically significant plant with immense economic value due to its applications in construction, textiles, and bioenergy. However, research on bamboo has been hindered by its long vegetative period, unpredictable flowering cycles, and challenges in genetic transformation. Recent developments in advanced sequencing and genetic engineering technologies have provided new insights into bamboo's evolutionary history, developmental biology, and stress resilience, paving the way for improved conservation and sustainable utilization. This review synthesizes the latest findings on bamboo's genomics, biotechnology, and the molecular mechanisms governing its growth, development, and stress response. Key genes and regulatory pathways controlling its rapid growth, internode elongation, rhizome development, culm lignification, flowering, and abiotic stress responses have been identified through multi-omics and functional studies. Complex interactions among transcription factors, epigenetic regulators, and functionally important genes shape bamboo's unique growth characteristics. Moreover, progress in genetic engineering techniques, including clustered regularly interspaced short palindromic repeats-based genome editing, has opened new avenues for targeted genetic improvements. However, technical challenges, particularly the complexity of polyploid bamboo genomes and inefficient regeneration systems, remain significant barriers to functional studies and large-scale breeding efforts. By integrating recent genomic discoveries with advancements in biotechnology, this review proposes potential strategies to overcome existing technological limitations and to accelerate the development of improved bamboo varieties. Continued efforts in multi-omics research, gene-editing applications, and sustainable cultivation practices will be essential for harnessing bamboo as a resilient and renewable resource for the future. The review presented here not only deepens our understanding of bamboo's genetic architecture but also provides a foundation for future research aimed at optimizing its ecological and industrial potential.

Mitochondrial Energy Homeostasis and Membrane Interaction Regulate the Rapid Growth of Moso Bamboo

The rapid growth of moso bamboo is primarily attributed to the swift elongation of its internodes. While mitochondria are known to provide energy for various cellular processes, the specific mechanisms by which they facilitate rapid growth in bamboo remain elusive. In this study, we optimised the procedures for mitochondria isolation and performed a comprehensive analysis of mitochondrial dynamics and proteomics from internodes at various growth stages, including the initial growth (IG) stage, the starting of cell division (SD), and the rapid elongation (RE). Confocal observation demonstrated that cells in the RE stage have a higher mitochondrial density and increased mitochondrial motility compared to other stages. Proteomic analysis of isolated mitochondria revealed an upregulation of the tricarboxylic acid cycle, along with a synchronous increase in both mitochondrial- and nuclear-encoded components of oxidative phosphorylation in RE cells. Moreover, the upregulation of various mitochondrial membrane transporters in RE cells suggests an enhanced exchange of metabolic intermediates and inorganic ions with the cytosol. Intriguingly, ultrastructural analysis and pharmacological treatments revealed membrane interactions between the endoplasmic reticulum (ER) and mitochondria in RE cells. In conclusion, our study provides novel insights into mitochondrial function and the intracellular dynamics that regulate the rapid growth of moso bamboo.

The relationship between growth, anatomical structure, and quality in different parts and stages of edible bamboo shoots of Dendrocalamus latiflorus

BACKGROUND

Dendrocalamus latiflorus is widely distributed in southern China and has high ornamental and edible value. The growth dynamics and the associations between growth and the distribution of nutrients or chemical components across various parts and stages of shoot development remain inadequately understood. In this study, tender shoots of D. latiflorus from Guangxi, China, were used to conduct experiments. During the edible growth period, the height, ground diameter, and morphology of the tender shoots were investigated, and the growth stages were classified by conducting ordered sample cluster analysis. The internal internode anatomy and nutritional/chemical components of the tender shoots at different growth stages and parts were measured and analyzed. The optimal harvesting stages and parts were determined by conducting a comprehensive analysis using the technique for order preference by similarity to the ideal solution (TOPSIS).

RESULTS

The height growth of D. latiflorus tender shoots lasted for 21 days and can be divided into four stages: I (0-9 d), II (10-13 d), III (14-17 d), and IV (18-21 d), while thickening growth lasted about 19 days. The moisture content of D. latiflorus tender shoots decreased as growth increased. Cell division and elongation increased the height of tender shoots. Among the four stages, cell division dominated in Stages I and II, whereas cell elongation dominated in Stages III and IV. The changes in nutrients and chemical components in different parts and stages of tender shoot development have distinct characteristics, and the differences are significant. The starch and reducing sugar contents reached a maximum value in the lower part of Stage II (10.19 mg·g-1, 18.87 mg·g-1), whereas the soluble sugar content reached a maximum value in the middle of Stage III (2.15 mg·g-1). The protein and fat contents were the highest in the upper part of Stage IV (3.84% and 4.8%). The contents of the chemical components of flavonoids and vitamin C were the highest in the middle of Stage IV (5.51 mg·g-1, 33.58 mg·100 g-1), whereas the contents of cellulose and lignin in the later part of Stage IV were the highest (9.43% and 13.67%, respectively). Stage II (10-13 d) was the best harvest stage for D. latiflorus tender shoots, according to the comprehensive TOPSIS analysis, and the comprehensive quality of the upper part was the best in this stage. Additionally, the middle part of Stage III and the lower part of Stage IV were also high quality and could also be harvested.

CONCLUSIONS

This study revealed the growth patterns of the tender shoots of D. latiflorus from morphological, anatomical, and physiological perspectives, as well as the dynamic changes in nutrient content during their growth. Within the 21-day edible stage, Stage II (10-13 days) was identified as the optimal harvesting stage, with the upper part of the shoot being the best section for harvest. This study provided a theoretical basis for further cultivating high-quality D. latiflorus for shoot production and has significant potential for increasing economic benefits.

Subgenome asymmetry of gibberellins-related genes plays important roles in regulating rapid growth of bamboos

Rapid growth is an innovative trait of woody bamboos that has been widely studied. However, the genetic basis and evolution of this trait are poorly understood. Taking advantage of genomic resources of 11 representative bamboos at different ploidal levels, we integrated morphological, physiological, and transcriptomic datasets to investigate rapid growth. In particular, these bamboos include two large-sized and a small-sized woody species, compared with a diploid herbaceous species. Our results showed that gibberellin A1 was important for the rapid shoot growth of the world's largest bamboo, Dendrocalamus sinicus, and indicated that two gibberellins (GAs)-related genes, KAO and SLRL1, were key to the rapid shoot growth and culm size in woody bamboos. The expression of GAs-related genes exhibited significant subgenome asymmetry with subgenomes A and C demonstrating expression dominance in the large-sized woody bamboos while the generally submissive subgenomes B and D dominating in the small-sized species. The subgenome asymmetry was found to be correlated with the subgenome-specific gene structure, particularly UTRs and core promoters. Our study provides novel insights into the molecular mechanism and evolution of rapid shoot growth following allopolyploidization in woody bamboos, particularly via subgenome asymmetry. These findings are helpful for understanding of how polyploidization in general and subgenome asymmetry in particular contributed to the origin of innovative traits in plants.

Direct RNA sequencing in plants: Practical applications and future perspectives

The transcriptome serves as a bridge that links genomic variation to phenotypic diversity. A vast number of studies using next-generation RNA sequencing (RNA-seq) over the last 2 decades have emphasized the essential roles of the plant transcriptome in response to developmental and environmental conditions, providing numerous insights into the dynamic changes, evolutionary traces, and elaborate regulation of the plant transcriptome. With substantial improvement in accuracy and throughput, direct RNA sequencing (DRS) has emerged as a new and powerful sequencing platform for precise detection of native and full-length transcripts, overcoming many limitations such as read length and PCR bias that are inherent to short-read RNA-seq. Here, we review recent advances in dissecting the complexity and diversity of plant transcriptomes using DRS as the main technological approach, covering many aspects of RNA metabolism, including novel isoforms, poly(A) tails, and RNA modification, and we propose a comprehensive workflow for processing of plant DRS data. Many challenges to the application of DRS in plants, such as the need for machine learning tools tailored to plant transcriptomes, remain to be overcome, and together we outline future biological questions that can be addressed by DRS, such as allele-specific RNA modification. This technology provides convenient support on which the connection of distinct RNA features is tightly built, sustainably refining our understanding of the biological functions of the plant transcriptome.

Evolution and post-transcriptional regulation insights of m6A writers, erasers, and readers in plant epitranscriptome

As a dynamic and reversible post-transcriptional marker, N6-methyladenosine (m6A) plays an important role in the regulation of biological functions, which are mediated by m6A pathway components including writers (MT-A70, FIP37, VIR and HAKAI family), erasers (ALKBH family) and readers (YTH family). There is an urgent need for a comprehensive analysis of m6A pathway components across species at evolutionary levels. In this study, we identified 4062 m6A pathway components from 154 plant species including green algae, utilizing large-scale phylogenetic to explore their origin and evolution. We discovered that the copy number of writers was conserved among different plant lineages, with notable expansions in the ALKBH and YTH families. Synteny network analysis revealed conserved genomic contexts and lineage-specific transpositions. Furthermore, we used Direct RNA Sequencing (DRS) to reveal the Poly(A) length (PAL) and m6A ratio profiles in six angiosperms species, with a particular focus on the m6A pathway components. The ECT1/2-Poeaece4 sub-branches (YTH family) with unique genomic contexts exhibited significantly higher expression level than genes of other ECT1/2 poeaece sub-branches (ECT1/2-Poeaece1-3), accompanied by lower m6A modification and PAL. Besides, conserved m6A sites distributed in CDS and 3'UTR were detected in the ECT1/2-Poaceae4, and the dual-luciferase assay further demonstrated that these conserved m6A sites in the 3'UTR negatively regulated the expression of Firefly luciferase (LUC) gene. Finally, we developed transcription factor regulatory networks for m6A pathway components, using yeast one-hybrid assay demonstrated that PheBPC1 could interact with the PheECT1/2-5 promoter. Overall, this study presents a comprehensive evolutionary and functional analysis of m6A pathway components and their modifications in plants, providing a valuable resource for future functional analysis in this field.

Lysine 2-hydroxyisobutyrylation proteomics analyses reveal the regulatory mechanism of CaMYB61-CaAFR1 module in regulating stem development in Capsicum annuum L

Plant stems constitute the most abundant renewable resource on earth. The function of lysine (K)-2-hydroxyisobutyrylation (Khib), a novel post-translational modification (PTM), has not yet been elucidated in plant stem development. Here, by assessing typical pepper genotypes with straight stem (SS) and prostrate stem (PS), we report the first large-scale proteomics analysis for protein Khib to date. Khib-modifications influenced central metabolic processes involved in stem development, such as glycolysis/gluconeogenesis and protein translation. The high Khib level regulated gene expression and protein accumulation associated with cell wall formation in the pepper stem. Specially, we found that CaMYB61 knockdown lines that exhibited prostrate stem phenotypes had high Khib levels. Most histone deacetylases (HDACs, e.g., switch-independent 3 associated polypeptide function related 1, AFR1) potentially function as the "erasing enzymes" involved in reversing Khib level. CaMYB61 positively regulated CaAFR1 expression to erase Khib and promote cellulose and hemicellulose accumulation in the stem. Therefore, we propose a bidirectional regulation hypothesis of "Khib modifications" and "Khib erasing" in stem development, and reveal a novel epigenetic regulatory network in which the CaMYB61-CaAFR1 molecular module participating in the regulation of Khib levels and biosynthesis of cellulose and hemicellulose for the first time.

Culm Morphological Analysis in Moso Bamboo Reveals the Negative Regulation of Internode Diameter and Thickness by Monthly Precipitation

The neglect of Moso bamboo's phenotype variations hinders its broader utilization, despite its high economic value globally. Thus, this study investigated the morphological variations of 16 Moso bamboo populations. The analysis revealed the culm heights ranging from 9.67 m to 17.5 m, with average heights under the first branch ranging from 4.91 m to 7.67 m. The total internode numbers under the first branch varied from 17 to 36, with internode lengths spanning 2.9 cm to 46.4 cm, diameters ranging from 5.10 cm to 17.2 cm, and wall thicknesses from 3.20 mm to 33.3 mm, indicating distinct attributes among the populations. Furthermore, strong positive correlations were observed between the internode diameter, thickness, length, and volume. The coefficient of variation of height under the first branch showed strong positive correlations with several parameters, indicating variability in their contribution to the total culm height. A regression analysis revealed patterns of covariation among the culm parameters, highlighting their influence on the culm height and structural characteristics. Both the diameter and thickness significantly contribute to the internode volume and culm height, and the culm parameters tend to either increase or decrease together, influencing the culm height. Moreover, this study also identified a significant negative correlation between monthly precipitation and the internode diameter and thickness, especially during December and January, impacting the primary thickening growth and, consequently, the internode size.

Exploring N6-methyladenosine (m6A) modification in tree species: opportunities and challenges

N 6-methyladenosine (m6A) in eukaryotes is the most common and widespread internal modification in mRNA. The modification regulates mRNA stability, translation efficiency, and splicing, thereby fine-tuning gene regulation. In plants, m6A is dynamic and critical for various growth stages, embryonic development, morphogenesis, flowering, stress response, crop yield, and biomass. Although recent high-throughput sequencing approaches have enabled the rapid identification of m6A modification sites, the site-specific mechanism of this modification remains unclear in trees. In this review, we discuss the functional significance of m6A in trees under different stress conditions and discuss recent advancements in the quantification of m6A. Quantitative and functional insights into the dynamic aspect of m6A modification could assist researchers in engineering tree crops for better productivity and resistance to various stress conditions.

Inhibition of DNA and RNA methylation disturbs root development of moso bamboo

DNA methylation (5mC) and N6-methyladenosine (m6A) are two important epigenetics regulators, which have a profound impact on plant growth development. Phyllostachys edulis (P. edulis) is one of the fastest spreading plants due to its well-developed root system. However, the association between 5mC and m6A has seldom been reported in P. edulis. In particular, the connection between m6A and several post-transcriptional regulators remains uncharacterized in P. edulis. Here, our morphological and electron microscope observations showed the phenotype of increased lateral root under RNA methylation inhibitor (DZnepA) and DNA methylation inhibitor (5-azaC) treatment. RNA epitranscriptome based on Nanopore direct RNA sequencing revealed that DZnepA treatment exhibits significantly decreased m6A level in the 3'-untranslated region (3'-UTR), which was accompanied by increased gene expression, full-length ratio, higher proximal poly(A) site usage and shorter poly(A) tail length. DNA methylation levels of CG and CHG were reduced in both coding sequencing and transposable element upon 5-azaC treatment. Cell wall synthesis was impaired under methylation inhibition. In particular, differentially expressed genes showed a high percentage of overlap between DZnepA and 5-azaC treatment, which suggested a potential correlation between two methylations. This study provides preliminary information for a better understanding of the link between m6A and 5mC in root development of moso bamboo.

Warmer temperature during asexual reproduction induce methylome, transcriptomic, and lasting phenotypic changes in Fragaria vesca ecotypes

Plants must adapt with increasing speed to global warming to maintain their fitness. One rapid adaptation mechanism is epigenetic memory, which may provide organisms sufficient time to adapt to climate change. We studied how the perennial Fragaria vesca adapted to warmer temperatures (28°C vs. 18°C) over three asexual generations. Differences in flowering time, stolon number, and petiole length were induced by warmer temperature in one or more ecotypes after three asexual generations and persisted in a common garden environment. Induced methylome changes differed between the four ecotypes from Norway, Iceland, Italy, and Spain, but shared methylome responses were also identified. Most differentially methylated regions (DMRs) occurred in the CHG context, and most CHG and CHH DMRs were hypermethylated at the warmer temperature. In eight CHG DMR peaks, a highly similar methylation pattern could be observed between ecotypes. On average, 13% of the differentially methylated genes between ecotypes also showed a temperature-induced change in gene expression. We observed ecotype-specific methylation and expression patterns for genes related to gibberellin metabolism, flowering time, and epigenetic mechanisms. Furthermore, we observed a negative correlation with gene expression when repetitive elements were found near (±2 kb) or inside genes. In conclusion, lasting phenotypic changes indicative of an epigenetic memory were induced by warmer temperature and were accompanied by changes in DNA methylation patterns. Both shared methylation patterns and transcriptome differences between F. vesca accessions were observed, indicating that DNA methylation may be involved in both general and ecotype-specific phenotypic variation.

Identification and Characterization of PRE Genes in Moso Bamboo (Phyllostachys edulis)

Basic helix-loop-helix (bHLH)/HLH transcription factors are involved in various aspects of the growth and development of plants. Here, we identified four HLH genes, PePRE1-4, in moso bamboo plants that are homologous to Arabidopsis PRE genes. In bamboo seedlings, PePRE1/3 were found to be highly expressed in the internode and lamina joint by using quantitative RT-PCR analysis. In the elongating internode of bamboo shoots, PePRE genes are expressed at higher levels in the basal segment than in the mature top segment. Overexpression of PePREs (PePREs-OX) in Arabidopsis showed longer petioles and hypocotyls, as well as earlier flowering. PePRE1 overexpression restored the phenotype due to the deficiency of AtPRE genes caused by artificial micro-RNA. PePRE1-OX plants showed hypersensitivity to propiconazole treatment compared with the wild type. In addition, PePRE1/3 but not PePRE2/4 proteins accumulated as punctate structures in the cytosol, which was disrupted by the vesicle recycling inhibitor brefeldin A (BFA). PePRE genes have a positive function in the internode elongation of moso bamboo shoots, and overexpression of PePREs genes promotes flowering and growth in Arabidopsis. Our findings provided new insights about the fast-growing mechanism of bamboo shoots and the application of PRE genes from bamboo.