Evolutionary Bioinformatics最新文献

{"title":"Transposable Elements-Derived MicroRNA Expression Patterns in TCGA Dataset for 10 Species.","authors":"Chan-Mi Lee,&nbsp;Sang Woo Jin,&nbsp;Byunghyun Jang,&nbsp;Young Kyung Ko,&nbsp;Jeong-An Gim","doi":"10.1177/11769343231194020","DOIUrl":"https://doi.org/10.1177/11769343231194020","url":null,"abstract":"<p><p>MicroRNAs (miRNAs) are a class of non-coding RNAs that act as regulators of disease. An evolutionary approach to the disease could reveal factors such as diagnosis, treatment, and prognosis prediction. The expression patterns of transposable element (TEs)-derived miRNAs could help elucidate diseases, and their evolutionary patterns are also valuable. The 34 miRNAs were compared in terms of stage survival and tumor status in 33 carcinomas from TCGA. Expression levels were compared using a <i>t</i>-test and presented as differentially expressed miRNAs (DEMs). For DEMs showing statistically specific expression patterns for 3 conditions (normal and cancer, early and advanced stage, and survival), interactions with related genes in 10 species, including humans, were compared. The enrichment term was discovered for the gene-miRNA interactions. In 18 out of the 33 carcinomas, at least one miRNA was retrieved with <i>P</i> < .05 and |fold change| >.05. A total of 128 DEMs for the 9 miRNAs were identified. Based on the TargetScan database, interactions between miRNAs and genes in 10 species, including humans, were confirmed. The evolutionarily conserved miR-130a was observed in all 10 species, whereas miR-151a was only observed in humans. GO terms of related genes were selected for the miRNAs commonly found in each species. Evolutionary analysis of TE-derived disease-associated miRNAs was performed, and the evolutionarily conserved miR-130a-related carcinomas included renal and thyroid cancers. Human and rhesus monkey-specific miR-625 is associated with various carcinomas.</p>","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":"19 ","pages":"11769343231194020"},"PeriodicalIF":2.6,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/99/11/10.1177_11769343231194020.PMC10426303.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10650845","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":"Utilizing In Silico Approaches to Investigate the Signaling Pathway’s Crucial Function in <i>Pennisetum glaucum</i> Under Thermal Stress","authors":"Faten Dhawi","doi":"10.1177/11769343231211072","DOIUrl":"https://doi.org/10.1177/11769343231211072","url":null,"abstract":"Pearl millet (Pennisetum glaucum (L.)) is a remarkable cereal crop known for its ability to thrive in challenging environmental conditions. Despite its resilience, the intricate molecular mechanisms behind its toughness remain a mystery. To address this knowledge gap, we conducted advanced next-generation RNA sequencing. This approach allowed us to compare the gene expression profiles of pearl millet seedlings exposed to heat stress with those grown under standard conditions. Our main focus was on the shoots of 13-day-old pearl millet plants, which we subjected to a brief heat stress episode at 50°C for 60 seconds. Within the vast genomic landscape comprising 36 041 genes, we successfully identified a set of 10 genes that exhibited significant fold changes, ranging from 11 to 14-fold compared to the control conditions. These 10 genes were previously unknown to have such substantial changes in expression compared to the control. To uncover the functional significance hidden within these transcriptomic findings, we utilized computational tools such as MEME, String, and phylogenetic tree analysis. These efforts collectively revealed conserved domains within the transcriptomic landscape, hinting at potential functions associated with these genetic sequences. Of particular note, the distinct transcriptomic patterns specific to pearl millet leaves under thermal stress shed light on intricate connections to fundamental biological processes. These processes included the Ethylene-activated signaling pathway, Regulation of intracellular signal transduction, Negative regulation of signal transduction, Protein autophosphorylation, and Intracellular signal transduction. Together, these processes provide insight into the molecular strategies employed by pearl millet to overcome thermal stress challenges. By integrating cutting-edge RNA sequencing techniques and computational analyses, we have embarked on unraveling the genetic components and pathways that empower pearl millet’s resilience in the face of adversity. This newfound understanding has the potential to not only advance our knowledge of plant stress responses but also contribute to enhancing crop resilience in challenging environmental conditions.","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":"39 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135710040","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":"New Insights Into The Evolution of Chloroplast Genomes in <i>Ochna</i> Species (Ochnaceae, Malpighiales)","authors":"Nguyen Nhat Nam, Nguyen Hoang Danh, Vu Minh Thiet, Hoang Dang Khoa Do","doi":"10.1177/11769343231210756","DOIUrl":"https://doi.org/10.1177/11769343231210756","url":null,"abstract":"Ochnaceae DC. includes more than 600 species that exhibit potential values for environmental ecology, ornamental, pharmaceutical, and timber industries. Although studies on phylogeny and phytochemicals have been intensively conducted, chloroplast genome data of Ochnaceae species have not been fully explored. In this study, the next-generation sequencing method was used to sequence the chloroplast genomes of Ochna integerrima and Ochna serrulata which were 157 329 and 157 835 bp in length, respectively. These chloroplast genomes had a quadripartite structure and contained 78 protein-coding genes, 30 tRNAs, and 4 rRNAs. Comparative analysis revealed 8 hypervariable regions, including trnK_UUU-trnQ_UUG, rpoB-psbM, trnS_GGA-rps4, accD-psaI, rpl33-rps18, rpl14-rpl16, ndhF-trnL_UAG, and rps15-ycf1 among 6 Ochnaceae taxa. Additionally, there were shared and unique repeats among 6 examined chloroplast genomes. The notable changes were the loss of rpl32 in Ochna species and the deletion of rps16 exon 2 in O. integerrima compared to other taxa. This study is the first comprehensive comparative genomic analysis of complete chloroplast genomes of Ochna species and related taxa in Ochnaceae. Consequently, the current study provides initial results for further research on genomic evolution, population genetics, and developing molecular markers in Ochnaceae and related taxa.","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":"139 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135710343","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":"Effects of Antibiotic Treatment on the Development and Bacterial Community of the <i>Wolbachia</i>-Infected Diamondback Moth.","authors":"Xiangyu Zhu,&nbsp;Ling Zhang,&nbsp;Jinyang Li,&nbsp;Ao He,&nbsp;Minsheng You,&nbsp;Shijun You","doi":"10.1177/11769343231175269","DOIUrl":"https://doi.org/10.1177/11769343231175269","url":null,"abstract":"<p><p>Based on the important role of antibiotic treatment in the research of the interaction between <i>Wolbachia</i> and insect hosts, this study aimed to identify the most suitable antibiotic and concentration for <i>Wolbachia</i> elimination in the <i>P. xylostella</i>, and to investigate the effect of <i>Wolbachia</i> and antibiotic treatment on the bacterial community of <i>P. xylostella</i>. Our results showed that the <i>Wolbachia</i>-infected strain was <i>plutWB1</i> of supergroup B in the <i>P. xylostella</i> population collected in Nepal in this study; 1 mg/mL rifampicin could remove <i>Wolbachia</i> infection in <i>P. xylostella</i> after 1 generation of feeding treatment and the toxic effect was relatively low; among the 29 samples of adult <i>P. xylostella</i> in our study (10 WU samples, 10 WA samples, and 9 WI samples), 52.5% of the sequences were of Firmicutes and 47.5% were of Proteobacteria, with the dominant genera being mainly <i>Carnobacterium</i> (46.2%), <i>Enterobacter</i> (10.1%), and <i>Enterococcus</i> (6.2%); Moreover, antibiotic removal of <i>Wolbachia</i> infection in <i>P. xylostella</i> and transfer to normal conditions for 10 generations no longer significantly affected the bacterial community of <i>P. xylostella</i>. This study provides a theoretical basis for the elimination method of <i>Wolbachia</i> in the <i>P. xylostella</i>, as well as a reference for the elimination method of <i>Wolbachia</i> in other <i>Wolbachia</i>-infected insect species, and a basis for the study of the extent and duration of the effect of antibiotic treatment on the bacterial community of the <i>P. xylostella</i>.</p>","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":"19 ","pages":"11769343231175269"},"PeriodicalIF":2.6,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/ce/d6/10.1177_11769343231175269.PMC10265341.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10646869","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":"The Prognostic Value of a lncRNA Risk Model Consists of 9 m6A Regulator-Related lncRNAs in Hepatocellular Carcinoma (HCC).","authors":"Zhen Deng,&nbsp;Jiaxing Hou,&nbsp;Hongbo Xu,&nbsp;Zhao Lei,&nbsp;Zhiqiang Li,&nbsp;Hongwei Zhu,&nbsp;Xiao Yu,&nbsp;Zhi Yang,&nbsp;Xiaoxin Jin,&nbsp;Jichun Sun","doi":"10.1177/11769343221142013","DOIUrl":"https://doi.org/10.1177/11769343221142013","url":null,"abstract":"<p><p>Hepatocellular carcinoma (HCC) is the most common primary malignancy of the liver. Although the RNA modification N6-methyladenine (m6A) has been reported to be involved in HCC carcinogenesis, early diagnostic markers and promising personalized therapeutic targets are still lacking. In this study, we identified that 19 m6A regulators and 34 co-expressed lncRNAs were significantly upregulated in HCC samples; based on these factors, we established a prognostic signal of HCC associated with 9 lncRNAs and 19 m6A regulators using LASSO Cox regression analysis. Kaplan-Meier survival estimate revealed correlations between the risk scores and patients' OS in the training and validation dataset. The ROC curve demonstrated that the risk score-based curve has satisfactory prediction efficiency for both training and validation datasets. Multivariate Cox's proportional hazard regression analysis indicated that the risk score was an independent risk factor within the training and validation dataset. In addition, the risk score could distinguish HCC patients from normal non-cancerous samples and HCC samples of different pathological grades. Eventually, 232 mRNAs were co-expressed with these 9 lncRNAs according to GSE101685 and GSE112790; these mRNAs were enriched in cell cycle and cell metabolic activities, drug metabolism, liver disease-related pathways, and some important cancer related pathways such as p53, MAPK, Wnt, RAS and so forth. The expression of the 9 lncRNAs was significantly higher in HCC samples than that in the neighboring non-cancerous samples. Altogether, by using the Consensus Clustering, PCA, ESTIMATE algorithm, LASSO regression model, Kaplan-Meier survival assessment, ROC curve analysis, and multivariate Cox's proportional hazard regression model analysis, we established a prognostic marker consisting of 9 m6A regulator-related lncRNAs that markers may have prognostic and diagnostic potential for HCC.</p>","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":"19 ","pages":"11769343221142013"},"PeriodicalIF":2.6,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/1a/64/10.1177_11769343221142013.PMC9841875.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10555929","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":"Characterization and Expression Analysis of <i>B12D-Like</i> Gene From Pearl Millet.","authors":"Zainab M Almutairi","doi":"10.1177/11769343221142285","DOIUrl":"https://doi.org/10.1177/11769343221142285","url":null,"abstract":"<p><p><i>B12D-Like</i> is a member of the B12D domain-containing protein family, which includes several transmembrane proteins in plants. In this study, the cDNA of <i>PgB12D-Like</i> from <i>Pennisetum glaucum subsp. monodii</i> (Maire) Brunken was sequenced and characterized. The 446-bp cDNA for <i>PgB12D-Like</i> encodes for a deduced protein of 95 amino acids. The PgB12D-Like protein contains a B12D domain and a transmembrane helix embedded in the mitochondrial membrane. Cis-regulatory elements analysis reveals binding sites for various transcription factors involved in responses to stress, light, and plant hormones in the putative promoter sequence for <i>PgB12D-Like</i>. Several proteins involved in floral organ development were also found to have binding sites in the <i>PgB12D-Like</i> promoter, such as agamous-like proteins and squamosa promoter binding proteins. Real-time PCR reveals high expression of <i>PgB12D-Like</i> in flowers during heading, whereas its expression in a 4-day-old seedling shoot was the lowest. Moreover, cold, drought, and heat stress were found to upregulate <i>PgB12D-Like</i>, whereas gibberellic acid downregulated its expression in seedlings. The present study helps to uncover the function of the <i>B12D-Like</i> in response to plant hormones and abiotic stress during <i>P. glaucum</i> development.</p>","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":"18 ","pages":"11769343221142285"},"PeriodicalIF":2.6,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/f9/c6/10.1177_11769343221142285.PMC9793006.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10455657","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":"Biological Computation and Compatibility Search in the Possibility Space as the Mechanism of Complexity Increase During Progressive Evolution","authors":"A. Kozlov","doi":"10.1177/11769343221110654","DOIUrl":"https://doi.org/10.1177/11769343221110654","url":null,"abstract":"The idea of computational processes, which take place in nature, for example, DNA computation, is discussed in the literature. DNA computation that is going on in the immunoglobulin locus of vertebrates shows how the computations in the biological possibility space could operate during evolution. We suggest that the origin of evolutionarily novel genes and genome evolution constitute the original intrinsic computation of the information about new structures in the space of unrealized biological possibilities. Due to DNA computation, the information about future structures is generated and stored in DNA as genetic information. In evolving ontogenies, search algorithms are necessary, which can search for information about evolutionary innovations and morphological novelties. We believe that such algorithms include stochastic gene expression, gene competition, and compatibility search at different levels of structural organization. We formulate the increase in complexity principle in terms of biological computation and hypothesize the possibility of in silico computing of future functions of evolutionarily novel genes.","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":"18 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48990834","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":"Diversity in Expression Biases of Lineage-Specific Genes During Development and Anhydrobiosis Among Tardigrade Species.","authors":"Jean-Christophe Metivier,&nbsp;Frédéric J J Chain","doi":"10.1177/11769343221140277","DOIUrl":"https://doi.org/10.1177/11769343221140277","url":null,"abstract":"<p><p>Lineage-specific genes can contribute to the emergence and evolution of novel traits and adaptations. Tardigrades are animals that have adapted to tolerate extreme conditions by undergoing a form of cryptobiosis called anhydrobiosis, a physical transformation to an inactive desiccated state. While studies to understand the genetics underlying the interspecies diversity in anhydrobiotic transitions have identified tardigrade-specific genes and family expansions involved in this process, the contributions of species-specific genes to the variation in tardigrade development and cryptobiosis are less clear. We used previously published transcriptomes throughout development and anhydrobiosis (5 embryonic stages, 7 juvenile stages, active adults, and tun adults) to assess the transcriptional biases of different classes of genes between 2 tardigrade species, <i>Hypsibius exemplaris</i> and <i>Ramazzottius varieornatus</i>. We also used the transcriptomes of 2 other tardigrades, <i>Echiniscoides sigismundi</i> and <i>Richtersius coronifer</i>, and data from 3 non-tardigrade species (<i>Adenita vaga</i>, <i>Drosophila melanogaster</i>, and <i>Caenorhabditis elegans</i>) to help identify lineage-specific genes. We found that lineage-specific genes have generally low and narrow expression but are enriched among biased genes in different stages of development depending on the species. Biased genes tend to be specific to early and late development, but there is little overlap in functional enrichment of biased genes between species. Gene expansions in the 2 tardigrades also involve families with different functions despite homologous genes being expressed during anhydrobiosis in both species. Our results demonstrate the interspecific variation in transcriptional contributions and biases of lineage-specific genes during development and anhydrobiosis in 2 tardigrades.</p>","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":"18 ","pages":"11769343221140277"},"PeriodicalIF":2.6,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/51/e1/10.1177_11769343221140277.PMC9791283.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10509846","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":"Stability of scRNA-Seq Analysis Workflows is Susceptible to Preprocessing and is Mitigated by Regularized or Supervised Approaches.","authors":"Arda Durmaz,&nbsp;Jacob G Scott","doi":"10.1177/11769343221123050","DOIUrl":"https://doi.org/10.1177/11769343221123050","url":null,"abstract":"<p><strong>Background: </strong>Statistical methods developed to address various questions in single-cell datasets show increased variability to different parameter regimes. In order to delineate further the robustness of commonly utilized methods for single-cell RNA-Seq, we aimed to comprehensively review scRNA-Seq analysis workflows in the setting of dimension reduction, clustering, and trajectory inference.</p><p><strong>Methods: </strong>We utilized datasets with temporal single-cell transcriptomics profiles from public repositories. Combining multiple methods at each level of the workflow, we have performed over 6<i>k</i> analysis and evaluated the results of clustering and pseudotime estimation using adjusted rand index and rank correlation metrics. We have further integrated neural network methods to assess whether models with increased complexity can show increased bias/variance trade-off.</p><p><strong>Results: </strong>Combinatorial workflows showed that utilizing non-linear dimension reduction techniques such as t-SNE and UMAP are sensitive to initial preprocessing steps hence clustering results on dimension reduced space of single-cell datasets should be utilized carefully. Similarly, pseudotime estimation methods that depend on previous non-linear dimension reduction steps can result in highly variable trajectories. In contrast, methods that avoid non-linearity such as WOT can result in repeatable inferences of temporal gene expression dynamics. Furthermore, imputation methods do not improve clustering or trajectory inference results substantially in terms of repeatability. In contrast, the selection of the normalization method shows an increased effect on downstream analysis where ScTransform reduces variability overall.</p>","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":"18 ","pages":"11769343221123050"},"PeriodicalIF":2.6,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/07/96/10.1177_11769343221123050.PMC9527995.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9743388","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":"Evolutionary Dynamics of Indels in SARS-CoV-2 Spike Glycoprotein.","authors":"R Shyama Prasad Rao, Nagib Ahsan, Chunhui Xu, Lingtao Su, Jacob Verburgt, Luca Fornelli, Daisuke Kihara, Dong Xu","doi":"10.1177/11769343211064616","DOIUrl":"10.1177/11769343211064616","url":null,"abstract":"<p><p>SARS-CoV-2, responsible for the current COVID-19 pandemic that claimed over 5.0 million lives, belongs to a class of enveloped viruses that undergo quick evolutionary adjustments under selection pressure. Numerous variants have emerged in SARS-CoV-2, posing a serious challenge to the global vaccination effort and COVID-19 management. The evolutionary dynamics of this virus are only beginning to be explored. In this work, we have analysed 1.79 million spike glycoprotein sequences of SARS-CoV-2 and found that the virus is fine-tuning the spike with numerous amino acid insertions and deletions (indels). Indels seem to have a selective advantage as the proportions of sequences with indels steadily increased over time, currently at over 89%, with similar trends across countries/variants. There were as many as 420 unique indel positions and 447 unique combinations of indels. Despite their high frequency, indels resulted in only minimal alteration of N-glycosylation sites, including both gain and loss. As indels and point mutations are positively correlated and sequences with indels have significantly more point mutations, they have implications in the evolutionary dynamics of the SARS-CoV-2 spike glycoprotein.</p>","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":"17 ","pages":"11769343211064616"},"PeriodicalIF":2.6,"publicationDate":"2021-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/18/95/10.1177_11769343211064616.PMC8655444.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39718297","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}