International journal of plant genomics最新文献_第3页

Local assemblies of paired-end reduced representation libraries sequenced with the illumina genome analyzer in maize. 用illumina基因组分析仪对玉米配对端简化表示文库的局部片段进行测序。

International journal of plant genomics Pub Date : 2012-01-01 Epub Date: 2012-10-09 DOI: 10.1155/2012/360598

Stéphane Deschamps, Kishore Nannapaneni, Yun Zhang, Kevin Hayes

{"title":"Local assemblies of paired-end reduced representation libraries sequenced with the illumina genome analyzer in maize.","authors":"Stéphane Deschamps, Kishore Nannapaneni, Yun Zhang, Kevin Hayes","doi":"10.1155/2012/360598","DOIUrl":"https://doi.org/10.1155/2012/360598","url":null,"abstract":"The use of next-generation DNA sequencing technologies has greatly facilitated reference-guided variant detection in complex plant genomes. However, complications may arise when regions adjacent to a read of interest are used for marker assay development, or when reference sequences are incomplete, as short reads alone may not be long enough to ascertain their uniqueness. Here, the possibility of generating longer sequences in discrete regions of the large and complex genome of maize is demonstrated, using a modified version of a paired-end RAD library construction strategy. Reads are generated from DNA fragments first digested with a methylation-sensitive restriction endonuclease, sheared, enriched with biotin and a selective PCR amplification step, and then sequenced at both ends. Sequences are locally assembled into contigs by subgrouping pairs based on the identity of the read anchored by the restriction site. This strategy applied to two maize inbred lines (B14 and B73) generated 183,609 and 129,018 contigs, respectively, out of which at least 76% were >200 bps in length. A subset of putative single nucleotide polymorphisms from contigs aligning to the B73 reference genome with at least one mismatch was resequenced, and 90% of those in B14 were confirmed, indicating that this method is a potent approach for variant detection and marker development in species with complex genomes or lacking extensive reference sequences.","PeriodicalId":73471,"journal":{"name":"International journal of plant genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2012/360598","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30999591","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 6

Poor Homologous Synapsis 1 Interacts with Chromatin but Does Not Colocalise with ASYnapsis 1 during Early Meiosis in Bread Wheat. 在面包小麦减数分裂早期，差同源突触 1 与染色质相互作用，但不与 ASYnapsis 1 共定位。

International journal of plant genomics Pub Date : 2012-01-01 Epub Date: 2012-02-06 DOI: 10.1155/2012/514398

Kelvin H P Khoo, Amanda J Able, Jason A Able

{"title":"Poor Homologous Synapsis 1 Interacts with Chromatin but Does Not Colocalise with ASYnapsis 1 during Early Meiosis in Bread Wheat.","authors":"Kelvin H P Khoo, Amanda J Able, Jason A Able","doi":"10.1155/2012/514398","DOIUrl":"10.1155/2012/514398","url":null,"abstract":"Chromosome pairing, synapsis, and DNA recombination are three key processes that occur during early meiosis. A previous study of Poor Homologous Synapsis 1 (PHS1) in maize suggested that PHS1 has a role in coordinating these three processes. Here we report the isolation of wheat (Triticum aestivum) PHS1 (TaPHS1), and its expression profile during and after meiosis. While the TaPHS1 protein has sequence similarity to other plant PHS1/PHS1-like proteins, it also possesses a unique region of oligopeptide repeat units. We show that TaPHS1 interacts with both single- and double-stranded DNA in vitro and provide evidence of the protein region that imparts the DNA-binding ability. Immunolocalisation data from assays conducted using antisera raised against TaPHS1 show that TaPHS1 associates with chromatin during early meiosis, with the signal persisting beyond chromosome synapsis. Furthermore, TaPHS1 does not appear to colocalise with the asynapsis protein (TaASY1) suggesting that these proteins are probably independently coordinated. Significantly, the data from the DNA-binding assays and 3-dimensional immunolocalisation of TaPHS1 during early meiosis indicates that TaPHS1 interacts with DNA, a function not previously observed in either the Arabidopsis or maize PHS1 homologues. As such, these results provide new insight into the function of PHS1 during early meiosis in bread wheat.","PeriodicalId":73471,"journal":{"name":"International journal of plant genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3303760/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40170528","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Evolutionary history of LTR retrotransposon chromodomains in plants. 植物LTR反转录转座子染色体域的进化历史。

International journal of plant genomics Pub Date : 2012-01-01 Epub Date: 2012-04-29 DOI: 10.1155/2012/874743

Anton Novikov, Georgiy Smyshlyaev, Olga Novikova

{"title":"Evolutionary history of LTR retrotransposon chromodomains in plants.","authors":"Anton Novikov, Georgiy Smyshlyaev, Olga Novikova","doi":"10.1155/2012/874743","DOIUrl":"https://doi.org/10.1155/2012/874743","url":null,"abstract":"Chromodomain-containing LTR retrotransposons are one of the most successful groups of mobile elements in plant genomes. Previously, we demonstrated that two types of chromodomains (CHDs) are carried by plant LTR retrotransposons. Chromodomains from group I (CHD_I) were detected only in Tcn1-like LTR retrotransposons from nonseed plants such as mosses (including the model moss species Physcomitrella) and lycophytes (the Selaginella species). LTR retrotransposon chromodomains from group II (CHD_II) have been described from a wide range of higher plants. In the present study, we performed computer-based mining of plant LTR retrotransposon CHDs from diverse plants with an emphasis on spike-moss Selaginella. Our extended comparative and phylogenetic analysis demonstrated that two types of CHDs are present only in the Selaginella genome, which puts this species in a unique position among plants. It appears that a transition from CHD_I to CHD_II and further diversification occurred in the evolutionary history of plant LTR retrotransposons at approximately 400 MYA and most probably was associated with the evolution of chromatin organization.","PeriodicalId":73471,"journal":{"name":"International journal of plant genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2012/874743","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30631800","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 20

SNP Discovery through Next-Generation Sequencing and Its Applications. 新一代测序SNP发现及其应用

International journal of plant genomics Pub Date : 2012-01-01 Epub Date: 2012-11-22 DOI: 10.1155/2012/831460

Santosh Kumar, Travis W Banks, Sylvie Cloutier

{"title":"SNP Discovery through Next-Generation Sequencing and Its Applications.","authors":"Santosh Kumar, Travis W Banks, Sylvie Cloutier","doi":"10.1155/2012/831460","DOIUrl":"https://doi.org/10.1155/2012/831460","url":null,"abstract":"The decreasing cost along with rapid progress in next-generation sequencing and related bioinformatics computing resources has facilitated large-scale discovery of SNPs in various model and nonmodel plant species. Large numbers and genome-wide availability of SNPs make them the marker of choice in partially or completely sequenced genomes. Although excellent reviews have been published on next-generation sequencing, its associated bioinformatics challenges, and the applications of SNPs in genetic studies, a comprehensive review connecting these three intertwined research areas is needed. This paper touches upon various aspects of SNP discovery, highlighting key points in availability and selection of appropriate sequencing platforms, bioinformatics pipelines, SNP filtering criteria, and applications of SNPs in genetic analyses. The use of next-generation sequencing methodologies in many non-model crops leading to discovery and implementation of SNPs in various genetic studies is discussed. Development and improvement of bioinformatics software that are open source and freely available have accelerated the SNP discovery while reducing the associated cost. Key considerations for SNP filtering and associated pipelines are discussed in specific topics. A list of commonly used software and their sources is compiled for easy access and reference.","PeriodicalId":73471,"journal":{"name":"International journal of plant genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2012/831460","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31109061","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 292

Application of phosphoproteomics to find targets of casein kinase 1 in the flagellum of chlamydomonas. 应用磷蛋白组学在衣藻鞭毛中寻找酪蛋白激酶1靶点。

International journal of plant genomics Pub Date : 2012-01-01 Epub Date: 2012-12-18 DOI: 10.1155/2012/581460

Jens Boesger, Volker Wagner, Wolfram Weisheit, Maria Mittag

{"title":"Application of phosphoproteomics to find targets of casein kinase 1 in the flagellum of chlamydomonas.","authors":"Jens Boesger, Volker Wagner, Wolfram Weisheit, Maria Mittag","doi":"10.1155/2012/581460","DOIUrl":"https://doi.org/10.1155/2012/581460","url":null,"abstract":"The green biflagellate alga Chlamydomonas reinhardtii serves as model for studying structural and functional features of flagella. The axoneme of C. reinhardtii anchors a network of kinases and phosphatases that control motility. One of them, Casein Kinase 1 (CK1), is known to phosphorylate the Inner Dynein Arm I1 Intermediate Chain 138 (IC138), thereby regulating motility. CK1 is also involved in regulating the circadian rhythm of phototaxis and is relevant for the formation of flagella. By a comparative phosphoproteome approach, we determined phosphoproteins in the flagellum that are targets of CK1. Thereby, we applied the specific CK1 inhibitor CKI-7 that causes significant changes in the flagellum phosphoproteome and reduces the swimming velocity of the cells. In the CKI-7-treated cells, 14 phosphoproteins were missing compared to the phosphoproteome of untreated cells, including IC138, and four additional phosphoproteins had a reduced number of phosphorylation sites. Notably, inhibition of CK1 causes also novel phosphorylation events, indicating that it is part of a kinase network. Among them, Glycogen Synthase Kinase 3 is of special interest, because it is involved in the phosphorylation of key clock components in flies and mammals and in parallel plays an important role in the regulation of assembly in the flagellum.","PeriodicalId":73471,"journal":{"name":"International journal of plant genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2012/581460","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31159650","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 11

SNP markers and their impact on plant breeding. SNP标记及其对植物育种的影响。

International journal of plant genomics Pub Date : 2012-01-01 Epub Date: 2012-12-18 DOI: 10.1155/2012/728398

Jafar Mammadov, Rajat Aggarwal, Ramesh Buyyarapu, Siva Kumpatla

{"title":"SNP markers and their impact on plant breeding.","authors":"Jafar Mammadov, Rajat Aggarwal, Ramesh Buyyarapu, Siva Kumpatla","doi":"10.1155/2012/728398","DOIUrl":"https://doi.org/10.1155/2012/728398","url":null,"abstract":"The use of molecular markers has revolutionized the pace and precision of plant genetic analysis which in turn facilitated the implementation of molecular breeding of crops. The last three decades have seen tremendous advances in the evolution of marker systems and the respective detection platforms. Markers based on single nucleotide polymorphisms (SNPs) have rapidly gained the center stage of molecular genetics during the recent years due to their abundance in the genomes and their amenability for high-throughput detection formats and platforms. Computational approaches dominate SNP discovery methods due to the ever-increasing sequence information in public databases; however, complex genomes pose special challenges in the identification of informative SNPs warranting alternative strategies in those crops. Many genotyping platforms and chemistries have become available making the use of SNPs even more attractive and efficient. This paper provides a review of historical and current efforts in the development, validation, and application of SNP markers in QTL/gene discovery and plant breeding by discussing key experimental strategies and cases exemplifying their impact.","PeriodicalId":73471,"journal":{"name":"International journal of plant genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2012/728398","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31159651","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 388

Gel-based and gel-free quantitative proteomics approaches at a glance. 基于凝胶和无凝胶的定量蛋白质组学方法概述。

International journal of plant genomics Pub Date : 2012-01-01 Epub Date: 2012-11-20 DOI: 10.1155/2012/494572

Cosette Abdallah, Eliane Dumas-Gaudot, Jenny Renaut, Kjell Sergeant

{"title":"Gel-based and gel-free quantitative proteomics approaches at a glance.","authors":"Cosette Abdallah, Eliane Dumas-Gaudot, Jenny Renaut, Kjell Sergeant","doi":"10.1155/2012/494572","DOIUrl":"https://doi.org/10.1155/2012/494572","url":null,"abstract":"Two-dimensional gel electrophoresis (2-DE) is widely applied and remains the method of choice in proteomics; however, pervasive 2-DE-related concerns undermine its prospects as a dominant separation technique in proteome research. Consequently, the state-of-the-art shotgun techniques are slowly taking over and utilising the rapid expansion and advancement of mass spectrometry (MS) to provide a new toolbox of gel-free quantitative techniques. When coupled to MS, the shotgun proteomic pipeline can fuel new routes in sensitive and high-throughput profiling of proteins, leading to a high accuracy in quantification. Although label-based approaches, either chemical or metabolic, gained popularity in quantitative proteomics because of the multiplexing capacity, these approaches are not without drawbacks. The burgeoning label-free methods are tag independent and suitable for all kinds of samples. The challenges in quantitative proteomics are more prominent in plants due to difficulties in protein extraction, some protein abundance in green tissue, and the absence of well-annotated and completed genome sequences. The goal of this perspective assay is to present the balance between the strengths and weaknesses of the available gel-based and -free methods and their application to plants. The latest trends in peptide fractionation amenable to MS analysis are as well discussed.","PeriodicalId":73471,"journal":{"name":"International journal of plant genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2012/494572","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31099608","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 200

A Bayesian Framework for Functional Mapping through Joint Modeling of Longitudinal and Time-to-Event Data. 通过对纵向数据和事件时间数据进行联合建模的贝叶斯功能映射框架。

International journal of plant genomics Pub Date : 2012-01-01 Epub Date: 2012-05-22 DOI: 10.1155/2012/680634

Kiranmoy Das, Runze Li, Zhongwen Huang, Junyi Gai, Rongling Wu

{"title":"A Bayesian Framework for Functional Mapping through Joint Modeling of Longitudinal and Time-to-Event Data.","authors":"Kiranmoy Das, Runze Li, Zhongwen Huang, Junyi Gai, Rongling Wu","doi":"10.1155/2012/680634","DOIUrl":"10.1155/2012/680634","url":null,"abstract":"The most powerful and comprehensive approach of study in modern biology is to understand the whole process of development and all events of importance to development which occur in the process. As a consequence, joint modeling of developmental processes and events has become one of the most demanding tasks in statistical research. Here, we propose a joint modeling framework for functional mapping of specific quantitative trait loci (QTLs) which controls developmental processes and the timing of development and their causal correlation over time. The joint model contains two submodels, one for a developmental process, known as a longitudinal trait, and the other for a developmental event, known as the time to event, which are connected through a QTL mapping framework. A nonparametric approach is used to model the mean and covariance function of the longitudinal trait while the traditional Cox proportional hazard (PH) model is used to model the event time. The joint model is applied to map QTLs that control whole-plant vegetative biomass growth and time to first flower in soybeans. Results show that this model should be broadly useful for detecting genes controlling physiological and pathological processes and other events of interest in biomedicine.","PeriodicalId":73471,"journal":{"name":"International journal of plant genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3364578/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30679665","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Chromosomal Location of HCA1 and HCA2, Hybrid Chlorosis Genes in Rice. 水稻杂交萎黄基因HCA1和HCA2的染色体定位

International journal of plant genomics Pub Date : 2012-01-01 Epub Date: 2012-02-12 DOI: 10.1155/2012/649081

Katsuyuki Ichitani, Yuma Takemoto, Kotaro Iiyama, Satoru Taura, Muneharu Sato

引用次数: 15

Comparative Genomics in Perennial Ryegrass (Lolium perenne L.): Identification and Characterisation of an Orthologue for the Rice Plant Architecture-Controlling Gene OsABCG5. 多年生黑麦草(Lolium perenne L.)的比较基因组学:水稻植株结构控制基因OsABCG5同源物的鉴定和表征。

International journal of plant genomics Pub Date : 2011-01-01 Epub Date: 2011-09-15 DOI: 10.1155/2011/291563

Hiroshi Shinozuka, Noel O I Cogan, German C Spangenberg, John W Forster

{"title":"Comparative Genomics in Perennial Ryegrass (Lolium perenne L.): Identification and Characterisation of an Orthologue for the Rice Plant Architecture-Controlling Gene OsABCG5.","authors":"Hiroshi Shinozuka, Noel O I Cogan, German C Spangenberg, John W Forster","doi":"10.1155/2011/291563","DOIUrl":"https://doi.org/10.1155/2011/291563","url":null,"abstract":"Perennial ryegrass is an important pasture grass in temperate regions. As a forage biomass-generating species, plant architecture-related characters provide key objectives for breeding improvement. In silico comparative genomics analysis predicted colocation between a previously identified QTL for plant type (erect versus prostrate growth) and the ortholocus of the rice OsABCG5 gene (LpABCG5), as well as related QTLs in other Poaceae species. Sequencing of an LpABCG5-containing BAC clone identified presence of a paralogue (LpABCG6) in the vicinity of the LpABCG5 locus, in addition to three other gene-like sequences. Comparative genomics involving five other 5 grass species (rice, Brachypodium, sorghum, maize, and foxtail millet) revealed conserved microsynteny in the ABCG5 ortholocus-flanking region. Gene expression profiling and phylogenetic analysis suggested that the two paralogues are functionally distinct. Fourteen additional ABCG5 gene family members, which may interact with the LpABCG5 gene, were identified through sequencing of transcriptomes from perennial ryegrass leaf, anther, and pistils. A larger-scale phylogenetic analysis of the ABCG gene family suggested conservation between major branches of the Poaceae family. This study identified the LpABCG5 gene as a candidate for the plant type determinant, suggesting that manipulation of gene expression may provide valuable phenotypes for perennial ryegrass breeding.","PeriodicalId":73471,"journal":{"name":"International journal of plant genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2011/291563","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30015821","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 6