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The edible jelly fungus Dacryopinax spathularia (Dacrymycetaceae) is wood-decaying and can be commonly found worldwide. It has found application in food additives, given its ability to synthesize long-chain glycolipids, among other uses. In this study, we present the genome assembly of D. spathularia using a combination of PacBio HiFi reads and Omni-C data. The genome size is 29.2 Mb. It has high sequence contiguity and completeness, with a scaffold N50 of 1.925 Mb and a 92.0% BUSCO score. A total of 11,510 protein-coding genes and 474.7 kb repeats (accounting for 1.62% of the genome) were predicted. The D. spathularia genome assembly generated in this study provides a valuable resource for understanding their ecology, such as their wood-decaying capability, their evolutionary relationships with other fungi, and their unique biology and applications in the food industry. © 2024 GigaScience Press. All rights reserved.

The golden birdwing Troides aeacus (Lepidoptera, Papilionidae), a significant species in Asia, faces habitat loss due to urbanization and human activities, necessitating its protection. However, the lack of genomic resources hinders our understanding of their biology and diversity, and impedes our conservation efforts based on genetic information or markers. Here, we present the first chromosomal-level genome assembly of T. aeacus using PacBio SMRT and Omni-C scaffolding technologies. The assembled genome (351 Mb) contains 98.94% of the sequences anchored to 30 pseudo-molecules. The genome assembly has high sequence continuity with contig length N50 = 11.67 Mb and L50 = 14, and scaffold length N50 = 12.2 Mb and L50 = 13. A total of 24,946 protein-coding genes were predicted, with high BUSCO score completeness (98.8% and 94.7% of genome and proteome BUSCO, respectively. This genome offers a significant resource for understanding the swallowtail butterfly biology and carrying out its conservation. © 2024 GigaScience Press. All rights reserved.

Grantham’s camellia (Camellia granthamiana Sealy) is a rare and endangered tea species discovered in Hong Kong in 1955 and endemic to southern China. Despite its high conservation value, the genomic resources of C. granthamiana are limited. Here, we present a chromosome-scale draft genome of the tetraploid C. granthamiana (2n = 4x = 60), combining PacBio long-read sequencing and Omni-C data. The assembled genome size is ∼2.4 Gb, with most sequences anchored to 15 pseudochromosomes resembling a monoploid genome. The genome has high contiguity, with a scaffold N50 of 139.7 Mb, and high completeness (97.8% BUSCO score). Our gene model prediction resulted in 68,032 protein-coding genes (BUSCO score of 90.9%). We annotated 1.65 Gb of repeat content (68.48% of the genome). Our Grantham’s camellia genome assembly is a valuable resource for investigating Grantham’s camellia’s biology, ecology, and phylogenomic relationships with other Camellia species, and provides a foundation for further conservation measures. © 2024 GigaScience Press. All rights reserved.

Chitons (Polyplacophora) are marine molluscs that can be found worldwide from cold waters to the tropics, and play important ecological roles in the environment. However, only two chiton genomes have been sequenced to date. The chiton Liolophura japonica (Lischke, 1873) is one of the most abundant polyplacophorans found throughout East Asia. Our PacBio HiFi reads and Omni-C sequencing data resulted in a high-quality near chromosome-level genome assembly of ∼609 Mb with a scaffold N50 length of 37.34 Mb (96.1% BUSCO). A total of 28,233 genes were predicted, including 28,010 protein-coding ones. The repeat content (27.89%) was similar to that of other Chitonidae species and approximately three times lower than that of the Hanleyidae chiton genome. The genomic resources provided by this work will help to expand our understanding of the evolution of molluscs and the ecological adaptation of chitons.

The long-spined sea urchin Diadema setosum is an algal and coral feeder widely distributed in the Indo-Pacific that can cause severe bioerosion on the reef community. However, the lack of genomic information has hindered the study of its ecology and evolution. Here, we report the chromosomal-level genome (885.8 Mb) of the long-spined sea urchin D. setosum using a combination of PacBio long-read sequencing and Omni-C scaffolding technology. The assembled genome contains a scaffold N50 length of 38.3 Mb, 98.1% of complete BUSCO (Geno, metazoa_odb10) genes (the single copy score is 97.8% and the duplication score is 0.3%), and 98.6% of the sequences are anchored to 22 pseudo-molecules/chromosomes. A total of 27,478 gene models have were annotated, reaching a total of 28,414 transcripts, including 5,384 tRNA and 23,030 protein-coding genes. The high-quality genome of D. setosum presented here is a valuable resource for the ecological and evolutionary studies of this coral reef-associated sea urchin.

The milky mangrove Excoecaria agallocha is a latex-secreting mangrove that are distributed in tropical and subtropical regions. While its poisonous latex is regarded as a potential source of phytochemicals for biomedical applications, the genomic resources of E. agallocha remains limited. Here, we present a chromosomal level genome of E. agallocha, assembled from the combination of PacBio long-read sequencing and Omni-C data. The resulting assembly size is 1,332.45 Mb and has high contiguity and completeness with a scaffold N50 of 58.9 Mb and a BUSCO score of 98.4%, with 86.08% of sequences anchored to 18 pseudomolecules. 73,740 protein-coding genes were also predicted. The milky mangrove genome provides a useful resource for further understanding the biosynthesis of phytochemical compounds in E. agallocha.

Wei Y, Liao Y, Deng Y, Zu Y, Zhao B, Li F. Onco Targets Ther. 2019;12:9005–9016. We, the Editors and Publisher of OncoTargets and Therapy, have retracted the following article. Following publication of the article, concerns were raised about the duplication of images from Figures 2, 5 and 7 with images from other unrelated articles. Specifically, The image for Figure 2B, PC9, NC inhibitor, has been duplicated with the image for Figure 2D, PANC1, Solasodine 10µg/mL, from Fan Y, Li Z, Wu L, et al. Solasodine, Isolated from Solanum sisymbriifolium Fruits, Has a Potent Anti-Tumor Activity Against Pancreatic Cancer. Drug Des Devel Ther. 2021;15:1509–1519. https://doi.org/10.2147/DDDT.S266746. Images for Figure 3A have been duplicated with images for Figure 4D from Wang M, Yu R, Ling X, et al. COPB2 promotes metastasis and inhibits apoptosis of lung adenocarcinoma cells through functioning as a target of miR-216a-3p JF. Translational Cancer Research. 2020; 9(4): 2648–2659. https://doi.org/10.21037/tcr.2020.02.65 and Figure 5B from Jia Yy, Yu Y, Li HJ. POSTN promotes proliferation and epithelial-mesenchymal transition in renal cell carcinoma through ILK/AKT/mTOR pathway. J Cancer. 2021;12(14):4183–4195. https://doi.org/10.7150/jca.51253. The image for Figure 5C, A549, miR-503+PDK1, has been duplicated with the image for Figure 3C, NB4 cell, inhibitors, from Wang D, Chen J, Ding Y, et al. miR-188-5p Promotes Tumor Growth by Targeting CD2AP Through PI3K/AKT/mTOR Signaling in Children with Acute Promyelocytic Leukemia. Onco Targets Ther. 2020;13:6681–6697. https://doi.org/10.2147/OTT.S244813. The authors did not respond to our queries and were unable to provide an explanation for the duplicated images or provide data for the study. As verifying the validity of published work is core to the integrity of the scholarly record, we are therefore retracting the article and the authors were notified of this. We have b

Yingying Wei,1,&ast; Jiahuan Peng,2,&ast; Han Li,1 Mengtian Wei,1 Hao Peng,1 Kai Wang,1 Yongfu Yu,2 Qizhi He3 1Clinical and Translational Research Center, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China; 2Department of Biostatistics, School of Public Health, Fudan University, Shanghai, People’s Republic of China; 3Department of Pathology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China&ast;These authors contributed equally to this workCorrespondence: Qizhi He, Department of Pathology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, No. 2699, West Gaoke Road, Pudong District, Shanghai, 201204, People’s Republic of China, Fax +86-2120261141, Email qizhihe2013@163.comPurpose: Infants with macrosomia are more likely to be born to mothers with gestational diabetes mellitus (GDM). This study aimed to investigate the associations between maternal blood glucose levels and fetal weight, placental weight, and risk of macrosomia in mothers with GDM.Patients and Methods: This retrospective study included 3211 singletons of mothers with GDM at the Shanghai First Maternity and Infant Hospital between January 2017 and December 2019. All women underwent an oral glucose tolerance test (OGTT) during the 24– 28 weeks gestation period. Data on fetal and placental parameters were collected at delivery. Multiple linear regression models were used to evaluate the associations of maternal blood glucose levels with fetal weight and placental weight, while multiple logistic regression model was used to estimate the association between maternal blood glucose levels and the risk of macrosomia.Results: The prevalence of GDM in our study was 7%. Fasting plasma glucose (FPG) was positively correlated with fetal weight (r2=0.0329, P< 0.001

In epigenome-wide association studies, the measured signals for each sample are a mixture of methylation profiles from different cell types. Current approaches to the association detection claim whether a cytosine-phosphate-guanine (CpG) site is associated with the phenotype or not at aggregate level and can suffer from low statistical power. Here, we propose a statistical method, HIgh REsolution (HIRE), which not only improves the power of association detection at aggregate level as compared to the existing methods but also enables the detection of risk-CpG sites for individual cell types.

In epigenome-wide association studies, the measured signals for each sample are a mixture of methylation profiles from different cell types. Current approaches to the association detection claim whether a cytosine-phosphate-guanine (CpG) site is associated with the phenotype or not at aggregate level and can suffer from low statistical power. Here, we propose a statistical method, HIgh REsolution (HIRE), which not only improves the power of association detection at aggregate level as compared to the existing methods but also enables the detection of risk-CpG sites for individual cell types.

In epigenome-wide association studies, the measured signals for each sample are a mixture of methylation profiles from different cell types. Current approaches to the association detection claim whether a cytosine-phosphate-guanine (CpG) site is associated with the phenotype or not at aggregate level and can suffer from low statistical power. Here, we propose a statistical method, HIgh REsolution (HIRE), which not only improves the power of association detection at aggregate level as compared to the existing methods but also enables the detection of risk-CpG sites for individual cell types.

This paper has been retracted. Wei Y, Liao Y, Deng Y, Zu Y, Zhao B, Li F. Onco Targets Ther. 2019;12:9005–9016. We, the Editors and Publisher of OncoTargets and Therapy, have retracted the following article. Following publication of the article, concerns were raised about the duplication of images from Figures 2, 5 and 7 with images from other unrelated articles. Specifically, The image for Figure 2B, PC9, NC inhibitor, has been duplicated with the image for Figure 2D, PANC1, Solasodine 10µg/mL, from Fan Y, Li Z, Wu L, et al. Solasodine, Isolated from Solanum sisymbriifolium Fruits, Has a Potent Anti-Tumor Activity Against Pancreatic Cancer. Drug Des Devel Ther. 2021;15:1509–1519. https://doi.org/10.2147/DDDT.S266746. Images for Figure 3A have been duplicated with images for Figure 4D from Wang M, Yu R, Ling X, et al. COPB2 promotes metastasis and inhibits apoptosis of lung adenocarcinoma cells through functioning as a target of miR-216a-3p JF. Translational Cancer Research. 2020; 9(4): 2648–2659. https://doi.org/10.21037/tcr.2020.02.65 and Figure 5B from Jia Yy, Yu Y, Li HJ. POSTN promotes proliferation and epithelial-mesenchymal transition in renal cell carcinoma through ILK/AKT/mTOR pathway. J Cancer. 2021;12(14):4183–4195. https://doi.org/10.7150/jca.51253. The image for Figure 5C, A549, miR-503+PDK1, has been duplicated with the image for Figure 3C, NB4 cell, inhibitors, from Wang D, Chen J, Ding Y, et al. miR-188-5p Promotes Tumor Growth by Targeting CD2AP Through PI3K/AKT/mTOR Signaling in Children with Acute Promyelocytic Leukemia. Onco Targets Ther. 2020;13:6681–6697. https://doi.org/10.2147/OTT.S244813. The authors did not respond to our queries and were unable to provide an explanation for the duplicated images or provide data for the study. As verifying the validity of published work is core to the integrity of the scholarly record, we are therefore retracting the article and the authors w

Over a half million new cases of Head and Neck Squamous Cell Carcinoma (HNSCC) are diagnosed annually worldwide, however, 5 year overall survival is only 50% for HNSCC patients. Recently, high throughput technologies have accelerated the genome-wide characterization of HNSCC. However, comprehensive pipelines with statistical algorithms that account for HNSCC biology and perform independent confirmatory and functional validation of candidates are needed to identify the most biologically relevant genes. We applied outlier statistics to high throughput gene expression data, and identified 76 top-scoring candidates with significant differential expression in tumors compared to normal tissues. We identified 15 epigenetically regulated candidates by focusing on a subset of the genes with a negative correlation between gene expression and promoter methylation. Differential expression and methylation of 3 selected candidates (BANK1, BIN2, and DTX1) were confirmed in an independent HNSCC cohorts from Johns Hopkins and TCGA (The Cancer Genome Atlas). We further performed functional evaluation of NOTCH regulator, DTX1, which was downregulated by promoter hypermethylation in tumors, and demonstrated that decreased expression of DTX1 in HNSCC tumors maybe associated with NOTCH pathway activation and increased migration potential.

Over a half million new cases of Head and Neck Squamous Cell Carcinoma (HNSCC) are diagnosed annually worldwide, however, 5 year overall survival is only 50% for HNSCC patients. Recently, high throughput technologies have accelerated the genome-wide characterization of HNSCC. However, comprehensive pipelines with statistical algorithms that account for HNSCC biology and perform independent confirmatory and functional validation of candidates are needed to identify the most biologically relevant genes. We applied outlier statistics to high throughput gene expression data, and identified 76 top-scoring candidates with significant differential expression in tumors compared to normal tissues. We identified 15 epigenetically regulated candidates by focusing on a subset of the genes with a negative correlation between gene expression and promoter methylation. Differential expression and methylation of 3 selected candidates (BANK1, BIN2, and DTX1) were confirmed in an independent HNSCC cohorts from Johns Hopkins and TCGA (The Cancer Genome Atlas). We further performed functional evaluation of NOTCH regulator, DTX1, which was downregulated by promoter hypermethylation in tumors, and demonstrated that decreased expression of DTX1 in HNSCC tumors maybe associated with NOTCH pathway activation and increased migration potential.

Head and Neck Squamous Cell Carcinoma (HNSCC) is the fifth most common cancer, annually affecting over half a million people worldwide. Presently, there are no accepted biomarkers for clinical detection and surveillance of HNSCC. In this work, a comprehensive genome-wide analysis of epigenetic alterations in primary HNSCC tumors was employed in conjunction with cancer-specific outlier statistics to define novel biomarker genes which are differentially methylated in HNSCC. The 37 identified biomarker candidates were top-scoring outlier genes with prominent differential methylation in tumors, but with no signal in normal tissues. These putative candidates were validated in independent HNSCC cohorts from our institution and TCGA (The Cancer Genome Atlas). Using the top candidates, ZNF14, ZNF160, and ZNF420, an assay was developed for detection of HNSCC cancer in primary tissue and saliva samples with 100% specificity when compared to normal control samples. Given the high detection specificity, the analysis of ZNF DNA methylation in combination with other DNA methylation biomarkers may be useful in the clinical setting for HNSCC detection and surveillance, particularly in high-risk patients. Several additional candidates identified through this work can be further investigated toward future development of a multi-gene panel of biomarkers for the surveillance and detection of HNSCC.

Head and Neck Squamous Cell Carcinoma (HNSCC) is the fifth most common cancer, annually affecting over half a million people worldwide. Presently, there are no accepted biomarkers for clinical detection and surveillance of HNSCC. In this work, a comprehensive genome-wide analysis of epigenetic alterations in primary HNSCC tumors was employed in conjunction with cancer-specific outlier statistics to define novel biomarker genes which are differentially methylated in HNSCC. The 37 identified biomarker candidates were top-scoring outlier genes with prominent differential methylation in tumors, but with no signal in normal tissues. These putative candidates were validated in independent HNSCC cohorts from our institution and TCGA (The Cancer Genome Atlas). Using the top candidates, ZNF14, ZNF160, and ZNF420, an assay was developed for detection of HNSCC cancer in primary tissue and saliva samples with 100% specificity when compared to normal control samples. Given the high detection specificity, the analysis of ZNF DNA methylation in combination with other DNA methylation biomarkers may be useful in the clinical setting for HNSCC detection and surveillance, particularly in high-risk patients. Several additional candidates identified through this work can be further investigated toward future development of a multi-gene panel of biomarkers for the surveillance and detection of HNSCC.