Current Genomics最新文献

{"title":"Identification of Potential Genes and Critical Pathways in Postoperative Recurrence of Crohn's Disease by Machine Learning And WGCNA Network Analysis.","authors":"Aruna Rajalingam, Kanagaraj Sekar, Anjali Ganjiwale","doi":"10.2174/1389202924666230601122334","DOIUrl":"10.2174/1389202924666230601122334","url":null,"abstract":"<p><strong>Background: </strong>Crohn's disease (CD) is a chronic idiopathic inflammatory bowel disease affecting the entire gastrointestinal tract from the mouth to the anus. These patients often experience a period of symptomatic relapse and remission. A 20 - 30% symptomatic recurrence rate is reported in the first year after surgery, with a 10% increase each subsequent year. Thus, surgery is done only to relieve symptoms and not for the complete cure of the disease. The determinants and the genetic factors of this disease recurrence are also not well-defined. Therefore, enhanced diagnostic efficiency and prognostic outcome are critical for confronting CD recurrence.</p><p><strong>Methods: </strong>We analysed ileal mucosa samples collected from neo-terminal ileum six months after surgery (M6=121 samples) from Crohn's disease dataset (GSE186582). The primary aim of this study is to identify the potential genes and critical pathways in post-operative recurrence of Crohn's disease. We combined the differential gene expression analysis with Recursive feature elimination (RFE), a machine learning approach to get five critical genes for the postoperative recurrence of Crohn's disease. The features (genes) selected by different methods were validated using five binary classifiers for recurrence and remission samples: Logistic Regression (LR), Decision tree classifier (DT), Support Vector Machine (SVM), Random Forest classifier (RF), and K-nearest neighbor (KNN) with 10-fold cross-validation. We also performed weighted gene co-expression network analysis (WGCNA) to select specific modules and feature genes associated with Crohn's disease postoperative recurrence, smoking, and biological sex. Combined with other biological interpretations, including Gene Ontology (GO) analysis, pathway enrichment, and protein-protein interaction (PPI) network analysis, our current study sheds light on the in-depth research of CD diagnosis and prognosis in postoperative recurrence.</p><p><strong>Results: </strong>PLOD2, ZNF165, BOK, CX3CR1, and ARMCX4, are the important genes identified from the machine learning approach. These genes are reported to be involved in the viral protein interaction with cytokine and cytokine receptors, lysine degradation, and apoptosis. They are also linked with various cellular and molecular functions such as Peptidyl-lysine hydroxylation, Central nervous system maturation, G protein-coupled chemoattractant receptor activity, BCL-2 homology (BH) domain binding, Gliogenesis and negative regulation of mitochondrial depolarization. WGCNA identified a gene co-expression module that was primarily involved in mitochondrial translational elongation, mitochondrial translational termination, mitochondrial translation, mitochondrial respiratory chain complex, mRNA splicing <i>via</i> spliceosome pathways, <i>etc</i>.; Both the analysis result emphasizes that the mitochondrial depolarization pathway is linked with CD recurrence leading to oxidative st","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2023-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10662376/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49542975","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Taxonomic Status and Phylogenetic Relationship of Family Charadriidae based on Complete Mitogenomes","authors":"Weiya Qian, Yizheng Liu, Keer Miao, Qing Chang, Chaochao Hu","doi":"10.2174/0113892029273517231017051819","DOIUrl":"https://doi.org/10.2174/0113892029273517231017051819","url":null,"abstract":"Background: The Charadriiformes provide a good source for researching evolution owing to their diverse distribution, behavior, morphology, and ecology. However, in the Charadrii, family-level relationships remain understudied, and the monophyly of Charadriidae is also a subject of controversy. Method: In the present study, we generated complete mitogenomes for two species, Charadrius leschenaultii and Charadrius mongolus, which were found to be 16,905 bp and 16,844 bp in length, respectively. Among the 13 protein codon genes, we observed variation in the rate of nonsynonymous substitution rates, with the slowest rate found in COI and the fastest rate observed in ATP8. The Ka/Ks ratio for all Charadriidae species was significantly lower than one, which inferred that the protein-coding genes underwent purifying selection. Result: Phylogenetic analysis based on the genes of Cyt b, 12S and ND2 revealed that the genus Pluvialis is the sister group of three families (Haematopodidae, Ibidorhynchidae, Recurvirostridae). However, the phylogenetic analysis based on complete mitogenomes indicated that the genus Pluvialis is within the Charadriidae family. Conclusion: This study highlights the importance of carefully selecting the number of genes used to obtain accurate estimates of the species tree. It also suggests that relying on partial mtDNA genes with fast-evolving rates may lead to misleading results when resolving the Pluvialis sister group. Future research should focus on sequencing more mitogenomes at different taxonomic levels to gain a better understanding of the features and phylogenetic relationships within the Charadriiformes order.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136316941","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":"Deciphering Target Protein Cascade in <i>Salmonella typhi</i> Biofilm using Genomic Data Mining, and Protein-protein Interaction.","authors":"Aditya Upadhyay, Dharm Pal, Awanish Kumar","doi":"10.2174/1389202924666230815144126","DOIUrl":"10.2174/1389202924666230815144126","url":null,"abstract":"<p><strong>Background: </strong><i>Salmonella typhi</i> biofilm confers a serious public health issue for lengthy periods and the rise in antibiotic resistance and death rate. Biofilm generation has rendered even the most potent antibiotics ineffective in controlling the illness, and the <i>S</i>. <i>typhi</i> outbreak has turned into a fatal disease typhoid. <i>S. typhi</i> infection has also been connected to other deadly illnesses, such as a gall bladder cancer. The virulence of this disease is due to the interaction of numerous genes and proteins of <i>S</i>. <i>typhi</i>.</p><p><strong>Objective: </strong>The study aimed to identify a cascade of target proteins in <i>S. typhi</i> biofilm condition with the help of genomic data mining and protein-protein interaction analysis.</p><p><strong>Methods: </strong>The goal of this study was to notice some important pharmacological targets in <i>S. typhi.</i> using genomic data mining, and protein-protein interaction approaches were used so that new drugs could be developed to combat the disease.</p><p><strong>Results: </strong>In this study, we identified 15 potential target proteins that are critical for <i>S. typhi</i> biofilm growth and maturation. Three proteins, CsgD, AdrA, and BcsA, were deciphered with their significant role in the synthesis of cellulose, a critical component of biofilm's extracellular matrix. The CsgD protein was also shown to have high interconnectedness and strong interactions with other important target proteins of <i>S. typhi</i>. As a result, it has been concluded that CsgD is involved in a range of activities, including cellulose synthesis, bacterial pathogenicity, quorum sensing, and bacterial virulence.</p><p><strong>Conclusion: </strong>All identified targets in this study possess hydrophobic properties, and their cellular localization offered proof of a potent therapeutic target. Overall results of this study, drug target shortage in <i>S. typhi</i> is also spotlighted, and we believe that obtained result could be useful for the design and development of some potent anti-salmonella agents for typhoid fever in the future.</p>","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2023-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10662377/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45301923","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Application of Feature Definition and Quantification in Biological Sequence Analysis.","authors":"Weiyang Chen, Weiwei Li","doi":"10.2174/1389202924666230816150732","DOIUrl":"10.2174/1389202924666230816150732","url":null,"abstract":"<p><p>Biological sequence analysis is the most fundamental work in bioinformatics. Many research methods have been developed in the development of biological sequence analysis. These methods include sequence alignment-based methods and alignment-free methods. In addition, there are also some sequence analysis methods based on the feature definition and quantification of the sequence itself. This editorial introduces the methods of biological sequence analysis and explores the significance of defining features and quantitative research of biological sequences.</p>","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2023-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10662379/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46676866","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High Prevalence of a c.5979dupA Variant in the Dysferlin Gene (DYSF) in Individuals from a Semiarid Region of Brazil","authors":"Isabella A. Motta, Maria Lucrécia A. Gouveia, Ana Paula M. Braga, Rafael S. Andrade, Mayra F.F. Montenegro, Sandra N. Gurgel, Keila M.F. Albuquerque, Priscilla A.N.G. Souto, Flávia P.B.F. Cardoso, Joseane S. Araujo, Mirella C.L. Pinheiro, Carlos E.P. da Silva, Pamella A.S. Gurgel, David Feder, Matheus M. Perez, Glaucia Luciano da Veiga, Beatriz C.A. Alves, Fernando L.A. Fonseca, Alzira A.S. Carvalho","doi":"10.2174/0113892029257856231013115036","DOIUrl":"https://doi.org/10.2174/0113892029257856231013115036","url":null,"abstract":"Background: Dysferlinopathies represent a group of limb girdle or distal muscular dystrophies with an autosomal-recessive inheritance pattern resulting from the presence of pathogenic variants in the dysferlin gene (DYSF). Objective: In this work, we describe a population from a small city in Brazil carrying the c.5979dupA pathogenic variant of DYSF responsible for limb girdle muscular dystrophy type 2R and distal muscular dystrophy. Methods: Genotyping analyses were performed by qPCR using customized probe complementary to the region with the duplication under analysis in the DYSF. Results: A total of 104 individuals were examined. c.5979dupA was identified in 48 (46.15%) individuals. Twenty-three (22%) were homozygotes, among whom 13 (56.5%) were female. A total of 91.3% (21) of homozygous individuals had a positive family history, and seven (30.4%) reported consanguineous marriages. Twenty-five (24%) individuals were heterozygous (25.8±16 years) for the same variant, among whom 15 (60%) were female. The mean CK level was 697 IU for homozygotes, 140.5 IU for heterozygotes and 176 IU for wild-type homo-zygotes. The weakness distribution pattern showed 17.3% of individuals with a proximal pattern, 13% with a distal pattern and 69.6% with a mixed pattern. Fatigue was present in 15 homozygotes and one heterozygote. Conclusion: The high prevalence of this variant in individuals from this small community can be explained by a possible founder effect associated with historical, geographical and cultural aspects.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135113544","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":"Pan-Cancer Analysis Identifies AIMP2 as a Potential Biomarker for Breast Cancer","authors":"Jie Qiu, Tao Zhou, Danhong Wang, Weimin Hong, Da Qian, Xiaozhen Liu, Xuli Meng","doi":"10.2174/0113892029255941231014142050","DOIUrl":"https://doi.org/10.2174/0113892029255941231014142050","url":null,"abstract":"Introduction:: Aminoacyl tRNA synthetase complex interacting with multifunctional protein 2 (AIMP2) is a significant regulator of cell proliferation and apoptosis. Despite its abnormal expression in various tumor types, the specific functions and effects of AIMP2 on tumor immune cell infiltration, proliferation, and migration remain unclear. background: AIMP2, Aminoacyl TRNA Synthetase Complex Interacting Multifunctional Protein 2, also known as JTV1, a multifunctional protein that forms a macromolecular complex with human aminoacyl tRNA synthetase, which consists of three non-enzymatic proteins, including p43, p38 and p18 proteins, of which p38 protein is AIMP2[1]. AIMP2 is necessary for the assembly and stability of aminoacyl tRNA synthetase complex[2]. Besides being important for efficient protein synthesis, additional physiological roles for AIMP2 have been discovered[3, 4]. For example, following DNA damage, AIMP2 is liberated from the ARS complex, phosphorylated in a JNK2-dependent pathway and translocated into the nucleus where it has been suggested to bind and sequester p53 from Mdm2-dependent ubiquitination[5]. AIMP2 has also been shown to be a substrate of E3 ligase Parkin[6]. Accumulation of AIMP2 as a result of Parkin mutation has been speculated to contribute to the characteristic dopaminergic cell death observed in Parkinson patients[7]. In addition, AIMP2 augments tumor necrosis factor-α-induced apoptotic signaling and exerts antiproliferative activities in TGF-β and Wnt pathways via distinct working mechanisms [8-10]. Therefore, we wonder that AIMP2 may play a crucial role in the occurrence and development of cancer. However, there are relatively few reseaches on AIMP2 in oncology. Current studies confirmed that AIMP2 may function as a multifunctional tumor suppressor[9, 11]. In this study, we analyzed the expression of AIMP2 and its relationship with the prognosis, Tumor Mutation Burden (TMB) and Microsatellite Instability (MSI) in 33 cancer types. In addition, we examined the correlation between AIMP2 and the immune microenvironment, immune-related antigens, and immune checkpoint genes. The results showed that AIMP2 was higher expressed in tumor tissue compared with normal tissue. Moreover, AIMP2 was associated with several tumor stages. Survival analysis showed that AIMP2 expression was strongly associated with OS in some cancer patients, where the high expression of AIMP2 was associated with a worse prognosis in five types of cancer. Then, we confirmed that the expression level of AIMP2 was associated with tumor immune infiltration and tumor microenvironment, especially in BRCA. Finally, si-RNA mediated knockdown of AIMP2 suppressed the proliferation and migration of BC cells in vitro. In conclusion, AIMP2 was found to be differentially expressed in the pan-cancer analysis and might play an important role in tumor immunity, which is expected to be a potential tumor prognostic marker, especially in BRCA. Method:: To assess AIMP","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135218841","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":"Unraveling the Concealed Transcriptomic Landscape of PTEN in Human Malignancies","authors":"Michaela A. Boti, Panagiotis G. Adamopoulos, Dido Vassilacopoulou, Andreas Scorilas","doi":"10.2174/0113892029265367231013113304","DOIUrl":"https://doi.org/10.2174/0113892029265367231013113304","url":null,"abstract":"Background: Phosphatase and tensin homolog, widely known as PTEN, is a major negative regulator of the PI3K/AKT/mTOR signaling pathway, involved in the regulation of a variety of important cellular processes, including cell proliferation, growth, survival, and metabolism. Since most of the molecules involved in this biological pathway have been described as key regulators in cancer, the study of the corresponding genes at several levels is crucial. Objective: Although previous studies have elucidated the physiological role of PTEN under normal conditions and its involvement in carcinogenesis and cancer progression, the transcriptional profile of PTEN has been poorly investigated. Methods: In this study, instead of conducting the “gold-standard” direct RNA sequencing that fails to detect less abundant novel mRNAs due to the decreased sequencing depth, we designed and implemented a multiplexed PTEN-targeted sequencing approach that combined both short- and longread sequencing. Results: Our study has highlighted a broad spectrum of previously unknown PTEN mRNA transcripts and assessed their expression patterns in a wide range of human cancer and non-cancer cell lines, shedding light on the involvement of PTEN in cell cycle dysregulation and thus tumor development. Conclusion: The identification of the described novel PTEN splice variants could have significant implications for understanding PTEN regulation and function, and provide new insights into PTEN biology, opening new avenues for monitoring PTEN-related diseases, including cancer.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135113985","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":"Complete Chloroplast Genomes of Pterodon emarginatus Vogel and Pterodon pubescens Benth: Comparative and Phylogenetic Analyses","authors":"Juliana Borges Pereira Brito, Adriana Maria Antunes, Ramilla dos Santos Braga Ferreira, Mariana Pires de Campos Telles, Cíntia Pelegrineti Targueta de Azevedo Brito, Thannya Nascimento Soares","doi":"10.2174/0113892029244147231016050434","DOIUrl":"https://doi.org/10.2174/0113892029244147231016050434","url":null,"abstract":"Background: The species Pterodon emarginatus and P. pubescens, popularly known as white sucupira or faveira, are native to the Cerrado biome and have the potential for medicinal use and reforestation. They are sister species with evolutionary proximity. Objective: The species Pterodon emarginatus and P. pubescens, popularly known as white sucupira or faveira, are native to the Cerrado biome and have the potential for medicinal use and reforestation. They are sister species with evolutionary proximity. Methods: The chloroplast genomes of P. emarginatus and P. pubescens were sequenced on the Illumina MiSeq platform. The genomes were assembled based on the de novo strategy. We performed the annotation of the genes and the repetitive regions of the genomes. The nucleotide diversity and phylogenetic relationships were analyzed using the gene sequences of these species and others of the Leguminosae family, whose genomes are available in databases. Results: The complete chloroplast genome of P. emarginatus is 159,877 bp, and that of P. pubescens is 159,873 bp. The genomes of both species have circular and quadripartite structures. A total of 127 genes were predicted in both species, including 110 single-copy genes and 17 duplicated genes in the inverted regions. 141 microsatellite regions were identified in P. emarginatus and 140 in P. pubescens. The nucleotide diversity estimates of the gene regions in twenty-one species of the Leguminosae family were 0.062 in LSC, 0.086 in SSC, and 0.036 in IR. The phylogenetic analysis demonstrated the proximity between the genera Pterodon and Dipteryx, both from the clade Dipterygeae. Ten pairs of primers with potential for the development of molecular markers were designed. Conclusion: The genetic information obtained on the chloroplast genomes of P. emarginatus and P. pubescens presented here reinforces the similarity and evolutionary proximity between these species, with a similarity percentage of 99.8%.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135218842","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":"Genome Sequencing and Organization of Three Geographically Different Isolates of Nucleopolyhedrovirus from the Gypsy Moth Reveal Significant Genomic Differences","authors":"Donus Gencer, Cihan Inan, Zeynep Bayramoglu, Remziye Nalcacioglu, Feifei Yin, Zheng Zhu, Jun Wang, Zhihong Hu, Lillian Pavlik, Basil Arif, Zihni Demirbag, Ismail Demir","doi":"10.2174/0113892029249830231014163829","DOIUrl":"https://doi.org/10.2174/0113892029249830231014163829","url":null,"abstract":"Background: The gypsy moth (Lymantria dispar L., Lepidoptera: Erebidae) is a worldwide pest of trees and forests. Lymantria dispar nucleopolyhedrovirus (LdMNPV) belongs to the Baculoviridae family and is an insect virus specific to gypsy moth larvae. In this study, we describe the complete genome sequences of three geographically diverse isolates, H2 (China), J2 (Japan), and T3 (Turkey), of Lymantria dispar multiple nucleopolyhedrovirus (LdMNPV). Method: The genomes of isolates H2, J2, and T3 were subjected to shotgun pyrosequencing using Roche 454 FLX and assembled using Roche GS De Novo Assembler. Comparative analysis of all isolates was performed using bioinformatics methods. Results: The genomes of LdMNPV-H2, J2, and T3 were 164,746, 162,249, and 162,614 bp in size, had GC content of 57.25%, 57.30%, and 57.46%, and contained 162, 165, and 164 putative open reading frames (ORFs ≥ 150 nt), respectively. Comparison between the reference genome LdMNPV-5/6 (AF081810) and the genomes of LdMNPV-H2, J2, and T3 revealed differences in gene content. Compared with LdMNPV-5/6, ORF5, 6, 8, 10, 31, and 67 were absent in LdMNPVH2, ORF5, 13, and 66 were absent in LdMNPV-J2, and ORF10, 13, 31, and 67 were absent in LdMNPV-T3. In addition, the gene encoding the mucin-like protein (ORF4) was split into two parts in isolates H2 and T3 and designated ORF4a and ORF4b. Phylogenetic analysis grouped isolates H2 and J2 in a different cluster than isolate T3, which is more closely related to the Turkish and Polish isolates. In addition, H2 was found to be closely related to a South Korean LdMNPV isolate. Conclusion: This study provided a more detailed overview of the relationships between different geographic LdMNPV isolates. The results showed remarkable differences between groups at the genome level.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135218848","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":"Using Chaos-Game-Representation for Analysing the SARS-CoV-2 Lineages, Newly Emerging Strains and Recombinants","authors":"Amarinder Singh Thind, Somdatta Sinha","doi":"10.2174/0113892029264990231013112156","DOIUrl":"https://doi.org/10.2174/0113892029264990231013112156","url":null,"abstract":"Background: Viruses have high mutation rates, facilitating rapid evolution and the emergence of new species, subspecies, strains and recombinant forms. Accurate classification of these forms is crucial for understanding viral evolution and developing therapeutic applications. Phylogenetic classification is typically performed by analyzing molecular differences at the genomic and sub-genomic levels. This involves aligning homologous proteins or genes. However, there is growing interest in developing alignment-free methods for whole-genome comparisons that are computationally efficient. Methods: Here we elaborate on the Chaos Game Representation (CGR) method, based on concepts of statistical physics and free of sequence alignment assumptions. We adopt the CGR method for classification of the closely related clades/lineages A and B of the SARS-Corona virus 2019 (SARS-CoV-2), which is one of the fastest evolving viruses. Results: Our study shows that the CGR approach can easily yield the SARS-CoV-2 phylogeny from the available whole genomes of lineage A and lineage B sequences. It also shows an accurate classification of eight different strains and the newly evolved XBB variant from its parental strains. Compared to alignment-based methods (Neighbour-Joining and Maximum Likelihood), the CGR method requires low computational resources, is fast and accurate for long sequences, and, being a K-mer based approach, allows simultaneous comparison of a large number of closely-related sequences of different sizes. Further, we developed an R pipeline CGRphylo, available on GitHub, which integrates the CGR module with various other R packages to create phylogenetic trees and visualize them. Conclusion: Our findings demonstrate the efficacy of the CGR method for accurate classification and tracking of rapidly evolving viruses, offering valuable insights into the evolution and emergence of new SARS-CoV-2 strains and recombinants.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135315919","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}