Next generation, sequencing & applications最新文献_第2页

Molecular Diversity of miR390-Guided Transacting siRNA Precursor Genes in Lower Land Plants: Experimental Approach and Bioinformatics Analysis mir390引导的低地植物siRNA前体基因的分子多样性:实验方法和生物信息学分析

Next generation, sequencing & applications Pub Date : 2011-12-21 DOI: 10.1155/2011/703683

M. Krasnikova, I. Milyutina, V. K. Bobrova, A. Troitsky, A. Solovyev, S. Morozov

{"title":"Molecular Diversity of miR390-Guided Transacting siRNA Precursor Genes in Lower Land Plants: Experimental Approach and Bioinformatics Analysis","authors":"M. Krasnikova, I. Milyutina, V. K. Bobrova, A. Troitsky, A. Solovyev, S. Morozov","doi":"10.1155/2011/703683","DOIUrl":"https://doi.org/10.1155/2011/703683","url":null,"abstract":"Transacting siRNA loci (TAS3-like) of a particular plant species are usually represented by several gene families. PCR-based approach was used as a phylogenetic profiling tool to probe genomic DNA samples from representatives of evolutionary distant Bryophyta taxa, namely, class Bryopsida (subclasses Bryidae and Dicranidae) and class Sphagnopsida. We found relatives of all four Physcomitrella patens (subclass Funariidae) TAS3-like loci in subclasses Bryidae and Dicranidae. Only representatives of subclass Bryidae encoded TAS3-like genes belonging to P. patens TAS3a and TAS3d families. On the other hand, only the members of order Grimmiales (subclass Dicranidae) encoded gene relatives of P. patens TAS3c family. These data indicate that moss ta-siRNA families have been long conserved during land plant evolution. However, P. patens TAS3-like loci were detected neither in two Sphagnum species from the earliest diverged moss class Sphagnopsida, nor in the Selaginella kraussiana from the earliest extant tracheophyta lineage, Lycopodiopsida.","PeriodicalId":90934,"journal":{"name":"Next generation, sequencing & applications","volume":"24 1","pages":"1-6"},"PeriodicalIF":0.0,"publicationDate":"2011-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81199245","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

Gene Expression in Leaves of Susceptible Glycine max during Infection with Phakopsora pachyrhizi Using Next Generation Sequencing 利用下一代测序技术研究厚根Phakopsora侵染过程中Glycine max敏感植株叶片的基因表达

Next generation, sequencing & applications Pub Date : 2011-01-01 DOI: 10.1155/2011/827250

Arianne Tremblay, Parsa Hosseini, N. Alkharouf, Shuxian Li, B. Matthews

引用次数: 21

KRAS Codons 12 and 13 Mutation Analysis: A Comparative Study between Direct Sequencing and a New Sensitive Real-Time PCR Assay KRAS密码子12和13突变分析:直接测序与新型灵敏实时PCR的比较研究

Next generation, sequencing & applications Pub Date : 2011-01-01 DOI: 10.1155/2011/895709

S. Marzinotto, F. Sessa, A. Franzoni, A. Anselmi, L. Gastaldo, Silvia Mason, G. Damante, C. Beltrami, L. Mariuzzi

引用次数: 4

Complete Genome Sequence of Rothia mucilaginosa DY-18: A Clinical Isolate with Dense Meshwork-Like Structures from a Persistent Apical Periodontitis Lesion 粘胶罗氏菌DY-18的全基因组序列:来自持续性根尖牙周炎病变的具有致密网状结构的临床分离物

Next generation, sequencing & applications Pub Date : 2010-10-24 DOI: 10.1155/2010/457236

K. Yamane, T. Nambu, T. Yamanaka, Chiho Mashimo, Chieko Sugimori, K. Leung, H. Fukushima

引用次数: 23

Increasing Prevalence of Unique Mutation Patterns in H5N1 Avian Influenza Virus HA and NA Glycoproteins from Human Infections in Egypt 埃及人感染H5N1禽流感病毒HA和NA糖蛋白的独特突变模式日益流行

Next generation, sequencing & applications Pub Date : 2010-07-19 DOI: 10.1155/2010/450823

E. Abdelwhab, H. Hafez, M. Aly, C. Grund, T. Harder

引用次数: 16

Identification and Quantification of Genomic Repeats and Sample Contamination in Assemblies of 454 Pyrosequencing Reads 454个焦磷酸测序Reads序列中基因组重复序列的鉴定和定量及样品污染

Next generation, sequencing & applications Pub Date : 2010-01-05 DOI: 10.1155/2010/782465

A. Nederbragt, T. Rounge, Kyrre Kausrud, K. Jakobsen

{"title":"Identification and Quantification of Genomic Repeats and Sample Contamination in Assemblies of 454 Pyrosequencing Reads","authors":"A. Nederbragt, T. Rounge, Kyrre Kausrud, K. Jakobsen","doi":"10.1155/2010/782465","DOIUrl":"https://doi.org/10.1155/2010/782465","url":null,"abstract":"Contigs assembled from 454 reads from bacterial genomes demonstrate a range of read depths, with a number of contigs having a depth that is far higher than can be expected. For reference genome sequence datasets, there exists a high correlation between the contig specific read depth and the number of copies present in the genome. We developed a sequence of applied statistical analyses, which suggest that the number of copies present can be reliably estimated based on the read depth distribution in de novo genome assemblies. Read depths of contigs of de novo cyanobacterial genome assemblies were determined, and several high read depth contigs were identified. These contigs were shown to mainly contain genes that are known to be present in multiple copies in bacterial genomes. For these assemblies, a correlation between read depth and copy number was experimentally demonstrated using real-time PCR. Copy number estimates, obtained using the statistical analysis developed in this work, are presented. Per-contig read depth analysis of assemblies based on 454 reads therefore enables de novo detection of genomic repeats and estimation of the copy number of these repeats. \u0000Additionally, our analysis efficiently identified contigs stemming from sample contamination, allowing for their removal from the assembly.","PeriodicalId":90934,"journal":{"name":"Next generation, sequencing & applications","volume":"188 1","pages":"1-12"},"PeriodicalIF":0.0,"publicationDate":"2010-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74434158","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: 16