Information Integration and Communication in Plant Growth Regulation.

Plants are equipped with the capacity to respond to a large number of diverse signals, both internal ones and those emanating from the environment, that are critical to their survival and adaption as sessile organisms. These signals need to be integrated through highly structured intracellular networks to ensure coherent cellular responses, and in addition, spatiotemporal actions of hormones and peptides both orchestrate local cell differentiation and coordinate growth and physiology over long distances. Further, signal interactions and signaling outputs vary significantly with developmental context. This review discusses our current understanding of the integrated intracellular and intercellular signaling networks that control plant growth.

Mapping the signaling network of BIN2 kinase using TurboID-mediated biotin labeling and phosphoproteomics.

Elucidating enzyme-substrate relationships in posttranslational modification (PTM) networks is crucial for understanding signal transduction pathways but is technically difficult because enzyme-substrate interactions tend to be transient. Here, we demonstrate that TurboID-based proximity labeling (TbPL) effectively and specifically captures the substrates of kinases and phosphatases. TbPL-mass spectrometry (TbPL-MS) identified over 400 proximal proteins of Arabidopsis thaliana BRASSINOSTEROID-INSENSITIVE2 (BIN2), a member of the GLYCOGEN SYNTHASE KINASE 3 (GSK3) family that integrates signaling pathways controlling diverse developmental and acclimation processes. A large portion of the BIN2-proximal proteins showed BIN2-dependent phosphorylation in vivo or in vitro, suggesting that these are BIN2 substrates. Protein-protein interaction network analysis showed that the BIN2-proximal proteins include interactors of BIN2 substrates, revealing a high level of interactions among the BIN2-proximal proteins. Our proteomic analysis establishes the BIN2 signaling network and uncovers BIN2 functions in regulating key cellular processes such as transcription, RNA processing, translation initiation, vesicle trafficking, and cytoskeleton organization. We further discovered significant overlap between the GSK3 phosphorylome and the O-GlcNAcylome, suggesting an evolutionarily ancient relationship between GSK3 and the nutrient-sensing O-glycosylation pathway. Our work presents a powerful method for mapping PTM networks, a large dataset of GSK3 kinase substrates, and important insights into the signaling network that controls key cellular functions underlying plant growth and acclimation.

The F-box Protein KIB1 Mediates Brassinosteroid-Induced Inactivation and Degradation of GSK3-like Kinases in Arabidopsis.

The glycogen synthase kinase-3 (GSK3) family kinases are central cellular regulators highly conserved in all eukaryotes. In Arabidopsis, the GSK3-like kinase BIN2 phosphorylates a range of proteins to control broad developmental processes, and BIN2 is degraded through unknown mechanism upon receptor kinase-mediated brassinosteroid (BR) signaling. Here we identify KIB1 as an F-box E3 ubiquitin ligase that promotes the degradation of BIN2 while blocking its substrate access. Loss-of-function mutations of KIB1 and its homologs abolished BR-induced BIN2 degradation and caused severe BR-insensitive phenotypes. KIB1 directly interacted with BIN2 in a BR-dependent manner and promoted BIN2 ubiquitination in vitro. Expression of an F-box-truncated KIB1 caused BIN2 accumulation but dephosphorylation of its substrate BZR1 and activation of BR responses because KIB1 blocked BIN2 binding to BZR1. Our study demonstrates that KIB1 plays an essential role in BR signaling by inhibiting BIN2 through dual mechanisms of blocking substrate access and promoting degradation.

Equilibrium Moisture Mediated Esterification Reaction to Achieve Over 100% Lignocellulosic Nanofibrils Yield.

Lignocellulosic nanofibrils (LCNFs) isolation is recognized as an efficient strategy for maximizing biomass utilization. Nevertheless, achieving a 100% yield presents a formidable challenge. Here, an esterification strategy mediated by the equilibrium moisture in biomass is proposed for LCNFs preparation without the use of catalysts, resulting in a yield exceeding 100%. Different from anhydrous chemical thermomechanical pulp (CTMP0%), the presence of moisture (moisture content of 7 wt%, denoted as CTMP7%) introduces a notably distinct process for the pretreatment of CTMP, comprising the initial disintegration and the post-esterification steps. The maleic acid, generated through maleic anhydride (MA) hydrolysis, degrades the recalcitrant lignin-carbohydrate complex (LCC) structures, resulting in esterified CTMP7% (E-CTMP7%). The highly grafted esters compensate for the mass loss resulting from the partial removal of hydrolyzed lignin and hemicellulose, ensuring a high yield. Following microfluidization, favorable LCNF7% with a high yield (114.4 ± 3.0%) and a high charge content (1.74 ± 0.09 mmol g-1) can be easily produced, surpassing most previous records for LCNFs. Additionally, LCNF7% presented highly processability for filaments, films, and 3D honeycomb structures preparation. These findings provide valuable insights and guidance for achieving a high yield in the isolation of LCNFs from biomass through the mediation of equilibrium moisture.

GMrepo v2: a curated human gut microbiome database with special focus on disease markers and cross-dataset comparison.

GMrepo (data repository for Gut Microbiota) is a database of curated and consistently annotated human gut metagenomes. Its main purposes are to increase the reusability and accessibility of human gut metagenomic data, and enable cross-project and phenotype comparisons. To achieve these goals, we performed manual curation on the meta-data and organized the datasets in a phenotype-centric manner. GMrepo v2 contains 353 projects and 71,642 runs/samples, which are significantly increased from the previous version. Among these runs/samples, 45,111 and 26,531 were obtained by 16S rRNA amplicon and whole-genome metagenomics sequencing, respectively. We also increased the number of phenotypes from 92 to 133. In addition, we introduced disease-marker identification and cross-project/phenotype comparison. We first identified disease markers between two phenotypes (e.g. health versus diseases) on a per-project basis for selected projects. We then compared the identified markers for each phenotype pair across datasets to facilitate the identification of consistent microbial markers across datasets. Finally, we provided a marker-centric view to allow users to check if a marker has different trends in different diseases. So far, GMrepo includes 592 marker taxa (350 species and 242 genera) for 47 phenotype pairs, identified from 83 selected projects. GMrepo v2 is freely available at: https://gmrepo.humangut.info.

Compared to histamine-2 receptor antagonist, proton pump inhibitor induces stronger oral-to-gut microbial transmission and gut microbiome alterations: a randomised controlled trial.

OBJECTIVE: We aim to compare the effects of proton pump inhibitors (PPIs) and histamine-2 receptor antagonists (H2RAs) on the gut microbiota through longitudinal analysis. DESIGN: Healthy volunteers were randomly assigned to receive either PPI (n=23) or H2RA (n=26) daily for seven consecutive days. We collected oral (saliva) and faecal samples before and after the intervention for metagenomic next-generation sequencing. We analysed intervention-induced alterations in the oral and gut microbiome including microbial abundance and growth rates, oral-to-gut transmissions, and compared differences between the PPI and H2RA groups. RESULTS: Both interventions disrupted the gut microbiota, with PPIs demonstrating more pronounced effects. PPI usage led to a significantly higher extent of oral-to-gut transmission and promoted the growth of specific oral microbes in the gut. This led to a significant increase in both the number and total abundance of oral species present in the gut, including the identification of known disease-associated species like Fusobacterium nucleatum and Streptococcus anginosus. Overall, gut microbiome-based machine learning classifiers could accurately distinguish PPI from non-PPI users, achieving an area under the receiver operating characteristic curve (AUROC) of 0.924, in contrast to an AUROC of 0.509 for H2RA versus non-H2RA users. CONCLUSION: Our study provides evidence that PPIs have a greater impact on the gut microbiome and oral-to-gut transmission than H2RAs, shedding light on the mechanism underlying the higher risk of certain diseases associated with prolonged PPI use. TRIAL REGISTRATION NUMBER: ChiCTR2300072310.

High-quality chromosome-level scaffolds of the plant bug Pachypeltis micranthus provide insights into the availability of Mikania micrantha control.

BACKGROUND: The plant bug, Pachypeltis micranthus Mu et Liu (Hemiptera: Miridae), is an effective potential biological control agent for Mikania micrantha H.B.K. (Asteraceae; one of the most notorious invasive weeds worldwide). However, limited knowledge about this species hindered its practical application and research. Accordingly, sequencing the genome of this mirid bug holds great significance in controlling M. micrantha. RESULTS: Here, 712.72 Mb high-quality chromosome-level scaffolds of P. micranthus were generated, of which 707.51 Mb (99.27%) of assembled sequences were anchored onto 15 chromosome-level scaffolds with contig N50 of 16.84 Mb. The P. micranthus genome had the highest GC content (42.43%) and the second highest proportion of repetitive sequences (375.82 Mb, 52.73%) than the three other mirid bugs (i.e., Apolygus lucorum, Cyrtorhinus lividipennis, and Nesidiocoris tenuis). Phylogenetic analysis showed that P. micranthus clustered with other mirid bugs and diverged from the common ancestor approximately 200 million years ago. Gene family expansion and/or contraction were analyzed, and significantly expanded gene families associated with P. micranthus feeding and adaptation to M. micrantha were manually identified. Compared with the whole body, transcriptome analysis of the salivary gland revealed that most of the upregulated genes were significantly associated with metabolism pathways and peptidase activity, particularly among cysteine peptidase, serine peptidase, and polygalacturonase; this could be one of the reasons for precisely and highly efficient feeding by the oligophagous bug P. micranthus on M. micrantha. CONCLUSION: Collectively, this work provides a crucial chromosome-level scaffolds resource to study the evolutionary adaptation between mirid bug and their host. It is also helpful in searching for novel environment-friendly biological strategies to control M. micrantha.

Functions and mechanisms of RNA helicases in plants.

RNA helicases (RHs) are a family of ubiquitous enzymes that alter RNA structures and remodel ribonucleoprotein complexes typically using energy from the hydrolysis of ATP. RHs are involved in various aspects of RNA processing and metabolism, exemplified by transcriptional regulation, pre-mRNA splicing, miRNA biogenesis, liquid-liquid phase separation, and rRNA biogenesis, among other molecular processes. Through these mechanisms, RHs contribute to vegetative and reproductive growth, as well as abiotic and biotic stress responses throughout the life cycle in plants. In this review, we systematically characterize RH-featured domains and signature motifs in Arabidopsis. We also summarize the functions and mechanisms of RHs in various biological processes in plants with a focus on DEAD-box and DEAH-box RNA helicases, aiming to present the latest understanding of RHs in plant biology.

Extracellular vesicles produced by avian pathogenic Escherichia coli (APEC) activate macrophage proinflammatory response and neutrophil extracellular trap (NET) formation through TLR4 signaling.

BACKGROUND: Avian pathogenic Escherichia coli (APEC) is the major pathogen causing important avian diseases in poultry. As an important subtype of extraintestinal pathogenic E. coli, APEC has zoonotic potential and is considered a foodborne pathogen. APEC extracellular vesicles (EVs) may play vital roles in the interaction of the pathogen with its host cells. However, the precise roles played by APEC EVs are still not completely clear, especially in immune cells. RESULTS: In this study, we investigated the relationships between APEC EVs and immune cells. The production and characteristics of the EVs of APEC isolate CT265 were identified. Toll like receptor 4 (TLR4) triggered the cellular immune responses when it interacted with APEC EVs. APEC EVs induced a significant release of proinflammatory cytokines in THP-1 macrophages. APEC EVs induced the macrophage inflammatory response via the TLR4/MYD88/NF-κB signaling pathway, which participated in the activation of the APEC-EV-induced NLRP3 inflammasome. However, the loss of lipopolysaccharide (LPS) from APEC EVs reduced the activation of the NLRP3 inflammasome mediated by TLR4/MYD88/NF-κB signaling. Because APEC EVs activated the macrophage inflammatory response and cytokines release, we speculated that the interaction between APEC EVs and macrophages activated and promoted neutrophil migration during APEC extraintestinal infection. This study is the first to report that APEC EVs induce the formation of neutrophil extracellular traps (NETs) and chicken heterophil extracellular traps. Treatment with APEC EVs induced SAPK/JNK activation in neutrophils. The inhibition of TLR4 signaling suppressed APEC-EV-induced NET formation. However, although APEC EVs activated the immune response of macrophages and initiated NET formation, they also damaged macrophages, causing their apoptosis. The loss of LPS from APEC EVs did not prevent this process. CONCLUSION: APEC-derived EVs induced inflammatory responses in macrophages and NETs in neutrophils, and that TLR4 was involved in the APEC-EV-activated inflammatory response. These findings provided a basis for the further study of APEC pathogenesis.

A Mobile Health-Based Management for Patients with Limited Lung Function to Improve Treatment Outcomes and Quality of Life After Minimally Invasive Thoracoscopic Lobectomy.

Objective: Limited lung function is an independent risk factor for postoperative respiratory failure in non-small cell lung cancer (NSCLC) patients. In this study, we developed a mobile health-based management for NSCLC patients with limited lung function who were scheduled to receive lobectomy and evaluated its effects on the patient's pulmonary function and quality of life. Methods: A total of 60 NSCLC patients scheduled to receive minimally invasive thoracoscopic lobectomy were enrolled and then randomized into the traditional management group and the program management group, with 30 patients per group. Based on the WeChat mini program, a management software for patients with limited lung function was established, including two portals: the patient portal and the nurse one. The pain assessment was performed using the Visual Analog Scale (VAS) scores, the cough assessment using the Leicester Cough Questionnaire, and the quality-of-life assessment using the EORTC QLQ-30 at 1 day before surgery, 1 week, 2 weeks, 1 month, 6 months, or 12 months after surgery. Results: The program management group exhibited an increased PaO2 (96.68 ± 7.92 vs. 87.69 vs. 5.50; P = .018) concomitant with a declined PaCO2 (38.55 ± 2.79 vs. 40.65 ± 2.17; p = 0.034) at 12 months after surgery compared with the traditional management group. The VAS scores showed significant differences at 2 weeks after surgery between the traditional management (median: 2; range: 2-3) and program management (median: 2; range: 1-2) groups (P = .012). The scores of Leicester Cough Questionnaire showed remarkable differences at 12 months after surgery between the traditional management (20.00 ± 1.54) and program management (18.99 ± 2.08) groups (P = .036). The total scores of EORTC QLQ-30 showed notable differences at 12 months after surgery between the traditional management (83.05 ± 14.09) and program management (90.55 ± 11.32) groups (P = .027). Conclusion: The study demonstrated improved pulmonary function and a better quality of life conferred by the mobile health-based management based on WeChat mini program for NSCLC patients with limited lung function and undergoing thoracoscopic lobectomy in a long follow up.

New method for measuring the pore sizes and pore size distributions of filter membranes-the fluorescence probe method.

A novel, simple, and rapid method is demonstrated for measuring the pore size and pore size distribution of filtration membranes (FMs) used in aqueous applications with fluorescence probes. Because the selected fluorescent probes are mixable and have strong signals, combined with the operation of dead-end filtration, this method only requires small amounts of reagents; additionally, it is time-efficient by avoiding multiple rounds of filtration. This method detects the size of a FM pore throat (i.e., the narrowest position of a pore tunnel), which is more consistent with the actual filtration situation. The conditions, such as probe concentration, temperature, transmembrane pressure difference, and types of surfactants, have been optimized. The experimental results show that the fluorescence probe method has good accuracy and reproducibility for measuring the pore size and pore size distribution of both organic and inorganic FMs. The method is particularly suitable for rapid testing of the filtration performance (nominal pore size≥0.02 µm) of purchased or synthetic membranes in the laboratory.

Glucosamine-Modified Reduction-Responsive Polymeric Micelles for Liver Cancer Therapy.

In this work, glucose transporter-1 (GLUT-1) and glutathione (GSH) over-expression in liver cancer was utilized to design a reduction-responsive and active targeting drug delivery system AG-PEG-SS-PCL (APSP) for the delivery of sorafenib (SF). The SF-APSP micelles were prepared using the thin film hydration method and characterized by various techniques. In vitro release experiments showed that the cumulative release of SF-APSP micelles in the simulated tumor microenvironment (pH 7.4 with GSH) reached 94.76 ± 1.78% at 48 h, while it was only 20.32 ± 1.67% in the normal physiological environment (pH 7.4 without GSH). The in vitro study revealed that glucosamine (AG) enhanced the antitumor effects of SF, and SF-APSP micelles inhibited proliferation by targeting HepG2 cells and suppressing cyclin D1 expression. The in vivo antitumor efficacy study further confirmed that the SF-APSP micelles had excellent antitumor effects and better tolerance against nude mouse with HepG2 cells than other treatment groups. All in all, these results indicated that SF-APSP micelles could be a promising drug delivery system for anti-hepatoma treatment.

M-Sn-Q (M = Zn, Cd; Q = S, Se) Compounds Templated by (Alkyl)ammonium Species: Synthesis, Crystal Structure, and Sr2+ Adsorption Property.

Deep investigations on the synthetic and structural chemistry of heterometallic chalcogenidostannates bear fundamental significance for the establishment of the structure-property relationship that would offer guidance on the functional material innovation. Presented here are four ammonium- and/or alkylammonium-directed M-Sn-Q (M = Zn, Cd; Q = S, Se) compounds, namely, [NH4]7[H3O]3Zn4Sn4S17 (1), [NH4]5[(CH3)2NH2]Zn4Sn5S17 (2), [CH3CH2NH3]22Zn16Sn12Se51(H2O)4·16H2O (3), and [NH4]2CdSnSe4 (4). All four compounds were synthesized in deep eutectic solvents (DESs) or ethylamine aqueous solution, both of which function simultaneously as reaction media and structure-directing agents. Compound 1 consists of discrete P1-[Zn4Sn4S17]10- clusters templated by mixed [NH4]+/[H3O]+ cations. In compound 2, such P1 clusters are bridged by Sn4+ ions in a 4,4-connection mode to form a [Zn4Sn5S17]n6n- framework with three types of cavities (I-III) varying in size. The two smaller cavities (I and II) accommodate NH4+ while the larger one(III) is occupied by [(CH3)2NH2]+, reflecting the rational size-dependence of cations on cavities. Compound 3 features an [Zn16Sn12Se51(H2O)4]n22n- open framework constructed from the 4,3-connection of P1-[Zn4Sn4Se17]10- clusters and {Zn(H2O)}2+ bridges. This linkage mode contributes to a large cage-like subunit (inner dimension: 21.99 × 9.06 Å2) and therefore an ultrahigh porosity that are occupied by [CH3CH2NH3]+ cations and water molecules (volume fraction: 57.7%). Compound 4 exists as a stacking of [CdSnSe4]n2n- chains, which are composed of alternatively arranged {CdSe4} and {SnSe4} tetrahedra, in combination with [NH4]+ cations as both charge-compensating and space-filling agents. Detailed synthetic, structural, and topological analyses were performed on these solid materials, coupled with extensive investigations on their optical and thermal properties. Compound 3 exhibits an efficient Sr2+ adsorption performance, featuring ultrafast kinetics (94.69% in 5 min), high removal rate (98.57% in 20 min) at equilibrium, and high capacity (104.17 ± 23.53 mg g-1).

Comparative genomic analysis of ABC transporter genes in Tenebrio molitor and four other tenebrionid beetles (Coleoptera: Tenebrionidea).

ATP-binding cassette (ABC) transporters, one of the largest transmembrane protein families, transport a diverse number of substate across membranes. Details of their diverse physiological functions have not been established. Here, we identified 87 ABC transporter genes in the genomes of Tenebrio molitor along with those from Asbolus verrucosus (104), Hycleus cichorii (65), and Hycleus phaleratus (80). Combining these genes (336 in total) with genes reported in Tribolium castaneum (73), we analyzed the phylogeny of ABC transporter genes in all five Tenebrionids. They are assigned into eight subfamilies (ABCA-H). In comparison to other species, the ABCC subfamily in this group of beetles appears expanded. The expression profiles of the T. molitor genes at different life stages and in various tissues were also investigated using transcriptomic analysis. Most of them display developmental specific expression patterns, suggesting to us their possible roles in development. Most of them are highly expressed in detoxification-related tissues including gut and Malpighian tubule, from which we infer their roles in insecticide resistance. We detected specific or abundant expressions of many ABC transporter genes in various tissues such as salivary gland, ovary, testis, and antenna. This new information helps generate new hypotheses on their biological significance within tissues.

Characterization and expression profiling of serine protease inhibitors in the yellow mealworm Tenebrio molitor.

Serine protease inhibitors (SPIs) act in diverse biological processes in insects such as immunity, development, and digestion by preventing the unwanted proteolysis. So far, the repertoire of genes encoding SPIs has been identified from few insect species. In this study, 62 SPI genes were identified from the genome of the yellow mealworm, Tenebrio molitor. According to their modes of action, they were classified into three families, serpin (26), canonical SPI (31), and α-macroglobulins (A2M) (5). These SPIs feature eight domains including serpin, Kazal, TIL, Kunitz, WAP, Antistasin, pacifastin, and A2M. In total, 39 SPIs contain a single SPI domain, while the others encode at least two inhibitor units. Based on the amino acids in the cleaved reactive sites, the abilities of these SPIs to inhibit trypsin, chymotrypsin, or elastase-like enzymes are predicted. The expression profiling based on the RNA-seq data showed that these genes displayed stage-specific expression patterns during development, suggesting to us their significance in development. Some of the SPI genes were exclusively expressed in particular tissues such as hemocyte, fat body, gut, ovary, and testis, which may be involved in biological processes specific to the indicated tissues. These findings provide necessary information for further investigation of insect SPIs.

Genomic and transcriptomic analyses of chitin metabolism enzymes in Tenebrio molitor.

Chitin is of great importance in the cuticle and inner cuticular linings of insects. Chitin synthases (CHSs), chitin deacetylases (CDAs), chitinases (CHTs), and ß-N-acetylhexosaminidases (HEXs) are important enzymes required for chitin metabolism, and play essential roles in development and metamorphosis. Although chitin metabolism genes have been well characterized in limited insects, the information in the yellow mealworm, Tenebrio molitor, a model insect, is presently still unavailable. With the help of bioinformatics, we identified 54 genes that encode putative chitin metabolism enzymes, including 2 CHSs, 10 CDAs, 32 CHTs, and 10 HEXs in the genome of T. molitor. All these genes have the conserved domains and motifs of their corresponding protein family. Phylogenetic analyses indicated that CHS genes were divided into two groups. CDA genes were clustered into five groups. CHT genes were phylogenetically grouped into 11 clades, among which 1 in the endo-ß-N-acetylglucosaminidases group and the others were classified in the glycoside hydrolase family 18 groups. HEX genes were assorted into six groups. Developmental and tissue-specific expression profiling indicated that the identified chitin metabolism genes showed dynamical expression patterns concurrent with specific instar during molting period, suggesting their significant roles in molting and development. They were predominantly expressed in different tissues or body parts, implying their functional specialization and diversity. The results provide important information for further clarifying their biological functions using the yellow mealworm as an ideal experimental insect.

Identification and expression profiling of serine protease-related genes in Tenebrio molitor.

In insects, serine proteases and serine protease homologs (SPs/SPHs) are involved in a variety of physiological processes including digestion, development, and immunity. Here, we identified 112 SP and 88 SPH genes in the genome of the yellow mealworm, Tenebrio molitor. Based on the features of domain structure, they were divided into "S" group containing single Tryp-SPc or Tryp-SPHc domain, "C" group containing 1-4 CLIP domain (CLIPA-D) and "M" group containing the CBD, CUB, EGF, Fz, Gd, LDLa, PAN, SEA, SR, Sushi, and TSP domains, and have 115, 48, and 37 gene members, respectively. According to the active sites in the catalytic triad, the putative trypsin, chymotrypsin, or elastase-like enzyme specificity of the identified SPs/SPHs were predicted. Phylogenetic and genomic location analyses revealed that gene duplication exists in the large amount of SPs/SPHs. Gene expression profiling using RNA-seq data along with real time reverse transcription-polymerase chain reaction analysis showed that most SP/SPH genes display life stage specific expression patterns, indicating their important roles in development. Many SP/SPH genes are specifically or highly expressed in the gut, salivary gland, fat body, hemocyte, ovary, and testis, suggesting that they participate in digestion, immunity, and reproduction. The findings lay the foundation for further functional characterization of SPs/SPHs in T. molitor.

Genome-wide and expression-profiling analyses of the cytochrome P450 genes in Tenebrionidea.

Cytochrome P450 monooxygenases (CYPs) are present in almost all areas of the tree of life. As one of the largest and most diverse superfamilies of multifunctional enzymes, they play important roles in the metabolism of xenobiotics and biosynthesis of endogenous compounds, shaping the success of insects. In this study, the CYPome (an omics term for all the CYP genes in a genome) diversification was examined in the four Tenebrionidea species through genome-wide analysis. A total of 483 CYP genes were identified, of which 103, 157, 122, and 101 were respectively deciphered from the genomes of Tebebrio molitor, Asbolus verucosus, Hycleus cichorii and Hycleus phaleratus. These CYPs were classified into four major clans (mitochondrial, CYP2, CYP3, and CYP4), and clans CYP3 and CYP4 are most diverse. Phylogenetic analysis showed that most CYPs of these Tenebrionidea beetles from each clan had a very close 1:1 orthology to each other, suggesting that they originate closely and have evolutionally conserved function. Expression analysis at different developmental stages and in various tissues showed the life stage-, gut-, salivary gland-, fat body-, Malpighian tubule-, antennae-, ovary- and testis-specific expression patterns of T. molitor CYP genes, implying their various potential roles in development, detoxification, immune response, digestion, olfaction, and reproduction. Our studies provide a platform to understand the evolution of Tenebrionidea CYP gene superfamily, and a basis for further functional investigation of the T. molitor CYPs involved in various biological processes.

Comparative genomic analysis of carboxylesterase genes in Tenebrio molitor and other four tenebrionids.

Carboxylesterases (COEs) have various functions in wide taxons of organisms. In insects, COEs are important enzymes involved in the hydrolysis of a variety of ester-containing xenobiotics, neural signal transmission, pheromone degradation, and reproductive development. Understanding the diversity of COEs is basic to illustrate their functions. In this study, we identified 53, 105, 37, and 39 COEs from the genomes of Tenebrio molitor, Asbolus verucosus, Hycleus cichorii, and H. phaleratus in the superfamily of Tenebrionidea, respectively. Phylogenetic analysis showed that 234 COEs from these four species and those reported in Tribolium castaneum (63) could be divided into 12 clades and three major classes. The α-esterases significantly expanded in T. molitor, A. verucosus, and T. castaneum compared to dipteran and hymenopteran insects. In T. molitor, most COEs showed tissue and stage-specific but not a sex-biased expression. Our results provide insights into the diversity and evolutionary characteristics of COEs in tenebrionids, and lay a foundation for the functional characterization of COEs in the yellow mealworm.

The Wnt gene family in Tenebrio molitor and other coleopterans.

The Wnt gene family is involved in a wide range of developmental processes. Despite its significance, the evolution and function of Wnt genes remain largely unclear. Here, an exhaustive survey of Wnt genes was conducted in Tenebrio molitor and 17 other beetle genomes. A total of 146 Wnt genes were identified, creating a comprehensive coleopteran Wnt gene catalog. Comparative genomics indicates that dynamic evolutionary patterns of Wnt gene loss and duplication occurred in Coleoptera, leading to the diverse Wnt gene repertoire in various beetles. A striking loss of particular Wnt gene subfamilies occurs in Coleoptera. Remarkably, Wnt gene duplication was discovered for the first time in insects. Further analysis of Wnt gene expression in T. molitor indicates that each Wnt gene, including the duplicated ones, has a unique spatial or temporal expression pattern. The current study provides valuable insight into the evolution and functional validation of Wnt genes in Coleoptera.