Selection and Validation of Reference Genes in Dendrocalamus brandisii for Quantitative Real-Time PCR.

Dendrocalamus brandisii (Munro) Kurz is a sympodial bamboo species with a wide distribution in tropical and subtropical regions. Due to its remarkable regenerative ability and exceptional flavor, this species plays a pivotal role in bolstering the economies of numerous nations across these regions. We recently published a high-quality genome of this species. To date, no study results have identified the optimal reference genes for quantitative real-time polymerase chain reaction (qRT-PCR) normalization in Dendrocalamus brandisii. qRT-PCR offers a highly accurate and effective approach to analyzing gene expression. However, the precision of the resulting quantitative data hinges on the correct choice of reference genes. Twenty-one potential reference genes were identified from the D. brandisii transcriptomes. Their expression in 23 samples, including 8 different tissue organs and 15 samples of D. brandisii under various treatment conditions, were evaluated through qRT-PCR. Subsequently, four software programs-Delta CT, geNorm, NormFinder, and RefFinder-were employed to compare their expression stability. The results revealed that the selection of optimal reference genes varied based on the particular organ and condition being examined. EF-1-α-2 consistently exhibits the most stable expression across diverse tissues, while ACTIN-1, TUBULIN-1, and EF-1-α-2 were the most consistent reference genes in roots, culms, and leaves under various treatments, respectively. In this study, we identified and characterized appropriate internal genes utilized for calibrating qRT-PCR analyses of D. brandisii across different tissue organs and under various treatments. This research will provide key insights for advancing the study of gene functionality and molecular biology in D. brandisii and related species.

Knockdown of KCNQ1OT1 Alleviates the Activation of NLRP3 Inflammasome Through miR-17-5p/TXNIP Axis in Retinal Müller Cells.

PURPOSE: Diabetic retinopathy (DR) is one of the most severe and common complications caused by diabetic mellites. Inhibiting NLRP3 inflammasome activation displays a crucial therapeutic value in DR. Studies have shown that KCNQ1OT1 plays a critical role in regulating NLRP3 inflammasome activation and participates in the pathogenesis of diabetic complications. The present study aims to explore the role, and the potential mechanism of KCNQ1OT1 in regulating the activation of NLRP3 inflammasome in DR. METHODS: qRT-PCR was used to detect the expression of KCNQ1OT1, miR-17-5p, TXNIP, NLRP3, ASC, caspase-1 and IL-1ß. Western blot was performed to detect the expression of NLRP3, ASC, caspase-1, IL-1ß and TXNIP. Immunohistochemistry and immunostaining were performed to detect the expression of caspase-1. The levels of the inflammatory cytokine IL-1ß were determined by ELISA assay. FISH was used to detect the subcellular localisation of KCNQ1OT1. Bioinformatic analysis, luciferase reporter assay and in vitro studies were performed to elucidate the mechanism of KCNQ1OT1-mediated dysfunction. RESULTS: The expression of KCNQ1OT1 and the activation of NLRP3 inflammasome were increased in experimental DR models. KCNQ1OT1 knockdown alleviated NLRP3 inflammasome-associated molecules expression. In addition, KCNQ1OT1 was found to be localized mainly in the cytoplasm of Müller cells and facilitated TXNIP expression by acting as a miR-17-5p sponge. KCNQ1OT1 promoted the activation of NLRP3 inflammasome through miR-17-5p/TXNIP axis. CONCLUSIONS: In conclusion, it was found in this study that KCNQ1OT1 promoted the activation of NLRP3 inflammasome both in vitro and in vivo, which was mediated by miR-17-5p/TXNIP axis. KCNQ1OT1 might be an effective interference target for the prevention and treatment of DR.

Chromosomal-level genome and metabolome analyses of highly heterozygous allohexaploid Dendrocalamus brandisii elucidate shoot quality and developmental characteristics.

Dendrocalamus brandisii (Munro) Kurz is a sympodial bamboo species with inimitable taste and flavorful shoots. Its rapid growth and use as high-quality material make this bamboo species highly valued for both food processing and wood applications. However, genome information for D. brandisii is lacking, primarily due to its polyploidy and large genome size. Here, we assembled a high-quality genome for hexaploid D. brandisii, which comprises 70 chromosomes with a total size of 2,756 Mb, using long-read HiFi sequencing. Furthermore, we accurately separated the genome into its three constituent subgenomes. We used Oxford Nanopore Technologies long reads to construct a transcriptomic dataset covering 15 tissues for gene annotation to complement our genome assembly, revealing differential gene expression and post-transcriptional regulation. By integrating metabolome analysis, we unveiled that well-balanced lignin formation, as well as abundant flavonoid and fructose contents, contribute to the superior quality of D. brandisii shoots. Integrating genomic, transcriptomic, and metabolomic datasets provided a solid foundation for enhancing bamboo shoot quality and developing efficient gene-editing techniques. This study should facilitate research on D. brandisii and enhance its use as a food source and wood material by providing crucial genomic resources.

Single-cell transcriptome atlas reveals spatiotemporal developmental trajectories in the basal roots of moso bamboo (Phyllostachys edulis).

Roots are essential for plant growth and development. Bamboo is a large Poaceae perennial with 1642 species worldwide. However, little is known about the transcriptional atlas that underpins root cell-type differentiation. Here, we set up a modified protocol for protoplast preparation and report single-cell transcriptomes of 14 279 filtered single cells derived from the basal root tips of moso bamboo. We identified four cell types and defined new cell-type-specific marker genes for the basal root. We reconstructed the developmental trajectories of the root cap, epidermis, and ground tissues and elucidated critical factors regulating cell fate determination. According to in situ hybridization and pseudotime trajectory analysis, the root cap and epidermis originated from a common initial cell lineage, revealing the particularity of bamboo basal root development. We further identified key regulatory factors for the differentiation of these cells and indicated divergent root developmental pathways between moso bamboo and rice. Additionally, PheWOX13a and PheWOX13b ectopically expressed in Arabidopsis inhibited primary root and lateral root growth and regulated the growth and development of the root cap, which was different from WOX13 orthologs in Arabidopsis. Taken together, our results offer an important resource for investigating the mechanism of root cell differentiation and root system architecture in perennial woody species of Bambusoideae.

Phytohormone Crosstalk of Cytokinin Biosynthesis and Signaling Family Genes in Moso Bamboo (Phyllostachys edulis).

Cytokinin is widely involved in the regulation of plant growth, but its pathway-related genes have not been reported in Moso bamboo. In this study, a total of 129 candidate sequences were identified by bioinformatic methods. These included 15 IPT family genes, 19 LOG family genes, 22 HK family genes, 11 HP family genes and 62 RR family genes. Phylogenetic analysis revealed that the cytokinin pathway was closely related to rice, and evolutionary pattern analysis found that most of the genes have syntenic relationship with rice-related genes. The Moso bamboo cytokinin pathway was evolutionarily conservative and mainly underwent purifying selection, and that gene family expansion was mainly due to whole-gene duplication events. Analysis of transcriptome data revealed a tissue-specific expression pattern of Moso bamboo cytokinin family genes, with auxin and gibberellin response patterns. Analysis of co-expression patterns at the developmental stages of Moso bamboo shoots revealed the existence of a phytohormone co-expression pattern centered on cytokinin signaling genes. The auxin signaling factor PheARF52 was identified by yeast one-hybrid assay as regulating the PheRR3 gene through a P-box element in the PheRR3 promoter region. Auxin and cytokinin signaling crosstalk to regulate Moso bamboo growth. Overall, we systematically identified and analyzed key gene families of the cytokinin pathway in Moso bamboo and obtained key factors for auxin and cytokinin crosstalk, laying the foundation for the study of hormone regulation in Moso bamboo.

Phylogeny, transcriptional profile, and auxin-induced phosphorylation modification characteristics of conserved PIN proteins in Moso bamboo (Phyllostachys edulis).

Auxin polar transport is an important way for auxin to exercise its function, and auxin plays an irreplaceable role in the rapid growth of Moso bamboo. We identified and performed the structural analysis of PIN-FORMED auxin efflux carriers in Moso bamboo and obtained a total of 23 PhePIN genes from five gene subfamilies. We also performed chromosome localization and intra- and inter-species synthesis analysis. Phylogenetic analyses of 216 PIN genes showed that PIN genes are relatively conserved in the evolution of the Bambusoideae and have undergone intra-family segment replication in Moso bamboo. The PIN genes' transcriptional patterns showed that the PIN1 subfamily plays a major regulatory role. PIN genes and auxin biosynthesis maintain a high degree of consistency in spatial and temporal distribution. Phosphoproteomics analysis identified many phosphorylated protein kinases that respond to auxin regulation through autophosphorylation and phosphorylation of PIN proteins. The protein interaction network showed that there is a plant hormone interaction regulatory network with PIN protein as the core. We provide a comprehensive PIN protein analysis that complements the auxin regulatory pathway in Moso bamboo and paves the way for further auxin regulatory studies in bamboo.

TNF-α released from retinal Müller cells aggravates retinal pigment epithelium cell apoptosis by upregulating mitophagy during diabetic retinopathy.

Retinal pigment epithelium (RPE) cell damage, including mitophagy-associated cell apoptosis, accelerates the pathogenesis of diabetic retinopathy (DR), a common complication of diabetes that causes blindness. Müller cells interact with RPE cells via pro-inflammatory cytokines, such as tumor necrosis factor α (TNF-α). Herein, we investigated the role of the RPE cell epidermal growth factor receptor (EGFR)/p38 mitogen-activated protein kinase (p38)/nuclear factor kappa B (NF-κB) pathway in Müller cell-derived TNF-α-induced mitophagy-associated apoptosis during DR. Our results showed that TNF-α released from Müller cells activated the EGFR/p38/NF-κB/p62 pathway to increase mitophagy and apoptosis in RPE cells under high glucose (HG) conditions. Additionally, blockade of the TNF-α/EGFR axis alleviates blood-retina barrier breakdown in diabetic mice. Our data further illustrate the effects of the Müller cell inflammatory response on RPE cell survival, implying potential molecular targets for DR treatment.