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Journal articles on the topic 'Expressed sequence tags (EST)'

Author: Grafiati

Published: 3 June 2025

Last updated: 19 July 2025

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1

Györgyey, János, Danièle Vaubert, José I. Jiménez-Zurdo, et al. "Analysis of Medicago truncatula Nodule Expressed Sequence Tags." Molecular Plant-Microbe Interactions® 13, no. 1 (2000): 62–71. http://dx.doi.org/10.1094/mpmi.2000.13.1.62.

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Systematic sequencing of expressed sequence tags (ESTs) can give a global picture of the assembly of genes involved in the development and function of organs. Indeterminate nodules representing different stages of the developmental program are especially suited to the study of organogenesis. With the vector λHybriZAP, a cDNA library was constructed from emerging nodules of Medicago truncatula induced by Sinorhizobium meliloti. The 5′ ends of 389 cDNA clones were sequenced, then these ESTs were analyzed both by sequence homology search and by studying their expression in roots and nodules. Two

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2

Cutri, Lucas, and Marcelo Carnier Dornelas. "PASSIOMA: Exploring Expressed Sequence Tags during Flower Development inPassifloraspp." Comparative and Functional Genomics 2012 (2012): 1–11. http://dx.doi.org/10.1155/2012/510549.

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The genusPassifloraprovides a remarkable example of floral complexity and diversity. The extreme variation ofPassifloraflower morphologies allowed a wide range of interactions with pollinators to evolve. We used the analysis of expressed sequence tags (ESTs) as an approach for the characterization of genes expressed duringPassiflorareproductive development. Analyzing thePassiflorafloral EST database (named PASSIOMA), we found sequences showing significant sequence similarity to genes known to be involved in reproductive development such as MADS-box genes. Some of these sequences were studied u

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Ozdemir Ozgenturk, Nehir, Fatma Oruç, Ugur Sezerman, et al. "Generation and Analysis of Expressed Sequence Tags fromOlea europaeaL." Comparative and Functional Genomics 2010 (2010): 1–9. http://dx.doi.org/10.1155/2010/757512.

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Olive (Olea europaeaL.) is an important source of edible oil which was originated in Near-East region. In this study, two cDNA libraries were constructed from young olive leaves and immature olive fruits for generation of ESTs to discover the novel genes and search the function of unknown genes of olive. The randomly selected 3840 colonies were sequenced for EST collection from both libraries. Readable 2228 sequences for olive leaf and 1506 sequences for olive fruit were assembled into 205 and 69 contigs, respectively, whereas 2478 were singletons. Putative functions of all 2752 differentially

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Watanabe, Hajime, Norihisa Tatarazako, Shigeto Oda, et al. "Analysis of expressed sequence tags of the water flea Daphnia magna." Genome 48, no. 4 (2005): 606–9. http://dx.doi.org/10.1139/g05-038.

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To study gene expression in the water flea Daphnia magna we constructed a cDNA library and characterized the expressed sequence tags (ESTs) of 7210 clones. The EST sequences clustered into 2958 nonredundant groups. BLAST analyses of both protein and DNA databases showed that 1218 (41%) of the unique sequences shared significant similarities to known nucleotide or amino acid sequences, whereas the remaining 1740 (59%) showed no significant similarities to other genes. Clustering analysis revealed particularly high expression of genes related to ATP synthesis, structural proteins, and proteases.

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Bettini, Ezio, Angela R. Porta, Norbert Dahmen, Henry Wang, and Frank L. Margolis. "Expressed sequence tags (EST) identify genes preferentially expressed in catfish chemosensory tissues." Molecular Brain Research 23, no. 4 (1994): 285–91. http://dx.doi.org/10.1016/0169-328x(94)90237-2.

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6

Levi, Amnon, Angela Davis, Pat Wechter, Alvaro Hernandez, and Jyothi Thimmapuram. "DEVELOPING EXPRESSED SEQUENCED TAGS (ESTS) FOR WATERMELON FRUIT." HortScience 41, no. 3 (2006): 518F—519. http://dx.doi.org/10.21273/hortsci.41.3.518f.

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A cDNA library was assembled using mRNA of watermelon fruit. The cDNA library was normalized and subtracted by hybridization with leaf cDNA of the same watermelon cultivar (Illini Red). 1,046 cDNA clones were sequenced to identify genes associated with fruit development and quality. Of 1,046 cDNA clones sequenced, 832 were unique sequences and designated as expressed sequenced tags (ESTs). Of the 832 ESTs, 205 (24.6%) have not been reported in any other plant species. Additionally, 186 ESTs (22.4%) correspond to genes with unknown function, while 441 ESTs (53.0%) correspond to genes with known

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Dyhrman, Sonya T., Sheean T. Haley, Shanda R. Birkeland, Louie L. Wurch, Michael J. Cipriano, and Andrew G. McArthur. "Long Serial Analysis of Gene Expression for Gene Discovery and Transcriptome Profiling in the Widespread Marine Coccolithophore Emiliania huxleyi." Applied and Environmental Microbiology 72, no. 1 (2006): 252–60. http://dx.doi.org/10.1128/aem.72.1.252-260.2006.

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ABSTRACT The abundant and widespread coccolithophore Emiliania huxleyi plays an important role in mediating CO2 exchange between the ocean and the atmosphere through its impact on marine photosynthesis and calcification. Here, we use long serial analysis of gene expression (SAGE) to identify E. huxleyi genes responsive to nitrogen (N) or phosphorus (P) starvation. Long SAGE is an elegant approach for examining quantitative and comprehensive gene expression patterns without a priori knowledge of gene sequences via the detection of 21-bp nucleotide sequence tags. E. huxleyi appears to have a rob

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Das, Nabajit, Saswat Suvesh Rout, and Rajanikanta Mahapatra. "An In-silico attempt to catch hold of the novel microRNAs in the Bio Energy Plant (Jatropha curcus): A Big Search." Biomirror 3, no. 07 (2012): 21–24. https://doi.org/10.5281/zenodo.30713.

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The oil-rich and weedy plant Jatropha has been hailed as the most promising source of biofuel on the planet, as a non-food, droughtresistant and oil-rich crop, Jatropha curcas fulfils many of the requirements for biofuel industries. A better understanding of the biochemical pathway leading to the synthesis of Jatropha oil and its regulation both by exogenous and endogenous factors is essential for facilitating increased yield. Increasing evidence has shown that miRNAs play multiple roles in various biological processes. The research finds previously known miRNAs from various plant species expr

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Livingstone, J. M., P. Seguin, and M. V. Strömvik. "An in silico study of the genes for the isoflavonoid pathway enzymes in soybean reveals novel expressed homologues." Canadian Journal of Plant Science 90, no. 4 (2010): 453–69. http://dx.doi.org/10.4141/cjps08214.

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Soybean [Glycine max (L.) Merr.] is an important source of isoflavones used by the nutraceutical industry. The soybean genome (2n = 40, 975 Mb) has recently been sequenced, and over a million (redundant) gene tags (expressed sequence tags, ESTs) are available in public databases. Using bioinformatics, we investigated five key enzymes of the isoflavonoid pathway (i.e., chalcone isomerase, isoflavone synthase, 2-hydroxyisoflavanone dehydratase, isoflavanone-7-O-glycosyltransferase, and isoflavone-7-O-glucoside-6′′-O-malonyltransferase) to gain a better understanding of which gene homologues are

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10

Burki, Fabien, Sergey I. Nikolaev, Ignacio Bolivar, Jackie Guiard, and Jan Pawlowski. "Analysis of expressed sequence tags from a naked foraminiferan Reticulomyxa filosa." Genome 49, no. 8 (2006): 882–87. http://dx.doi.org/10.1139/g06-048.

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Foraminifers are a major component of modern marine ecosystems and one of the most important oceanic producers of calcium carbonate. They are a key phylogenetic group among amoeboid protists, but our knowledge of their genome is still mostly limited to a few conserved genes. Here, we report the first study of expressed genes by means of expressed sequence tag (EST) from the freshwater naked foraminiferan Reticulomyxa filosa. Cluster analysis of 1630 valid ESTs enabled the identification of 178 groups of related sequences and 871 singlets. Approximately 50% of the putative unique 1059 ESTs coul

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Yu, Ju-Kyung, Qi Sun, Mauricio La Rota, Hugh Edwards, Hailu Tefera, and Mark E. Sorrells. "Expressed sequence tag analysis in tef (Eragrostis tef (Zucc) Trotter)." Genome 49, no. 4 (2006): 365–72. http://dx.doi.org/10.1139/g05-118.

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Tef (Eragrostis tef (Zucc.) Trotter) is the most important cereal crop in Ethiopia; however, there is very little DNA sequence information available for this species. Expressed sequence tags (ESTs) were generated from 4 cDNA libraries: seedling leaf, seedling root, and inflorescence of E. tef and seedling leaf of Eragrostis pilosa, a wild relative of E. tef. Clustering of 3603 sequences produced 530 clusters and 1890 singletons, resulting in 2420 tef unigenes. Ap prox imately 3/4 of tef unigenes matched protein or nucleotide sequences in public databases. Annotation of unigenes associated 68%

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Chaves, L. D., J. A. Rowe, and K. M. Reed. "Survey of a cDNA library from the turkey (Meleagris gallopavo)." Genome 48, no. 1 (2005): 12–17. http://dx.doi.org/10.1139/g04-088.

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Genome characterization and analysis is an imperative step in identifying and selectively breeding for improved traits of agriculturally important species. Expressed sequence tags (ESTs) represent a transcribed portion of the genome and are an effective way to identify genes within a species. Downstream applications of EST projects include DNA microarray construction and interspecies comparisons. In this study, 694 ESTs were sequenced and analyzed from a library derived from a 24-day-old turkey embryo. The 437 unique sequences identified were divided into 76 assembled contigs and 361 singleton

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Wen-Zheng, Li, Song Li-Min, Li Yong-Ping, et al. "Expressed sequence tag analysis and cDNA array establishment of Nicotiana tabacum: application to salinity stress." Chinese Journal of Agricultural Biotechnology 6, no. 1 (2009): 81–89. http://dx.doi.org/10.1017/s1479236209002526.

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AbstractThis study aimed to explore high-throughput cDNA array monitoring technology and to apply it to the gene expression spectrum analysis of salinity-challenged tobacco plants. A Nicotiana tabacum cDNA library was sequenced and found to consist of 5927 high-quality sequences (GenBank accession nos CV015900-CV021826). By analysing the expressed sequence tags (ESTs), the proportion of N. tabacum genes was identified at the EST level. A cDNA array was constructed based on the tentative unique transcripts (TUTs) derived from EST assembling results. A total of 42 differentially expressed genes

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14

Lee, Y. H., G. M. Huang, R. A. Cameron, et al. "EST analysis of gene expression in early cleavage-stage sea urchin embryos." Development 126, no. 17 (1999): 3857–67. http://dx.doi.org/10.1242/dev.126.17.3857.

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A set of 956 expressed sequence tags derived from 7-hour (mid-cleavage) sea urchin embryos was analyzed to assess biosynthetic functions and to illuminate the structure of the message population at this stage. About a quarter of the expressed sequence tags represented repetitive sequence transcripts typical of early embryos, or ribosomal and mitochondrial RNAs, while a majority of the remainder contained significant open reading frames. A total of 232 sequences, including 153 different proteins, produced significant matches when compared against GenBank. The majority of these identified sequen

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Torto-Alalibo, Trudy A., Sucheta Tripathy, Brian M. Smith, et al. "Expressed Sequence Tags from Phytophthora sojae Reveal Genes Specific to Development and Infection." Molecular Plant-Microbe Interactions® 20, no. 7 (2007): 781–93. http://dx.doi.org/10.1094/mpmi-20-7-0781.

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Six unique expressed sequence tag (EST) libraries were generated from four developmental stages of Phytophthora sojae P6497. RNA was extracted from mycelia, swimming zoospores, germinating cysts, and soybean (Glycine max (L.) Merr.) cv. Harosoy tissues heavily infected with P. sojae. Three libraries were created from mycelia growing on defined medium, complex medium, and nutrient-limited medium. The 26,943 high-quality sequences obtained clustered into 7,863 unigenes composed of 2,845 contigs and 5,018 singletons. The total number of P. sojae unigenes matching sequences in the genome assembly

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16

Chen, Song Bo, Xin Lu Xie, Gong Li, and Hai Jin Liu. "Data Mining for Simple Sequence Repeats in Expressed Sequence Tags from Japanese Flounder (Paralichthys olivaceus)." Advanced Materials Research 765-767 (September 2013): 274–77. http://dx.doi.org/10.4028/www.scientific.net/amr.765-767.274.

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Based on ESTs of Japanese flounder (Paralichthys olivaceus) in the public database, EST-SSR makers were developed after mining and evaluating SSRs in them by bioinformatics methods. 5 927 non-redundant ESTs of Japanese flounder were screened and 390 SSRs were mined out. The frequency of these EST-SSRs was 7.95% and the average distance of distribution was 7.9 kb in non-redundant ESTs. The dinucleotide repest motif was dominant type (59.02%) with repeat motif AC being the most common (16.91%). The distribution of trinucleotide, tetranucleotide and hexanucleotide repeats were dispersive. 30 prim

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17

Ju, Zhenlin, Melissa C. Wells, Al Martinez, Leona Hazlewood, and Ronald B. Walter. "An in silico Mining for Simple Sequence Repeats from Expressed Sequence Tags of Zebrafish, Medaka, Fundulus, and Xiphophorus." In Silico Biology: Journal of Biological Systems Modeling and Multi-Scale Simulation 5, no. 5-6 (2005): 439–63. https://doi.org/10.3233/isb-00201.

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Teleost fish genome projects involving model species are resulting in a rapid accumulation of genomic and expressed DNA sequences in public databases. The expressed sequence tags (ESTs) collected in the databases can be mined for the analysis of both structural and functional genomics. In this study, we in silico analyzed 49,430 unigenes representing a total of 692,654 ESTs from four model fish for their potential use in developing simple sequence repeats (SSRs), or microsatellites. After bioinformatical mining, a total of 3,018 EST derived SSRs (EST-SSRs) were identified for 2,335 SSR contain

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18

Aliyeva, Elmira, Anneke M. Metz, and Karen S. Browning. "Sequences of two expressed sequence tags (EST) from rice encoding different cap-binding proteins." Gene 180, no. 1-2 (1996): 221–23. http://dx.doi.org/10.1016/s0378-1119(96)00418-0.

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19

Abad, Pierre, David Bird, John Jones, and James McCarter. "Rapid gene discovery in plant parasitic nematodes via Expressed Sequence Tags." Nematology 2, no. 7 (2000): 719–31. http://dx.doi.org/10.1163/156854100509574.

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AbstractProjects currently underway are generating thousands of publicly available DNA sequences representing numerous genes from plant parasitic nematodes. Use of these data has the potential to revolutionise gene discovery, as well as aiding in genome physical mapping and expression profiling experiments. This article introduces sequences called expressed sequence tags or ESTs, which are single-sequence reads from randomly-selected cDNA clones. We review the process used to create these sequences and outline the strengths and weaknesses of ESTs as research tools. Instructions on how to acces

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20

Huang, Q., X. Cheng, B. Xie, and R. Xu. "SSR data mined from expressed sequence tags of phytoparasitic nematodes." Helminthologia 47, no. 1 (2010): 8–19. http://dx.doi.org/10.2478/s11687-010-0002-2.

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AbstractSSR markers have become the most popular resource for studying population genetic variation in eukaryotes. However, few studies with SSR markers have been carried out with phytoparasitic nematodes. In this study a primary survey on EST-SSRs was made utilizing bioinformatics methods to derive SSRs from expressed sequence tags (ESTs) of 16 species of PPN, which belong to 7 genera and 5 families. The results showed that trinucleotide repeats were the most abundant SSRs in coding ESTs, while tetranucleotide SSRs were predominant in non-coding ESTs and genome sequences. AG/CT, AAC/GTT and (

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Pinto, Luciana Rossini, Karine Miranda Oliveira, Eugênio César Ulian, Antonio Augusto Franco Garcia, and Anete Pereira de Souza. "Survey in the sugarcane expressed sequence tag database (SUCEST) for simple sequence repeats." Genome 47, no. 5 (2004): 795–804. http://dx.doi.org/10.1139/g04-055.

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Sugarcane microsatellites or simple sequence repeats (SSR) were developed in an economical and practical way by mining EST databases. A survey in the SUCEST (sugarcane EST) database revealed a total of 2005 clusters out of 43 141 containing SSRs. Of these, 8.2% were dinucleotide, 30.5% were trinucleotide, and 61.3% were tetranucleotide repeats. Except for dinucleotides, the CG-rich motif types were the most common. Differences in abundance of trinucleotide motif types were observed between EST-SSRs and those isolated from sugarcane genomic libraries. Among the different cDNA libraries used for

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You, Na, Junmei Liu, and Chang Xuan Mao. "An Empirical Bayesian Method for Detecting Differentially Expressed Genes Using EST Data." International Journal of Plant Genomics 2008 (March 13, 2008): 1–4. http://dx.doi.org/10.1155/2008/817210.

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Detection of differentially expressed genes from expressed sequence tags (ESTs) data has received much attention. An empirical Bayesian method is introduced in which gene expression patterns are estimated and used to define detection statistics. Significantly differentially expressed genes can be declared given detection statistics. Simulation is done to evaluate the performance of proposed method. Two real applications are studied.

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Figueiredo, R. C., M. S. Brito, L. H. M. Figueiredo, et al. "Dissecting the sugarcane expressed sequence tag (SUCEST) database: unraveling flower-specific genes." Genetics and Molecular Biology 24, no. 1-4 (2001): 77–84. http://dx.doi.org/10.1590/s1415-47572001000100012.

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There are almost 260,000 independent clones sequenced from the 5’ end in the Sugarcane Expressed Sequence Tag (SUCEST) database, which have been obtained from 37 cDNA libraries prepared from different tissues. This large number of expressed sequence tags (ESTs) provides an opportunity, unprecedented in plants, to perform ‘digital differential screening’ on selected cDNA libraries. In general, the frequency of a particular EST correlates with transcript accumulation in the tissues from which the cDNA libraries were constructed, so it is possible to compare the whole transcriptome from different

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Fridolfsson, A. K., T. Hori, A. K. Winterø, et al. "Expansion of the pig comparative map by expressed sequence tags (EST) mapping." Mammalian Genome 8, no. 12 (1997): 907–12. http://dx.doi.org/10.1007/s003359900609.

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Telles, Guilherme P., Marília D. V. Braga, Zanoni Dias, et al. "Bioinformatics of the sugarcane EST project." Genetics and Molecular Biology 24, no. 1-4 (2001): 9–15. http://dx.doi.org/10.1590/s1415-47572001000100003.

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The Sugarcane EST project (SUCEST) produced 291,904 expressed sequence tags (ESTs) in a consortium that involved 74 sequencing and data mining laboratories. We created a web site for this project that served as a ‘meeting point’ for receiving, processing, analyzing, and providing services to help explore the sequence data. In this paper we describe the information pathway that we implemented to support this project and a brief explanation of the clustering procedure, which resulted in 43,141 clusters.

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Mullan, Daniel J., Amanda Platteter, Natasha L. Teakle, et al. "EST-derived SSR markers from defined regions of the wheat genome to identify Lophopyrum elongatum specific loci." Genome 48, no. 5 (2005): 811–22. http://dx.doi.org/10.1139/g05-040.

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Lophopyrum elongatum, a close relative of wheat, provides a source of novel genes for wheat improvement. Molecular markers were developed to monitor the introgression of L. elongatum chromosome segments into hexaploid wheat. Existing simple sequence repeats (SSRs) derived from genomic libraries were initially screened for detecting L. elongatum loci in wheat, but only 6 of the 163 markers tested were successful. To increase detection of L. elongatum specific loci, 165 SSRs were identified from wheat expressed sequence tags (ESTs), where their chromosomal positions in wheat were known from dele

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Ewing, Rob, Olivier Poirot, and Jean-Michel Claverie. "Comparative Analysis of the Arabidopsis and Rice Expressed Sequence Tag (EST) Sets." In Silico Biology: Journal of Biological Systems Modeling and Multi-Scale Simulation 1, no. 4 (2000): 197–213. https://doi.org/10.3233/isb-00018.

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Large numbers of expressed sequence tags (ESTs) have now been generated from a variety of model organisms. In plants, substantial collections of ESTs are available for Arabidopsis and rice, in each case representing significant proportions of the estimated total numbers of genes. Large-scale comparisons of Arabidopsis and rice sequences are especially interesting due to the fact that these two species are representatives of the two subclasses of the flowering plants (Dicotyledonae and Monocotyledonae, respectively). Here we present the results of systematic analysis of the Arabidopsis and rice

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28

Brazauskas, Gintaras, and Izolda Pašakinskienė. "Identification of Differentially Expressed Genes in Axillary Tillers of Perennial Ryegrass." Proceedings of the Latvian Academy of Sciences. Section B. Natural, Exact, and Applied Sciences. 63, no. 1-2 (2009): 25–28. http://dx.doi.org/10.2478/v10046-009-0008-7.

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Identification of Differentially Expressed Genes in Axillary Tillers of Perennial Ryegrass A PCR-based suppression subtractive hybridisation (SSH) technique was used to identify differentially expressed genes in the primary and axillary tillers of a perennial ryegrass (Lolium perenne L.) mutant with enhanced axillary tillering. A total of 310 expressed sequence tags (ESTs) were obtained representing 249 non-redundant sequences. The average EST sequence length was 249 nt and varied from 30 to 508 nt. Putative function was assigned to 152 ESTs by comparing sequences with publicly available datab

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Shen, Xiaorong, Michael G. Francki, and Herbert W. Ohm. "A resistance-like gene identified by EST mapping and its association with a QTL controlling Fusarium head blight infection on wheat chromosome 3BS." Genome 49, no. 6 (2006): 631–35. http://dx.doi.org/10.1139/g06-010.

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Fusarium head blight (FHB) is a major disease in the wheat growing regions of the world. A quantitative trait locus (QTL) on the short arm of chromosome 3B controls much of the variation for resistance. The cloning of candidate disease-resistance genes for FHB QTLs on chromosome 3B can provide further elucidation of the mechanisms that control resistance. However, rearrangements and divergence during plant genome evolution often hampers the identification of sequences with similarity to known disease-resistance genes. This study focuses on the use of wheat expressed sequence tags (ESTs) that m

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Sengoelge, Gürkan, Wensheng Luo, Derek Fine, et al. "A SAGE-based comparison between glomerular and aortic endothelial cells." American Journal of Physiology-Renal Physiology 288, no. 6 (2005): F1290—F1300. http://dx.doi.org/10.1152/ajprenal.00076.2004.

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Endothelial cells have many characteristics in common, but significant morphological and functional differences exist between endothelial cells from different anatomic sites. The specific glomerular endothelial (GEn) cell transcript repertoire is unknown. We sought to determine whether endothelial cells derived from bovine glomeruli display a distinct transcriptional profile compared with bovine aortic endothelium (BAE) under identical conditions. Serial analysis of gene expression (SAGE), which includes known and unknown transcripts, was used to make the comparison. The GEn and BAE SAGE libra

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Costa, Fábio L. S., Maria E. De Lima, Adriano C. Pimenta, Suely G. Figueiredo, Evanguedes Kalapothakis, and Carlos E. Salas. "Expressed sequence tags in venomous tissue of Scorpaena plumieri (Scorpaeniformes: Scorpaenidae)." Neotropical Ichthyology 12, no. 4 (2014): 871–78. http://dx.doi.org/10.1590/1982-0224-20130149.

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Species of the family Scorpaenidae are responsible for accidents and sporadic casualties by the shore they inhabit. The species Scorpaena plumierifrom this family populate the Northeastern and Eastern coast of Brazil causing human envenomation characterized by local and systemic symptoms. In experimental animals the venom induces cardiotoxic, hypotensive, and airway respiratory effects. As first step to identify the venom components we isolated gland mRNA to produce a cDNA library from the fish gland. This report describes the partial sequencing of 356 gland transcripts from S. plumieri. BLAST

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Fan-Yun, Lin, Hu Yin-Gang, Song Guo-Qi, Zhang Hong, Liu Tian-Ming, and He Bei-Ru. "Isolation and analysis of genes induced by rehydration after serious drought in broomcorn millet (Panicum miliaceum L.) by SSH." Chinese Journal of Agricultural Biotechnology 3, no. 3 (2006): 237–42. http://dx.doi.org/10.1079/cjb2006119.

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AbstractIn order to investigate the molecular mechanism of rehydration after serious drought in broomcorn millet (Panicum miliaceum L.), a forward subtracted cDNA library was constructed between normal watered leaves and rehydrated leaves after serious drought conditions, using the suppressive subtraction hybridization (SSH) technique. A total of 60 positive clones were picked out at random from the subtracted library and sequenced, and redundancy sequences were removed after sequence alignment. Based on the results of sequence homologous comparison and function querying, 32 expressed sequence

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He, X., J. Zheng, M. Serapiglia, L. Smart, S. Shi, and B. Wang. "Short note: Development, characterization and cross-amplification of eight EST-derived microsatellites in Salix." Silvae Genetica 63, no. 1-6 (2014): 113–15. http://dx.doi.org/10.1515/sg-2014-0015.

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Abstract A set of eight simple sequence repeat (SSR) markers were developed from 707 Salix expressed sequence tags (ESTs) deposited in GenBank. Each of the EST-SSR amplicons was identical to the original EST, with sequence identity 60.90-96.03% and presence of the expected repeat motifs. Of the eight EST-SSR loci, five were polymorphic among 14 individuals of S. eriocephala, with the number of alleles per locus (Na), observed heterozygosity (Ho), expected heterozygosity (He) and polymorphic information content (PIC) being 2-7 (mean 4.8), 0.29-0.85 (mean 0.65), 0.25-0.84 (mean 0.65) and 0.21-0.

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Ozdemir Ozgenturk, Nehir, Zehra Omeroglu Ulu, Salih Ulu, Cemal Un, Kemal Ozdem Oztabak, and Kemal Altunatmaz. "Preparing and Analyzing Expressed Sequence Tags (ESTs) Library for the Mammary Tissue of Local Turkish Kivircik Sheep." International Journal of Genomics 2017 (2017): 1–14. http://dx.doi.org/10.1155/2017/9604762.

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Kivircik sheep is an important local Turkish sheep according to its meat quality and milk productivity. The aim of this study was to analyze gene expression profiles of both prenatal and postnatal stages for the Kivircik sheep. Therefore, two different cDNA libraries, which were taken from the same Kivircik sheep mammary gland tissue at prenatal and postnatal stages, were constructed. Total 3072 colonies which were randomly selected from the two libraries were sequenced for developing a sheep ESTs collection. We used Phred/Phrap computer programs for analysis of the raw EST and readable EST se

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PANCHIN, ALEXANDER Y., SERGEY A. SPIRIN, SERGEY A. LUKYANOV, YURI B. LEBEDEV, and YURI V. PANCHIN. "HUMAN TRASH ESTs — SEQUENCES FROM cDNA COLLECTION THAT ARE NOT ALIGNED TO GENOME ASSEMBLY." Journal of Bioinformatics and Computational Biology 06, no. 04 (2008): 759–73. http://dx.doi.org/10.1142/s0219720008003709.

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Expressed sequence tags (ESTs) represent 500–1000-bp-long sequences corresponding to mRNAs derived from different sources (cell lines, tissues, etc.). The human EST database contains over 8,000,000 sequences, with over 4,000,000,000 total nucleotides. RNA molecules are transcribed from a genomic DNA template; therefore, all ESTs should match corresponding genomes. Nevertheless, we have found in the human EST database approximately 11,000 ESTs not matching sequences in the human genome database. The presence of "trash" ESTs (TESTs) in the EST database could result from DNA or RNA contamination

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van Zijll de Jong, Eline, Kathryn M. Guthridge, German C. Spangenberg, and John W. Forster. "Development and characterization of EST-derived simple sequence repeat (SSR) markers for pasture grass endophytes." Genome 46, no. 2 (2003): 277–90. http://dx.doi.org/10.1139/g03-001.

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Fungal endophytes of the genus Neotyphodium are common in temperate pasture grass species and confer both beneficial and deleterious agronomic characteristics to their hosts. The aim of this study was to develop molecular markers based on simple sequence repeat (SSR) loci for the identification and assessment of genetic diversity among Neotyphodium endophytes in grasses. Expressed sequence tags (ESTs) from both Neptyphodium coenophialum and Neotyphodium lolii were examined, and unique SSR loci were identified in 9.7% of the N. coenophialum sequences and 6.3% of the N. lolii sequences. A variet

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Sim, Sung-Chur, Ju-Kyung Yu, Young-ki Jo, Mark E. Sorrells, and Geunhwa Jung. "Transferability of cereal EST-SSR markers to ryegrass." Genome 52, no. 5 (2009): 431–37. http://dx.doi.org/10.1139/g09-019.

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A large number of expressed sequence tags (ESTs) in public databases have provided an opportunity for the systematic development of simple sequence repeat (SSR) markers. EST-SSRs derived from conserved coding sequences show considerable cross-species transferability in related species. In the present study, we assessed the utility of cereal EST-SSRs in ryegrass ( Lolium spp.). A total of 165 cereal EST-SSRs were tested; a high rate of transferability (57%) and polymorphism (67% of functional EST-SSRs) was demonstrated between cereals and ryegrass. A total of 46 segregating loci derived from 37

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Lambais, Marcio R. "In silico differential display of defense-related expressed sequence tags from sugarcane tissues infected with diazotrophic endophytes." Genetics and Molecular Biology 24, no. 1-4 (2001): 103–11. http://dx.doi.org/10.1590/s1415-47572001000100015.

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The expression patterns of 277 sugarcane expressed sequence tags (EST)-contigs encoding putative defense-related (DR) proteins were evaluated using the Sugarcane EST database. The DR proteins evaluated included chitinases, beta-1,3-glucanases, phenylalanine ammonia-lyases, chalcone synthases, chalcone isomerases, isoflavone reductases, hydroxyproline-rich glycoproteins, proline-rich glycoproteins, peroxidases, catalases, superoxide dismutases, WRKY-like transcription factors and proteins involved in cell death control. Putative sugarcane WRKY proteins were compared and their phylogenetic relat

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Dracatos, Peter M., Jeremy L. Dumsday, Rhiannon S. Olle, et al. "Development and characterization of EST-SSR markers for the crown rust pathogen of ryegrass (Puccinia coronata f.sp. lolii)." Genome 49, no. 6 (2006): 572–83. http://dx.doi.org/10.1139/g06-006.

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The causative organism of crown rust in ryegrasses (Puccinia coronata f.sp. lolii) is an obligate biotroph that causes significant economic losses within the temperate grazing industries of dairy, meat, and wool production. This study reports on the development, transferability, and utility of gene-associated simple sequence repeat (SSR) molecular markers for crown rust. Analysis of 1100 expressed sequence tag (EST) sequences from a urediniospore-derived cDNA library detected 55 SSR loci. The majority of EST-SSR arrays contained perfect trinucleotide repeats with consistently low repeat number

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Soanes, Darren M., Wendy Skinner, John Keon, John Hargreaves, and Nicholas J. Talbot. "Genomics of Phytopathogenic Fungi and the Development of Bioinformatic Resources." Molecular Plant-Microbe Interactions® 15, no. 5 (2002): 421–27. http://dx.doi.org/10.1094/mpmi.2002.15.5.421.

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Genomic resources available to researchers studying phytopathogenic fungi are limited. Here, we briefly review the genomic and bioinformatic resources available and the current status of fungal genomics. We also describe a relational database containing sequences of expressed sequence tags (ESTs) from three phytopathogenic fungi, Blumeria graminis, Magnaporthe grisea, and Mycosphaerella graminicola, and the methods and underlying principles required for its construction. The database contains significant annotation for each EST sequence and is accessible at http://cogeme.ex.ac.uk . An easy-to-

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Pinto, Fernanda de Oliveira, Mirian Perez Maluf, and Oliveiro Guerreiro-Filho. "Study of simple sequence repeat markers from coffee expressed sequences associated to leaf miner resistance." Pesquisa Agropecuária Brasileira 42, no. 3 (2007): 377–84. http://dx.doi.org/10.1590/s0100-204x2007000300011.

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The objective of this work was to identify expressed simple sequence repeats (SSR) markers associated to leaf miner resistance in coffee progenies. Identification of SSR markers was accomplished by directed searches on the Brazilian Coffee Expressed Sequence Tags (EST) database. Sequence analysis of 32 selected SSR loci showed that 65% repeats are of tetra-, 21% of tri- and 14% of dinucleotides. Also, expressed SSR are localized frequently in the 5'-UTR of gene transcript. Moreover, most of the genes containing SSR are associated with defense mechanisms. Polymorphisms were analyzed in progenie

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Jayashree, B., Ramu Punna, P. Prasad, et al. "A Database of Simple Sequence Repeats from Cereal and Legume Expressed Sequence Tags Mined in silico: Survey and Evaluation." In Silico Biology: Journal of Biological Systems Modeling and Multi-Scale Simulation 6, no. 6 (2006): 607–20. https://doi.org/10.3233/isb-00269.

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Simple sequence repeats (SSRs) or microsatellites are an important class of molecular markers for genome analysis and plant breeding applications. In this paper, the SSR distributions within ESTs from the legumes soybean (Glycine max, representing 135.86 Mb), medicago (Medicago truncatula, 121.1 Mb) and lotus (Lotus japonicus, 45.4 Mb) have been studied relative to the distributions in cereals such as sorghum (Sorghum bicolor, 98.9 Mb), rice (Oryza sativa, 143.9 Mb) and maize (Zea mays, 183.7 Mb). The relative abundance, density, composition and putative annotations of di-, tri-, tetra- and pe

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Oliveira, K. M., L. R. Pinto, T. G. Marconi, et al. "Characterization of new polymorphic functional markers for sugarcane." Genome 52, no. 2 (2009): 191–209. http://dx.doi.org/10.1139/g08-105.

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Expressed sequence tags (ESTs) offer the opportunity to exploit single, low-copy, conserved sequence motifs for the development of simple sequence repeats (SSRs). The authors have examined the Sugarcane Expressed Sequence Tag database for the presence of SSRs. To test the utility of EST-derived SSR markers, a total of 342 EST–SSRs, which represent a subset of over 2005 SSR-containing sequences that were located in the sugarcane EST database, could be designed from the nonredundant SSR-positive ESTs for possible use as potential genic markers. These EST–SSR markers were used to screen 18 sugarc

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Yang, Liming, Yuming Luo, Jifu Wei, Chongmiao Ren, Xin Zhou, and Shaoheng He. "Methods for protein identification using expressed sequence tags and peptide mass fingerprinting for seed crops without complete genome sequences." Seed Science Research 20, no. 4 (2010): 257–62. http://dx.doi.org/10.1017/s0960258510000243.

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AbstractProteomic approaches based on two-dimensional gel electrophoresis, mass spectrometry and database search are widely used to address questions about the development, physiology and quality of seeds. Identification of proteins is of great importance in proteomic analyses. For seed crops without full genome information, cross-species protein identification by mass spectrometry-driven sequence similarity search can be used. However, this approach is risky due to protein polymorphism between different species. Species-specific expressed sequence tag (EST) databases are an invaluable resourc

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Seong, Eun Soo, Ji Hye Yoo, Jae Hoo Choi, et al. "Expressed Sequence Tags Analysis and Design of Simple Sequence Repeats Markers from a Full-Length cDNA Library inPerilla frutescens(L.)." International Journal of Genomics 2015 (2015): 1–7. http://dx.doi.org/10.1155/2015/679548.

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Perilla frutescensis valuable as a medicinal plant as well as a natural medicine and functional food. However, comparative genomics analyses ofP. frutescensare limited due to a lack of gene annotations and characterization. A full-length cDNA library fromP. frutescensleaves was constructed to identify functional gene clusters and probable EST-SSR markers via analysis of 1,056 expressed sequence tags. Unigene assembly was performed using basic local alignment search tool (BLAST) homology searches and annotated Gene Ontology (GO). A total of 18 simple sequence repeats (SSRs) were designed as pri

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Zhang, Yuejin, Yuanyuan Chen, Ruihong Wang, et al. "Development of Microsatellite Markers Derived from Expressed Sequence Tags of Polyporales for Genetic Diversity Analysis of EndangeredPolyporus umbellatus." BioMed Research International 2015 (2015): 1–11. http://dx.doi.org/10.1155/2015/941357.

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A large scale of EST sequences of Polyporales was screened in this investigation in order to identify EST-SSR markers for various applications. The distribution of EST sequences and SSRs in five families of Polyporales was analyzed, respectively. Mononucleotide was the most abundant type, followed by trinucleotide. Among five families, Ganodermataceae occupied the most SSR markers, followed by Coriolaceae. Functional prediction of SSR marker-containing EST sequences inGanoderma lucidumobtained three main groups, namely, cellular component, biological process, and molecular function. Thirty EST

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Severson, D. W., and Y. Zhang. "Generation of expressed sequence tags and sequence-tagged sites as physical landmarks in the mosquito, Aedes aegypti, genome." Genome 39, no. 1 (1996): 224–29. http://dx.doi.org/10.1139/g96-030.

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Twenty-three clones were developed as expressed sequence tags (ESTs) and sequence-tagged sites (STSs) that provide broad coverage of the mosquito, Aedes aegypti, genome at an average spacing of about 7.2 cM. Each of these clones had been mapped previously as a restriction fragment length polymorphism (RFLP) marker. Nineteen of these clones represent anonymous cDNAs and 4 clones represent known genes. Forty-seven percent of the anonymous cDNAs showed significant deduced amino acid sequence similarity to previously described sequences from a wide variety of organisms. STSs developed from RFLPs w

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Ijaz, Siddra, Imran Ul Haq, and Bukhtawer Nasir. "In silico identification of expressed sequence tags based simple sequence repeats (EST-SSRs) markers in Trifolium species." ScienceAsia 46, no. 1 (2020): 6. http://dx.doi.org/10.2306/scienceasia1513-1874.2020.001.

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Qiu, Xuemei, Li Xu, Shaozhen Liu, Xiuli Wang, and Xiangying Meng. "Eleven polymorphic simple sequence repeat markers from expressed sequence tags of Pacific oyster Crassostrea gigas EST database." Conservation Genetics 10, no. 6 (2008): 1773–75. http://dx.doi.org/10.1007/s10592-008-9724-9.

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Hanai, Luiz Ricardo, Tatiana de Campos, Luis Eduardo Aranha Camargo, et al. "Development, characterization, and comparative analysis of polymorphism at common bean SSR loci isolated from genic and genomic sources." Genome 50, no. 3 (2007): 266–77. http://dx.doi.org/10.1139/g07-007.

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Microsatellites or SSRs (single sequence repeats) have been used to construct and integrate genetic maps in crop species, including Phaseolus vulgaris . In the present study, 3 cDNA libraries generated by the Bean EST project ( http://lgm.esalq.usp.br/BEST/ ), comprising a unigene collection of 3126 sequences and a genomic microsatellite-enriched library, were analyzed for the presence of SSRs. A total of 219 expressed sequence tags (ESTs) were found to carry 240 SSRs (named EST-SSR), whereas 714 genomic sequences contained 471 SSRs (named genomic-SSR). A subset of 80 SSRs, 40 EST-SSRs, and 40

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