scholarly journals The sugarcane signal transduction (SUCAST) catalogue: prospecting signal transduction in sugarcane

2001 ◽  
Vol 24 (1-4) ◽  
pp. 25-34 ◽  
Author(s):  
Glaucia Mendes Souza ◽  
Ana Carolina Quirino Simoes ◽  
Katia Cristina Oliveira ◽  
Humberto Miguel Garay ◽  
Leonardo Costa Fiorini ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Expressed Sequence Tags ◽  
Tissue Specificity ◽  
Expressed Sequence Tag ◽  
Large Family ◽  
Small Gtpases ◽  
Response Regulators ◽  
New Genes ◽  
Est Sequencing ◽  
Expressed Sequence

EST sequencing has enabled the discovery of many new genes in a vast array of organisms, and the utility of this approach to the scientific community is greatly increased by the establishment of fully annotated databases. The present study aimed to identify sugarcane ESTs sequenced in the sugarcane expressed sequence tag (SUCEST) project (<A HREF="http://sucest.lad.ic.unicamp.br/">http://sucest.lad.ic.unicamp.br</A>) that corresponded to signal transduction components. We also produced a sugarcane signal transduction (SUCAST) catalogue (<A HREF="http://sucest.lad.ic.unicamp.br/private/mining-reports/QG/QG-mining.htm">http://sucest.lad.ic.unicamp.br/private/mining-reports/QG/QG-mining.htm</A>) that covered the main categories and pathways. Expressed sequence tags (ESTs) encoding enzymes for hormone (gibberellins, ethylene, auxins, abscisic acid and jasmonic acid) biosynthetic pathways were found and tissue specificity was inferred from their relative frequency of occurrence in the different libraries. Whenever possible, transducers of hormones and plant peptide signaling were catalogued to the respective pathway. Over 100 receptors were found in sugarcane, which contains a large family of Ser/Thr kinase receptors and also photoreceptors, histidine kinase receptors and their response regulators. G-protein and small GTPases were analyzed and compared to known members of these families found in mammalian and plant systems. Major kinase and phosphatase pathways were mapped, with special attention being given to the MAP kinase and the inositol pathway, both of which are well known in plants.

Survey in the sugarcane expressed sequence tag database (SUCEST) for simple sequence repeats

Genome ◽  
2004 ◽  
Vol 47 (5) ◽  
pp. 795-804 ◽  
Author(s):  
Luciana Rossini Pinto ◽  
Karine Miranda Oliveira ◽  
Eugênio César Ulian ◽  
Antonio Augusto Franco Garcia ◽  
Anete Pereira de Souza
Keyword(s):  
Simple Sequence Repeats ◽  
Expressed Sequence Tags ◽  
Expressed Sequence Tag ◽  
Leaf Roll ◽  
Cdna Libraries ◽  
Genomic Libraries ◽  
Est Sequencing ◽  
Tetranucleotide Repeats ◽  
Expressed Sequence ◽  
Simple Sequence

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 EST sequencing, SSRs were more frequent in the ones derived from leaf roll (LR). Twenty-three out of 30 tested SSRs produced scorable polymorphisms in 18 sugarcane commercial clones. These EST-SSRs showed a moderate level of polymorphism with some SSRs producing unique fingerprints. The number of alleles observed among the 18 clones evaluated varied from 2 to 15, with an average of 6.04 alleles/locus. The polymorphism information content (PIC) values ranged from 0.28 to 0.90 with a mean of 0.66. The EST-SSRs screened over both parents (SP 80-180; SP 80-4966) and 6 F1 individuals produced 52 segregating markers that could potentially be used for sugarcane mapping. The EST-SSRs were found in clusters that had significant homology to proteins involved in important metabolic pathways such as sugar biosynthesis, proving that EST-SSRs are a valuable tool for the construction of a functional sugarcane map.Key words: sugarcane, polyploid, expressed sequence tags (ESTs), microsatellites (SSRs), genetic mapping.

Tc8, a Tourist-like Transposon in Caenorhabditis elegans

Genetics ◽  
2001 ◽  
Vol 158 (3) ◽  
pp. 1081-1088 ◽  
Author(s):  
Quang Hien Le ◽  
Kime Turcotte ◽  
Thomas Bureau
Keyword(s):  
Caenorhabditis Elegans ◽  
Expressed Sequence Tags ◽  
Large Family ◽  
Insertion Sequences ◽  
Normal Plant ◽  
Nematode Caenorhabditis Elegans ◽  
Plant Genomes ◽  
Plant Genes ◽  
Expressed Sequence ◽  
Eukaryotic Genomes

Abstract Members of the Tourist family of miniature inverted-repeat transposable elements (MITEs) are very abundant among a wide variety of plants, are frequently found associated with normal plant genes, and thus are thought to be important players in the organization and evolution of plant genomes. In Arabidopsis, the recent discovery of a Tourist member harboring a putative transposase has shed new light on the mobility and evolution of MITEs. Here, we analyze a family of Tourist transposons endogenous to the genome of the nematode Caenorhabditis elegans (Bristol N2). One member of this large family is 7568 bp in length, harbors an ORF similar to the putative Tourist transposase from Arabidopsis, and is related to the IS5 family of bacterial insertion sequences (IS). Using database searches, we found expressed sequence tags (ESTs) similar to the putative Tourist transposases in plants, insects, and vertebrates. Taken together, our data suggest that Tourist-like and IS5-like transposons form a superfamily of potentially active elements ubiquitous to prokaryotic and eukaryotic genomes.

Survey of a cDNA library from the turkey (Meleagris gallopavo)

Genome ◽  
2005 ◽  
Vol 48 (1) ◽  
pp. 12-17 ◽  
Author(s):  
L D Chaves ◽  
J A Rowe ◽  
K M Reed
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Expressed Sequence Tags ◽  
Expressed Sequence Tag ◽  
Meleagris Gallopavo ◽  
Whole Genome Sequence ◽  
Snp Discovery ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Important Species ◽  
Expressed Sequence

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 singletons. The majority of significant comparative matches occurred between the turkey sequences and sequences reported from the chicken. Whole genome sequence from the chicken was used to identify potential exon–intron boundaries for selected turkey clones and intron-amplifying primers were developed for sequence analysis and single nucleotide polymorphism (SNP) discovery. Identified SNPs were genotyped for linkage analysis on two turkey reference populations. This study significantly increases the number of EST sequences available for the turkey.Key words: turkey, cDNA, expressed sequence tag, single nucleotide polymorphism.

Expressed sequence tag analysis and cDNA array establishment of Nicotiana tabacum: application to salinity stress

2009 ◽  
Vol 6 (1) ◽  
pp. 81-89 ◽  
Author(s):  
Li Wen-Zheng ◽  
Song Li-Min ◽  
Li Yong-Ping ◽  
Lu Xiu-Ping ◽  
Luo Hong-Mei ◽  
...  
Keyword(s):  
Nicotiana Tabacum ◽  
Expressed Sequence Tags ◽  
Expressed Sequence Tag ◽  
Cdna Array ◽  
Biological Response ◽  
Mrna Splicing ◽  
Saline Stress ◽  
Plasma Membrane Intrinsic Protein ◽  
Expressed Sequence Tag Analysis ◽  
Expressed Sequence

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 were identified, including plasma membrane intrinsic protein 2a, ethylene-responsive proteinase and pre-mRNA splicing factor prp31 gene, suggesting that there was a complicated biological response in N. tabacum under saline stress.

scholarly journals Analysis of Genes Expressed at the Infective Larval Stage Validates Utility of Litomosoides sigmodontis as a Murine Model for Filarial Vaccine Development

2000 ◽  
Vol 68 (9) ◽  
pp. 5454-5458 ◽  
Author(s):  
Judith E. Allen ◽  
Jennifer Daub ◽  
David Guiliano ◽  
Amanda McDonnell ◽  
Michelle Lizotte-Waniewski ◽  
...  
Keyword(s):  
Murine Model ◽  
Larval Stage ◽  
Vaccine Development ◽  
Expressed Sequence Tag ◽  
Filarial Infection ◽  
Vaccine Candidates ◽  
Infective Larvae ◽  
New Genes ◽  
Litomosoides Sigmodontis ◽  
Expressed Sequence

ABSTRACT We used an expressed sequence tag approach to analyze genes expressed by the infective larvae of the rodent filarial parasiteLitomosoides sigmodontis. One hundred fifty two new genes were identified, including several proposed as vaccine candidates in studies with human filarial parasites. Our findings have important implications for the use of L. sigmodontis as a model for filarial infection.

scholarly journals Trimming and clustering sugarcane ESTs

2001 ◽  
Vol 24 (1-4) ◽  
pp. 17-23 ◽  
Author(s):  
Guilherme P. Telles ◽  
Felipe R. da Silva
Keyword(s):  
Expressed Sequence Tags ◽  
Expressed Sequence Tag ◽  
Expressed Sequence

The original clustering procedure adopted in the Sugarcane Expressed Sequence Tag project (SUCEST) had many problems, for instance too many clusters, the presence of ribosomal sequences, etc. We therefore redesigned the clustering procedure entirely, including a much more careful initial trimming of the reads. In this paper the new trimming and clustering strategies are described in detail and we give the new official figures for the project, 237,954 expressed sequence tags and 43,141 clusters.

scholarly journals Identification of 14-3-3-like protein in sugarcane (Saccharum officinarum)

2001 ◽  
Vol 24 (1-4) ◽  
pp. 43-48 ◽  
Author(s):  
Eiko Eurya Kuramae ◽  
Roseli Chela Fenille ◽  
Vicente Eugenio de Rosa Jr.
Keyword(s):  
Expressed Sequence Tags ◽  
Expressed Sequence Tag ◽  
Saccharum Officinarum ◽  
Full Length ◽  
Encoded Proteins ◽  
Expressed Sequence

In a search of the sugarcane expressed sequence tag (SUCEST) database we located three full-length cDNAs (SCCCLR1022D05.g, SCCCRZ1001D02.g and SCBFLR1026E02.g) encoding the 14-3-3 proteins from sugarcane (Saccharum officinarum). The encoded proteins were identified based on the clustering of the expressed sequence tags and were shown to encode proteins similar to 14-3-3 proteins of other monocotyledonous plants. Cluster SCCCLR1022D05.g was 99% similar to the maize 14-3-3-like protein (gi|1345587) while cluster SCCCRZ1001D02.g shared 96% and SCBFLR1026E02.g 94% similarity with the 14-3-3 protein of rice (gi|7435022). Although 14-3-3 proteins have been reported to be specific to particular species, tissue or organ from which they were isolated, all three sugarcane clusters were found to be expressed in several tissues.

scholarly journals The Surface of Toxoplasma Tachyzoites Is Dominated by a Family of Glycosylphosphatidylinositol-Anchored Antigens Related to SAG1

1998 ◽  
Vol 66 (5) ◽  
pp. 2237-2244 ◽  
Author(s):  
Ian D. Manger ◽  
Adrian B. Hehl ◽  
John C. Boothroyd
Keyword(s):  
Common Ancestor ◽  
Expressed Sequence Tag ◽  
Host Cells ◽  
Complex Life Cycle ◽  
Est Database ◽  
Related Sequence ◽  
New Genes ◽  
Selection For ◽  
Major Surface ◽  
Expressed Sequence

ABSTRACT Toxoplasma gondii is an Apicomplexan parasite with a complex life cycle that includes a rapidly dividing asexual stage known as the tachyzoite. The tachyzoite surface has been reported to comprise five major antigens, the most abundant of which is designated SAG1 (for surface antigen 1). At least one of the other four (SAG3) and another recently described minor antigen (SRS1 [for SAG1-related sequence 1]) have previously been shown to be structurally related to SAG1. To determine if further SAG1 homologs exist, we searched aToxoplasma expressed sequence tag (EST) database and found numerous ESTs corresponding to at least three new genes related toSAG1. Like SAG1, these new SRSgenes encode apparently glycosylphosphatidylinositol-anchored proteins that share several motifs and a set of conserved cysteine residues. This family appears to have arisen by divergence from a common ancestor under selection for the conservation of overall topology. The products of two of these new genes (SRS2 and SRS3) are shown to be expressed on the surface of Toxoplasmatachyzoites by immunofluorescence. We also identified strain-specific differences in relative expression levels. A total of 10 members of theSAG1 gene family have now been identified, which apparently include three of the five major surface antigens previously described and one antigen expressed only in bradyzoites. The function of this family may be to provide a redundant system of receptors for interaction with host cells and/or to direct the immune responses that limit acute T. gondii infections.

Sign in / Sign up

Export Citation Format

Share Document