Genomics最新文献

{"title":"Unraveling the complexity of asymmetric DNA replication: Advancements in ribonucleotide mapping techniques and beyond","authors":"Alberto Bugallo ,&nbsp;Mónica Segurado","doi":"10.1016/j.ygeno.2024.110908","DOIUrl":"10.1016/j.ygeno.2024.110908","url":null,"abstract":"<div><p>DNA replication is a fundamental process for cell proliferation, governed by intricate mechanisms involving leading and lagging strand synthesis. In eukaryotes, canonical DNA replication occurs during the S phase of the cell cycle, facilitated by various components of the replicative machinery at sites known as replication origins. Leading and lagging strands exhibit distinct replication dynamics, with leading strand replication being relatively straightforward compared to the complex synthesis of lagging strands involving Okazaki fragment maturation. Central to DNA synthesis are DNA polymerases, with Polα, Polε, and Polδ playing pivotal roles, each specializing in specific tasks during replication. Notably, leading and lagging strands are replicated by different polymerases, contributing to the division of labor in DNA replication. Understanding the enzymology of asymmetric DNA replication has been challenging, with methods relying on ribonucleotide incorporation and next-generation sequencing techniques offering comprehensive insights. These methodologies, such as HydEn-seq, PU-seq, ribose-seq, and emRiboSeq, offer insights into polymerase activity and strand synthesis, aiding in understanding DNA replication dynamics. Recent advancements include novel conditional mutants for ribonucleotide excision repair, enzymatic cleavage alternatives, and unified pipelines for data analysis. Further developments in adapting techniques to different organisms, studying non-canonical polymerases, and exploring new sequencing platforms hold promise for expanding our understanding of DNA replication dynamics. Integrating strand-specific information into single-cell studies could offer novel insights into enzymology, opening avenues for future research and applications in repair and replication biology.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 5","pages":"Article 110908"},"PeriodicalIF":3.4,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001290/pdfft?md5=b151a928ffaf0efcc9a705417da239dd&pid=1-s2.0-S0888754324001290-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141897248","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enhancing schizophrenia phenotype prediction from genotype data through knowledge-driven deep neural network models","authors":"Daniel Martins ,&nbsp;Maryam Abbasi ,&nbsp;Conceição Egas ,&nbsp;Joel P. Arrais","doi":"10.1016/j.ygeno.2024.110910","DOIUrl":"10.1016/j.ygeno.2024.110910","url":null,"abstract":"<div><p>This article explores deep learning model design, drawing inspiration from the omnigenic model and genetic heterogeneity concepts, to improve schizophrenia prediction using genotype data. It introduces an innovative three-step approach leveraging neural networks' capabilities to efficiently handle genetic interactions. A locally connected network initially routes input data from variants to their corresponding genes. The second step employs an Encoder-Decoder to capture relationships among identified genes. The final model integrates knowledge from the first two and incorporates a parallel component to consider the effects of additional genes. This expansion enhances prediction scores by considering a larger number of genes. Trained models achieved an average AUC of 0.83, surpassing other genotype-trained models and matching gene expression dataset-based approaches. Additionally, tests on held-out sets reported an average sensitivity of 0.72 and an accuracy of 0.76, aligning with schizophrenia heritability predictions. Moreover, the study addresses genetic heterogeneity challenges by considering diverse population subsets.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 5","pages":"Article 110910"},"PeriodicalIF":3.4,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001319/pdfft?md5=05dc9164810795ff25d26a05f27f02e0&pid=1-s2.0-S0888754324001319-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141901499","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Screening of novel disease genes of sepsis-induced myocardial Disfunction by RNA sequencing and bioinformatics analysis","authors":"Hanyi Yao ,&nbsp;Zixi Xiao ,&nbsp;Shufang Liu ,&nbsp;Xingjian Gao ,&nbsp;Zehong Wu ,&nbsp;Dongping Li ,&nbsp;Zhangqing Yi ,&nbsp;Haojie Zhou ,&nbsp;Weizhi Zhang","doi":"10.1016/j.ygeno.2024.110911","DOIUrl":"10.1016/j.ygeno.2024.110911","url":null,"abstract":"<div><h3>Background</h3><p>There is still a lack of effective treatment for sepsis-induced myocardial dysfunction (SIMD), while the pathogenesis of SIMD still remains largely unexplained.</p></div><div><h3>Methods</h3><p>RNA sequencing results (GSE267388 and GSE79962) were used for cross-species integrative analysis. Bioinformatic analyses were used to delve into function, tissue- and cell- specificity, and interactions of genes. External datasets and qRT-PCR experiments were used for validation. L1000 FWD was used to predict targeted drugs, and 3D structure files were used for molecular docking.</p></div><div><h3>Results</h3><p>Based on bioinformatic analyses, ten differentially expressed genes were selected as genes of interest, seven of which were verified to be significantly differential expression. Bucladesine was considered as a potential targeted drug for SIMD, which banded to seven target proteins primarily by forming hydrogen bonds.</p></div><div><h3>Conclusion</h3><p>It was considered that <em>Cebpd</em>, <em>Timp1</em>, <em>Pnp</em>, <em>Osmr</em>, <em>Tgm2</em>, <em>Cp,</em> and <em>Asb2</em> were novel disease genes, while bucladesine was a potential therapeutic drug, of SIMD.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 5","pages":"Article 110911"},"PeriodicalIF":3.4,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001320/pdfft?md5=cca2d967557214ef34591f2420bd9b5c&pid=1-s2.0-S0888754324001320-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141901500","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dissecting transposable elements and endogenous retroviruses upregulation by HDAC inhibitors in leiomyosarcoma cells: Implications for the interferon response","authors":"Nicolò Gualandi,&nbsp;Martina Minisini,&nbsp;Alessio Bertozzo,&nbsp;Claudio Brancolini","doi":"10.1016/j.ygeno.2024.110909","DOIUrl":"10.1016/j.ygeno.2024.110909","url":null,"abstract":"<div><p>Transposable elements (TEs) are of interest as immunomodulators for cancer therapies. TEs can fold into dsRNAs that trigger the interferon response. Here, we investigated the effect of different HDAC inhibitors (HDACIs) on the expression of TEs in leiomyosarcoma cells. Our data show that endogenous retroviruses (ERVs), especially ERV1 elements, are upregulated after treatment with HDAC1/2/3-specific inhibitors. Surprisingly, the interferon response was not activated. We observed an increase in A-to-I editing of upregulated ERV1. This could have an impact on the stability of dsRNAs and the activation of the interferon response. We also found that H3K27ac levels are increased in the LTR12 subfamilies, which could be regulatory elements controlling the expression of proapoptotic genes such as <em>TNFRSF10B</em>. In summary, we provide a detailed characterization of TEs modulation in response to HDACIs and suggest the use of HDACIs in combination with ADAR inhibitors to induce cell death and support immunotherapy in cancer.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 5","pages":"Article 110909"},"PeriodicalIF":3.4,"publicationDate":"2024-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001307/pdfft?md5=6f2801b75ee2c5d7fd35841f95f86b6b&pid=1-s2.0-S0888754324001307-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141893237","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomic analysis of different intramuscular fat contents on the flavor of the longissimus dorsi tissues from Guangling donkey","authors":"Wufeng Li ,&nbsp;LiLi ,&nbsp;Xi Wang","doi":"10.1016/j.ygeno.2024.110905","DOIUrl":"10.1016/j.ygeno.2024.110905","url":null,"abstract":"<div><h3>Background</h3><p>In this study, researchers aimed to explore the impact of intramuscular fat (IMF) concentration on the flavor of donkey meat, specifically in the longissimus dorsi muscle of Guangling donkeys. The internal volatile organic compounds that cause the flavor differences between donkey muscles are not clear at present. Transcriptomic technologies were utilized to analyze gene expression and its relationship to donkey meat flavor.</p></div><div><h3>Method</h3><p>Thirty Guangling donkeys had their IMF content evaluated in the longissimus dorsi muscle. Based on IMF content, 16 donkeys of similar ages were divided into two groups: low-fat (L) and high-fat (H). Headspace solid-phase microextraction Gas chromatography-mass spectrometry (HS-SPME-GC–MS) and headspace solid phase microextraction mass spectrometry were used to identify potential flavor components that differed between the two groups.</p></div><div><h3>Results</h3><p>Five key volatile substances were identified, and WGCNA and KEGG analysis was conducted to analyze the genes associated with these substances. The results showed that pathways like PPAR signaling, nucleotide excision repair, glucagon signaling, arachidonic acid metabolism, and glycolysis/glycogenesis were involved in lipid deposition. Additionally, a gene-gene interaction network map was constructed, highlighting the importance of hub genes such as <em>EEF2, DDX49, GAP43, SNAP25, NDUFS8, MRPS11, RNASEH2A, POLR2E, POLR2C</em> and <em>ALB</em> in regulating key flavor substances.</p></div><div><h3>Conclusion</h3><p>This study provided valuable insights into the regulation of genes and protein expression related to flavor substances in donkey meat. It also deepened understanding of the influence of IMF on flavor and laid a foundation for future molecular breeding improvements in Guangling donkeys.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 5","pages":"Article 110905"},"PeriodicalIF":3.4,"publicationDate":"2024-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001265/pdfft?md5=bd806337e79ad9945333abd324d2c576&pid=1-s2.0-S0888754324001265-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141859506","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"W2V-repeated index: Prediction of enhancers and their strength based on repeated fragments","authors":"Weiming Xie ,&nbsp;Zhaomin Yao ,&nbsp;Yizhe Yuan ,&nbsp;Jingwei Too ,&nbsp;Fei Li ,&nbsp;Hongyu Wang ,&nbsp;Ying Zhan ,&nbsp;Xiaodan Wu ,&nbsp;Zhiguo Wang ,&nbsp;Guoxu Zhang","doi":"10.1016/j.ygeno.2024.110906","DOIUrl":"10.1016/j.ygeno.2024.110906","url":null,"abstract":"<div><p>Enhancers are crucial in gene expression regulation, dictating the specificity and timing of transcriptional activity, which highlights the importance of their identification for unravelling the intricacies of genetic regulation. Therefore, it is critical to identify enhancers and their strengths. Repeated sequences in the genome are repeats of the same or symmetrical fragments. There has been a great deal of evidence that repetitive sequences contain enormous amounts of genetic information. Thus, We introduce the W2V-Repeated Index, designed to identify enhancer sequence fragments and evaluates their strength through the analysis of repeated K-mer sequences in enhancer regions. Utilizing the word2vector algorithm for numerical conversion and Manta Ray Foraging Optimization for feature selection, this method effectively captures the frequency and distribution of K-mer sequences. By concentrating on repeated K-mer sequences, it minimizes computational complexity and facilitates the analysis of larger K values. Experiments indicate that our method performs better than all other advanced methods on almost all indicators.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 5","pages":"Article 110906"},"PeriodicalIF":3.4,"publicationDate":"2024-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001277/pdfft?md5=0d0ea4c1427e7c0c571c9c7409b124e9&pid=1-s2.0-S0888754324001277-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141859507","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide association analysis reveals the genetic basis of thermal tolerance in dwarf surf clam Mulinia lateralis","authors":"Haoran Wang ,&nbsp;Zujing Yang ,&nbsp;Shenhai Wang ,&nbsp;Ang Zhao ,&nbsp;Hao Wang ,&nbsp;Zhi Liu ,&nbsp;Mingyi Sui ,&nbsp;Lijingjing Bao ,&nbsp;Qifan Zeng ,&nbsp;Jingjie Hu ,&nbsp;Zhenmin Bao ,&nbsp;Xiaoting Huang","doi":"10.1016/j.ygeno.2024.110904","DOIUrl":"10.1016/j.ygeno.2024.110904","url":null,"abstract":"<div><p>Recently, elevated seawater temperatures have resulted numerous adverse effects, including significant mortality among bivalves. The dwarf surf clam, <em>Mulinia lateralis</em>, is considered a valuable model species for bivalve research due to its rapid growth and short generation time. The successful cultivation in laboratory setting throughout its entire life cycle makes it an ideal candidate for exploring the potential mechanisms underlying bivalve responses to thermal stress. In this study, a total of 600 clams were subjected to a 17-day thermal stress experiment at a temperature of 30 °C which is the semi-lethal temperature for this species. Ninety individuals who perished initially were classified as heat-sensitive populations (HSP), while 89 individuals who survived the experiment were classified as heat-tolerant populations (HTP). Subsequently, 179 individuals were then sequenced, and 21,292 single nucleotide polymorphisms (SNPs) were genotyped for downstream analysis. The heritability estimate for survival status was found to be 0.375 ± 0.127 suggesting a genetic basis for thermal tolerance trait. Furthermore, a genome-wide association study (GWAS) identified three SNPs and 10 candidate genes associated with thermal tolerance trait in <em>M. lateralis</em>. These candidate genes were involved in the <em>ETHR</em>/<em>EHF</em> signaling pathway and played pivotal role in signal sensory, cell adhesion, oxidative stress, DNA damage repair, etc. Additionally, qPCR results indicated that, excluding <em>MGAT4A</em>, <em>ZAN</em>, and <em>RFC1</em> genes, all others exhibited significantly higher expression in the HTP (<em>p</em> &lt; 0.05), underscoring the critical involvement of the <em>ETHR</em>/<em>EHF</em> signaling pathway in <em>M. lateralis</em>' thermal tolerance. These results unveil the presence of standing genetic variations associated with thermal tolerance in <em>M. lateralis</em>, highlighting the regulatory role of the <em>ETHR</em>/<em>EHF</em> signaling pathway in the bivalve's response to thermal stress, which contribute to comprehension of the genetic basis of thermal tolerance in bivalves.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 5","pages":"Article 110904"},"PeriodicalIF":3.4,"publicationDate":"2024-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001253/pdfft?md5=da29085f952a8ca872e24d3ac5be6b91&pid=1-s2.0-S0888754324001253-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141859505","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The aminophospholipid transporter, ATP8B3, as a potential biomarker and target for enhancing the therapeutic effect of PD-L1 blockade in colon adenocarcinoma","authors":"Weihao Zhang ,&nbsp;Yongjie Xie ,&nbsp;Ziyun Liu ,&nbsp;Jie Zhang ,&nbsp;Bo Ni ,&nbsp;Wei Gao ,&nbsp;Wenge Xing ,&nbsp;Yaoyao Zhou ,&nbsp;Tongguo Si","doi":"10.1016/j.ygeno.2024.110907","DOIUrl":"10.1016/j.ygeno.2024.110907","url":null,"abstract":"<div><h3>Background</h3><p>Colon adenocarcinoma (COAD) is a prevalent malignant tumor globally, contributing significantly to cancer-related mortality. COAD guidelines label MSI (Microsatellite instability) and MSS (Microsatellite stability) subtypes as global classification criteria and treatment strategy selection criteria for COAD. Various combination therapies involving PD-L1 inhibitors and adjuvant therapy to enhance anti-tumor efficacy.</p></div><div><h3>Methods</h3><p>Datasets from single-cell RNA sequencing and bulk RNA sequencing in the TCGA and GEO databases were utilized to identify differentially expressed genes (DEGs). Furthermore, the correlation between ATP8B3 and PD-L1 was validated using siRNA, shRNA, and western blot analysis. Additionally, the association between ATP8B3 and immune checkpoint blockade (ICB) therapy was investigated through immune infiltration analysis and flow cytometry in both in vivo and in vitro assays.</p></div><div><h3>Results</h3><p>In the COAD patient group, ATP8B3 significantly contributed to the establishment of an immunosuppressive microenvironment. Inhibiting ATP8B3 led to a reduction in PD-L1 expression in colon cancer cell lines. Additionally, ATP8B3 expression levels could serve as a potential guide for PD-L1 treatment in MSI-H COAD patients, with higher ATP8B3 expression associated with increased sensitivity to PD-L1 therapy. However, due to the lack of immuno-killer cells in the microenvironment of MSS subtypes, elevated ATP8B3 expression couldn't increase the sensitivity of MSS COAD patients to PD-L1 inhibitors.</p></div><div><h3>Conclusion</h3><p>Our research results support that Inhibiting ATP8B3 could enhance TIL (tumor-infiltrating lymphocyte) infiltration by reducing PD-L1 expression in MSI-H COAD, thereby serving as an effective strategy to improve PD-L1 blocker efficacy. The treatment strategy of combining ATP8B3 inhibitors and immunotherapy for MSI/MSS COAD patients will be the best choice.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 5","pages":"Article 110907"},"PeriodicalIF":3.4,"publicationDate":"2024-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001289/pdfft?md5=5635c02dfd33eab8800ad87fe4783f19&pid=1-s2.0-S0888754324001289-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141792367","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"miR-10167-3p targets TCF7L1 to inhibit bovine adipocyte differentiation and promote bovine adipocyte proliferation","authors":"Chunli Hu,&nbsp;Mengli Yang,&nbsp;Xue Feng,&nbsp;Shuzhe Wang,&nbsp;Yanfen Ma,&nbsp;Yun Ma","doi":"10.1016/j.ygeno.2024.110903","DOIUrl":"10.1016/j.ygeno.2024.110903","url":null,"abstract":"<div><p>MicroRNAs (miRNAs) are widely involved in various lipogenic processes, including adipocyte proliferation and differentiation, lipid droplet formation, and adipocyte-specific gene activation. The present study aimed to investigate the gene expression profiles of bovine preadipocytes under high miR-10167-3p expression using the RNA-seq technique and to verify the functions of its downstream target genes on the proliferation and differentiation of bovine preadipocytes. First, RNA-seq identified 573 differentially expressed genes (DEGs), of which 243 were downregulated and 330 were upregulated. Then, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that 15.19% of the DEGs were enriched in pathways related to lipid metabolism. Meanwhile, dual-luciferase reporter gene assay verified the target-binding relationship between miR-10167-3p and <em>TCF7L1</em>. The function of <em>TCF7L1</em> was assessed using several experiments in adipocytes with high <em>TCF7L1</em> expression and RNA interference. The mRNA and protein expression of proliferation, differentiation, and apoptosis marker genes were detected using qPCR and western blot, respectively; lipid droplet synthesis was detected using oil red O, Nile red, and bodipy staining; adipocyte proliferation was detected by EdU; and apoptosis was detected using flow cytometry. The results revealed that <em>TCF7L1</em> overexpression inhibited bovine preadipocyte differentiation and apoptosis and promoted their proliferation, with opposite results obtained with its RNA interference. These results may provide a reference for the subsequent investigation of the molecular mechanism of bovine fat deposition.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 5","pages":"Article 110903"},"PeriodicalIF":3.4,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001241/pdfft?md5=cb5d0b6fde740e95307390a61567622c&pid=1-s2.0-S0888754324001241-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141787782","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"De novo assembly and comprehensive analysis of the mitochondrial genome of Taxus wallichiana reveals different repeats mediate recombination to generate multiple conformations","authors":"Kai Qu ,&nbsp;Dan Liu ,&nbsp;Limin Sun ,&nbsp;Meng Li ,&nbsp;Tiantian Xia ,&nbsp;Weixia Sun ,&nbsp;Yufei Xia","doi":"10.1016/j.ygeno.2024.110900","DOIUrl":"10.1016/j.ygeno.2024.110900","url":null,"abstract":"<div><p><em>Taxus</em> plants are the exclusive source of paclitaxel, an anticancer drug with significant medicinal and economic value. Interspecies hybridization and gene introgression during evolution have obscured distinctions among <em>Taxus</em> species, complicating their phylogenetic classification. While the chloroplast genome of <em>Taxus wallichiana</em>, a widely distributed species in China, has been sequenced, its mitochondrial genome (mitogenome) remains uncharacterized.We sequenced and assembled the <em>T. wallichiana</em> mitogenome using BGI short reads and Nanopore long reads, facilitating comparisons with other gymnosperm mitogenomes. The <em>T. wallichiana</em> mitogenome spanning 469,949 bp, predominantly forms a circular configuration with a GC content of 50.51%, supplemented by 3 minor configurations mediated by one pair of LRs and two pairs of IntRs. It includes 32 protein-coding genes, 7 tRNA genes, and 3 rRNA genes, several of which exist in multiple copies.We detailed the mitogenome's structure, codon usage, RNA editing, and sequence migration between organelles, constructing a phylogenetic tree to elucidate evolutionary relationships. Unlike typical gymnosperm mitochondria, <em>T. wallichiana</em> shows no evidence of mitochondrial-plastid DNA transfer (MTPT), highlighting its unique genomic architecture. Synteny analysis indicated extensive genomic rearrangements in <em>T. wallichiana</em>, likely driven by recombination among abundant repetitive sequences. This study offers a high-quality <em>T. wallichiana</em> mitogenome, enhancing our understanding of gymnosperm mitochondrial evolution and supporting further cultivation and utilization of <em>Taxus</em> species.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 5","pages":"Article 110900"},"PeriodicalIF":3.4,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001216/pdfft?md5=151a70eb7e8c78a2bfff1f7303b4fa30&pid=1-s2.0-S0888754324001216-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141787783","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}