Genes & genomics最新文献

{"title":"Population genetics reveals new introgression in the nucleus herd of min pigs.","authors":"Tianxin Liu, Dongqing Ji, Xinyuan Li, Jiadong Liu, Fei Xu, Zhiying Miao, Yang Chang, Ming Tian, Chunzhu Xu","doi":"10.1007/s13258-024-01490-1","DOIUrl":"10.1007/s13258-024-01490-1","url":null,"abstract":"<p><strong>Objective: </strong>Min pigs are a unique genetic resource among local pig breeds in China. They have more excellent characteristics in cold and stress resistance, good meat quality, and a high reproductive rate. However, the genetic structure and driving factors remain unclear in the nucleus herd. In this study, the genetic diversity of Min pigs was studied to reveal the formation mechanism of its unique genetic structure. We hope to protect and develop the genetic resources of Min pigs.</p><p><strong>Methods: </strong>We analyzed different types of genes to identify the genetic structure and gene introgression pattern of Min pigs. The nuclear DNA dataset includes information on 21 microsatellite loci and 6 Y-chromosome genes, and the mitochondrial D-loop gene is selected to represent maternal lineages. The above genes are all from the nucleus herd of Min pigs.</p><p><strong>Results: </strong>The results of genetic structure identification and analysis of potential exogenous gene introgression patterns indicate that the nucleus herd of Min pigs maintains a high level of genetic diversity (polymorphism information content = 0.713, expected heterozygosity = 0.662, observed heterozygosity = 0.612). Compared with other Asian pig breeds, the formation of Min pig breeds is more special. Gene introgression from European pig breeds to Min pigs has occurred, which is characterized by complete introgression of paternal genes and incomplete introgression of maternal genes.</p><p><strong>Conclusion: </strong>Gene introgression caused by cross-breeding is not the main factor leading to the formation of the current genetic structure of Min pigs, but this process has increased the level of genetic diversity in the nucleus herd. Compared with the influence of gene introgression, our research suggest that artificial selection and environmental adaptive evolution make Min pigs form unique genetic characteristics.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139912410","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":"Transcriptome profiling and characterization of genes associated with tuberization under high temperature in aeroponics in potato cv. Kufri Anand.","authors":"Rasna Zinta, Jagesh Kumar Tiwari, Tanuja Buckseth, Umesh Goutam, Rajesh Kumar Singh, Vinod Kumar, Ajay Kumar Thakur","doi":"10.1007/s13258-024-01503-z","DOIUrl":"10.1007/s13258-024-01503-z","url":null,"abstract":"<p><strong>Background: </strong>High temperature stress is an important abiotic factor, which affects tuberization and ultimately causes heavy yield reduction in potato.</p><p><strong>Objectives: </strong>Identification and characterization of genes associated with tuberization under high temperature stress is essential for future management through biotechnology.</p><p><strong>Methodology: </strong>Two contrasting potato varieties Kufri Anand (profuse tuber-bearing) versus Kufri Frysona (very less/scanty tuber-bearing, control) were cultivated in aeroponics under high temperature stress, and transcriptomes were analyzed.</p><p><strong>Results: </strong>Potato cv. Kufri Anand was found superior over control (Kufri Frysona) for tuber yield and its component traits along with root morphology under aeroponics. Transcriptomes of tuber and leaf tissues were analyzed. Statistically significant (p < 0.05) differentially expressed genes (DEGs) were categorised into up-regulated (> 2 log₂ fold change, FC) and down-regulated (< -2 log2 FC) genes. DEGs were annotated by gene ontology and KEGG pathways. A few selected up-regulated genes of both tissues were identified, and phylogeny tree and motif analysis were analysed based on 36 peptide sequences representing 15 selected DEGs in this study. Further, gene expression markers were developed and validated by real time qPCR analysis for the identification of high temperature tolerant genotypes.</p><p><strong>Conclusion: </strong>A few key genes associated in tuberization under high temperature conditions were heat shock proteins (e.g. 18.5 kDa class I heat shock protein), sugar metabolism (e.g. glucosyltransferase), transcription factor (e.g. WRKY), and phytohormones (e.g. auxin-induced beta-glucosidase). Our study provides an overview of key genes involved in tuberization under high temperature stress in potato cv. Kufri Anand under aeroponics.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139912411","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":"Correlation analysis of cancer stem cell marker CD133 and human endogenous retrovirus (HERV)-K env in SKOV3 ovarian cancer cells.","authors":"Do-Ye Kim, Heungyeol Kim, Eun-Ji Ko, Suk Bong Koh, Hongbae Kim, Ji Young Lee, Chul Min Lee, Wan Kyu Eo, Ki Hyung Kim, Hee-Jae Cha","doi":"10.1007/s13258-024-01499-6","DOIUrl":"10.1007/s13258-024-01499-6","url":null,"abstract":"<p><strong>Background: </strong>Human endogenous retrovirus (HERV)-K is a type of retrovirus that is present in the human genome, and its expression is usually silenced in healthy tissues. The precise mechanism by which HERV-K env influences cancer stemness is not fully understood, but it has been suggested that HERV-K env may activate various signaling pathways that promote stemness traits in cancer cells.</p><p><strong>Objective: </strong>To establish the connection between HERV-K env expression and cancer stemness in ovarian cancer cells, we carried out correlation analyses between HERV-K env and the cancer stem cell (CSC) marker known as the cluster of differentiation 133 (CD133) gene in SKOV3 ovarian cancer cells.</p><p><strong>Method: </strong>To perform correlation analysis between HERV-K env and CSCs, ovarian cancer cells were cultured in a medium designed for cancer stem cell induction. The expression of HERV-K env and CD133 genes was verified using quantitative real-time polymerase chain reaction (RT-qPCR) and Western blot analyses. Additionally, the expression of stemness-related markers, such as OCT-4 and Nanog, was also confirmed using RT-qPCR.</p><p><strong>Results: </strong>In the stem cell induction medium, the number of tumorsphere-type SKOV3 cells increased, and the expression of CD133 and HERV-K env genes was up-regulated. Additionally, other stemness-related markers like OCT-4 and Nanog also exhibited increased expression when cultured in the cancer stem cell induction medium. However, when HERV-K env knockout (KO) SKOV3 cells were cultured in the same cancer stem cell induction medium, there was a significant decrease in the number of tumorsphere-type cells compared to mock SKOV3 cells subjected to the same conditions. Furthermore, the expression of CD133, Nanog, and OCT-4 did not show a significant increase in HERV-K env KO SKOV3 cells compared to mock SKOV3 cells cultured in the same cancer stem cell induction medium.</p><p><strong>Conclusion: </strong>These findings indicate that the expression of HERV-K env increased in SKOV3 cells when cultured in cancer stem cell induction media, and cancer stem cell induction was inhibited by KO of HERV-K env in SKOV3 cells. These results suggest a strong association between HERV-K env and stemness in SKOV3 ovarian cancer cells.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140059120","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":"T-DNA insertion mutants of Arabidopsis DA1 orthologous genes displayed altered plant height and yield-related traits in rice (O. Sativa L.).","authors":"Kyu-Chan Shim, Ngoc Ha Luong, Thomas H Tai, Gyu-Ri Lee, Sang-Nag Ahn, Inkyu Park","doi":"10.1007/s13258-024-01501-1","DOIUrl":"10.1007/s13258-024-01501-1","url":null,"abstract":"<p><strong>Background: </strong>The Arabidopsis DA1 gene is a key player in the regulation of organ and seed development. To extend our understanding of its functional counterparts in rice, this study investigates the roles of orthologous genes, namely DA1, HDR3, HDR3.1, and the DA2 ortholog GW2, through the analysis of T-DNA insertion mutants.</p><p><strong>Objective: </strong>The aim of this research is to elucidate the impact of T-DNA insertions in DA1, HDR3, HDR3.1, and GW2 on agronomic traits in rice. By evaluating homozygous plants, we specifically focus on key parameters such as plant height, tiller number, days to heading, and grain size.</p><p><strong>Methods: </strong>T-DNA insertion locations were validated using PCR, and subsequent analyses were conducted on homozygous plants. Agronomic traits, including plant height, tiller number, days to heading, and grain size, were assessed. Additionally, leaf senescence assays were performed under dark incubation conditions to gauge the impact of T-DNA insertions on this physiological aspect.</p><p><strong>Results: </strong>The study revealed distinctive phenotypic outcomes associated with T-DNA insertions in HDR3, HDR3.1, GW2, and DA1. Specifically, HDR3 and HDR3.1 mutants exhibited significantly reduced plant height and smaller grain size, while GW2 and DA1 mutants displayed a notable increase in both plant height and grain size compared to the wild type variety Dongjin. Leaf senescence assays further indicated delayed leaf senescence in hdr3.1 mutants, contrasting with slightly earlier leaf senescence observed in hdr3 mutants under dark incubation.</p><p><strong>Conclusions: </strong>The findings underscore the pivotal roles of DA1 orthologous genes in rice, shedding light on their significance in regulating plant growth and development. The observed phenotypic variations highlight the potential of these genes as targets for crop improvement strategies, offering insights that could contribute to the enhancement of agronomic traits in rice and potentially other crops.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140021411","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":"Comparative whole genome analysis of face-derived Streptococcus infantis CX-4 unravels the functions related to skin barrier.","authors":"Haeun Lee, Dong-Geol Lee, HyungWoo Jo, Young Mok Heo, Chaeyun Baek, Hye-Been Kim, Geunhwa Park, Seunghyun Kang, Wooseok Lee, Seyoung Mun, Kyudong Han","doi":"10.1007/s13258-024-01495-w","DOIUrl":"10.1007/s13258-024-01495-w","url":null,"abstract":"<p><strong>Background: </strong>The skin microbiome is essential in guarding against harmful pathogens and responding to environmental changes by generating substances useful in the cosmetic and pharmaceutical industries. Among these microorganisms, Streptococcus is a bacterial species identified in various isolation sources. In 2021, a strain of Streptococcus infantis, CX-4, was identified from facial skin and found to be linked to skin structure and elasticity. As the skin-derived strain differs from other S. infantis strains, which are usually of oral origin, it emphasizes the significance of bacterial variation by the environment.</p><p><strong>Objective: </strong>This study aims to explore the unique characteristics of the CX-4 compared to seven oral-derived Streptococcus strains based on the Whole-Genome Sequencing data, focusing on its potential role in skin health and its possible application in cosmetic strategies.</p><p><strong>Methods: </strong>The genome of the CX-4 strain was constructed using PacBio Sequencing, with the assembly performed using the SMRT protocol. Comparative whole-genome analysis was then performed with seven closely related strains, utilizing web-based tools like PATRIC, OrthoVenn3, and EggNOG-mapper, for various analyses, including protein association analysis using STRING.</p><p><strong>Results: </strong>Our analysis unveiled a substantial number of Clusters of Orthologous Groups in diverse functional categories in CX-4, among which sphingosine kinase (SphK) emerged as a unique product, exclusively present in the CX-4 strain. SphK is a critical enzyme in the sphingolipid metabolic pathway, generating sphingosine-1-phosphate. The study also brought potential associations with isoprene formation and retinoic acid synthesis, the latter being a metabolite of vitamin A, renowned for its crucial function in promoting skin cell growth, differentiation, and maintaining of skin barrier integrity. These findings collectively suggest the potential of the CX-4 strain in enhancing of skin barrier functionality.</p><p><strong>Conclusion: </strong>Our research underscores the potential of the skin-derived S. infantis CX-4 strain by revealing unique bacterial compounds and their potential roles on human skin.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140059119","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":"In silico identification and expression analyses of peroxidases in Tenebrio molitor","authors":"Ho Am Jang, Sung Min Ku, Jae Hui Kim, Sang Mok Jung, Jongdae Lee, Yong Seok Lee, Yeon Soo Han, Yong Hun Jo","doi":"10.1007/s13258-024-01498-7","DOIUrl":"https://doi.org/10.1007/s13258-024-01498-7","url":null,"abstract":"<p>Human advancements in agriculture, urbanization, and industrialization have led to various forms of environmental pollution, including heavy metal pollution. Insects, as highly adaptable organisms, can survive under various environmental stresses, which induce oxidative damage and impair antioxidant systems. To investigate the peroxidase (POX) family in <i>Tenebrio molitor</i>, we characterized two POXs, namely <i>Tm</i>POX-iso1 and <i>Tm</i>POX-iso2. The full-length cDNA sequences of <i>TmPox-iso1</i> and <i>TmPox-iso2</i> respectively consisted of an open reading frame of 1815 bp encoding 605 amino acids and an open reading frame of 2229 bp encoding 743 amino acids. <i>Tm</i>POX-iso1 and <i>Tm</i>POX-iso2 homologs were found in five distinct insect orders. In the phylogenetic tree analysis, <i>Tm</i>POX-iso1 was clustered with the predicted POX protein of <i>T. castaneum</i>, and <i>Tm</i>POX-iso2 was clustered with the POX precursor protein of <i>T. castaneum</i>. During development, the highest expression level of <i>TmPox-iso1</i> was observed in the pre-pupal stage, while that of <i>TmPox-iso2</i> expression were observed in the pre-pupal and 4-day pupal stages. <i>TmPox-iso1</i> was primarily expressed in the early and late larval gut, while <i>TmPox-iso2</i> mRNA expression was higher in the fat bodies and Malpighian tubules. In response to cadmium chloride treatment, <i>TmPox-iso1</i> expression increased at 3 hours and then declined until 24 hours, while in the zinc chloride-treated group, <i>TmPox-iso1</i> expression peaked 24 hours after the treatment. Both treated groups showed increases in <i>TmPox-iso2</i> expression 24 hours after the treatments.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140313303","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":"Feature selection for effective prediction of SARS-COV-2 using machine learning.","authors":"Gagan Punacha, Rama Adiga","doi":"10.1007/s13258-023-01467-6","DOIUrl":"10.1007/s13258-023-01467-6","url":null,"abstract":"<p><strong>Background: </strong>With rise in variants of SARS-CoV-2, it is necessary to classify the emerging SARS-CoV-2 for early detection and thereby reduce human transmission. Genomic and proteomic information have less frequently been used for classifying in a machine learning (ML) approach for detection of SARS-CoV-2.</p><p><strong>Objective: </strong>With this aim we used nucleoprotein and viral proteomic evolutionary information of SARS-CoV-2 along with the charge and basicity distribution of amino acids from various strains of SARS-CoV-2 to generate a disease severity model based on ML.</p><p><strong>Methods: </strong>All sequence and clinical data were obtained from GISAID. Proteomic level calculations were added to comprise the dataset. The training set was used for feature selection. Select K- Best feature selection method was employed which was cross validated with testing set and performance evaluated. Delong's test was also done. We also employed BIRCH clustering on SARS-CoV-2 for clustering the strains.</p><p><strong>Results: </strong>Out of six ML models four were successful in training and testing. Extra Trees algorithm generated a micro-averaged F1-score of 74.2% and a weighted averaged area under the receiver operating characteristic curve (AUC-ROC) score of 73.7% with multi-class option. The feature selection set to 5, enhanced the ROC AUC from 73.7 to 76.4%. Accuracy of the selected model of 86.9% was achieved.</p><p><strong>Conclusion: </strong>The unique features identified in the ML approach was able to classify disease severity into classes and had potential for predicting risk in newer variants.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138176066","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":"PSMD12 promotes non-small cell lung cancer progression through activating the Nrf2/TrxR1 pathway.","authors":"Junqi Lv, Shengmao Ma, Xiaowen Wang, Jifang Dang, Fuchun Ma","doi":"10.1007/s13258-023-01484-5","DOIUrl":"10.1007/s13258-023-01484-5","url":null,"abstract":"<p><strong>Background: </strong>Non-small cell lung cancer (NSCLC) contributes to the vast majority of cancer-related deaths. Proteasome 26S subunit, non-ATPase 12 (PSMD12), a subunit of 26S proteasome complex, is known to play the tumor-promoting role in several types of cancer but its function in NSCLC remains elusive.</p><p><strong>Objective: </strong>To explore the role and underlying mechanisms of PSMD12 in NSCLC.</p><p><strong>Methods: </strong>The PSMD12 expression in human normal lung epithelial cell line (BEAS-2B) and four NSCLC cell lines (A549, NCI-H1299, NCI-H1975, Calu-1) were determined by qRT-PCR and western blot. Malignant phenotypes of NSCLC cells were detected by CCK-8, EdU staining, immunofluorescence staining for E-cadherin, flow cytometry, and Transwell assays to assess cell viability, proliferation, epithelial-mesenchymal transition (EMT), apoptosis, migration and invasion. Dual luciferase assay was used to verify the regulatory role of transcription factor on the promoter.</p><p><strong>Results: </strong>We identified the upregulation of PSMD12 in NSCLC tissues based on the GEO datasets, which further verified in NSCLC and BEAS-2B cell lines. PSMD12 knockdown significantly suppressed malignant behaviors of NSCLC cells, including cell growth, invasion, and migration, while PSMD12 overexpression presented the opposite effects. Interestingly, we found that PSMD12 upregulated the tumor-promoting factor TrxR1 mRNA expression. For its potential mechanisms, we demonstrated that PSMD12 elevated transcription factor Nrf2 protein level and promoted Nrf2 nuclear translocation. And Nrf2 further increased TrxR1 promoter activity and enhanced TrxR1 transcription. Meanwhile, we proved that TrxR1 overexpression erased the inhibitory effect of PSMD12 knockdown.</p><p><strong>Conclusion: </strong>PSMD12 promotes NSCLC progression by activating the Nrf2/TrxR1 pathway, providing a novel prognostic and therapeutic target for NSCLC treatment.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139502340","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":"Characterization and comparative analysis of the complete organelle genomes of three red macroalgae species (Neoporphyra dentata, Neoporphyra seriata, and Neopyropia yezoensis) and development of molecular makers for their identification.","authors":"Yong Jin Lee, Yo Ram Uh, Yeon Mi Kim, Cheol Min Kim, Cheol Seong Jang","doi":"10.1007/s13258-023-01472-9","DOIUrl":"10.1007/s13258-023-01472-9","url":null,"abstract":"<p><strong>Background: </strong>Many species of red algae belonging to the phylum Rhodophyta are consumed by humans as raw materials for nutrition and medicine. As the seaweed market grows, the importance of the laver species has increased. The classification of red algal species has changed significantly, and the accuracy of this classification has improved significantly in recent years. Here, we report the complete circular genomes of the chloroplasts (cp) and mitochondria (mt) of three laver species (Neoporphyra dentata, Neoporphyra seriata, and Neopyropia yezoensis).</p><p><strong>Objective: </strong>This study aims to assemble, annotate, and characterize the organization of the organelle genomes of three laver species, conduct comparative genomic studies, and develop molecular markers based on SNPs.</p><p><strong>Methods: </strong>We analyzed organelle genome structures, repeat sequences, sequence divergence, gene rearrangements, and phylogenetic relationships of three laver species.</p><p><strong>Results: </strong>The chloroplast genomes of the three species contained an average of 212 protein-coding genes (PCGs), while the mitochondrial genomes contained an average of 25 PCGs. We reconstructed the phylogenetic trees based on both chloroplast and mitochondrial genomes using 201 and 23 PCGs (in cp and mt genomes, respectively) shared in the class Bangiophyceae (and five species of Florideophyceae class used as an outgroup). In addition, 12 species-specific molecular markers were developed for qRT-PCR analysis.</p><p><strong>Conclusions: </strong>This is the first report of Neoporphyra seriata complete organellar genomes. With the results, this study provides useful genetic information regarding taxonomic discrepancies, the reconstruction of phylogenetic trees, and the evolution of red algae. Moreover, the species-specific markers can be used as fast and easy methods to identify a target species.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138294997","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 novel CHD7 variant in a chinese family with CHARGE syndrome.","authors":"Yanhong Shan, LingFang Yao, Linli Li, Xueping Gao, Jinghan Jiang","doi":"10.1007/s13258-023-01411-8","DOIUrl":"10.1007/s13258-023-01411-8","url":null,"abstract":"<p><strong>Objective: </strong>CHARGE syndrome is a rare autosomal dominant (AD) multi-system disorder with a broad and variable clinical manifestation and occurs in approximately 1/10,000 newborns in the world. Mutations in the CHD7 gene are the genetic cause of over 90% of patients with typical CHARGE syndrome. The present study reported a novel variant in the CHD7 gene in a Chinese family with an abnormal fetus.</p><p><strong>Methods: </strong>Routine prenatal ultrasound screening showed fetal heart abnormality and left foot varus. Chromosomal microarray analysis (CMA) and fetus-parent whole-exome sequencing (trio-WES) were performed to determine the genetic cause of the fetus. The candidate variant was further verified using Sanger sequencing.</p><p><strong>Results: </strong>CMA analysis revealed normal results. However, WES analysis identified a de novo heterozygous variant of c.2919_2922del (NM_017780.4) on exon 11 of CHD7 gene, resulting in a premature truncation of the CHD7 protein (p.Gly975*). The variant was classified as Pathogenic (PVS1 + PS2_Moderate + PM2_Supporting) based on the ACMG guidelines. Combined with the clinical phenotype of fetal heart abnormalities, it was confirmed CHARGE syndrome.</p><p><strong>Conclusion: </strong>We identified a novel heterozygous variant c.2919_2922del in CHD7 of a Chinese fetus with CHARGE syndrome, enriching the genotype-phenotype spectrum of CHD7. These results suggest that genetic testing could help facilitate prenatal diagnosis of CHARGE syndrome, thus promoting the appropriate genetic counseling.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9946256","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}