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 Construction of a cDNA Library of Vitis pseudoreticulata Native to China Inoculated with Uncinula necator and the Analysis of Potential Defense-related Expressed Sequence Tags

HortScience ◽  
2006 ◽  
Vol 41 (4) ◽  
pp. 993C-993
Author(s):  
Yan Xu ◽  
Yuejin Wang
Keyword(s):  
Cdna Library ◽  
Plant Species ◽  
Expressed Sequence Tags ◽  
Cdna Clones ◽  
Sequence Information ◽  
Uncinula Necator ◽  
The Public ◽  
Perennial Plant ◽  
Vitis Pseudoreticulata ◽  
Expressed Sequence

Expressed sequence tags (ESTs) constitute a rapid and informative strategy for studying gene-expression profiles of specific stages of annual and perennial plant species. Compared with annual plants, the NCBI database has very little sequence information from perennial plant species. To date, only ∼145 ESTs of Vitis pseudoreticulata W.T. Wang have been deposited in databases. This is insufficient to understand the biology and development of this species. In this report, a cDNA library constructed from young leaf inoculated with powdery mildew pathogen [Uncinula necator (Schw.) Burr.] of Chinese wild Vitis pseudoreticulata. Leaf was harvested at various times after inoculation for total RNA extraction, which was used to generate ESTs. In our study, 107 cDNA clones were sequenced either from 5' or 3' end of the cDNAs. Among them, 60 unigenes (56%) were functionally characterized by the BLASTX matches to known function proteins, and 20 unigenes (18.6 %) matched significantly with those having unknown function in the public databases. The remaining 27 unigenes (25.2%) failed to show significant homology to any proteins in the public databases, suggesting that they represent novel sequences. Some functional genes identified from the cDNA library to be potentially associated with plant defence-related responses are discussed.

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.

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.

Analysis and comparison of a set of expressed sequence tags of the parthenogenetic water flea Daphnia carinata

2009 ◽  
Vol 282 (2) ◽  
pp. 197-203 ◽  
Author(s):  
Xiaoqian Xu ◽  
Shuhui Song ◽  
Qun Wang ◽  
Fen Qin ◽  
Kan Liu ◽  
...  
Keyword(s):  
Expressed Sequence Tags ◽  
Water Flea ◽  
Daphnia Carinata ◽  
Expressed Sequence

Development and application of a bovine cDNA microarray for expression profiling of muscle and adipose tissue

2004 ◽  
Vol 44 (11) ◽  
pp. 1127 ◽  
Author(s):  
S. A. Lehnert ◽  
Y. H. Wang ◽  
K. A. Byrne
Keyword(s):  
Expressed Sequence Tags ◽  
Expression Profiling ◽  
Protein Turnover ◽  
Animal Experiments ◽  
Cdna Libraries ◽  
Cdna Clones ◽  
Beef Quality ◽  
New Knowledge ◽  
New Evidence ◽  
Expressed Sequence

In order to gain new knowledge of the genetic control of biochemical and developmental processes that contribute to beef quality, we constructed a bovine microarray of 9600 elements comprising about 2000 expressed sequence tags (ESTs) and 7300 anonymous cDNA clones from muscle and fat-derived cDNA libraries. The microarray was used in 2 animal experiments aimed at uncovering gene expression differences associated with adipogenesis and protein turnover. The results obtained so far show that expression profiling of bovine muscle using the microarray can reliably identify differentially expressed genes and confirm existing hypotheses. Moreover, the technique can provide new evidence on the detailed involvement of well-characterised genes and can identify genes that have not previously been described as having a role in these processes.

scholarly journals Sequences of Probes Revealing Mapped Restriction Fragment-length Polymorphisms in Cucumber

HortScience ◽  
2005 ◽  
Vol 40 (2) ◽  
pp. 323-324
Author(s):  
Michael J. Havey
Keyword(s):  
Restriction Fragment ◽  
Fragment Length ◽  
Expressed Sequence Tags ◽  
Restriction Fragment Length Polymorphisms ◽  
Cdna Clones ◽  
Chromosome 4 ◽  
Sequence Comparisons ◽  
Length Polymorphisms ◽  
Expressed Sequence ◽  
Restriction Fragment Length

PstI-genomic and cDNA clones revealing mapped restriction fragment-length polymorphisms (RFLP) in cucumber (Cucumis sativus L.) were sequenced in order to ensure that these clones remain available and to determine if any clones showing genetic linkage in cucumber are physically linked in Arabidopsis thaliana. Sequence comparisons using translated searches revealed that 80% of the cucumber cDNA clones showed significant (≤e-20) similarities to Arabidopsis expressed sequence tags (ESTs) or genomic sequences, as opposed to relatively few (32%) of the cucumber genomic clones. Two clones revealing RFLPs linked at 2 cM in cucumber showed significant (≤e-20) similarities to sequences separated by 347,616 basepairs on chromosome 4 of Arabidopsis.

scholarly journals Expressed Sequence Tags (ESTs) from a Jute (Corchorus olitorius) cDNA Library

1970 ◽  
Vol 16 (2) ◽  
pp. 95-104 ◽  
Author(s):  
J Matthew Taliaferro ◽  
Ahmad S Islam ◽  
Kanagasabapathi Sathasivan
Keyword(s):  
Arabidopsis Thaliana ◽  
Cdna Library ◽  
Expressed Sequence Tags ◽  
Higher Plants ◽  
Open Reading Frame ◽  
Sequence Information ◽  
Corchorus Olitorius ◽  
Reading Frame ◽  
Partial Cdna ◽  
Expressed Sequence

Analysis of the genome of jute (Corchorus olitorius) was done by creating a new cDNA library of expressed sequence tags (ESTs) in pBluescript as the previous libraries reported earlier in this journal yielded only small DNA fragments from chloroplast and mitochondrial DNA. This report discusses results from a cDNA library constructed using poly A+ mRNA purified from 7-day old etiolated jute seedlings. Out of 700 recombinant plasmids obtained, 250 were analyzed using WU-BLAST (www.arabidopsis.org) for similar EST sequences in Arabidopsis thaliana and other higher plants. So far the analysis of the library has yielded several significant sequences, including the complete open reading frame of the 60S acidic ribosomal protein P3 and a partial cDNA of Class I chitinase. These results and future EST sequences from this library will be made available in Genbank and the sequence information will be used to clone full length DNA through PCR.  DOI = 10.3329/ptcb.v16i2.1110Plant Tissue Cult. & Biotech. 16(2): 95-104, 2006 (December)

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