共查询到20条相似文献,搜索用时 15 毫秒
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Peter Wenzl Haobing Li Jason Carling Meixue Zhou Harsh Raman Edie Paul Phillippa Hearnden Christina Maier Ling Xia Vanessa Caig Jaroslava Ovesná Mehmet Cakir David Poulsen Junping Wang Rosy Raman Kevin P Smith Gary J Muehlbauer Ken J Chalmers Andris Kleinhofs Eric Huttner Andrzej Kilian 《BMC genomics》2006,7(1):1-22
Background
Wheat is an excellent species to study freezing tolerance and other abiotic stresses. However, the sequence of the wheat genome has not been completely characterized due to its complexity and large size. To circumvent this obstacle and identify genes involved in cold acclimation and associated stresses, a large scale EST sequencing approach was undertaken by the Functional Genomics of Abiotic Stress (FGAS) project.Results
We generated 73,521 quality-filtered ESTs from eleven cDNA libraries constructed from wheat plants exposed to various abiotic stresses and at different developmental stages. In addition, 196,041 ESTs for which tracefiles were available from the National Science Foundation wheat EST sequencing program and DuPont were also quality-filtered and used in the analysis. Clustering of the combined ESTs with d2_cluster and TGICL yielded a few large clusters containing several thousand ESTs that were refractory to routine clustering techniques. To resolve this problem, the sequence proximity and "bridges" were identified by an e-value distance graph to manually break clusters into smaller groups. Assembly of the resolved ESTs generated a 75,488 unique sequence set (31,580 contigs and 43,908 singletons/singlets). Digital expression analyses indicated that the FGAS dataset is enriched in stress-regulated genes compared to the other public datasets. Over 43% of the unique sequence set was annotated and classified into functional categories according to Gene Ontology.Conclusion
We have annotated 29,556 different sequences, an almost 5-fold increase in annotated sequences compared to the available wheat public databases. Digital expression analysis combined with gene annotation helped in the identification of several pathways associated with abiotic stress. The genomic resources and knowledge developed by this project will contribute to a better understanding of the different mechanisms that govern stress tolerance in wheat and other cereals. 相似文献3.
Josine L Min Amy Barrett Tim Watts Fredrik H Pettersson Helen E Lockstone Cecilia M Lindgren Jennifer M Taylor Maxine Allen Krina T Zondervan Mark I McCarthy 《BMC genomics》2010,11(1):1-14
Background
Infection of plants by pathogens and the subsequent disease development involves substantial changes in the biochemistry and physiology of both partners. Analysis of genes that are expressed during these interactions represents a powerful strategy to obtain insights into the molecular events underlying these changes. We have employed expressed sequence tag (EST) analysis to identify rice genes involved in defense responses against infection by the blast fungus Magnaporthe oryzae and fungal genes involved in infectious growth within the host during a compatible interaction.Results
A cDNA library was constructed with RNA from rice leaves (Oryza sativa cv. Hwacheong) infected with M. oryzae strain KJ201. To enrich for fungal genes, subtraction library using PCR-based suppression subtractive hybridization was constructed with RNA from infected rice leaves as a tester and that from uninfected rice leaves as the driver. A total of 4,148 clones from two libraries were sequenced to generate 2,302 non-redundant ESTs. Of these, 712 and 1,562 ESTs could be identified to encode fungal and rice genes, respectively. To predict gene function, Gene Ontology (GO) analysis was applied, with 31% and 32% of rice and fungal ESTs being assigned to GO terms, respectively. One hundred uniESTs were found to be specific to fungal infection EST. More than 80 full-length fungal cDNA sequences were used to validate ab initio annotated gene model of M. oryzae genome sequence.Conclusion
This study shows the power of ESTs to refine genome annotation and functional characterization. Results of this work have advanced our understanding of the molecular mechanisms underpinning fungal-plant interactions and formed the basis for new hypothesis. 相似文献4.
Shaolin Wang Eric Peatman Jason Abernathy Geoff Waldbieser Erika Lindquist Paul Richardson Susan Lucas Mei Wang Ping Li Jyothi Thimmapuram Lei Liu Deepika Vullaganti Huseyin Kucuktas Christopher Murdock Brian C Small Melanie Wilson Hong Liu Yanliang Jiang Yoona Lee Fei Chen Jianguo Lu Wenqi Wang Peng Xu Benjaporn Somridhivej Puttharat Baoprasertkul Jonas Quilang Zhenxia Sha Baolong Bao Yaping Wang Qun Wang Tomokazu Takano Samiran Nandi Shikai Liu Lilian Wong Ludmilla Kaltenboeck Sylvie Quiniou Eva Bengten Norman Miller John Trant Daniel Rokhsar Zhanjiang Liu 《Genome biology》2010,11(1):1-14
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Brian J Haas Jennifer R Wortman Catherine M Ronning Linda I Hannick Roger K Smith Jr Rama Maiti Agnes P Chan Chunhui Yu Maryam Farzad Dongying Wu Owen White Christopher D Town 《BMC biology》2005,3(1):1-19
Background
Since the initial publication of its complete genome sequence, Arabidopsis thaliana has become more important than ever as a model for plant research. However, the initial genome annotation was submitted by multiple centers using inconsistent methods, making the data difficult to use for many applications.Results
Over the course of three years, TIGR has completed its effort to standardize the structural and functional annotation of the Arabidopsis genome. Using both manual and automated methods, Arabidopsis gene structures were refined and gene products were renamed and assigned to Gene Ontology categories. We present an overview of the methods employed, tools developed, and protocols followed, summarizing the contents of each data release with special emphasis on our final annotation release (version 5).Conclusion
Over the entire period, several thousand new genes and pseudogenes were added to the annotation. Approximately one third of the originally annotated gene models were significantly refined yielding improved gene structure annotations, and every protein-coding gene was manually inspected and classified using Gene Ontology terms. 相似文献8.
Ali N Dana Maureen E Hillenmeyer Neil F Lobo Marcia K Kern Patricia A Romans Frank H Collins 《BMC genomics》2006,7(1):1-24
Background
Large scale sequencing of cDNA libraries can provide profiles of genes expressed in an organism under defined biological and environmental circumstances. We have analyzed sequences of 4541 Expressed Sequence Tags (ESTs) from 3 different cDNA libraries created from abdomens from Plasmodium infection-susceptible adult female Anopheles gambiae. These libraries were made from sugar fed (S), rat blood fed (RB), and P. berghei-infected (IRB) mosquitoes at 30 hours after the blood meal, when most parasites would be transforming ookinetes or very early oocysts.Results
The S, RB and IRB libraries contained 1727, 1145 and 1669 high quality ESTs, respectively, averaging 455 nucleotides (nt) in length. They assembled into 1975 consensus sequences - 567 contigs and 1408 singletons. Functional annotation was performed to annotate probable molecular functions of the gene products and the biological processes in which they function. Genes represented at high frequency in one or more of the libraries were subjected to digital Northern analysis and results on expression of 5 verified by qRT-PCR.Conclusion
13% of the 1965 ESTs showing identity to the A. gambiae genome sequence represent novel genes. These, together with untranslated regions (UTR) present on many of the ESTs, will inform further genome annotation. We have identified 23 genes encoding products likely to be involved in regulating the cellular oxidative environment and 25 insect immunity genes. We also identified 25 genes as being up or down regulated following blood feeding and/or feeding with P. berghei infected blood relative to their expression levels in sugar fed females. 相似文献9.
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To obtain an initial overview of gene diversity and expression pattern in porcine thymus, 11,712 ESTs (Expressed Sequence Tags) from 100-day-old porcine thymus (FTY) were sequenced and 7,071 cleaned ESTs were used for gene expression analysis. Clustered by the PHRAP program, 959 contigs and 3,074 singlets were obtained. Blast search showed that 806 contigs and 1,669 singlets (totally 5,442 ESTs) had homologues in GenBank and 1,629 ESTs were novel. According to the Gene Ontology classification, 36.99% ESTs were cataloged into the gene expression group, indicating that although the functional gene (18.78% in defense group) of thymus is expressed in a certain degree, the 100-day-old porcine thymus still exists in a developmental stage. Comparative analysis showed that the gene expression pattern of the 100-day-old porcine thymus is similar to that of the human infant thymus. 相似文献
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Liu S Rexroad CE Couch CR Cordes JF Reece KS Sullivan CV 《Marine biotechnology (New York, N.Y.)》2012,14(2):237-244
The striped bass (Morone saxatilis) and its relatives (genus Morone) are of great importance to fisheries and aquaculture in North America. As part of a collaborative effort to employ molecular
genetics technologies in striped bass breeding programs, we previously developed nearly 500 microsatellite markers. The objectives
of this study were to construct a microsatellite linkage map of striped bass and to examine conserved synteny between striped
bass and three-spined stickleback (Gasterosteus aculeatus). Of 480 microsatellite markers screened for polymorphism, 289 informative markers were identified and used to genotype two
half-sib mapping families. Twenty-six linkage groups were assembled, and only two markers remain unlinked. The sex-averaged
map spans 1,623.8 cM with an average marker density of 5.78 cM per marker. Among 287 striped bass microsatellite markers assigned
to linkage groups, 169 (58.9%) showed homology to sequences on stickleback chromosomes or scaffolds. Comparison between the
stickleback genome and the striped bass linkage map revealed conserved synteny between these two species. This is the first
linkage map for any of the Morone species. This map will be useful for molecular mapping and marker-assisted selection of genes of interest in striped bass
breeding programs. The conserved synteny between striped bass and stickleback will facilitate fine mapping of genome regions
of interest and will serve as a new resource for comparative mapping with other Perciform fishes such as European sea bass
(Dicentrarchus labrax), gilthead sea bream (Sparus aurata), and tilapia (Oreochromis ssp.). 相似文献
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Bo-Young Lee Aimee E Howe Matthew A Conte Helena D'Cotta Elodie Pepey Jean-Francois Baroiller Federica di Palma Karen L Carleton Thomas D Kocher 《BMC genomics》2010,11(1):278
Background
Large collections of expressed sequence tags (ESTs) are a fundamental resource for analysis of gene expression and annotation of genome sequences. We generated 116,899 ESTs from 17 normalized and two non-normalized cDNA libraries representing 16 tissues from tilapia, a cichlid fish widely used in aquaculture and biological research.Results
The ESTs were assembled into 20,190 contigs and 36,028 singletons for a total of 56,218 unique sequences and a total assembled length of 35,168,415 bp. Over the whole project, a unique sequence was discovered for every 2.079 sequence reads. 17,722 (31.5%) of these unique sequences had significant BLAST hits (e-value < 10-10) to the UniProt database.Conclusion
Normalization of the cDNA pools with double-stranded nuclease allowed us to efficiently sequence a large collection of ESTs. These sequences are an important resource for studies of gene expression, comparative mapping and annotation of the forthcoming tilapia genome sequence.15.
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A nucleotide sequence analysis of a fragment of a Morone MHC class Ia gene detected high levels of polymorphism in striped bass Morone saxatilis, white perch Morone americana and yellow bass Morone mississippiensis. Extremely low levels of MHC diversity, however, were detected in white bass Morone chrysops, suggesting the possibility of a severe population bottleneck for this species. 相似文献
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