A drosophila genetic resource of mutants to study mechanisms underlying human genetic diseases.

Invertebrate model systems are powerful tools for studying human disease owing to their genetic tractability and ease of screening. We conducted a mosaic genetic screen of lethal mutations on the Drosophila X chromosome to identify genes required for the development, function, and maintenance of the nervous system. We identified 165 genes, most of whose function has not been studied in vivo. In parallel, we investigated rare variant alleles in 1,929 human exomes from families with unsolved Mendelian disease. Genes that are essential in flies and have multiple human homologs were found to be likely to be associated with human diseases. Merging the human data sets with the fly genes allowed us to identify disease-associated mutations in six families and to provide insights into microcephaly associated with brain dysgenesis. This bidirectional synergism between fly genetics and human genomics facilitates the functional annotation of evolutionarily conserved genes involved in human health.

Disruptive CHD8 mutations define a subtype of autism early in development.

Autism spectrum disorder (ASD) is a heterogeneous disease in which efforts to define subtypes behaviorally have met with limited success. Hypothesizing that genetically based subtype identification may prove more productive, we resequenced the ASD-associated gene CHD8 in 3,730 children with developmental delay or ASD. We identified a total of 15 independent mutations; no truncating events were identified in 8,792 controls, including 2,289 unaffected siblings. In addition to a high likelihood of an ASD diagnosis among patients bearing CHD8 mutations, characteristics enriched in this group included macrocephaly, distinct faces, and gastrointestinal complaints. chd8 disruption in zebrafish recapitulates features of the human phenotype, including increased head size as a result of expansion of the forebrain/midbrain and impairment of gastrointestinal motility due to a reduction in postmitotic enteric neurons. Our findings indicate that CHD8 disruptions define a distinct ASD subtype and reveal unexpected comorbidities between brain development and enteric innervation.

Regulators of the cohesin network.

Chromosome cohesion is the term used to describe the cellular process in which sister chromatids are held together from the time of their replication until the time of separation at the metaphase to anaphase transition. In this capacity, chromosome cohesion, especially at centromeric regions, is essential for chromosome segregation. However, cohesion of noncentromeric DNA sequences has been shown to occur during double-strand break (DSB) repair and the transcriptional regulation of genes. Cohesion for the purposes of accurate chromosome segregation, DSB repair, and gene regulation are all achieved through a similar network of proteins, but cohesion for each purpose may be regulated differently. In this review, we focus on recent developments regarding the regulation of this multipurpose network for tying DNA sequences together. In particular, regulation via effectors and posttranslational modifications are reviewed. A picture is emerging in which complex regulatory networks are capable of differential regulation of cohesion in various contexts.

Prospective Comparison of Standard and Deep Learning-reconstructed Turbo Spin-Echo MRI of the Shoulder.

Background Deep learning (DL)-based MRI reconstructions can reduce imaging times for turbo spin-echo (TSE) examinations. However, studies that prospectively use DL-based reconstructions of rapidly acquired, undersampled MRI in the shoulder are lacking. Purpose To compare the acquisition time, image quality, and diagnostic confidence of DL-reconstructed TSE (TSEDL) with standard TSE in patients indicated for shoulder MRI. Materials and Methods This prospective single-center study included consecutive adult patients with various shoulder abnormalities who were clinically referred for shoulder MRI between February and March 2023. Each participant underwent standard TSE MRI (proton density- and T1-weighted imaging; conventional TSE sequence was used as reference for comparison), followed by a prospectively undersampled accelerated TSEDL examination. Six musculoskeletal radiologists evaluated images using a four-point Likert scale (1, poor; 4, excellent) for overall image quality, perceived signal-to-noise ratio, sharpness, artifacts, and diagnostic confidence. The frequency of major pathologic features and acquisition times were also compared between the acquisition protocols. The intergroup comparisons were performed using the Wilcoxon signed rank test. Results Overall, 135 shoulders in 133 participants were evaluated (mean age, 47.9 years ± 17.1 [SD]; 73 female participants). The median acquisition time of the TSEDL protocol was lower than that of the standard TSE protocol (288 seconds [IQR, 288-288 seconds] vs 926 seconds [IQR, 926-950 seconds], respectively; P < .001), achieving a 69% lower acquisition time. TSEDL images were given higher scores for overall image quality, perceived signal-to-noise ratio, and artifacts (all P < .001). Similar frequency of pathologic features (P = .48 to > .99), sharpness (P = .06), or diagnostic confidence (P = .05) were noted between images from the two protocols. Conclusion In a clinical setting, TSEDL led to reduced examination time and higher image quality with similar diagnostic confidence compared with standard TSE MRI in the shoulder. © RSNA, 2024 Supplemental material is available for this article. See also the editorial by Chang and Chow in this issue.

AutoDeconJ: a GPU-accelerated ImageJ plugin for 3D light-field deconvolution with optimal iteration numbers predicting.

MOTIVATION: Light-field microscopy (LFM) is a compact solution to high-speed 3D fluorescence imaging. Usually, we need to do 3D deconvolution to the captured raw data. Although there are deep neural network methods that can accelerate the reconstruction process, the model is not universally applicable for all system parameters. Here, we develop AutoDeconJ, a GPU-accelerated ImageJ plugin for 4.4× faster and more accurate deconvolution of LFM data. We further propose an image quality metric for the deconvolution process, aiding in automatically determining the optimal number of iterations with higher reconstruction accuracy and fewer artifacts. RESULTS: Our proposed method outperforms state-of-the-art light-field deconvolution methods in reconstruction time and optimal iteration numbers prediction capability. It shows better universality of different light-field point spread function (PSF) parameters than the deep learning method. The fast, accurate and general reconstruction performance for different PSF parameters suggests its potential for mass 3D reconstruction of LFM data. AVAILABILITY AND IMPLEMENTATION: The codes, the documentation and example data are available on an open source at: https://github.com/Onetism/AutoDeconJ.git. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Realizing highly efficient vertical coupling with dielectric deflective metasurfaces.

Using dielectric deflective metasurfaces, we propose a novel, to the best of our knowledge, out-of-plane modulation scheme to realize vertical coupling on a 220 nm silicon-on-insulator platform. The metasurface is used to deflect vertical incident light to an oblique angle with high efficiency in the cladding layer. This deflection introduces a lateral wave vector component, thus preventing bi-directional transmission of traditional vertical coupling due to the second-order Bragg reflection of the grating. Additionally, an apodized design is employed for the subwavelength grating to improve mode matching with a deflection angle incident. The integration of the metasurface and subwavelength grating enables a new vertical coupling scheme with high efficiency. After global optimization, we achieved a simulation coupling efficiency of -2.19 dB. The measured coupling efficiency is -3.36 dB with a center wavelength of 1545.6 nm and a 1-dB bandwidth of 32 nm. The results confirm the feasibility of the proposed new architecture.

Supplementation of spermidine enhances the quality of postovulatory aged porcine oocytes.

BACKGROUND: Spermidine (SPD) is an intermediate compound in the polyamine metabolism which takes critical part in a variety of cellular processes. In particular, it has been reported to exert anti-aging effects, suppress the age-related diseases, and extend lifespan across species. However, whether it has the favorable influence on the quality of postovulatory aged oocytes remains elusive. METHODS: Immunostaining and fluorescence intensity measurement were used to evaluate the effects of postovulatory aging and SPD supplementation on the oocyte fragmentation, spindle/chromosome structure, actin polymerization, dynamics of cortical granules (CGs) and ovastacin, mitochondrial distribution and function, as well as autophagy levels. In addition, in vitro sperm binding assay and in vitro fertilization (IVF) experiment were applied to assess the impacts of postovulatory aging and SPD supplementation on the sperm binding ability and fertilization capacity of oocytes. RESULTS: Here, we showed that supplementation of SPD during postovulatory aging could relieve the deterioration of porcine oocytes. Specifically, we found that postovulatory aging impaired the oocyte quality by damaging the morphological integrity of oocytes, maintenance of spindle/chromosome structure, and dynamics of actin cytoskeleton. Postovulatory aging also weakened the sperm binding ability and fertilization capacity of oocytes by compromising the distribution pattern of CGs and their content ovastacin. Notably, supplementation of SPD attenuated these defects in postovulatory aged porcine oocytes via strengthening mitochondrial function, eliminating excessive reactive oxygen species (ROS), inhibiting apoptosis, and enhancing autophagy levels. CONCLUSION: Altogether, our findings demonstrate that SPD supplementation is a feasible approach to ameliorate the quality of postovulatory aged oocytes, which can be potentially applied to the human assisted reproductive technology (ART) and in vitro production of animal embryos.

Astrocyte-derived exosomal lncRNA 4933431K23Rik modulates microglial phenotype and improves post-traumatic recovery via SMAD7 regulation.

Astrocyte-microglial interaction plays a crucial role in brain injury-associated neuroinflammation. Our previous data illustrated that astrocytes secrete microRNA, leading to anti-inflammatory effects on microglia. Long non-coding RNAs participate in neuroinflammation regulation after traumatic brain injury. However, the effect of astrocytes on microglial phenotype via long non-coding RNAs and the underlying molecular mechanisms remain elusive. We used long non-coding RNA sequencing on murine astrocytes and found that exosomal long non-coding RNA 4933431K23Rik attenuated traumatic brain injury-induced microglial activation in vitro and in vivo and ameliorated cognitive function deficiency. Furthermore, microRNA and messenger RNA sequencing together with binding prediction illustrated that exosomal long non-coding RNA 4933431K23Rik up-regulates E2F7 and TFAP2C expression by sponging miR-10a-5p. Additionally, E2F7 and TFAP2C, as transcription factors, regulated microglial Smad7 expression. Using Cx3cr1-Smad7 overexpression of adeno-associated virus, microglia specifically overexpressed Smad7 in the attenuation of neuroinflammation, resulting in less cognitive deficiency after traumatic brain injury. Mechanically, overexpressed Smad7 physically binds to IκBα and inhibits its ubiquitination, preventing NF-κB signaling activation. The Smad7 activator asiaticoside alleviates neuroinflammation and protects neuronal function in traumatic brain injury mice. This study revealed that an exosomal long non-coding RNA from astrocytes attenuates microglial activation after traumatic brain injury by up-regulating Smad7, providing a potential therapeutic target.

Cinchophen induces RPA1 related DNA damage and apoptosis to impair ENS development of zebrafish.

Nonsteroidal anti-inflammatory drugs (NSAIDs) have become contaminants widely distributed in the environment due to improper disposal and discharge. Previous study has found several components might involve in impairing enteric nervous system (ENS) development of zebrafish, including NSAIDs cinchophen. Deficient ENS development in fetal could lead to Hirschsprung disease (HSCR), a congenital neurocristopathy characterized by absence of enteric neurons in hindgut. However, the intrinsic mechanism of neurotoxicity of cinchophen is unclear. We confirmed that cinchophen could impair ENS development of zebrafish and transcriptome sequencing revealed that disfunction of Replication protein A1 (RPA1), which is involved in DNA replication and repairment, might be relevant to the neurotoxicity effects induced by cinchophen. Based on previous data of single cell RNA sequencing (scRNA-seq) of zebrafish gut cells, we observed that rpa1 mainly expressed in proliferating, differentiating ENS cells and neural crest progenitors. Interestingly, cinchophen induced apoptosis and impaired proliferation. Furthermore, cinchophen caused DNA damage and abnormal activation of ataxia telangiectasia mutated/ Rad3 related (ATM/ATR) and checkpoint kinase 2 (CHK2). Finally, molecular docking indicated cinchophen could bind and antagonize RPA1 more effectively. Our study might provide a better understanding and draw more attention to the role of environmental factors in the pathogenesis of HSCR. And the mechanism of cinchophen neurotoxicity would give theoretical guidance for clinical pharmacy.

Unveiling NRlncRNAs as prognostic biomarkers and therapeutic targets for head-and-neck squamous cell carcinoma through machine learning.

Head-and-neck squamous cell carcinoma (HNSCC) patients often exhibit insensitivity to immunotherapy, leading to treatment failure. Identifying potential biomarkers that can predict prognosis and improve the efficacy of treatment is crucial. In this study, we aimed to identify necroptosis-related long noncoding RNAs (NRlncRNAs) as potential therapeutic targets to improve the prognosis of HNSCC patients. By exploring the Genotype-Tissue Expression Project (GTEx) and the Cancer Genome Atlas (TCGA) databases, we identified NRlncRNAs and developed a risk model comprising 17 NRlncRNAs to predict the prognosis of HNSCC patients and to classify patients into two clusters based on their expression levels. We conducted various analyses, such as the Kaplan-Meier analysis, GSEA and IC50 prediction, to evaluate the differences in sensitivity to immunotherapy between the two clusters. Our findings suggest that NRlncRNAs have potential as therapeutic targets for improving the prognosis of HNSCC patients, and that individualized treatment approaches based on NRlncRNA expression levels can improve the sensitivity of immunotherapy and overall treatment outcomes. This study highlights new perspectives within clinical cancer informatics and provides insight into potential therapeutic strategies for HNSCC patients.

Genetic and Environmental Factors Co-Contributing to Behavioral Abnormalities in adnp/adnp2 Mutant Zebrafish.

Human mutations of ADNP and ADNP2 are known to be associated with neural developmental disorders (NDDs), including autism spectrum disorders (ASDs) and schizophrenia (SZ). However, the underlying mechanisms remain elusive. In this study, using CRISPR/Cas9 gene editing technology, we generated adnp and adnp2 mutant zebrafish models, which exhibited developmental delays, brain deficits, and core behavioral features of NDDs. RNA sequencing analysis of adnpa-/-; adnpb-/- and adnp2a-/-; adnp2b-/- larval brains revealed altered gene expression profiles affecting synaptic transmission, autophagy, apoptosis, microtubule dynamics, hormone signaling, and circadian rhythm regulation. Validation using whole-mount in situ hybridization (WISH) and real-time quantitative PCR (qRT-PCR) corroborated these findings, supporting the RNA-seq results. Additionally, loss of adnp and adnp2 resulted in significant downregulation of pan-neuronal HuC and neuronal fiber network α-Tubulin signals. Importantly, prolonged low-dose exposure to environmental endocrine disruptors (EEDs) aggravated behavioral abnormalities in adnp and adnp2 mutants. This comprehensive approach enhances our understanding of the complex interplay between genetic mutations and environmental factors in NDDs. Our findings provide novel insights and experimental foundations into the roles of adnp and adnp2 in neurodevelopment and behavioral regulation, offering a framework for future preclinical drug screening aimed at elucidating the pathogenesis of NDDs and related conditions.

Multifaceted anomaly detection framework for leachate monitoring in landfills.

The imperative to preserve environmental resources has transcended traditional conservation efforts, becoming a crucial element for sustaining life. Our deep interconnectedness with the natural environment, which directly impacts our well-being, emphasizes this urgency. Contaminants such as leachate from landfills are increasingly threatening groundwater, a vital resource that provides drinking water for nearly half of the global population. This critical environmental threat requires advanced detection and monitoring solutions to effectively safeguard our groundwater resources. To address this pressing need, we introduce the Multifaceted Anomaly Detection Framework (MADF), which integrates Electrical Resistivity Tomography (ERT) with advanced machine learning models-Isolation Forest (IF), One-Class Support Vector Machines (OC-SVM), and Local Outlier Factor (LOF). MADF processes and analyzes ERT data, employing these hybrid machine learning models to identify and quantify anomaly signals accurately via the majority vote strategy. Applied to the Chaling landfill site in Zhuzhou, China, MADF demonstrated significant improvements in detection capability. The framework enhanced the precision of anomaly detection, evidenced by higher Youden Index values (≈ 6.216%), with a 30% increase in sensitivity and a 25% reduction in false positives compared to traditional ERT inversion methods. Indeed, these enhancements are crucial for effective environmental monitoring, where the cost of missing a leak could be catastrophic, and for reducing unnecessary interventions that can be resource-intensive. These results underscore MADF's potential as a robust tool for proactive environmental management, offering a scalable and adaptable solution for comprehensive landfill monitoring and pollution prevention across varied environmental settings.

Polarization-insensitive EDG demultiplexer combined with a polarization beam splitter.

Polarization dependence is an inherent challenge for wavelength-division multiplexing transceivers on silicon photonic platforms, causing severe problems with polarization-dependent losses and hindering the implementation of monolithic integrated receivers. In this study, we developed a polarization-insensitive demultiplexer on a silicon nitride (Si3N4) platform, which provides a promising solution to the polarization challenge. Comprising an etched diffraction grating (EDG) and a polarization beam splitter (PBS), the demultiplexer can achieve polarization insensitivity by introducing an additional optical path difference for polarization compensation. The fabricated demultiplexers were experimentally measured to have minimum insertion losses of 1.5 dB, cross talks of better than -25 dB, and polarization-dependent losses of better than 0.7 dB. This is the first, to the best of our knowledge, proposed solution for a polarization-insensitive EDG demultiplexer combined with a PBS on a Si3N4 platform.

Impaired fertility in 4930590J08Rik mutant male mice is associated with defective sperm energy metabolism.

Testis-specifically expressed genes are important for male reproduction according to their unique expression patterns. However, the functions of most of these genes in reproduction are unclear. Here, we showed that mouse 4930590J08Rik was a testis-specifically expressed gene. 4930590J08Rik knockout mice exhibited a delay in the first wave of spermatogenesis and a reduction of cauda epididymal sperm. Furthermore, knockout spermatozoa exhibited defective acrosome reactions and decreased progressive motility, which led to impaired in vivo fertilization. Transcriptome analysis of testes revealed that most of the differentially expressed genes in knockout testes were associated with metabolic processes. 4930590J08Rik knockout sperm exhibited oxidative phosphorylation deficiency and were highly dependent on increased anaerobic glycolysis to compensate for ATP demands. Taken together, the 4930590J08Rik-disrupted mouse partially mimics the phenotypes of human asthenospermia and oligozoospermia, which provides a new model for further understanding the pathogenesis of idiopathic male infertility.

Isovalent electronic systems B+13 and BeB12: structural interchange of GM and TS.

Fluxional Wankel motor molecules have received considerable attention in recent years in both chemistry and nanoscience. Based on extensive first-principles theory calculations, we present herein the smallest neutral quasi-planar alkaline-earth metal-doped Wankel motor complex Cs BeB12 (BeB2@B10), which is isovalent with C2v B+13 (B3@B10+). The global minimum (GM) Cs BeB12 (1) and transition state (TS) Cs BeB12 (2) correspond to the C2v TS (4) and C2v GM (3) of B+13, respectively. Molecular dynamics simulations show that, with ten equivalent GMs and ten equivalent TSs intervals, the B10 outer ring in BeB12 (1/2) overcomes the rotational energy barrier to rotate almost freely around the BeB2 triangular core above 800 K in a rotation angle of 36° in each step. Detailed bonding analyses indicate that, in addition to the ten localized periphery B-B bonds, both Cs BeB12 (1) and Cs BeB12 (2) possess three delocalized bonding systems over the molecular framework satisfying the (4n+2) Hückel rule, making the neutral complex 2σ + π triply aromatic in nature and highly stable in thermodynamics.

Deep brain stimulation in Lesch-Nyhan syndrome: a systematic review.

Given the good results of deep brain stimulation (DBS) in the treatment of movement disorders, DBS was initially tried to treat Lesch-Nyhan syndrome (LNS) with the aim to alleviate LNS-related dystonia. Some cases have reported clinical results of DBS in LNS thus far. This systematic review was conducted to comprehensively summarize cases of LNS treated with DBS and evaluate the efficacy and safety of DBS in LNS. Eight publications covering 12 LNS patients were included in this review. DBS improved dystonia of the LNS to varying degrees. All the included cases achieved partial or complete control of self-injurious behavior (SIB). Overall, DBS is a promising treatment for both motor and behavior disorders of LNS patients, but the results reported thus far have varied widely, especially for motor outcomes. The ultimate clinical benefits in LNS patients were still unpredictable. DBS-related complications were rather common, which raised questions about the safety of the procedure in LNS. More research is needed to further clarify the safety and effectiveness of this treatment.

Spinal cord stimulation and deep brain stimulation for disorders of consciousness: a systematic review and individual patient data analysis of 608 cases.

The application of spinal cord stimulation (SCS) and deep brain stimulation (DBS) for disorders of consciousness (DoC) has been increasingly reported. However, there is no sufficient evidence to determine how effective and safe SCS and DBS are for DoC owing to various methodological limitations. We conducted a systematic review to elucidate the safety and efficacy of SCS and DBS for DoC by systematically reviewing related literature by searching PubMed, EMBASE, Medline, and Cochrane Library. Twenty eligible studies with 608 patients were included in this study. Ten studies with 508 patients reported the efficacy of SCS for DoC, and the estimated overall effectiveness rate was 37%. Five studies with 343 patients reported the efficacy of SCS for VS, and the estimated effectiveness rate was 30%. Three studies with 53 patients reported the efficacy of SCS for MCS, and the estimated effectiveness rate was 63%. Five studies with 92 patients reported the efficacy of DBS for DoC, and the estimated overall effectiveness rate was 40%. Four studies with 63 patients reported the efficacy of DBS for VS, and the estimated effectiveness rate was 26%. Three studies with 19 patients reported the efficacy of DBS for MCS, and the estimated effectiveness rate was 74%. The adverse event rate of DoC was 8.1% and 18.2% after SCS and DBS, respectively. These results suggest that SCS and DBS can be considered reasonable treatments for DoC with considerable efficacy and safety.

The Effect of Transversus Abdominis Plane Block in Kidney Transplantation: A Systematic Review and Meta-Analysis.

INTRODUCTION: The aim of the study was to evaluate the effect of transversus abdominal (TAP) block for postoperative analgesia after renal transplantation. METHODS: We searched PubMed, Embase, the Cochrane Library, and the Chinese Biomedical Literature Database for relevant studies. The related trials that met the inclusion criteria were analysed using RevMan 5.4 software. RESULTS: We found 15 randomized controlled trials and two retrospective studies that, on meta-analysis, showed that TAP block group had significantly lower requirement of opioid consumption (MD -11.89, 95% CI -17.13∼-6.65) at 24 h for pain mitigation and pain intensity VAS at rest at 6h (MD -1.13, 95% CI -1.76∼-0.49), 12 h (MD -0.83, 95% CI -1.30∼-0.36) and 24 h (MD -0.47, 95% CI -0.75∼-0.20). Also, postoperative nausea and vomiting were not statistically significant (RR 1.00, 95% CI 0.78∼1.27). CONCLUSION: TAP block appears to significantly reduce renal transplantation pain and the amount of opioid use on the first postoperative day after renal transplantation.

Exposure to diisononyl phthalate deteriorates the quality of porcine oocytes by inducing the apoptosis.

Diisononyl phthalate (DINP), a mixture of chemical compounds composed of diverse isononyl esters of phthalic acid, is commonly applied as a plasticizer to substitute for di (2-ethylhexyl) phthalate (DEHP). It has been demonstrated that DINP exposure impairs the functions of kidney and liver in animals. However, the effects and potential mechanisms of DINP exposure on the female reproduction, especially the oocyte quality are still poorly understood. Here, we discovered that DINP exposure weakened the porcine oocyte meiotic competency (78.9% vs 53.6%, P < 0.001) and fertilization ability (78.5% vs 34.1%, P < 0.0001) during in vitro maturation. Specifically, DINP exposure induced the persistent spindle assembly checkpoint (SAC) activation caused by the disorganized spindle/chromosome apparatus (spindle: 20.0% vs 83.3%, P < 0.001; chromosome: 20.0% vs 80.0%, P < 0.01) to arrest meiotic progression of oocytes at metaphase I stage. In addition, DINP exposure disturbed the dynamics of sperm binding (146.7 vs 58.6, P < 0.0001) and fusion proteins (19.5 vs 11.6, P < 0.0001) in oocytes to compromise their fertilization ability. In particular, transcriptome data uncovered that the action mechanism of DINP on the oocyte maturation was associated with oxidative phosphorylation, apoptosis and autophagy pathways. Lastly, we validated that DINP exposure resulted in the mitochondrial dysfunction (27.2 vs 19.8, P < 0.0001) and elevated levels of reactive oxygen species (ROS; 8.9 vs 19.9, P < 0.0001) to trigger the occurrence of apoptosis (7.2 vs 13.1, P < 0.0001) and protective autophagy (68.6 vs 139.3, P < 0.01). Altogether, our findings not only testify that DINP has a potentially adverse impact on the mammalian oocyte quality, but also provide a scientific reference regarding how environment pollutants act on the female germ cell development.

Analysis of Codon Usage Bias in Xyloglucan Endotransglycosylase (XET) Genes.

Xyloglucan endotransglycosylase (XET) genes are widely distributed in most plants, but the codon usage bias of XET genes has remained uncharacterized. Thus, we analyzed the codon usage bias using 4500 codons of 20 XET genes to elucidate the genetic and evolutionary patterns. Phylogenetic and hierarchical cluster analyses revealed that the 20 XET genes belonged to two groups. The closer the genetic distance, the more similar the codon usage preference. The codon usage bias of most XET genes was weak, but there was also some codon usage bias. AGA, AGG, AUC, and GUG were the top four codons (RSCU > 1.5) in the 20 XET genes. CitXET had a stronger codon usage bias, and there were eight optimal codons of CitXET (i.e., AGA, AUU, UCU, CUU, CCA, GCU, GUU, and AAA). The RSCU values underwent a correspondence analysis. The two main factors affecting codon usage bias (i.e., Axes 1 and 2) accounted for 54.8% and 17.6% of the total variation, respectively. Multiple correspondence analysis revealed that XET genes were widely distributed, with Group 1 genes being closer to Axis 1 than Group 2 genes, which were closer to Axis 2. Codons with A/U at the third codon position were distributed closer to Axis 1 than codons with G/C at the third codon position. PgXET, ZmXET, VlXET, VrXET, and PcXET were biased toward codons ending with G/C. In contrast, CitXET, DpXET, and BrpXET were strongly biased toward codons ending with A/U, indicating that these XET genes have a strong codon usage bias. Translational selection and base composition (especially A and U at the third codon position), followed by mutation pressure and natural selection, may be the most important factors affecting codon usage of 20 XET genes. These results may be useful in clarifying the codon usage bias of XET genes and the relevant evolutionary characteristics.