Biochemical Genetics最新文献

{"title":"Optimizing Genomic DNA Extraction from Avian Feathers: A Modified Phenol-Chloroform Approach for Enhanced Efficiency and Cost-Effectiveness.","authors":"Demir Ozdemir, Leyla Bener, Emine Toparslan Akcay","doi":"10.1007/s10528-024-10957-5","DOIUrl":"https://doi.org/10.1007/s10528-024-10957-5","url":null,"abstract":"<p><p>The procurement of blood and tissue samples for DNA extraction in avian species intended for molecular studies is associated with the induction of discomfort and pain in the subjects, compounded by practical challenges in application and ethical considerations. Consequently, feathers have emerged as a more prevalent source for molecular investigations, particularly in the fields of poultry and ornithology. However, the effective extraction of DNA from feathers necessitates the breakdown of the hard keratinized tissue within the feather structure. This study aimed to devise a highly efficient, cost-effective, and easily adaptable Modified Phenol-Chloroform (MPC) approach for genomic DNA extraction from feathers, addressing shortcomings identified in previous studies on feather-based DNA isolation. The MPC method was employed to extract genomic DNA from feather samples obtained from six distinct avian species (chicken, guinea fowl, canary, pigeon, emu, and goose). Comparative evaluation of DNA isolation efficiency was conducted by employing two different commercial DNA kits alongside the MPC method. The results showed significantly higher DNA concentrations (ng/ml) from chicken feathers using the MPC method compared to those obtained with commercial kits (p < 0.05), along with high DNA purity (1.83 ± 0.11). Subsequent PCR experiments, employing nuclear and mitochondrial DNA-specific primers, illustrated the effective amplification of short and long fragments from MPC-isolated DNA samples. In contrast to commercial kits, the findings underscore the successful application of the MPC method in isolating high-quality genomic DNA from feathers characterized by elevated keratin content.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142611859","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic Surveillance and Molecular Characterization of SARS-CoV-2 Variants During the Peak of the Pandemic in Türkiye.","authors":"Faruk Berat Akçeşme, Tuğba Kul Köprülü, Burçin Erkal Çam, Şeyma İş, Birsen Cevher Keskin, Betül Akçeşme, Kürşad Nuri Baydili, Bahar Gezer, Jülide Balkan, Bihter Uçar, Osman Gürsoy, Mehmet Taha Yıldız, Halil Kurt, Nevzat Ünal, Celalettin Korkmaz, Özlem Bayraktar Saral, Barış Demirkol, Yasemin Çağ, Hilal Abakay, Şükran Köse, Hasan Türkez, Kenan Çadırcı, Mustafa Altındiş, Yasemin Derya Gülseren, Nuray Aslan, Abdulkadir Özel, Muhammet Atıf Karagöl, Neslihan Mutluay, Şaban Tekin","doi":"10.1007/s10528-024-10962-8","DOIUrl":"https://doi.org/10.1007/s10528-024-10962-8","url":null,"abstract":"<p><p>SARS-CoV-2 is a highly transmissible coronavirus and has caused a pandemic of acute respiratory disease. Genomic characterization of SARS-CoV-2 is important for monitoring and assessing its evolution. A total of 1.346 nasopharyngeal swab samples were collected but only 879 SARS-CoV-2 high-quality genomes were isolated, subjected to Next Generation Sequencing and analyzed both statistically and regarding mutations comprehensively. The distribution of clades and lineages in different cities of Türkiye and the association of SARS-CoV-2 variants with age groups and clinical characteristics of COVID-19 were also examined. Furthermore, the frequency of the clades and lineages was observed in 10 months. Finally, non-synonymous mutations not defined in specific SARS-CoV-2 variants (during that period) were identified by performing mutation analysis. B.1.1.7 (Alpha) and B.1.617.2 (Delta) SARS-CoV-2 variants which have also been identified in our study from March to December 2021. We observed a significant association of SARS-CoV-2 variants with age groups and cities. Also, E:T9I, S:A27S, S:A67V, S:D796Y, S:K417N, S:N440K, S:R158X, S:S477N (below 1%-frequency) were determined as specific mutations belonging and shared with the Omicron variant that appeared later. Our study has highlighted the importance of constant monitoring of the genetic diversity of SARS-CoV-2 to provide better prevention strategies and it contributes to the understanding of SARS-CoV-2 from the past to the present.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142611853","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Cuproptosis-Related LncRNA Risk Model for Predicting Prognosis and Immunotherapeutic Efficacy in Patients with Hepatocellular Carcinoma.","authors":"Shuo Wang, Hongyan Bai, Sujuan Fei, Bei Miao","doi":"10.1007/s10528-023-10539-x","DOIUrl":"10.1007/s10528-023-10539-x","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Cuproptosis is a novel programmed cell death pathway that is initiated by direct binding of copper to lipoylated tricarboxylic acid (TCA) cycle proteins. Recent studies have demonstrated that cuproptosis-related genes regulate tumorigenesis. However, the potential role and clinical significance of cuproptosis-related long noncoding RNAs (lncRNAs) in hepatocellular carcinoma (HCC) have not been established. We performed a bioinformatics analyses of RNA-sequencing data of HCC patients extracted from The Cancer Genome Atlas (TCGA) dataset to identify and validate a cuproptosis-related lncRNA prognostic signature. Furthermore, we analyzed the clinical significance of the prognostic signature of cuproptosis-related lncRNA in predicting the immunotherapeutic efficacy and the status of the tumor immune microenvironment. The RNA-sequencing data, genomic mutations, and clinical information were downloaded for 374 HCC samples and 50 normal liver samples from TCGA-Liver Hepatocellular Carcinoma (TCGA-LIHC) dataset. Co-expression analysis of Gene-lncRNA pairs with 49 known cuproptosis-related prognostic genes was used to define cuproptosis-related prognostic lncRNAs. We performed the LASSO algorithm and univariate and multivariate Cox regression analysis, respectively, to gradually identify the prognostic risk models of cuproptosis-related lncRNA based on the TCGA-LIHC dataset. Subsequently, the predictive performance of the model was evaluated using receiver operation characteristic (ROC) curves, Kaplan-Meier survival curves, and prognostic nomogram. The analysis of gene-lncRNA co-expression with 49 known cuproptosis-related genes identified 1359 cuproptosis-related lncRNAs in the TCGA-LIHC data set. A prognostic model was constructed with nine cuproptosis-related prognostic lncRNAs (AC007998.3, AC003086.1, AC009974.2, IQCH-AS1, LINC0256 1, AC105345.1, ZFPM2-AS1, AL353708.1 and WAC-AS1) using LASSO regression and Cox regression analyses. Risk scores were calculated for all HCC patient samples based on the four cuproptosis-related lncRNA prognostic models. All HCC patients were divided into high-risk and low-risk subgroups according to a 1:1 ratio column. The Kaplan-Meier survival curve analysis showed that the overall survival rate (OS) of the high-risk group patients was significantly lower than that of the low-risk group. The principal component analysis (PCA) confirmed that the prognostic lncRNA model accurately distinguished between high- and low-risk HCC patients. Furthermore, regression analysis as well as ROC curves confirmed the prognostic value of the risk score. A nomogram with risk scores and other clinicopathological characteristics was constructed. The nomogram accurately predicted the probability of 1-, 3-, and 5-year OS in HCC patients. Tumor mutation burden (TMB) scores were higher for high-risk patients than for low-risk patients. HCC patients in the low-risk group showed lower TIDE scores and greater sensitivity to antitumor drugs th","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"2332-2351"},"PeriodicalIF":2.4,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71410068","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Aurantio-obtusin Alleviates Dry Eye Disease by Targeting NF-κB/NLRP3 Signaling in Rodent Models.","authors":"Dan Zhu, Na Zheng, Kebin Deng, Liangchang Li","doi":"10.1007/s10528-023-10471-0","DOIUrl":"10.1007/s10528-023-10471-0","url":null,"abstract":"<p><p>Dry eye disease (DED) is a common inflammatory ocular surface disorder, seriously affecting the quality of life of patients. Aurantio-obtusin (AO) is a bioactive anthraquinone compound isolated from Semen Cassiae which has multiple pharmacological activities. Nonetheless, the specific function of AO in DED is unclarified. In this study, a rodent DED model was established by benzalkonium chloride (BAC) induction, followed by topical administration of AO. The results showed that topical application of AO increased tear production, mitigated ocular surface disruption and maintained the number of goblet cells in BAC-induced DED rats (p˂0.05). ELISA revealed that AO treatment significantly (p˂0.001) reduced the production of proinflammatory cytokines and chemokines in the conjunctiva and cornea of BAC-induced DED rats. Immunohistochemical staining and western blotting showed that AO treatment suppressed the expression levels of NLR family pyrin domain containing 3 (NLRP3) inflammasome-related proteins, and inhibited activation of nuclear factor kappa B (NF-κB) signaling pathway in rat conjunctiva and cornea (p˂0.001). In conclusion, AO treatment alleviates BAC-induced DED in rats by inhibiting NF-κB/NLRP3 inflammasome signaling pathway.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"1-14"},"PeriodicalIF":2.1,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10073470","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"TLR4 Polymorphisms (T399I/D299G) Association with Schizophrenia and Bipolar Disorder in a Tunisian Population","authors":"Youssef Aflouk,&nbsp;Hana Saoud,&nbsp;Oumaima Inoubli,&nbsp;Saloua Yacoub,&nbsp;Ferid Zaafrane,&nbsp;Lotfi Gaha,&nbsp;Besma Bel Hadj Jrad","doi":"10.1007/s10528-023-10553-z","DOIUrl":"10.1007/s10528-023-10553-z","url":null,"abstract":"<div><p>Immune dysregulation has been widely described in the pathophysiology of schizophrenia (SCZ) and bipolar disorder (BD). Particularly, TLR4-altered activation was proposed as one of the underlying processes of psychosis onset. Since TLR4 activation was altered by T399I and D299G polymorphisms, we hypothesized that those variants could present common genetic factors of SCZ and BD. A total of 293 healthy volunteers and 335 psychotic patients were genotyped using PCR–RFLP. Genotype, allele, and haplotype distribution between controls and patients were evaluated according to clinical parameters. Statistical analyses were adjusted by logistic regression. In dominant model, T399I CT + TT and allele frequency were significantly higher in controls compared to psychotic population (<i>p</i> = 0.004, <i>p</i> = 0.002, respectively), SCZ (<i>p</i> = 0.02, <i>p</i> = 0.01, respectively), and BD (<i>p</i> = 0.03, p = 0.02, respectively). Similarly, D299G AG + GG and allele frequency were significantly higher in controls compared to psychotic population (<i>p</i> = 0.04, <i>p</i> = 0.04, respectively) and SCZ (<i>p</i> = 0.04, p = 0.03, respectively). T399I CT + TT and T allele were overrepresented in controls compared to paranoid subgroup (P_adjusted = 0.04, <i>p</i> = 0.04, respectively) and type I BD (<i>p</i> = 0.04). Moreover, T399I and D299G were less prevalent in SCZ late-onset age (<i>p</i> = 0.03, <i>p</i> = 0.02, respectively). TA haplotype was associated with protection from psychoses (<i>p</i> = 0.02) and particularly from schizophrenia (<i>p</i> = 0.04). In conclusion, <i>TLR4</i> polymorphisms could present a preventive genetic background against psychoses onset in a Tunisian population. While T399I could be associated with protection against SCZ and BD, presenting an overlapping genetic factor between those psychoses, D299G was suggested to be associated with protection only from schizophrenia.</p></div>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":"62 4","pages":"2418 - 2436"},"PeriodicalIF":2.1,"publicationDate":"2023-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72012960","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Comprehensive Analysis of NRP1 in Malignancies Provide Therapeutic Implication for Treating Cancer Patients Infected with SARS-CoV-2","authors":"Shuzhao Chen,&nbsp;Limei Zhang,&nbsp;Yiling Song,&nbsp;Kunying Xie,&nbsp;Yun Wang,&nbsp;Yang Liang","doi":"10.1007/s10528-023-10518-2","DOIUrl":"10.1007/s10528-023-10518-2","url":null,"abstract":"<div><p>COVID-19 (Coronavirus disease 2019) is caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2), which can lead to pneumonia, cytokine storms, and lymphopenia. Patients with cancer are more susceptible to SARS-CoV-2 infection and severe COVID-19 due to immunosuppression. Recent studies have indicated that NRP1 (Neuropilin 1) may act as a novel mediator of SARS-CoV-2 entry into the host cell. As no systematic review has been performed investigating the characteristics of NRP1 in pan-carcinoma, we comprehensively analyzed NRP1 in patients with pan-cancer. Using a bioinformatics approach, we aimed to systematically examine NRP1 expression profiles in both pan-carcinoma and healthy tissues. We found that lung and genitourinary cancers have a relatively higher NRP-1 expression than other cancer patients, suggesting that these patients may be more susceptible to SARS-CoV-2. Our analysis further revealed that NRP1 expression was downregulated in Vero E6 cells, whole blood, lung organoids, testis tissue, and alveolospheres infected with SARS-CoV-2. Notably, NRP1 was associated with immune cell infiltration, immune checkpoint genes, and immune-related genes in most patients with cancer. These findings suggest that, in patients with specific types of cancer, especially lung and genitourinary, high expression of NRP1 contributes to greater susceptibility to SARS-CoV-2 infection and an increased risk of damage due to cytokine storms. Overall, NRP1 appears to play a critical role in regulating immunological properties and metabolism in many tumor types. Specific inhibitors of the NRP1 antigen (pegaptanib, EG00229, or MNRP1685A) combined with other anti-SARS-CoV-2 strategies may aid in treating patients with lung and genitourinary cancers following SARS-CoV-2 infection.</p></div>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":"62 4","pages":"2399 - 2417"},"PeriodicalIF":2.1,"publicationDate":"2023-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71476602","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrated Transcriptomics and Network Analysis Identified Altered Neural Mechanisms in Frontal Aging Brain-Associated Alzheimer’s Disease","authors":"Suthipong Chujan,&nbsp;Wanida Cholpraipimolrat,&nbsp;Jutamaad Satayavivad","doi":"10.1007/s10528-023-10549-9","DOIUrl":"10.1007/s10528-023-10549-9","url":null,"abstract":"<div><p>Alzheimer’s disease (AD) is the most common neurodegenerative disease. The late stage of AD typically develops after 60 years of age and AD pathogenesis can be detected predominately in the frontal lobe, which is responsible for memory. Multiple alterations in cellular mechanisms have been associated with AD, but there is no clear information on AD pathogenesis during brain aging. This study aimed to explore the differentially expressed genes (DEGs) in the frontal lobe of aging brains and to identify shared crucial mechanisms in the aging brain linked to AD pathogenesis. Three datasets were downloaded from the Gene Expression Omnibus (GEO). Biological function analysis was performed by DAVID and KEGG databases. An AD patient’s cohort (GSE150696) was collected for verification of the enriched pathway. The results demonstrated that multiple neurochemical synapsis and regulation of the cytoskeleton are linked to AD pathogenesis during aging. Taken together, this study contributes to our further understanding of neural alterations during aging in AD that could be used to develop therapeutics for early intervention to prevent or slow progression.</p></div>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":"62 4","pages":"2382 - 2398"},"PeriodicalIF":2.1,"publicationDate":"2023-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71476604","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CircRNA circ_0013339 Regulates the Progression of Colorectal Cancer Through miR-136-5p/SOX9 Axis","authors":"Juan Jin,&nbsp;Min Du,&nbsp;Ding Ding,&nbsp;Ran Xuan","doi":"10.1007/s10528-023-10540-4","DOIUrl":"10.1007/s10528-023-10540-4","url":null,"abstract":"<div><h3>Background</h3><p>Colorectal cancer (CRC) is a common gastrointestinal malignancy. Dysregulation of circular RNAs (circRNAs) is associated with the progression of CRC. However, the role of circ_0013339 (hsa_circ_0013339) in CRC is still not clear.</p><h3>Methods</h3><p>The levels of circ_0013339, miR-136-5p, and SRY-box transcription factor 9 (SOX9) in CRC were gauged by quantitative real-time polymerase chain reaction (qRT-PCR). Colony formation and 5-Ethynyl-2’-deoxyuridine (EdU) assays were used to detect cell proliferation. Cell counting kit-8 (CCK8) assay was used to measure cell viability. Western blot assay was performed to examine protein expression. The relationship between miR-136-5p and circ_0013339 or SOX9 was tested by dual-luciferase reporter assay. The effect of sh-circ_0013339 on tumor growth in vivo was examined by xenograft experiments.</p><h3>Results</h3><p>Circ_0013339 expression was elevated in CRC tissues and cells, and circ_0013339 knockdown diminished the growth of CRC cells. MiR-136-5p was regulated by circ_0013339. MiR-136-5p deficiency ameliorated the effects of circ_0013339 silencing on CRC cell malignant behaviors. Circ_0013339 modulated SOX9 expression through miR-136-5p. SOX9 addition reversed the effects of miR-136-5p overexpression on CRC cell behaviors. Moreover, silencing of circ_0013339 suppressed the growth of xenograft tumors in vivo.</p><h3>Conclusion</h3><p>Circ_0013339 regulates the progression of CRC through miR-136-5p-dependent regulation of SOX9, uncovering a novel regulatory mechanism of circ_0013339 in CRC.</p></div>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":"62 4","pages":"2362 - 2380"},"PeriodicalIF":2.1,"publicationDate":"2023-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71476603","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Angiotensin-Converting Enzyme Insertion/Deletion Polymorphism and the Risk of Leukoaraiosis in a South Chinese Han Population: A Case–Control Study","authors":"Dong-can Mo,&nbsp;Xiao-ju Wu,&nbsp;Xiao-ling Li,&nbsp;Liu-yu Liu,&nbsp;Yi-ying Jiang,&nbsp;Guo-qiu Zhou,&nbsp;Li-jie Chen,&nbsp;Jiao-xing Li,&nbsp;Man Luo","doi":"10.1007/s10528-023-10505-7","DOIUrl":"10.1007/s10528-023-10505-7","url":null,"abstract":"<div><p>Leukoaraiosis (LA) appears as white matter hyperintensities on T2-weighted brain magnetic resonance imaging scans. Age and hypertension are considered the primary risk factors for LA, but its pathogenesis remains uncertain. This study aims to investigate the correlation between the angiotensin-converting enzyme (ACE) insertion/deletion (I/D) polymorphism and LA. A total of 140 patients with LA and 136 neuroimaging alteration-free controls were recruited in a case–control study. ACE I/D polymorphism was determined using the polymerase chain reaction method. The allele and genotype distributions of the ACE I/D polymorphism were significantly different between subjects with and without LA. Significant difference was observed in the genotypic distribution between LA patients and controls for recessive and additive models. A statistically significant association remained apparent after adjusting for potential risk factors (D/D vs. I/D + I/I: adjusted OR 3.251, 95% CI 1.185–8.918; D/D vs. I/I: adjusted OR 3.277, 95% CI 1.187–9.047). Our results indicate that the D/D genotype and D allele are important risk factors for LA. Future studies with larger populations are needed to validate our results.</p></div>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":"62 4","pages":"2353 - 2361"},"PeriodicalIF":2.1,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71419430","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The First Genome-Wide Survey of Shortbelly Eel (Dysomma anguillare Barnard, 1923) to Provide Genomic Characteristics, Microsatellite Markers and Complete Mitogenome Information","authors":"Tian-yan Yang,&nbsp;Zi-yan Zhu,&nbsp;Yu-ping Liu,&nbsp;Si-ge Wang","doi":"10.1007/s10528-023-10543-1","DOIUrl":"10.1007/s10528-023-10543-1","url":null,"abstract":"<div><p><i>Dysomma anguillare</i> is a demersal eel widespread distributing in tropical waters of the Indo-West Pacific and Atlantic. As an important component of the coastal fishery and marine ecosystem, the lack of genomic information for this species severely restricts the progress of relevant researches. In this study, the abecedarian genome-wide characteristics and phylogenetic relationships analyses were carried out based on next-generation sequencing (NGS) platform. The revised genome size was approximately 1 310 Mb, with the largest scaffold length reaching 23 878 bp through K-mer (<i>K</i> = 17) method. The heterozygosity, repetitive rate and average GC content were about 0.94%, 51.93% and 42.23%, respectively. A total of 1 160 104 microsatellite motifs were identified from the de novo assembled genome of <i>D. anguillare</i>, in which dinucleotide repeats accounted for the largest proportion (592 234, 51.05%), the highest occurrence frequency (14.58%) as well as the largest relative abundance (379.27/Mb). The high-polymorphic and moderate-polymorphic loci composed around 73% of the total single sequence repeats (SSRs), showing a latent capacity for subsequent population genetic structure and genetic diversity appraisal researches. Another byproduct of whole-genome sequencing, the double-stranded and circular mitogenome (16 690 bp) was assembled to investigate the evolutionary relationships of <i>D. anguillare.</i> The phylogenic tree constructed with maximum likelihood (ML) method showed that <i>D. anguillare</i> was closely related to Synaphobranchidae species, and the molecular systematic results further supported classical taxonomy status of <i>D. anguillare.</i></p></div>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":"62 3","pages":"2296 - 2313"},"PeriodicalIF":2.1,"publicationDate":"2023-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71419432","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}