Comparative and Functional Genomics最新文献

{"title":"Genome-Wide Identification and Characterization of PRR Gene Family and their Diurnal Rhythmic Expression Profile in Maize","authors":"Cuiling Wang,&nbsp;Leili Wang,&nbsp;Qingqing Liu,&nbsp;Yanling Zhang,&nbsp;Keqing Dong","doi":"10.1155/2022/6941607","DOIUrl":"10.1155/2022/6941607","url":null,"abstract":"<div>\u0000 <p>As essential components of the circadian clock, the pseudo-response regulator (PRR) gene family plays critical roles in plant photoperiod pathway. In this study, we performed a genome-wide identification and a systematic analysis of the PRR gene family in maize. Nine <i>ZmPRR</i>s were identified, and the gene structure, conserved motif, evolution relationship, and expression pattern of <i>ZmPRRs</i> were analyzed comprehensively. Phylogenetic analysis indicated that the nine <i>ZmPRR</i> genes were divided into three groups, except for <i>ZmPRR73</i>, two of which were highly homologous to each of the <i>AtPRR</i> or <i>OsPRR</i> quintet members. Promoter cis-element analysis of <i>ZmPRRs</i> demonstrated that they might be involved in multiple signaling transduction pathways, such as light response, biological or abiotic stress response, and hormone response. qRT-PCR analysis revealed that the levels of <i>ZmPRRs</i> transcripts varied considerably and exhibited a diurnal rhythmic oscillation expression pattern in the given 24-h period under both SD and LD conditions, which indicated that the level of transcription of <i>ZmPRRs</i> expression is subjected to a circadian rhythm and modulated by light and the circadian clock. The present study will provide an insight into further exploring the biological function and regulatory mechanism of <i>ZmPRR</i> genes in circadian rhythm and response to photoperiod in maize.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2022 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/2022/6941607","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48577592","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification and Validation of Inflammatory Response-Related Gene Signatures to Predict the Prognosis of Neuroblastoma","authors":"Jiye Song,&nbsp;Liang Song,&nbsp;Zhenmei Lv,&nbsp;Jianke Liu,&nbsp;Xuan Feng,&nbsp;Song Zhang,&nbsp;Aiqin Song","doi":"10.1155/2022/2417351","DOIUrl":"10.1155/2022/2417351","url":null,"abstract":"<div>\u0000 <p><i>Background</i>. Neuroblastoma (NB) is the third most common malignant tumor in children. The inflammation is believed to be closely related to NB patients’ prognosis. However, there is no comprehensive research to study the role of inflammatory response-related gene (IRRG) in NB patients. <i>Methods</i>. We downloaded the gene expression profiles of NB patients from GEO and TARGET database, and the expression of 200 IRRGs was extracted. Then, we performed differentially analysis between INSS stage 4 and INSS stage 4S NB patients. The univariate and multivariate Cox regression analyses were performed to screen out the overall survival- (OS-) and event-free survival- (EFS-) related IRRGs in GSE49710, and two signatures were constructed; both signatures were evaluated by Kaplan-Meier (K-M) survival curve and receiver operating characteristic (ROC) curve. Finally, the TARGET cohort was used to validate IRRG signatures, and the independence of the prognostic IRRG signatures was evaluated by integrating clinical information. <i>Results</i>. We screened out 10 OS-related IRRGs and 11 EFS-related IRRGs. Then, we identified that OS- and EFS-related IRRG signatures and found that the OS and EFS of NB patients in the low-risk group were significantly superior than those in the high-risk group (both <i>P</i> value &lt; 0.0001). The AUC values of 3-, 5-, and 7-year OS are 0.910, 0.933, and 0.921, respectively, and 3-, 5-, and 7-year EFS are 0.840, 0.835, and 0.837, respectively. In addition, we found that both IRRG signatures can be used as independent prognostic indicators for patients with NB. Both IRRG signatures still have good predictive ability in validation cohort. <i>Conclusions</i>. We constructed and validated two prognostic gene signatures based on IRRGs. Our study helped us to better understand the role of inflammation in NB and provided new insights for the prognosis assessment and treatment strategy for NB patients.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2022 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/2022/2417351","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47657487","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"NEIL3 Mediates Lung Cancer Progression and Modulates PI3K/AKT/mTOR Signaling: A Potential Therapeutic Target","authors":"Hongbo Huang,&nbsp;Qingwang Hua","doi":"10.1155/2022/8348499","DOIUrl":"10.1155/2022/8348499","url":null,"abstract":"<div>\u0000 <p><i>Background</i>. Nei endonuclease VIII-like 3 (NEIL3) is widely involved in pathophysiological processes of the body; however, its role in lung cancer has not been conclusively determined. <i>Objective</i>. This study is aimed at exploring the role of NEIL3 in lung cancer. <i>Methods</i>. The public data used in this study were downloaded from The Cancer Genome Atlas (TCGA) database. “Limma” in R was used for the analysis of differentially expressed genes. Clinical correlations and prognostic analyses were performed using the survival package in R. The proliferative abilities of lung cancer cells were evaluated by the CCK8 and colony formation assays while their invasive and migration abilities were assessed by the transwell and wound healing assays. Quantitative real-time PCR (qRT-PCR) and western blot analyses were utilized to detect RNA and protein levels. Biological differences between groups were determined by gene set enrichment analysis (GSEA). Tumor Immune Dysfunction and Exclusion (TIDE) as well as Genomics of Drug Sensitivity in Cancer (GDSC) was used for immunotherapeutic and chemotherapeutic sensitivity analyses. <i>Results</i>. NEIL3 was upregulated in NSCLC tissues and cell lines, implying that it is involved in lung cancer initiation and progression. Clinical correlation and prognostic analyses showed that NEIL3 was associated with worse clinical features (stage and T and N classifications) and poor prognostic outcomes. <i>In vitro</i>, NEIL3 significantly enhanced NSCLC proliferation, invasion, and migration. GSEA indicated that NEIL3 might be involved in PI3K/AKT/mTOR, G2/M checkpoints, and E2F target pathways. Inhibition of NEIL3 suppressed cyclinD1 and p-AKT protein levels; however, it had no effects on AKT levels, indicating that NEIL3 can partially activate the PI3K/AKT/mTOR signaling pathway. The predicted result of TIDE indicated that immunotherapeutic nonresponders had elevated NEIL3 levels. Moreover, there was a positive correlation between NEIL3 levels and chemosensitivity to cisplatin and paclitaxel. <i>Conclusion</i>. In general, NEIL3 mediates NSCLC progression and affects sensitivity to immunotherapy and chemotherapy; therefore, it is a potential molecular target for treatment.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2022 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/2022/8348499","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48726341","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome Editing: A Promising Approach for Achieving Abiotic Stress Tolerance in Plants","authors":"Navdeep Kaur,&nbsp;Shubham Sharma,&nbsp;Mirza Hasanuzzaman,&nbsp;Pratap Kumar Pati","doi":"10.1155/2022/5547231","DOIUrl":"10.1155/2022/5547231","url":null,"abstract":"<div>\u0000 <p>The susceptibility of crop plants towards abiotic stresses is highly threatening to assure global food security as it results in almost 50% annual yield loss. To address this issue, several strategies like plant breeding and genetic engineering have been used by researchers from time to time. However, these approaches are not sufficient to ensure stress resilience due to the complexity associated with the inheritance of abiotic stress adaptive traits. Thus, researchers were prompted to develop novel techniques with high precision that can address the challenges connected to the previous strategies. Genome editing is the latest approach that is in the limelight for improving the stress tolerance of plants. It has revolutionized crop research due to its versatility and precision. The present review is an update on the different genome editing tools used for crop improvement so far and the various challenges associated with them. It also highlights the emerging potential of genome editing for developing abiotic stress-resilient crops.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2022 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/2022/5547231","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43980322","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prostate Cancer Susceptibility Loci Identified in GATA2 and ZMIZ1 in Chinese Population","authors":"Hui-Jing Zhang,&nbsp;Zhongyuan Liu,&nbsp;Liang Kan","doi":"10.1155/2022/8553530","DOIUrl":"10.1155/2022/8553530","url":null,"abstract":"<div>\u0000 <p><i>Background</i>. Common genetic risk variants for prostate cancer (PCa) have been identified at approximately 170 loci using genome-wide association studies (GWAS), most of which were identified in European populations. Recently, GWAS were applied to a large Japanese cohort and identified 12 novel susceptibility loci associated with PCa risk. In this study, we aim to investigate PCa susceptibility loci in the Chinese population. The study data will be used to promote PCa risk control in China. <i>Methods</i>. A total of 235 PCa patients and 252 control subjects (all unrelated) were enrolled in this case-control PCa study. Nine single nucleotide polymorphisms (SNPs) were genotyped in <i>GATA2</i> (rs73862213, rs2335052, and rs10934857), <i>ZMIZ1</i> (rs704017, rs77911174, and rs3740259), and <i>SUN2</i> (rs78397383, rs5750680, and rs138705) genes. The associations between the candidate SNPs and PCa were analyzed using multiple-factor logistic regression and haplotype analysis. <i>Results</i>. The allele frequency distributions of rs73862213 and rs2335052 in the <i>GATA2</i> gene and rs704017 and rs77911174 in the <i>ZMIZ1</i> gene were found to be significantly different between PCa cases and controls. Haplotype analysis revealed that the G-C-A haplotype of the <i>GATA2</i> gene (order of SNPs: rs73862213-rs2335052-rs10934857) and the G-G-G haplotype of the <i>ZMIZ1</i> gene (order of SNPs: rs704017-rs77911174-rs3740259) were associated with increased PCa risk. None of the <i>SUN2</i> haplotypes were associated with PCa. <i>Conclusions</i>. Our study data indicates that the minor alleles of rs73862213 and rs2335052 in the <i>GATA2</i> gene and rs704017 and rs77911174 in the <i>ZMIZ1</i> gene were associated with increased PCa risk. These findings greatly extended our knowledge of the etiology of PCa.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2022 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/2022/8553530","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46542393","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Upregulation of Yin-Yang-1 Associates with Proliferation and Glutamine Metabolism in Esophageal Carcinoma","authors":"Can Luo,&nbsp;Xin Chen,&nbsp;Yuting Bai,&nbsp;Lei Xu,&nbsp;Shuqi Wang,&nbsp;Lihua Yao,&nbsp;Xiaolan Guo,&nbsp;Dongsheng Wang,&nbsp;Xiaowu Zhong","doi":"10.1155/2022/9305081","DOIUrl":"10.1155/2022/9305081","url":null,"abstract":"<div>\u0000 <p><i>Objective</i>. To investigate the expression of Yin-Yang-1 (YY1) in esophageal carcinoma (ESCA) and its effect on glutamine metabolism in ESCA. <i>Methods</i>. The expression and roles of YY1 in ESCA were investigated using a series of bioinformatics databases and tools. The expression of YY1 between ESCA tissues with the corresponding adjacent tissues was validated using real-time PCR, western blot, and immunohistochemical staining method. Furthermore, the effects of YY1 on ESCC cell proliferation and migration were examined. The correlation between the YY1 and glutamine metabolism was evaluated by western blot. <i>Results</i>. YY1 gene was highly conserved in evolution and upregulated in ESCA tissues and ESCC cell lines (ECA109 and TE-1). In addition, YY1 may affect the level of immune cell infiltration and promote tumor cell immune escape. Functional enrichment analysis found that YY1 involved in many biological processes, such as cell division and glutathione and glutamine metabolism. After siRNA knockdown of YY1 in ECA109 and TE-1, the proliferation and the migration of ECA109 and TE-1 were suppressed. The glutamine consumption and glutamate production were significantly decreased. The protein expression of alanine-, serine-, cysteine-preferring transporter 2 (ASCT2), glutaminase (GLS), and glutamate dehydrogenase (GLUD1) was significantly downregulated. <i>Conclusion</i>. YY1 is highly expressed in ESCA and may promote glutamine metabolism of ESCC cells, indicating it may be as a diagnostic biomarker for ESCA.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2022 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/2022/9305081","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41760903","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Circ_0078767 Inhibits the Progression of Non-Small-Cell Lung Cancer by Regulating the GPX3 Expression by Adsorbing miR-665","authors":"Xiting Liu,&nbsp;Ze Chen,&nbsp;Yuqiang Wu,&nbsp;Feng Gu,&nbsp;Dong Yan,&nbsp;Lei Yang,&nbsp;Qin Ma,&nbsp;Caihong Fu","doi":"10.1155/2022/6361256","DOIUrl":"10.1155/2022/6361256","url":null,"abstract":"<div>\u0000 <p>Non-small-cell lung cancer (NSCLC) is one of the most serious cancers. The circular RNA_0078767 (circ_0078767) expression was decreased in NSCLC tissues. However, the molecular mechanism of circ_0078767 remains unknown. The expression of circ_0078767, microRNA-665 (miR-665), and glutathione peroxidase 3 (GPX3) was detected by quantitative real-time fluorescence polymerase chain reaction (qRT-PCR). Cell proliferation, migration, and invasion were detected by colony formation assay and transwell assay, respectively. The lactate production and glucose consumption were tested by glycolysis. Western blot examined the protein levels of hexokinase-2 (HK2), matrix metalloproteinase-9 (MMP9), and GPX3 cells. Circinteractome predicted the relationship between miR-665 and circ_0078767 or GPX3 and was verified by dual luciferase reporter assays. The xenotransplantation model was established to study the role of circ_0078767 in vivo. The expression of circ_0078767 and GPX3 was decreased in NSCLC tissues, while the expression of miR-665 was increased. Circ_0078767 can sponge miR-665, and GPX3 is the target of miR-665. In vitro complement experiments showed that knockdown of circ_0078767 significantly promoted malignant behavior of NSCLC, while cotransfection of miR-665 inhibitor partially reduced this change. In addition, the GPX3 overexpression decreased the promoting effects of miR-665 upregulation on proliferation, migration, and invasion of NSCLC cells. Mechanically, circ_0078767 regulates the GPX3 expression in NSCLC cells by spongy miR-665. In addition, in vivo studies have shown that downregulation of circ_0078767 promotes tumor growth. Circ_0078767 silencing promotes proliferation, migration, invasion, and glycolysis of NSCLC cells by regulating the miR-665/GPX3 axis, suggesting that circ_0078767/miR-665/GPX3 axis may be a potential regulatory mechanism for the treatment of NSCLC.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2022 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/2022/6361256","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45092714","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-Wide Identification and Characterization of the Shaker-Type K+ Channel Genes in Prunus persica (L.) Batsch","authors":"Yong Yang,&nbsp;Jinlong Han,&nbsp;Yue Zhang,&nbsp;Shizhuo Lin,&nbsp;Meixia Liang,&nbsp;Lizi Zhao,&nbsp;Zhizhong Song","doi":"10.1155/2022/5053838","DOIUrl":"10.1155/2022/5053838","url":null,"abstract":"<div>\u0000 <p>Shaker-type K⁺ channels are critical for plant K⁺ acquisition and translocation that play key roles during plant growth and development. However, molecular mechanisms towards K⁺ channels are extremely rare in fruit trees, especially in peach. In this study, we identified 7 putative shaker-type K⁺ channel genes from peach, which were unevenly distributed on 5 chromosomes. The peach shaker K⁺ channel proteins were classified into 5 subfamilies, I-V, and were tightly clustered with pear homologs in the phylogenetic tree. Various <i>cis</i>-acting regulatory elements were detected in the promoter region of the shaker-type K⁺ channel genes, including phytohormone-responsive, abiotic stress-responsive, and development regulatory elements. The peach shaker K⁺ channel genes were expressed differentially in distinct tissues, and <i>PpSPIK</i> was specifically expressed in the full-bloom flowers; <i>PpKAT1</i> and <i>PpGORK</i> were predominantly expressed in the leaves, while <i>PpAKT1</i>, <i>PpKC1</i>, and <i>PpSKOR</i> were majorly expressed in the roots. The peach shaker K⁺ channel genes were differentially regulated by abiotic stresses in that K⁺ deficiency, and ABA treatment mainly increased the shaker K⁺ channel gene expression throughout the whole seedling, whereas NaCl and PEG treatment reduced the shaker K⁺ channel gene expression, especially in the roots. Moreover, electrophysiological analysis demonstrated that PpSKOR is a typical voltage-dependent outwardly rectifying K⁺ channel in peach. This study lays a molecular basis for further functional studies of the shaker-type K⁺ channel genes in peach and provides a theoretical foundation for K⁺ nutrition and balance research in fruit trees.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2022 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8926527/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40306933","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Early Breast Cancer Evolution by Autosomal Broad Copy Number Alterations","authors":"Joseph R. Larsen,&nbsp;Peter Kuhn,&nbsp;James B. Hicks","doi":"10.1155/2022/9332922","DOIUrl":"10.1155/2022/9332922","url":null,"abstract":"<div>\u0000 <p>The availability of comprehensive genomic datasets across patient populations enables the application of novel methods for reconstructing tumor evolution within individual patients. To this end, we propose studying autosomal broad copy number alterations (CNAs) as a framework to better understand early tumor evolution. We compared the broad CNAs and somatic mutations of patients with 1 to 10 autosomal broad CNAs against the full set of patients, using data from The Cancer Genome Atlas breast cancer project. We reveal here that the frequency of a chromosome arm obtaining a broad CNA and a genome acquiring somatic mutations changes as autosomal broad CNAs accumulate. Therefore, we propose that the number of autosomal broad CNAs is an important characteristic of breast tumors that needs to be taken into consideration when studying breast tumors. To investigate this idea more in-depth, we next studied the frequency that specific chromosome arms acquire broad CNAs in patients with 1 to 10 broad CNAs. With this process, we identified the broad CNAs that exhibit the fastest rates of accumulation across all patients. This finding suggests a likely order of occurrence of these alterations in patients, which is apparent when we consider a subset of patients with few broad CNAs. Here, we lay the foundation for future studies to build upon our findings and use autosomal broad CNAs as a method to monitor breast tumor progression in vivo to further our understanding of how early tumor evolution unfolds.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2022 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/2022/9332922","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48032230","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome Sequencing of Hericium coralloides by a Combination of PacBio RS II and Next-Generation Sequencing Platforms","authors":"Caixia Zhang,&nbsp;Lijun Xu,&nbsp;Jian Li,&nbsp;Jiansong Chen,&nbsp;Manjun Yang","doi":"10.1155/2022/4017654","DOIUrl":"10.1155/2022/4017654","url":null,"abstract":"<div>\u0000 <p>The fruiting bodies or mycelia of <i>Hericium coralloides</i> (<i>H. coralloides</i>) contain many physiologically active compounds that are used to treat various diseases, including cardiovascular disorders and cancers. However, the genome of <i>H. coralloides</i> has not been sequenced, which hinders further investigations into aspects, such as bioactivity or evolutionary events. The present study is aimed at (i) performing <i>de novo</i> sequencing of the assembled genome; (ii) mapping the reads from PE400 DNA into the assembled genome; (iii) identifying the full length of all the repeated sequences; and (iv) annotating protein-coding genes using GO, eggNOG, and KEGG databases. The assembled genome comprised 5,59,05,675 bp, including 307 contigs. The mapping rate of reads obtained from PE400 DNA in the assembled genome was 92.46%. We identified 2,525 repeated sequences of 14,23,274 bp length. We predicted ncRNAs of 48,895 bp and 11,736 genes encoding proteins that were annotated in the GO, eggNOG, and KEGG databases. We are the first to sequence the entire <i>H. coralloides</i> genome (NCBI; Assembly: ASM367540v1), which will serve as a reference for studying the evolutionary diversification of edible and medicinal mushrooms and facilitate the application of bioactivity in <i>H. coralloides</i>.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2022 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8820905/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39905247","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}