Evolutionary Bioinformatics Online最新文献_第10页

Gene Tree Affects Inference of Sites Under Selection by the Branch-Site Test of Positive Selection 正选择分支位点检验对基因树选择位点推断的影响

Evolutionary Bioinformatics Online Pub Date : 2015-01-01 DOI: 10.4137/EBO.S30902

Y. Diekmann, J. Pereira-Leal

引用次数: 14

Phylotranscriptomic Analysis Based on Coalescence was Less Influenced by the Evolving Rates and the Number of Genes: A Case Study in Ericales 基于聚结的系统转录组学分析受进化速率和基因数量的影响较小——以稻属植物为例

Evolutionary Bioinformatics Online Pub Date : 2015-01-01 DOI: 10.4137/EBO.S22448

Luchong Zhang, Wei Wu, Haifei Yan, X. Ge

{"title":"Phylotranscriptomic Analysis Based on Coalescence was Less Influenced by the Evolving Rates and the Number of Genes: A Case Study in Ericales","authors":"Luchong Zhang, Wei Wu, Haifei Yan, X. Ge","doi":"10.4137/EBO.S22448","DOIUrl":"https://doi.org/10.4137/EBO.S22448","url":null,"abstract":"Advances in high-throughput sequencing have generated a vast amount of transcriptomic data that are being increasingly used in phylogenetic reconstruction. However, processing the vast datasets for a huge number of genes and even identifying optimal analytical methodology are challenging. Through de novo sequenced and retrieved data from public databases, we identified 221 orthologous protein-coding genes to reconstruct the phylogeny of Ericales, an order characterized by rapid ancient radiation. Seven species representing different families in Ericales were used as in-groups. Both concatenation and coalescence methods yielded the same well-supported topology as previous studies, with only two nodes conflicting with previously reported relationships. The results revealed that a partitioning strategy could improve the traditional concatenation methodology. Rapidly evolving genes negatively affected the concatenation analysis, while slowly evolving genes slightly affected the coalescence analysis. The coalescence methods usually accommodated rate heterogeneity better and required fewer genes to yield well-supported topologies than the concatenation methods with both real and simulated data.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"79 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132557257","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 9

Comparative Genomics of Amphibian-like Ranaviruses, Nucleocytoplasmic Large DNA Viruses of Poikilotherms 两栖类病毒、变温动物核胞质大DNA病毒的比较基因组学研究

Evolutionary Bioinformatics Online Pub Date : 2015-01-01 DOI: 10.4137/EBO.S33490

S. J. Price

引用次数: 8

Forward-in-Time, Spatially Explicit Modeling Software to Simulate Genetic Lineages Under Selection 向前在时间，空间显式建模软件模拟遗传谱系下的选择

Evolutionary Bioinformatics Online Pub Date : 2015-01-01 DOI: 10.4137/EBO.S33488

M. Currat, P. Gerbault, D. Di, J. M. Nunes, A. Sanchez‐Mazas

{"title":"Forward-in-Time, Spatially Explicit Modeling Software to Simulate Genetic Lineages Under Selection","authors":"M. Currat, P. Gerbault, D. Di, J. M. Nunes, A. Sanchez‐Mazas","doi":"10.4137/EBO.S33488","DOIUrl":"https://doi.org/10.4137/EBO.S33488","url":null,"abstract":"SELECTOR is a software package for studying the evolution of multiallelic genes under balancing or positive selection while simulating complex evolutionary scenarios that integrate demographic growth and migration in a spatially explicit population framework. Parameters can be varied both in space and time to account for geographical, environmental, and cultural heterogeneity. SELECTOR can be used within an approximate Bayesian computation estimation framework. We first describe the principles of SELECTOR and validate the algorithms by comparing its outputs for simple models with theoretical expectations. Then, we show how it can be used to investigate genetic differentiation of loci under balancing selection in interconnected demes with spatially heterogeneous gene flow. We identify situations in which balancing selection reduces genetic differentiation between population groups compared with neutrality and explain conflicting outcomes observed for human leukocyte antigen loci. These results and three previously published applications demonstrate that SELECTOR is efficient and robust for building insight into human settlement history and evolution.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"122 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124457580","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 9

Using Disease-Associated Coding Sequence Variation to Investigate Functional Compensation by Human Paralogous Proteins 利用疾病相关编码序列变异研究人类同源蛋白的功能代偿

Evolutionary Bioinformatics Online Pub Date : 2015-01-01 DOI: 10.4137/EBO.S30594

Sayaka Miura, Stephanie Tate, Sudhir Kumar

{"title":"Using Disease-Associated Coding Sequence Variation to Investigate Functional Compensation by Human Paralogous Proteins","authors":"Sayaka Miura, Stephanie Tate, Sudhir Kumar","doi":"10.4137/EBO.S30594","DOIUrl":"https://doi.org/10.4137/EBO.S30594","url":null,"abstract":"Gene duplication enables the functional diversification in species. It is thought that duplicated genes may be able to compensate if the function of one of the gene copies is disrupted. This possibility is extensively debated with some studies reporting proteome-wide compensation, whereas others suggest functional compensation among only recent gene duplicates or no compensation at all. We report results from a systematic molecular evolutionary analysis to test the predictions of the functional compensation hypothesis. We contrasted the density of Mendelian disease-associated single nucleotide variants (dSNVs) in proteins with no discernable paralogs (singletons) with the dSNV density in proteins found in multigene families. Under the functional compensation hypothesis, we expected to find greater numbers of dSNVs in singletons due to the lack of any compensating partners. Our analyses produced an opposite pattern; paralogs have over 35% higher dSNV density than singletons. We found that these patterns are concordant with similar differences in the rates of amino acid evolution (ie, functional constraints), as the proteins with paralogs have evolved 33% slower than singletons. Our evolutionary constraint explanation is robust to differences in family sizes, ages (young vs. old duplicates), and degrees of amino acid sequence similarities among paralogs. Therefore, disease-associated human variation does not exhibit significant signals of functional compensation among paralogous proteins, but rather an evolutionary constraint hypothesis provides a better explanation for the observed patterns of disease-associated and neutral polymorphisms in the human genome.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"11 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123832305","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Using uniformat and gene[rate] to Analyze Data with Ambiguities in Population Genetics 用统一格式和基因率分析群体遗传学中存在歧义的数据

Evolutionary Bioinformatics Online Pub Date : 2015-01-01 DOI: 10.4137/EBO.S32415

J. M. Nunes

引用次数: 41

Discovering All Transcriptome Single-Nucleotide Polymorphisms and Scanning for Selection Signatures in Ducks (Anas platyrhynchos) 鸭(Anas platyrhynchos)所有转录组单核苷酸多态性的发现和选择特征的扫描

Evolutionary Bioinformatics Online Pub Date : 2015-01-01 DOI: 10.4137/EBO.S21545

R. Lin, Xiaoyong Du, Sixue Peng, Liubin Yang, Yunlong Ma, Y. Gong, Shijun Li

{"title":"Discovering All Transcriptome Single-Nucleotide Polymorphisms and Scanning for Selection Signatures in Ducks (Anas platyrhynchos)","authors":"R. Lin, Xiaoyong Du, Sixue Peng, Liubin Yang, Yunlong Ma, Y. Gong, Shijun Li","doi":"10.4137/EBO.S21545","DOIUrl":"https://doi.org/10.4137/EBO.S21545","url":null,"abstract":"The duck is one of the most economically important waterfowl as a source of meat, eggs, and feathers. Characterizing the genetic variation in duck species is an important step toward linking genes or genomic regions with phenotypes. Human-driven selection during duck domestication and subsequent breed formation has likely left detectable signatures in duck genome. In this study, we employed a panel of >1.4 million single-nucleotide polymorphisms (SNPs) identified from the RNA sequencing (RNA-seq) data of 15 duck individuals. The density of the resulting SNPs is significantly positively correlated with the density of genes across the duck genome, which demonstrates that the usage of the RNA-seq data allowed us to enrich variant functional categories, such as coding exons, untranslated regions (UTRs), introns, and downstream/upstream. We performed a complete scan of selection signatures in the ducks using the composite likelihood ratio (CLR) and found 76 candidate regions of selection, many of which harbor genes related to phenotypes relevant to the function of the digestive system and fat metabolism, including TCF7L2, EIF2AK3, ELOVL2, and fatty acid-binding protein family. This study illustrates the potential of population genetic approaches for identifying genomic regions affecting domestication-related phenotypes and further helps to increase the known genetic information about this economically important animal.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"40 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115150925","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 8

In Silico Gene Regulatory Network of the Maurer’s Cleft Pathway in Plasmodium falciparum 恶性疟原虫毛雷尔裂孔通路基因调控网络的研究

Evolutionary Bioinformatics Online Pub Date : 2015-01-01 DOI: 10.4137/EBO.S25585

Itunuoluwa Isewon, Jelili Oyelade, B. Brors, E. Adebiyi

引用次数: 2

Segmenting the Human Genome into Isochores 将人类基因组分割成同工

Evolutionary Bioinformatics Online Pub Date : 2015-01-01 DOI: 10.4137/EBO.S27693

P. Cozzi, L. Milanesi, G. Bernardi

引用次数: 24

Screening of Transcription Factors Involved in Fetal Hemoglobin Regulation Using Phylogenetic Footprinting 利用系统发育足迹筛选参与胎儿血红蛋白调节的转录因子

Evolutionary Bioinformatics Online Pub Date : 2015-01-01 DOI: 10.4137/EBO.S15364

Gisele Cristine de Souza Carrocini, L. Venâncio, C. Bonini-Domingos

{"title":"Screening of Transcription Factors Involved in Fetal Hemoglobin Regulation Using Phylogenetic Footprinting","authors":"Gisele Cristine de Souza Carrocini, L. Venâncio, C. Bonini-Domingos","doi":"10.4137/EBO.S15364","DOIUrl":"https://doi.org/10.4137/EBO.S15364","url":null,"abstract":"Fetal hemoglobin (Hb F) is an important genetic modulator of the beta-hemoglobinopathies. The regulation of Hb F levels is influenced by transcription factors. We used phylogenetic footprinting to screen transcription factors that have binding sites in HBG1 and HBG2 genes’ noncoding regions in order to know the genetic determinants of the Hb F expression. Our analysis showed 354 conserved motifs in the noncoding regions of HBG1 gene and 231 motifs in the HBG2 gene between the analyzed species. Of these motifs, 13 showed relation to Hb F regulation: cell division cycle-5 (CDC5), myeloblastosis viral oncogene homolog (c-MYB), transcription factor CP2 (TFCP2), GATA binding protein 1 (GATA-1), GATA binding protein 2 (GATA-2), nuclear factor erythroid 2 (NF-E2), nuclear transcription factor Y (NF-Y), runt-related transcription factor 1 (RUNX-1), T-cell acute lymphocytic leukemia 1 (TAL-1), YY1 transcription factor (YY1), beta protein 1 (BP1), chicken ovalbumin upstream promoter-transcription factor II (COUP-TFII), and paired box 1 (PAX-1). The last three motifs were conserved only in the noncoding regions of the HBG1 gene. The understanding of genetic elements involved in the maintenance of high Hb F levels may provide new efficient therapeutic strategies in the beta-hemoglobinopathies treatment, promoting reduction in clinical complications of these genetic disorders.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"4 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126839260","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 7