expressed sequence tags
Summary: Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.
Publications313 found, 100 shown here
- High-throughput functional annotation and data mining with the Blast2GO suiteStefan Götz
Bioinformatics Department, Centro de Investigacion Principe Felipe, Valencia, Spain
Nucleic Acids Res 36:3420-35. 2008..Our aim is to offer biologists useful information to take into account when addressing the task of functionally characterizing their sequence data...
- Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTsBastien Chevreux
Department of Molecular Biophysics, German Cancer Research Centre Heidelberg, 69120 Heidelberg, Germany
Genome Res 14:1147-59. 2004....
- Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencingJ Cristobal Vera
Department of Biology, 208 Mueller Laboratory, Pennsylvania State University, University Park, PA 16802, USA
Mol Ecol 17:1636-47. 2008..DNA collections from a genetically diverse pool of larvae, pupae, and adults yielded 608,053 expressed sequence tags (mean length = 110 nucleotides), which assembled into 48,354 contigs (sets of overlapping DNA segments) ..
- TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasetsGeo Pertea
The Institute for Genomic Research, Rockville, MD 20850, USA
Bioinformatics 19:651-2. 2003TGICL is a pipeline for analysis of large Expressed Sequence Tags (EST) and mRNA databases in which the sequences are first clustered based on pairwise sequence similarity, and then assembled by individual clusters (optionally with ..
- Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discoveryThomas L Parchman
Department of Botany, University of Wyoming, Laramie, WY 82071, USA
BMC Genomics 11:180. 2010..Here we describe a sequencing study of expressed genes from P. contorta, including their assembly and annotation, and their potential for molecular marker development to support population and association genetic studies...
- High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genomeEvandro Novaes
School of Forest Resources and Conservation, University of Florida, PO Box 110410, Gainesville, USA
BMC Genomics 9:312. 2008..However, it is questionable how effective the sequencing of large numbers of short reads for species with essentially no prior gene sequence information will support contig assemblies and sequence annotation...
- Comparing de novo assemblers for 454 transcriptome dataSujai Kumar
Institute of Evolutionary Biology, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK
BMC Genomics 11:571. 2010..We have carried out a systematic comparison of five assemblers (CAP3, MIRA, Newbler, SeqMan and CLC) to establish best practices for transcriptome assemblies, using a new dataset from the parasitic nematode Litomosoides sigmodontis...
- The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)G A Tuskan
Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
Science 313:1596-604. 2006..Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport...
- Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.)T Thiel
Institute of Plant Genetics and Crop Plant Research IPK, Corrensstrasse 3, D 06466 Gatersleben, Germany
Theor Appl Genet 106:411-22. 2003....
- Conservation and divergence of plant microRNA genesBaohong Zhang
The Institute of Environmental and Human Health TIEHH, and Department of Environmental Toxicology, Texas Tech University, Lubbock, TX 79409 1163, USA
Plant J 46:243-59. 2006..Regulation of gene expression by miRNAs appears to have existed at the earliest stages of plant evolution and has been tightly constrained (functionally) for more than 425 million years...
- Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequencesWeizhong Li
Burnham Institute for Medical Research La Jolla, CA 92037, USA
Bioinformatics 22:1658-9. 2006..All these programs can handle huge datasets with millions of sequences and can be hundreds of times faster than methods based on the popular sequence comparison and database search tools, such as BLAST...
- De novo transcriptome sequencing in Anopheles funestus using Illumina RNA-seq technologyJacob E Crawford
Department of Entomology, Cornell University, Ithaca, New York, United States of America
PLoS ONE 5:e14202. 2010..funestus from a newly founded colony in Burkina Faso, West Africa, using the Illumina GAIIx next generation sequencing platform...
- De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversityMassimo Iorizzo
Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, WI 53706, USA
BMC Genomics 12:389. 2011..The scope of this study was to develop a de novo assembly of carrot ESTs from multiple genotypes using the Illumina platform, and to identify polymorphisms...
- Transcriptomics of the bed bug (Cimex lectularius)Xiaodong Bai
Department of Entomology, Ohio Agricultural and Research Development Center, The Ohio State University, Wooster, Ohio, United States of America
PLoS ONE 6:e16336. 2011..lectularius. Hence, we subjected the C. lectularius transcriptome to 454 pyrosequencing in order to identify potential genes involved in pesticide resistance...
- Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markersWenliang Wei
Key Laboratory of Oil Crops Biology of the Ministry of Agriculture, Sesame Germplasm and Genetic Breeding Laboratory, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences OCRI CAAS, Wuhan, 430062, China
BMC Genomics 12:451. 2011..High-throughput transcriptomic sequencing is essential to generate a large transcriptome sequence dataset for gene discovery and molecular marker development...
- Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencingMartin Trick
John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
Plant Biotechnol J 7:334-46. 2009..of a polyploid crop, and the Solexa sequencing system was used to generate approximately 20 million expressed sequence tags (ESTs) from each of two cultivars: Tapidor and Ningyou 7...
- Using native and syntenically mapped cDNA alignments to improve de novo gene findingMario Stanke
Center for Biomolecular Science and Engineering, University of California Santa Cruz UCSC, Santa Cruz, CA 95064, USA
Bioinformatics 24:637-44. 2008..For many eukaryotic genomes, expressed sequence tags (ESTs) are available as evidence for genes...
- Transcript-specific, single-nucleotide polymorphism discovery and linkage analysis in hexaploid bread wheat (Triticum aestivum L.)Alexandra M Allen
School of Biological Sciences, University of Bristol, Bristol, UK
Plant Biotechnol J 9:1086-99. 2011..To mine selected elite wheat germplasm for intervarietal single-nucleotide polymorphisms, we have used expressed sequence tags derived from public sequencing programmes and next-generation sequencing of normalized wheat ..
- Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.)Susan R McCouch
Plant Breeding Dept, Cornell University, Ithaca, NY 14853 1901, USA
DNA Res 9:199-207. 2002..In combination with the pool of 500 previously mapped SSR markers, this release makes available a total of 2740 experimentally confirmed SSR markers for rice, or approximately one SSR every 157 kb...
- Stem cell transcriptome profiling via massive-scale mRNA sequencingNicole Cloonan
Expression Genomics Laboratory, Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, St Lucia, Queensland, 4072, Australia
Nat Methods 5:613-9. 2008....
- GMAP: a genomic mapping and alignment program for mRNA and EST sequencesThomas D Wu
Department of Bioinformatics Genentech, Inc, South San Francisco, CA 94080, USA
Bioinformatics 21:1859-75. 2005....
- Identification of soybean microRNAs and their targetsBaohong Zhang
Department of Biology, East Carolina University, Greenville, NC 27858, USA
Planta 229:161-82. 2008....
- Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised trainingVardges Ter-Hovhannisyan
School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
Genome Res 18:1979-90. 2008..By eliminating the effort necessary to build comprehensive training sets, the new algorithm can streamline and accelerate the process of annotation in a large number of fungal genome sequencing projects...
- Comparative 454 pyrosequencing of transcripts from two olive genotypes during fruit developmentFiammetta Alagna
CNR Institute of Plant Genetics, Via Madonna Alta 130, 06128 Perugia, Italy
BMC Genomics 10:399. 2009..454 pyrosequencing was used to enrich the very few sequence data currently available for the Olea europaea species and to identify genes involved in expression of fruit quality traits...
- Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and ArabidopsisL Duret
Laboratoire de Biometrie, Génétique et Biologie des Populations, Unité Mixte de Recherche Centre National de la Recherche Scientifique 5558, Villeurbanne Cedex, France
Proc Natl Acad Sci U S A 96:4482-7. 1999..This puzzling observation is not predicted by any of the current models of selection on codon usage and thus raises the question of how translation efficiency affects fitness in multicellular organisms...
- Global characterization of Artemisia annua glandular trichome transcriptome using 454 pyrosequencingWei Wang
Department of Biology and the State Key Lab for Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, PR China
BMC Genomics 10:465. 2009..The most prominent anti-malarial drug artemisinin, a sesquiterpene lactone, is produced in glandular trichomes of Artemisia annua. However, only limited genomic information is currently available in this non-model plant species...
- Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishesK R Elmer
Department of Biology, University of Konstanz, Germany
Mol Ecol 19:197-211. 2010..next-generation sequencing (Roche 454 massively parallel pyrosequencing) to characterize the diversity of expressed sequence tags between ecologically divergent, endemic and sympatric species of cichlid fishes from crater lake Apoyo, ..
- Comparison of the transcriptomes of American chestnut (Castanea dentata) and Chinese chestnut (Castanea mollissima) in response to the chestnut blight infectionAbdelali Barakat
The School of Forest Resources, Department of Horticulture, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
BMC Plant Biol 9:51. 2009....
- Identification and characterization of new plant microRNAs using EST analysisBao Hong Zhang
The Institute of Environmental and Human Health, and Department of Environmental Toxicology, Texas Tech University, Lubbock, TX 79409 1163, USA
Cell Res 15:336-60. 2005..A total of 18,694 plant expressed sequence tags (EST) were found in the GenBank EST databases by comparing all previously known Arabidopsis miRNAs to ..
- Characterization of the rainbow trout transcriptome using Sanger and 454-pyrosequencing approachesMohamed Salem
Laboratory of Animal Biotechnology and Genomics, Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA
BMC Genomics 11:564. 2010..Although a large number (258,973) of EST sequences are publicly available, the nature of rainbow trout duplicated genome hinders assembly and complicates annotation...
- Identification and characterization of nucleotide-binding site-leucine-rich repeat genes in the model plant Medicago truncatulaCarine Ameline-Torregrosa
Laboratoire des Interactions Plantes Microorganismes, UMR CNRS INRA 442 2594, 31326, Castanet Tolosan, France
Plant Physiol 146:5-21. 2008..This analysis shows the gene family not only is important functionally and agronomically, but also plays a structural role in the genome...
- Multiple sequence alignment using partial order graphsChristopher Lee
Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095 1570, USA
Bioinformatics 18:452-64. 2002..Progressive Multiple Sequence Alignment (MSA) methods depend on reducing an MSA to a linear profile for each alignment step. However, this leads to loss of information needed for accurate alignment, and gap scoring artifacts...
- Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding superfamilyB C Meyers
Department of Vegetable Crops, University of California, Davis 95616, USA
Plant J 20:317-32. 1999..Sequence inferences suggest that these genes encode a novel class of nucleotide-binding proteins...
- Transcriptome sequencing of lentil based on second-generation technology permits large-scale unigene assembly and SSR marker discoverySukhjiwan Kaur
Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, La Trobe University Research and Development Park, Bundoora, Australia
BMC Genomics 12:265. 2011..There is hence a significant need to enhance such resources in order to identify novel genes and alleles for molecular breeding to increase crop productivity and quality...
- Genic microsatellite markers in plants: features and applicationsRajeev K Varshney
Institute of Plant Genetics and Crop Plant Research IPK, Corrensstrasse 3, D 06466 Gatersleben, Germany
Trends Biotechnol 23:48-55. 2005..Applications and potential uses of EST-SSRs in plant genetics and breeding are discussed...
- Transcriptome sequencing and comparative analysis of cucumber flowers with different sex typesShaogui Guo
1National Engineering Research Center for Vegetables, Beijing 100097, China
BMC Genomics 11:384. 2010....
- Integration of physical and genetic maps in apple confirms whole-genome and segmental duplications in the apple genomeYuepeng Han
Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Moshan, Wuhan, 430074, PR China
J Exp Bot 62:5117-30. 2011..These findings demonstrated the presence of both genome-wide and segmental duplications in the apple genome and provided further insights into the complex polyploid ancestral origin of the apple...
- SNP discovery and linkage map construction in cultivated tomatoKenta Shirasawa
Kazusa DNA Research Institute, 2 6 7 Kazusa Kamatari, Kisarazu, Chiba 292 0818, Japan
DNA Res 17:381-91. 2010..In this study, we developed SNP markers based on expressed sequence tags for the construction of intraspecific linkage maps in tomato...
- Development of a EST dataset and characterization of EST-SSRs in a traditional Chinese medicinal plant, Epimedium sagittatum (Sieb. Et Zucc.) MaximShaohua Zeng
Key Laboratory of Pant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
BMC Genomics 11:94. 2010..Here, we report a set of expressed sequence tags (ESTs) and simple sequence repeats (SSRs) identified in these ESTs for E. sagittatum.
- GENCODE: producing a reference annotation for ENCODEJennifer Harrow
Wellcome Trust Sanger Institute, Wellcome Trust Campus, Hinxton, Cambridge CB10 1SA, UK
Genome Biol 7:S4.1-9. 2006..This was achieved by a combination of initial manual annotation by the HAVANA team, experimental validation by the GENCODE consortium and a refinement of the annotation based on these experimental results...
- High-density integrated linkage map based on SSR markers in soybeanTae Young Hwang
National Agricultural Research Center for Hokkaido Region, Sapporo, Hokkaido 062 8555, Japan
DNA Res 16:213-25. 2009..8. Our high-density linkage map should facilitate ongoing and future genomic research such as analysis of quantitative trait loci and positional cloning in addition to marker-assisted selection in soybean breeding...
- A consensus genetic map of cowpea [Vigna unguiculata (L) Walp.] and synteny based on EST-derived SNPsWellington Muchero
Departments of Nematology and Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
Proc Natl Acad Sci U S A 106:18159-64. 2009..These results support evolutionary closeness between cowpea and soybean and identify regions for synteny-based functional genomics studies in legumes...
- An approach to transcriptome analysis of non-model organisms using short-read sequencesLesley J Collins
Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
Genome Inform 21:3-14. 2008..Our approach demonstrates that transcriptome analysis using high-throughput short-read sequencing need not be restricted to the genomes of model organisms...
- Large-scale transcriptome analysis in chickpea (Cicer arietinum L.), an orphan legume crop of the semi-arid tropics of Asia and AfricaPavana J Hiremath
International Crops Research Institute for the Semi Arid Tropics ICRISAT, Patancheru, India
Plant Biotechnol J 9:922-31. 2011..tentative unique sequences (TUSs) have been produced from 435,018 Roche/454 reads and 21,491 Sanger expressed sequence tags (ESTs). Putative functions were determined for 49,437 (47...
- Comparative transcriptome and metabolite analysis of oil palm and date palm mesocarp that differ dramatically in carbon partitioningFabienne Bourgis
Université de Bordeaux Ségalen, Laboratoire de Biogenese Membranaire, Bordeaux, France
Proc Natl Acad Sci U S A 108:12527-32. 2011....
- Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oakSaneyoshi Ueno
INRA, UMR 1202 BIOGECO, 69 route d Arcachon, F 33612 Cestas, France
BMC Genomics 11:650. 2010....
- Tissue-specific transcriptomics of the exotic invasive insect pest emerald ash borer (Agrilus planipennis)Omprakash Mittapalli
Department of Entomology, Ohio Agricultural and Research Development Center, The Ohio State University, Wooster, Ohio, United States of America
PLoS ONE 5:e13708. 2010..primarily in the Midwestern United States and Ontario, Canada. However, despite its high impact status little knowledge exists for A. planipennis at the molecular level...
- Generation and analysis of a 29,745 unique Expressed Sequence Tags from the Pacific oyster (Crassostrea gigas) assembled into a publicly accessible database: the GigasDatabaseElodie Fleury
UMR M100 Ifremer Université de Caen Basse Normandie Physiologie et Ecophysiologie des Mollusques Marins, Centre de Brest, B, P, 70, 29280 Plouzané IBFA, IFR ICORE 146, Esplanade de la Paix, 14032 Caen Cedex, France
BMC Genomics 10:341. 2009..cDNA sequencing projects for the Pacific oyster Crassostrea gigas initiated to provide a large number of expressed sequence tags that were subsequently compiled in a publicly accessible database...
- In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal speciesRajeev K Varshney
Institute of Plant Genetics and Crop Plant Research IPK, Corrensstrasse 3, D 06466 Gatersleben, Germany
Cell Mol Biol Lett 7:537-46. 2002..sequencing and genomics programmes in various cereal species at different laboratories, a large set of expressed sequence tags (ESTs) is being generated, which can be used to search for microsatellites...
- A soybean transcript map: gene distribution, haplotype and single-nucleotide polymorphism analysisIk Young Choi
Soybean Genomics and Improvement Laboratory, USDA, ARS, Beltsville, Maryland 20705, USA
Genetics 176:685-96. 2007....
- Computational identification of novel microRNAs and targets in Brassica napusFu Liang Xie
Department of Biochemistry and Molecular Biology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
FEBS Lett 581:1464-74. 2007..We used previously known miRNAs from Arabidopsis, rice and other plant species against both expressed sequence tags (EST) and genomic survey sequence (GSS) databases to search for potential miRNAs in B. napus...
- Phylogenomics reshuffles the eukaryotic supergroupsFabien Burki
Department of Zoology and Animal Biology, University of Geneva, Geneva, Switzerland
PLoS ONE 2:e790. 2007..Yet, the composition of these large assemblages and their relationships remain controversial...
- A SSR-based composite genetic linkage map for the cultivated peanut (Arachis hypogaea L.) genomeYanbin Hong
Guangdong Academy of Agricultural Sciences, Crops Research Institute, Guangzhou, PR China
BMC Plant Biol 10:17. 2010..was to construct a genetic linkage map of cultivated peanut using simple sequence repeat (SSR) markers derived primarily from peanut genomic sequences, expressed sequence tags (ESTs), and by "data mining" sequences released in GenBank.
- Scanning the genome for gene single nucleotide polymorphisms involved in adaptive population differentiation in white spruceMarie Claire Namroud
Canada Research Chair in Forest and Environmental Genomics and Arborea, Forest Research Centre, Pavillon Charles Eugène Marchand, Universite Laval, Quebec, Quebec, CanadaP4
Mol Ecol 17:3599-613. 2008..The results suggest that an approach separating the locus and population effects is useful to identify genes potentially under selection. These candidates are worth exploring in more details at the physiological and ecological levels...
- Transcriptional regulation of biomass-degrading enzymes in the filamentous fungus Trichoderma reeseiPamela K Foreman
Genencor International, Inc, Palo Alto, California 94304, USA
J Biol Chem 278:31988-97. 2003..However, genes whose products are involved in protein processing and secretion were not highly regulated during cellulase induction...
- An oligo-based microarray offers novel transcriptomic approaches for the analysis of pathogen resistance and fruit quality traits in melon (Cucumis melo L.)Albert Mascarell-Creus
Molecular Genetics Department, Centre for Research in Agricultural Genomics CRAG CSIC IRTA UAB, Barcelona 08034, Spain
BMC Genomics 10:467. 2009..However, the unprecedented existence of a transcriptomic approaches in melon, highlight the importance of designing new tools for high-throughput analysis of gene expression...
- Gene discovery and annotation using LCM-454 transcriptome sequencingScott J Emrich
Bioinformatics and Computational Biology Graduate Program, Iowa State University, Ames, IA 50010, USA
Genome Res 17:69-73. 2007..We conclude that the coupling of LCM and 454 sequencing technologies facilitates the discovery of rare, possibly cell-type-specific transcripts...
- Nucleotide divergence vs. gene expression differentiation: comparative transcriptome sequencing in natural isolates from the carrion crow and its hybrid zone with the hooded crowJochen B W Wolf
Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plon, Germany
Mol Ecol 19:162-75. 2010..These results suggest that gene expression differences may indeed be a sensitive indicator of initial species divergence...
- Gene expression and protein length influence codon usage and rates of sequence evolution in Populus tremulaPar K Ingvarsson
Umea Plant Science Centre, Department of Ecology and Environmental Science, Umea University, Umea, Sweden
Mol Biol Evol 24:836-44. 2007..Using expression data for 558 genes derived from expressed sequence tags (EST) libraries from 19 different tissues and developmental stages, I study how gene expression levels ..
- GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics dataSook Jung
Department of Horticulture and Landscape Architecture, Washington State University, Pullman, WA 99164 6414, USA
Nucleic Acids Res 36:D1034-40. 2008..GDR also provides online analysis tools such as a batch BLAST/FASTA server for the GDR datasets, a sequence assembly server and microsatellite and primer detection tools. GDR is available at http://www.rosaceae.org...
- Development and analysis of EST-SSRs for flax (Linum usitatissimum L.)Sylvie Cloutier
Cereal Research Centre, Agriculture and Agri Food Canada, Winnipeg, MB, Canada
Theor Appl Genet 119:53-63. 2009A set of 146,611 expressed sequence tags (ESTs) were generated from 10 flax cDNA libraries...
- De novo sequencing and analysis of the American ginseng root transcriptome using a GS FLX Titanium platform to discover putative genes involved in ginsenoside biosynthesisChao Sun
Institute of Medicinal Plant Development IMPLAD, Chinese Academy of Medical Sciences, Haidian District, Beijing, China
BMC Genomics 11:262. 2010..Its major bioactive constituents are the triterpene saponins known as ginsenosides. However, little is known about ginsenoside biosynthesis in American ginseng, especially the late steps of the pathway...
- The odorant binding protein gene family from the genome of silkworm, Bombyx moriDa Ping Gong
The Key Sericultural Laboratory of Agricultural Ministry, Southwest University, Chongqing, PR China
BMC Genomics 10:332. 2009..Insect chemoreception is mediated by two large and diverse gene superfamilies, chemoreceptors and odorant binding proteins (OBPs). OBPs are believed to transport hydrophobic odorants from the environment to the olfactory receptors...
- Gene discovery using next-generation pyrosequencing to develop ESTs for Phalaenopsis orchidsYu Yun Hsiao
Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
BMC Genomics 12:360. 2011..We aimed to use massively parallel 454 pyrosequencing for a global characterization of the Phalaenopsis transcriptome...
- An Expressed Sequence Tag collection from the male antennae of the Noctuid moth Spodoptera littoralis: a resource for olfactory and pheromone detection researchFabrice Legeai
1IRISA, Equipe Symbiose, Campus Universitaire de Beaulieu, 35042 Rennes Cedex, France
BMC Genomics 12:86. 2011..Here, we describe an Expressed Sequence Tag (EST) project to characterize the antennal transcriptome of the noctuid pest model, Spodoptera littoralis, and to identify candidate genes involved in odour/pheromone detection...
- Model SNP development for complex genomes based on hexaploid oat using high-throughput 454 sequencing technologyRebekah E Oliver
USDA ARS, Small Grains and Potato Germplasm Research Unit, Aberdeen, ID, USA
BMC Genomics 12:77. 2011....
- Gene expression analysis of flax seed developmentPrakash Venglat
Plant Biotechnology Institute, NRC, 110 Gymnasium Place, Saskatoon, Saskatchewan, S7N 0W9, Canada
BMC Plant Biol 11:74. 2011..Here, we describe flax embryo and seed development and generation of comprehensive genomic resources for the flax seed...
- Transcriptome profiling and molecular marker discovery in red pepper, Capsicum annuum L. TF68Fu hao Lu
Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 340 802, Republic of Korea
Mol Biol Rep 39:3327-35. 2012..The SSR motifs corresponded to di- and tri- nucleotide motifs (27.03 and 61.92%, respectively). These molecular markers may be of great value for application in linkage mapping and association mapping research...
- Comparative gene expression analysis of susceptible and resistant near-isogenic lines in common wheat infected by Puccinia triticinaAlagu Manickavelu
Kihara Institute for Biological Research, Yokohama City University, Yokohama 244 0813, Japan
DNA Res 17:211-22. 2010..The molecular pathogenicity of leaf rust in wheat was studied and the EST data generated made a foundation for future studies...
- Synteny mapping between common bean and soybean reveals extensive blocks of shared lociPhillip E McClean
Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND 58105, USA
BMC Genomics 11:184. 2010..Determining the syntentic relationship between these two species will allow researchers to leverage not only genomic resources but also genetic data for important agronomic traits to improve both of these species...
- Transcriptome and proteome analysis of Pinctada margaritifera calcifying mantle and shell: focus on biomineralizationCaroline Joubert
Ifremer Laboratoire de Biotechnologie et de Qualité de Perle, Centre Océanologique du Pacifique BP 7004, 98719 Taravao, French Polynesia
BMC Genomics 11:613. 2010..margaritifera, high-throughput Expressed Sequence Tag (EST) pyrosequencing was undertaken on the calcifying mantle, combined with a proteomic analysis of the shell...
- A linkage map for the B-genome of Arachis (Fabaceae) and its synteny to the A-genomeMarcio C Moretzsohn
EMBRAPA Recursos Geneticos e Biotecnologia, Brasilia, DF, Brazil
BMC Plant Biol 9:40. 2009..This can be overcome by the utilization of wild species of Arachis, which present the A- and B-genomes in the diploid state, and show high levels of genetic variability...
- Arabidopsis genes involved in acyl lipid metabolism. A 2003 census of the candidates, a study of the distribution of expressed sequence tags in organs, and a web-based databaseFrédéric Beisson
Department of Plant Biology, Michigan State University, East Lansing 48824, USA
Plant Physiol 132:681-97. 2003....
- EST-SSRs as a resource for population genetic analysesJ R Ellis
Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
Heredity (Edinb) 99:125-32. 2007..in the production of vast amounts of publicly available DNA sequence data, including large collections of expressed sequence tags (ESTs) from a variety of different taxa...
- Microarray analysis identifies candidate genes for key roles in coral developmentLauretta C Grasso
Centre for the Molecular Genetics of Development, Research School of Biological Sciences, Australian National University, Canberra, Australia
BMC Genomics 9:540. 2008....
- Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barleyMauricio La Rota
Department of Plant Breeding and Genetics, 240 Emerson Hall, Cornell University, Ithaca, NY 14853, USA
BMC Genomics 6:23. 2005..sequences containing simple sequence repeats (SSR or microsatellites) by length and motif for wheat, barley and rice and to determine in-silico rice genome locations for primer sets developed for wheat and barley Expressed Sequence Tags.
- High-throughput sequencing and analysis of the gill tissue transcriptome from the deep-sea hydrothermal vent mussel Bathymodiolus azoricusRaul Bettencourt
Department of Oceanography and Fisheries, University of the Azores, 9901 861 Horta, Portugal
BMC Genomics 11:559. 2010....
- Transcriptome profiling of a toxic dinoflagellate reveals a gene-rich protist and a potential impact on gene expression due to bacterial presenceAhmed Moustafa
Ecology, Evolution and Natural Resources, Institute of Marine and Coastal Sciences, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, United States of America
PLoS ONE 5:e9688. 2010..Here, we used massively parallel signature sequencing (MPSS) to understand global transcriptional regulation patterns in Alexandrium tamarense cultures that were grown under four different conditions...
- Comparative analysis of detoxification enzymes in Acyrthosiphon pisum and Myzus persicaeJ S Ramsey
Boyce Thompson Institute for Plant Research, Ithaca, NY, USA
Insect Mol Biol 19:155-64. 2010..However, given the incomplete M. persicae cDNA data set, the number of identified detoxification genes in this species is likely to be an underestimate...
- SNP discovery via 454 transcriptome sequencingW Brad Barbazuk
Donald Danforth Plant Science Center, St Louis, MO 63132, USA
Plant J 51:910-8. 2007..These results demonstrate that 454-based transcriptome sequencing is an excellent method for the high-throughput acquisition of gene-associated SNPs...
- "Stemness": transcriptional profiling of embryonic and adult stem cellsMiguel Ramalho-Santos
Department of Molecular and Cellular Biology and Howard Hughes Medical Institute HHMI, Harvard University, Cambridge, MA 02138, USA
Science 298:597-600. 2002..to differentiated cell types, stem cells express a significantly higher number of genes (represented by expressed sequence tags) whose functions are unknown...
- Quality assessment parameters for EST-derived SNPs from catfishShaolin Wang
The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, USA
BMC Genomics 9:450. 2008..This project was designed to answer some of the questions relevant to quality assessment of EST-derived SNPs...
- A Brassica rapa linkage map of EST-based SNP markers for identification of candidate genes controlling flowering time and leaf morphological traitsFeng Li
Laboratory of Plant Breeding and Genetics, Graduate School of Agricultural Science, Tohoku University, 1 1 Tsutsumidori Amamiyamachi, Aoba, Sendai, Miyagi 981 8555, Japan
DNA Res 16:311-23. 2009..Analysis of nucleotide sequences and expression of these genes suggested possible involvement of these genes in leaf morphological traits...
- Deep sampling of the Palomero maize transcriptome by a high throughput strategy of pyrosequencingJulio C Vega-Arreguín
Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Campus Guanajuato, Carretera Irapuato León, Irapuato, Gto, Mexico
BMC Genomics 10:299. 2009..In some cases, deep parallel sequencing of Expressed Sequence Tags (ESTs), although not yet optimized for the sequencing of cDNAs, has represented an efficient procedure ..
- Next generation transcriptomes for next generation genomes using est2assemblyAlexie Papanicolaou
Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
BMC Bioinformatics 10:447. 2009..This rapid growth in data has outstripped the ability of researchers working on non-model species to analyze and mine transcriptome data efficiently...
- The TIGR Rice Genome Annotation Resource: improvements and new featuresShu Ouyang
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
Nucleic Acids Res 35:D883-7. 2007..Enhanced data access is available through web interfaces, FTP downloads and a Data Extractor tool developed in order to support discrete dataset downloads...
- A high-density transcript linkage map of barley derived from a single populationK Sato
Research Institute for Bioresources, Okayama University, Chuo, Kurashiki, Japan
Heredity (Edinb) 103:110-7. 2009..linkage map of barley was created using a single doubled haploid (DH) mapping population, only 3'-end expressed sequence tags (ESTs) and only PCR-based assays...
- Gene discovery using massively parallel pyrosequencing to develop ESTs for the flesh fly Sarcophaga crassipalpisDaniel A Hahn
Department of Entomology and Nematology, The University of Florida, Gainesville, FL 32611 0620, USA
BMC Genomics 10:234. 2009..To maximize sequence diversity, we pooled RNA extracted from whole bodies of all life stages and normalized the cDNA pool after reverse transcription...
- OrchidBase: a collection of sequences of the transcriptome derived from orchidsChih Hsiung Fu
Department of Engineering Science, National Cheng Kung University, Tainan 701, Taiwan
Plant Cell Physiol 52:238-43. 2011..Among them, 41,310 expressed sequence tags (ESTs) were obtained by using Sanger sequencing, whereas 37,908,032 reads were obtained by using next-..
- A comprehensive resource of drought- and salinity- responsive ESTs for gene discovery and marker development in chickpea (Cicer arietinum L.)Rajeev K Varshney
International Crops Research Institute for the Semi Arid Tropics ICRISAT, Patancheru, Greater Hyderabad, AP, India
BMC Genomics 10:523. 2009..This study reports generation and analysis of comprehensive resource of drought- and salinity-responsive expressed sequence tags (ESTs) and gene-based markers.
- Pyrosequencing the Manduca sexta larval midgut transcriptome: messages for digestion, detoxification and defenceY Pauchet
School of Biosciences, University of Exeter, Cornwall Campus, Penryn, UK
Insect Mol Biol 19:61-75. 2010..Following a recent pyrosequencing study generating immune related expressed sequence tags (ESTs), here we use this new technology to define the M. sexta larval midgut transcriptome...
- Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plantsTheresa M Fulton
Department of Plant Breeding, Cornell University, Ithaca, New York 14853, USA
Plant Cell 14:1457-67. 2002..This set of COS markers, identified computationally and experimentally, may further studies on comparative genomes and phylogenetics and elucidate the nature of genes conserved throughout plant evolution...
- High throughput SNP discovery and genotyping in grapevine (Vitis vinifera L.) by combining a re-sequencing approach and SNPlex technologyDiego Lijavetzky
Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Cientificas CSIC, C Darwin 3, 28049 Madrid, Spain
BMC Genomics 8:424. 2007..b>Expressed sequence tags (EST) sequencing projects in grapevine are allowing for the in silico detection of multiple putative ..
- Combining next-generation pyrosequencing with microarray for large scale expression analysis in non-model speciesDiana Bellin
Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
BMC Genomics 10:555. 2009..We describe here an innovative approach for this purpose and demonstrate its potential also for non-model species...
- MytiBase: a knowledgebase of mussel (M. galloprovincialis) transcribed sequencesPaola Venier
Department of Biology, University of Padova, Via U Bassi 58 B, Padova, Italy
BMC Genomics 10:72. 2009....
- QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid speciesJifeng Tang
Plant Research International, PO Box 16, 6700 AA Wageningen, The Netherlands
BMC Bioinformatics 7:438. 2006..for SNP discovery make use of the large number of sequences present in public databases (in most cases as expressed sequence tags (ESTs)) and are considered to be faster and more cost-effective than experimental procedures...
- From stop to start: tandem gene arrangement, copy number and trans-splicing sites in the dinoflagellate Amphidinium carteraeTsvetan R Bachvaroff
Center of Marine Biotechnology, University of Maryland Biotechnology Institute, Baltimore, Maryland, United States of America
PLoS ONE 3:e2929. 2008..This combination of features appears to be unique among eukaryotes...
- Genomic resources for Myzus persicae: EST sequencing, SNP identification, and microarray designJohn S Ramsey
Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, NY 14853, USA
BMC Genomics 8:423. 2007..However, despite the significant damage inflicted by M. persicae in agricultural systems through direct feeding damage and by its ability to transmit plant viruses, limited genomic information is available for this species...
- Insights into corn genes derived from large-scale cDNA sequencingNickolai N Alexandrov
Ceres, Inc, 1535 Rancho Conejo Blvd, Thousand Oaks, CA 91320, USA
Plant Mol Biol 69:179-94. 2009..All of the sequence data from this study have been submitted to DDBJ/GenBank/EMBL under accession numbers EU940701-EU977132 (FLI cDNA) and FK944382-FL482108 (EST)...
- A conifer genomics resource of 200,000 spruce (Picea spp.) ESTs and 6,464 high-quality, sequence-finished full-length cDNAs for Sitka spruce (Picea sitchensis)Steven G Ralph
Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
BMC Genomics 9:484. 2008..Sequence-finished full-length (FL)cDNAs and large collections of expressed sequence tags (ESTs) are essential for gene discovery, functional genomics, and for future efforts of conifer genome ..
- Identification and functional characterization of effectors in expressed sequence tags from various life cycle stages of the potato cyst nematode Globodera pallidaJohn T Jones
Plant Pathology Programme, SCRI, Invergowrie, Dundee DD2 5DA, UK
Mol Plant Pathol 10:815-28. 2009In this article, we describe the analysis of over 9000 expressed sequence tags (ESTs) from cDNA libraries obtained from various life cycle stages of Globodera pallida. We have identified over 50 G...
- Shotgun Sequencing of the Trichomonas Vaginalis GenomeJane Carlton; Fiscal Year: 2003..In addition, we will generate 30,000 Expressed Sequence Tags (ESTs) to aid in gene identification...
- Metabolic Pathways and Defects in Fructose MetabolismDEAN TOLAN; Fiscal Year: 2009..The large database of expressed sequence tags (dbEST) will be analyzed for overlapping expression profiles of the GLUT5, GLUT2, ketohexokinase, ..
- Metabolic Pathways and Defects in Fructose MetabolismDEAN TOLAN; Fiscal Year: 2007..The large database of expressed sequence tags (dbEST) will be analyzed for overlapping expression profiles of the GLUT5, GLUT2, ketohexokinase, ..
- Genetic Heterogeneity and Protein Function in DBAColin Sieff; Fiscal Year: 2003..screen by cytogenetic techniques for deletions and translocations; (2) use cDNA arrays of the genes and expressed sequence tags (ESTs) in the critical region to define candidate genes by examining their pattern of expressed RNAs in ..
- The Tetrahymena Genome ProjectEduardo Orias; Fiscal Year: 2004..4,000 expressed sequence tags (ESTs) will constitute the backbone of the physical map...
- A GENOMIC APPROACH TO PARASITES FROM THE PHYLUM NEMATODAMakedonka Mitreva; Fiscal Year: 2007..University's Genome Sequencing Center (GSC) has generated and immediately made public over 210,000 expressed sequence tags (ESTs) from 25 nematode species, including representatives of all the major groups of human parasites ..
- CHROMATIN-TELOMERE STRUCTURE AND AT GENOMIC SENSITIVITYTEJ PANDITA; Fiscal Year: 2005..We found six expressed sequence tags aberrantly expressed in Atm null mice as compared to the normal control, and we will characterize them ..
- CHARACTERIZING THE ZEBRAFISH GENOMELeonard Zon; Fiscal Year: 2002..500 expressed sequence tags (ESTs) derived from cDNA libraries of various tissues and developmental stages will be mapped using this ..
- AUTOSOMAL DOMINANT FOCAL SEGMENTAL GLOMERULOSCLEROSISMichelle Winn; Fiscal Year: 2004..PACs and BACs will in turn be used to map expressed sequence tags (ESTs), microsatellites and genes in the MCR...
- Identification of Metastasis-related Gene in Oral CancerZhuo Chen; Fiscal Year: 2003..The preliminary experiments revealed the existence of several genes and expressed sequence tags whose expressions were significantly altered in the selected metastatic cell lines...
- EFFECTS OF GENE PATENTS ON GENETIC TESTING AND RESEARCHMildred Cho; Fiscal Year: 2002..Many gene sequences, including expressed sequence tags and single nucleotide polymorphisms are particularly useful for developing predictive or diagnostic tests ..
- Resources for Teleost Gene Duplicates and Human DiseaseJOHN HARVEY POSTLETHWAIT; Fiscal Year: 2010..Aim 2 is to construct a resource of expressed sequence tags (ESTs) for gar and to develop bioinformatics that assign ESTs to thousands of markers on the linkage map...
- Songbird Neurogenomics InitiativeDavid Clayton; Fiscal Year: 2005..a) a collection of cDNA clones representing the mRNAs in the zebra finch brain; b) a database of expressed sequence tags (ESTs) derived by high-throughput sequencing of the collection; c) a web-based publicly accessible server ..
- Comprehensive Assessment of Endocrine Active MixturesTimothy Zacharewski; Fiscal Year: 2003..cDNA clones or expressed sequence tags (ESTs) for the estrogen responsive genes will be used to construct a custom estrogen responsive cDNA/EST ..