EST mining for structure and expression of genes in the region of the wheat high-molecular-weight glutenin loci

Genome ◽  
2009 ◽  
Vol 52 (8) ◽  
pp. 726-740 ◽  
Author(s):  
O. D. Anderson
Keyword(s):  
Expressed Sequence Tags ◽  
Genomic Region ◽  
Chromatin Domain ◽  
Gene Sequences ◽  
Orthologous Genes ◽  
Coding Regions ◽  
Expression Of Genes ◽  
Depth Analysis ◽  
Genes Encoding ◽  
Expressed Sequence

An in-depth analysis was carried out with expressed sequence tags (ESTs) for genes in and near the HMW-GS loci. Considerations for using ESTs are discussed, including the occurrence of chimeric and aberrant HMW-GS ESTs. Complete gene sequences demonstrated the feasibility of constructing accurate full-length coding regions from EST assemblies and found, or supported, errors in several previously reported HMW-GS gene sequences. New complete HMW-GS gene sequences are reported for the cultivars Chinese Spring and Glenlea. The Ay subunit gene, which is considered null in cultivated wheats, was shown to transcribe in at least two germplasms. Analyses support the conclusion that of the five known genes within this genomic region, the two HMW-GS genes and the globulin gene are highly expressed. The other two genes, encoding a receptor kinase and a protein kinase, have one and no identifiable wheat EST, respectively, although ESTs are found for the orthologous genes in barley. The ESTs of all five genes within the HMW-GS region are either definitely associated with the endosperm or possibly originate from imbibed seed, suggesting the four distinct gene classes in this region are part of a seed or endosperm chromatin domain. EST resources were also used to determine relative abundance of ESTs for all classes of wheat prolamines and indicated differential levels of expression both among germplasms and among the three genomes of hexaploid wheats.

scholarly journals Suppressed expression of genes involved in transcription and translation in in vitro compared with in vivo cultured bovine embryos

Reproduction ◽  
2006 ◽  
Vol 131 (4) ◽  
pp. 651-660 ◽  
Author(s):  
D Corcoran ◽  
T Fair ◽  
S Park ◽  
D Rizos ◽  
O V Patel ◽  
...  
Keyword(s):  
Expressed Sequence Tags ◽  
Differentially Expressed ◽  
Bovine Embryos ◽  
Quantitative Real Time Pcr ◽  
Expression Of Genes ◽  
Mrna Transcripts ◽  
Induced Changes ◽  
Expressed Sequence

In vivo-derived bovine embryos are of higher quality than those derivedin vitro. Many of the differences in quality can be related to culture environment-induced changes in mRNA abundance. The aim of this study was to identify a range of mRNA transcripts that are differentially expressed between bovine blastocysts derived fromin vitroversusin vivoculture. Microarray (BOTL5) comparison betweenin vivo- andin vitro-cultured bovine blastocysts identified 384 genes and expressed sequence tags (ESTs) that were differentially expressed; 85% of these were down-regulated inin vitrocultured blastocysts, showing a much reduced overall level of mRNA expression inin vitro- compared within vivo-cultured blastocysts. Relative expression of 16 out of 23 (70%) differentially expressed genes (according toPvalue) were verified in new pools ofin vivo- andin vitro-cultured blastocysts, using quantitative real-time PCR. Most (10 out of 16) are involved in transcription and translation events, suggesting that the reason whyin vitro-derived embryos are of inferior quality compared within vivo-derived embryos is due to a deficiency of the machinery associated with transcription and translation.

Isolation of peanut genes encoding arachins and conglutins by expressed sequence tags

Plant Science ◽  
2005 ◽  
Vol 169 (2) ◽  
pp. 439-445 ◽  
Author(s):  
Yong-Sheng Yan ◽  
Xiao-Dong Lin ◽  
Yi-Shun Zhang ◽  
Lei Wang ◽  
Keqiang Wu ◽  
...  
Keyword(s):  
Expressed Sequence Tags ◽  
Genes Encoding ◽  
Expressed Sequence

Analysis of expressed sequence tags of the water flea Daphnia magna

Genome ◽  
2005 ◽  
Vol 48 (4) ◽  
pp. 606-609 ◽  
Author(s):  
Hajime Watanabe ◽  
Norihisa Tatarazako ◽  
Shigeto Oda ◽  
Hiroyo Nishide ◽  
Ikuo Uchiyama ◽  
...  
Keyword(s):  
Daphnia Magna ◽  
Expressed Sequence Tags ◽  
Atp Synthesis ◽  
Amino Acid Sequences ◽  
Cdna Clones ◽  
Sequence Information ◽  
Water Flea ◽  
Expression Of Genes ◽  
Study Gene Expression ◽  
Expressed Sequence

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. The cDNA clones and EST sequence information should be useful for future functional analysis of daphnid biology and investigation of the links between ecology and genomics.Key words: Daphnia magna, EST, classification, ATP synthesis.

scholarly journals The Two TpsB-like Proteins in Anabaena sp. PCC 7120 Are Involved in Secretion of Selected Substrates.

2020 ◽  
Author(s):  
Giang Ngo ◽  
Melis Girbas ◽  
Hannah Schätzle ◽  
Andreas Hammer ◽  
Schara Safarian ◽  
...  
Keyword(s):  
Outer Membrane ◽  
Pathogenic Bacteria ◽  
Carbon Fixation ◽  
Membrane Integrity ◽  
Genomic Region ◽  
Secretion System ◽  
Secretion Systems ◽  
Expression Of Genes ◽  
Genes Encoding ◽  
Pcc 7120

The outer membrane of Gram-negative bacteria acts as an initial diffusion barrier that shields the cell from the environment. It contains many membrane-embedded proteins required for functionality of this system. These proteins serve as solute and lipid transporters or as machines for membrane insertion or secretion of proteins. The genome of Anabaena sp. PCC 7120 codes for two outer membrane transporters termed TpsB1 and TpsB2. Those belong to the family of the two-partner secretion system proteins which are characteristic for pathogenic bacteria. Because pathogenicity of Anabaena sp. PCC 7120 has not been reported, the function of these two cyanobacterial TpsB proteins was analyzed. TpsB1 is encoded by alr1659, while TpsB2 is encoded by all5116. The latter is part of a genomic region containing 11 genes encoding TpsA-like proteins. However, tpsB2 is transcribed independently of a tpsA gene-cluster. Bioinformatics analysis revealed the presence of at least 22 genes in Anabaena sp. PCC 7120 putatively coding for substrates of the TpsB-system suggesting a rather global function of the two TpsB proteins. Insertion of a plasmid into each of the two genes, respectively, resulted in phenotypes of altered outer membrane integrity and antibiotic resistance. In addition, the expression of genes coding for the Clp and Deg proteases is dysregulated in these mutants. Moreover, for two of the putative substrates a dependence of the secretion on functional TpsB proteins could be confirmed. We confirm the existence of a two-partner secretion system in Anabaena sp. PCC 7120 and predict a large pool of putative substrates. IMPORTANCE Cyanobacteria are important organisms for the ecosystem considering their contribution to carbon fixation and oxygen production, while at the same time some species produce compounds that are toxic to their environment. As a consequence, cyanobacteria overpopulation might negatively impact the diversity of natural communities. Thus, a detailed understanding of cyanobacterial interaction with the environment including other organisms is required to define their impact on ecosystems. While two-partner secretion systems are well known from pathogenic bacteria, we provide a first description of the cyanobacterial two-partner secretion system.

Comparative gene-based in silico analysis of transcriptomes in different bovine tissues and (or) organs

Genome ◽  
2004 ◽  
Vol 47 (6) ◽  
pp. 1164-1172 ◽  
Author(s):  
Zhihua Jiang ◽  
Xiao-Lin Wu ◽  
Matthew D Garcia ◽  
Kirsten B Griffin ◽  
Jennifer J Michal ◽  
...  
Keyword(s):  
Expressed Sequence Tags ◽  
In Silico ◽  
Expression Patterns ◽  
In Silico Analysis ◽  
Orthologous Genes ◽  
Functional Relations ◽  
Human Genes ◽  
Expressed Sequence ◽  
Silico Analysis ◽  
Tissue Library

A gene-based approach was used to annotate 322 168 cattle expressed sequence tags (ESTs) based on human genes in order to census the transcriptomes, analyze their expression similarities, and identify genes preferentially expressed in different bovine tissues and (or) organs. Of the 34 157 human coding genes used in a standalone BLAST search, 14 928 could be matched with provisional orthologous sequences in a total of 230 135 bovine ESTs. The remaining 92 033 bovine ESTs were estimated to represent an additional 5970 genes in cattle. On average, ~8600 genes were estimated to be expressed in a single tissue and (or) organ and 13 000 in a pooled tissue library. On the basis of the estimated numbers of genes, no more than 3% of genes would be missed when ~34 000 ESTs were sequenced from a single tissue and (or) organ library and ~40 000 ESTs from a pooled source, respectively. Cluster analyses of the gene expression patterns among 12 single tissues and (or) organs in cattle revealed that their expression similarities would depend on physiological functions. In addition, a total of 1502 genes were identified as preferentially expressed genes in these 12 single tissues and (or) organs with LOD (logarithm of the odds, base 10) ≥ 3.0. Therefore, our study provides some insights for further investigating the developmental and functional relations of various tissues and organs in mammals.Key words: cattle, expressed sequence tags (ESTs), orthologous genes, comparative gene-based approach, in silico census, tissue/organs, transcriptomes.

scholarly journals Genomics of Phytopathogenic Fungi and the Development of Bioinformatic Resources

2002 ◽  
Vol 15 (5) ◽  
pp. 421-427 ◽  
Author(s):  
Darren M. Soanes ◽  
Wendy Skinner ◽  
John Keon ◽  
John Hargreaves ◽  
Nicholas J. Talbot
Keyword(s):  
Relational Database ◽  
Expressed Sequence Tags ◽  
Magnaporthe Grisea ◽  
Mycosphaerella Graminicola ◽  
Phytopathogenic Fungi ◽  
Current Status ◽  
Gene Sequences ◽  
Fungal Genomics ◽  
Est Sequence ◽  
Expressed Sequence

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-use interface allows the user to identify gene sequences by using simple text queries or homology searches. New querying functions and large sequence sets from a variety of phytopathogenic species will be incorporated in due course.

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