Evolutionary Bioinformatics Online最新文献_第5页

Structural Diversity of a Novel LTR Retrotransposon, RTPOSON, in the Genus Oryza 水稻属LTR反转录转座子RTPOSON的结构多样性

Evolutionary Bioinformatics Online Pub Date : 2016-01-01 DOI: 10.4137/EBO.S35158

Y. Hsu, Chang-Sheng Wang, Yann-rong Lin, Yong-pei Wu

{"title":"Structural Diversity of a Novel LTR Retrotransposon, RTPOSON, in the Genus Oryza","authors":"Y. Hsu, Chang-Sheng Wang, Yann-rong Lin, Yong-pei Wu","doi":"10.4137/EBO.S35158","DOIUrl":"https://doi.org/10.4137/EBO.S35158","url":null,"abstract":"Retrotransposons with long terminal repeats (LTRs) are the most abundant transposable elements in plant genomes. A novel LTR retrotransposon named RTPOSON primarily occurs in the genus Oryza and in several species of the Poaceae family. RTPOSON has been identified in the Ty1-copia group of retrotransposons because two of its open reading frames encode an uncharacterized protein and UBN2_2 and zinc knuckle, respectively. More than 700 RTPOSONs were identified in Oryza genomes; 127 RTPOSONs with LTRs and gag-pol elements were classified into three subgroups. The subgroup RTPOSON_sub3 had the smallest DNA size and 97% (32/33) of RTPOSON elements from Oryza punctata are classified in this group. The insertion time of these RTPOSONs varied and their proliferation occurred within the last 8 Mya, with two bursting periods within the last 1.5-5.0 Mya. A total of 37 different orthologous insertions of RTPOSONs, with different nested transposable elements and gene fragments, were identified by comparing the genomes of ssp. japonica cv. Nipponbare and ssp. indica cv. 93-11. A part of intact RTPOSON elements was evolved independently after the divergence of indica and japonica. In addition, intact RTPOSONs and homologous fragments were preferentially retained or integrated in genic regions. This novel LTR retrotransposon, RTPOSON, might have an impact on genome evolution, genic innovation, and genetic variation.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"12 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129064398","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: 2

A Comparative In Silico Study of the Antioxidant Defense Gene Repertoire of Distinct Lifestyle Trypanosomatid Species 不同生活方式锥虫种抗氧化防御基因库的计算机对比研究

Evolutionary Bioinformatics Online Pub Date : 2016-01-01 DOI: 10.4137/EBO.S40648

I. T. Beltrame-Botelho, C. Talavera-López, B. Andersson, E. Grisard, P. H. Stoco

引用次数: 7

A Novel Method for Alignment-free DNA Sequence Similarity Analysis Based on the Characterization of Complex Networks 基于复杂网络特征的无比对DNA序列相似性分析新方法

Evolutionary Bioinformatics Online Pub Date : 2016-01-01 DOI: 10.4137/EBO.S40474

Jie Zhou, Pianyu Zhong, Tinghui Zhang

{"title":"A Novel Method for Alignment-free DNA Sequence Similarity Analysis Based on the Characterization of Complex Networks","authors":"Jie Zhou, Pianyu Zhong, Tinghui Zhang","doi":"10.4137/EBO.S40474","DOIUrl":"https://doi.org/10.4137/EBO.S40474","url":null,"abstract":"Determination of sequence similarity is one of the major steps in computational phylogenetic studies. One of the major tasks of computational biologists is to develop novel mathematical descriptors for similarity analysis. DNA clustering is an important technology that automatically identifies inherent relationships among large-scale DNA sequences. The comparison between the DNA sequences of different species helps determine phylogenetic relationships among species. Alignment-free approaches have continuously gained interest in various sequence analysis applications such as phylogenetic inference and metagenomic classification/clustering, particularly for large-scale sequence datasets. Here, we construct a novel and simple mathematical descriptor based on the characterization of cis sequence complex DNA networks. This new approach is based on a code of three cis nucleotides in a gene that could code for an amino acid. In particular, for each DNA sequence, we will set up a cis sequence complex network that will be used to develop a characterization vector for the analysis of mitochondrial DNA sequence phylogenetic relationships among nine species. The resulting phylogenetic relationships among the nine species were determined to be in agreement with the actual situation.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"12 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130016362","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: 13

A Multilayered Screening Method for the Identification of Regulatory Genes in Rice by Agronomic Traits 利用农艺性状鉴定水稻调控基因的多层筛选方法

Evolutionary Bioinformatics Online Pub Date : 2016-01-01 DOI: 10.4137/EBO.S40622

Y. Seol, S. Won, Y. Shin, Jong-Yeol Lee, J. Chun, Yong-Kab Kim, Chang-Kug Kim

{"title":"A Multilayered Screening Method for the Identification of Regulatory Genes in Rice by Agronomic Traits","authors":"Y. Seol, S. Won, Y. Shin, Jong-Yeol Lee, J. Chun, Yong-Kab Kim, Chang-Kug Kim","doi":"10.4137/EBO.S40622","DOIUrl":"https://doi.org/10.4137/EBO.S40622","url":null,"abstract":"We developed a multilayered screening method that integrates both genome and transcriptome data to effectively identify regulatory genes in rice (Oryza sativa). We tested our method using eight rice accessions that differed in three important nutritional and agricultural traits, anthocyanin biosynthesis, amylose content, and heading date. In the genome resequencing of eight rice accessions with 24 RNA sequencing experiments, 98% of the preprocessed reads could be uniquely mapped to the reference genome, resulting in the identification of 42,699 unique transcripts. Comparison between black and white rice cultivars showed evidence of intensive selective sweeps in chromosomes 3, 10, and 12. A total of 131 genes were differentially expressed among the black rice cultivars and found to be associated with three Gene Ontology terms (secondary metabolic process, biosynthetic process, and response to stimulus). We identified nonsynonymous Single Nucleotide Polymorphism (SNP) that likely play an important role in determining the agronomic traits differences, two upregulated and three downregulated genes in the black cultivars, and two downregulated genes in the white cultivars. The three agronomic traits were clearly grouped together by the developmental stages, regardless of any other traits, suggesting that the developmental stage is the most important factor that triggers global changes in gene expression. Interestingly, glutinous and nonglutinous black rice cultivars were distinguished from one another by different heading dates.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133788166","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: 4

Support Vector Machines Trained with Evolutionary Algorithms Employing Kernel Adatron for Large Scale Classification of Protein Structures 基于核Adatron进化算法训练的支持向量机用于大规模蛋白质结构分类

Evolutionary Bioinformatics Online Pub Date : 2016-01-01 DOI: 10.4137/EBO.S40912

N. Arana-Daniel, Alberto A. Gallegos, C. López-Franco, A. Alanis, J. Morales, Adriana Lopez-Franco

{"title":"Support Vector Machines Trained with Evolutionary Algorithms Employing Kernel Adatron for Large Scale Classification of Protein Structures","authors":"N. Arana-Daniel, Alberto A. Gallegos, C. López-Franco, A. Alanis, J. Morales, Adriana Lopez-Franco","doi":"10.4137/EBO.S40912","DOIUrl":"https://doi.org/10.4137/EBO.S40912","url":null,"abstract":"With the increasing power of computers, the amount of data that can be processed in small periods of time has grown exponentially, as has the importance of classifying large-scale data efficiently. Support vector machines have shown good results classifying large amounts of high-dimensional data, such as data generated by protein structure prediction, spam recognition, medical diagnosis, optical character recognition and text classiffication, etc. Most state of the art approaches for large-scale learning use traditional optimization methods, such as quadratic programming or gradient descent, which makes the use of evolutionary algorithms for training support vector machines an area to be explored. The present paper proposes an approach that is simple to implement based on evolutionary algorithms and Kernel-Adatron for solving large-scale classiffication problems, focusing on protein structure prediction. The functional properties of proteins depend upon their three-dimensional structures. Knowing the structures of proteins is crucial for biology and can lead to improvements in areas such as medicine, agriculture and biofuels.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"10 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114531429","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: 11

Commensal Viruses of Mosquitoes: Host Restriction, Transmission, and Interaction with Arboviral Pathogens 蚊子的共生病毒:宿主限制、传播和与虫媒病毒病原体的相互作用

Evolutionary Bioinformatics Online Pub Date : 2016-01-01 DOI: 10.4137/EBO.S40740

R. Hall, H. Bielefeldt-Ohmann, Breeanna J McLean, Caitlin A. O’Brien, Agathe M. G. Colmant, Thisun B. H. Piyasena, J. Harrison, N. Newton, R. Barnard, N. Prow, J. Deerain, Marcus G. Mah, J. Hobson-Peters

{"title":"Commensal Viruses of Mosquitoes: Host Restriction, Transmission, and Interaction with Arboviral Pathogens","authors":"R. Hall, H. Bielefeldt-Ohmann, Breeanna J McLean, Caitlin A. O’Brien, Agathe M. G. Colmant, Thisun B. H. Piyasena, J. Harrison, N. Newton, R. Barnard, N. Prow, J. Deerain, Marcus G. Mah, J. Hobson-Peters","doi":"10.4137/EBO.S40740","DOIUrl":"https://doi.org/10.4137/EBO.S40740","url":null,"abstract":"Recent advances in virus detection strategies and deep sequencing technologies have enabled the identification of a multitude of new viruses that persistently infect mosquitoes but do not infect vertebrates. These are usually referred to as insect-specific viruses (ISVs). These novel viruses have generated considerable interest in their modes of transmission, persistence in mosquito populations, the mechanisms that restrict their host range to mosquitoes, and their interactions with pathogens transmissible by the same mosquito. In this article, we discuss studies in our laboratory and others that demonstrate that many ISVs are efficiently transmitted directly from the female mosquito to their progeny via infected eggs, and, moreover, that persistent infection of mosquito cell cultures or whole mosquitoes with ISVs can restrict subsequent infection, replication, and transmission of some mosquito-borne viral pathogens. This suggests that some ISVs may act as natural regulators of arboviral transmission. We also discuss viral and host factors that may be responsible for their host restriction.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"12 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129646395","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: 68

pATsi: Paralogs and Singleton Genes from Arabidopsis thaliana 拟南芥的同源基因和单基因

Evolutionary Bioinformatics Online Pub Date : 2016-01-01 DOI: 10.4137/EBO.S32536

Luca Ambrosino, H. Bostan, Pasquale di Salle, Mara Sangiovanni, A. Vigilante, M. Chiusano

引用次数: 10

HTSFinder: Powerful Pipeline of DNA Signature Discovery by Parallel and Distributed Computing HTSFinder:基于并行和分布式计算的DNA签名发现的强大管道

Evolutionary Bioinformatics Online Pub Date : 2016-01-01 DOI: 10.4137/EBO.S35545

Ramin Karimi, A. Hajdu

{"title":"HTSFinder: Powerful Pipeline of DNA Signature Discovery by Parallel and Distributed Computing","authors":"Ramin Karimi, A. Hajdu","doi":"10.4137/EBO.S35545","DOIUrl":"https://doi.org/10.4137/EBO.S35545","url":null,"abstract":"Comprehensive effort for low-cost sequencing in the past few years has led to the growth of complete genome databases. In parallel with this effort, a strong need, fast and cost-effective methods and applications have been developed to accelerate sequence analysis. Identification is the very first step of this task. Due to the difficulties, high costs, and computational challenges of alignment-based approaches, an alternative universal identification method is highly required. Like an alignment-free approach, DNA signatures have provided new opportunities for the rapid identification of species. In this paper, we present an effective pipeline HTSFinder (high-throughput signature finder) with a corresponding k-mer generator GkmerG (genome k-mers generator). Using this pipeline, we determine the frequency of k-mers from the available complete genome databases for the detection of extensive DNA signatures in a reasonably short time. Our application can detect both unique and common signatures in the arbitrarily selected target and nontarget databases. Hadoop and MapReduce as parallel and distributed computing tools with commodity hardware are used in this pipeline. This approach brings the power of high-performance computing into the ordinary desktop personal computers for discovering DNA signatures in large databases such as bacterial genome. A considerable number of detected unique and common DNA signatures of the target database bring the opportunities to improve the identification process not only for polymerase chain reaction and microarray assays but also for more complex scenarios such as metagenomics and next-generation sequencing analysis.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"21 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130454669","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: 5

Genomics Study of Mycobacterium tuberculosis Strains from Different Ethnic Populations in Taiwan 台湾不同族群结核分枝杆菌基因组学研究

Evolutionary Bioinformatics Online Pub Date : 2016-01-01 DOI: 10.4137/EBO.S40152

Horng-Yunn Dou, Yih-Yuan Chen, Ying-Tsong Chen, Jia-Ru Chang, Chien-Hsing Lin, Keh-Ming Wu, Ming-shian Lin, I. Su, S. Tsai

{"title":"Genomics Study of Mycobacterium tuberculosis Strains from Different Ethnic Populations in Taiwan","authors":"Horng-Yunn Dou, Yih-Yuan Chen, Ying-Tsong Chen, Jia-Ru Chang, Chien-Hsing Lin, Keh-Ming Wu, Ming-shian Lin, I. Su, S. Tsai","doi":"10.4137/EBO.S40152","DOIUrl":"https://doi.org/10.4137/EBO.S40152","url":null,"abstract":"To better understand the transmission and evolution of Mycobacterium tuberculosis (MTB) in Taiwan, six different MTB isolates (representatives of the Beijing ancient sublineage, Beijing modern sublineage, Haarlem, East-African Indian, T1, and Latin-American Mediterranean (LAM)) were characterized and their genomes were sequenced. Discriminating among large sequence polymorphisms (LSPs) that occur once versus those that occur repeatedly in a genomic region may help to elucidate the biological roles of LSPs and to identify the useful phylogenetic relationships. In contrast to our previous LSP-based phylogeny, the sequencing data allowed us to determine actual genetic distances and to define precisely the phylogenetic relationships between the main lineages of the MTB complex. Comparative genomics analyses revealed more nonsynonymous substitutions than synonymous changes in the coding sequences. Furthermore, MTB isolate M7, a LAM-3 clinical strain isolated from a patient of Taiwanese aboriginal origin, is closely related to F11 (LAM), an epidemic tuberculosis strain isolated in the Western Cape of South Africa. The PE/PPE protein family showed a higher dn/ds ratio compared to that for all protein-coding genes. Finally, we found Haarlem-3 and LAM-3 isolates to be circulating in the aboriginal community in Taiwan, suggesting that they may have originated with post-Columbus Europeans. Taken together, our results revealed an interesting association with historical migrations of different ethnic populations, thus providing a good model to explore the global evolution and spread of MTB.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"136 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125237677","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: 2

Phylogeny Inference of Closely Related Bacterial Genomes: Combining the Features of Both Overlapping Genes and Collinear Genomic Regions 近缘细菌基因组的系统发育推断:结合重叠基因和共线基因组区域的特征

Evolutionary Bioinformatics Online Pub Date : 2015-01-01 DOI: 10.4137/EBO.S33491

Yancong Zhang, Kui Lin

{"title":"Phylogeny Inference of Closely Related Bacterial Genomes: Combining the Features of Both Overlapping Genes and Collinear Genomic Regions","authors":"Yancong Zhang, Kui Lin","doi":"10.4137/EBO.S33491","DOIUrl":"https://doi.org/10.4137/EBO.S33491","url":null,"abstract":"Overlapping genes (OGs) represent one type of widespread genomic feature in bacterial genomes and have been used as rare genomic markers in phylogeny inference of closely related bacterial species. However, the inference may experience a decrease in performance for phylogenomic analysis of too closely or too distantly related genomes. Another drawback of OGs as phylogenetic markers is that they usually take little account of the effects of genomic rearrangement on the similarity estimation, such as intra-chromosome/genome translocations, horizontal gene transfer, and gene losses. To explore such effects on the accuracy of phylogeny reconstruction, we combine phylogenetic signals of OGs with collinear genomic regions, here called locally collinear blocks (LCBs). By putting these together, we refine our previous metric of pairwise similarity between two closely related bacterial genomes. As a case study, we used this new method to reconstruct the phylogenies of 88 Enterobacteriale genomes of the class Gammaproteobacteria. Our results demonstrated that the topological accuracy of the inferred phylogeny was improved when both OGs and LCBs were simultaneously considered, suggesting that combining these two phylogenetic markers may reduce, to some extent, the influence of gene loss on phylogeny inference. Such phylogenomic studies, we believe, will help us to explore a more effective approach to increasing the robustness of phylogeny reconstruction of closely related bacterial organisms.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"1 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":"115437593","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