Expressed Sequence Tags: Normalization and Subtraction of cDNA Libraries Expressed sequence tags normalization and subtraction of cDNA libraries

To further increase our understanding of responses in potato to abiotic stress and the potato transcriptome in general, we generated 20 756 expressed sequence tags (ESTs) from a cDNA library constructed by pooling mRNA from heat-, cold-, salt-, and drought-stressed potato leaves and roots. These ESTs were clustered and assembled into a collection of 5240 unique sequences with 3344 contigs and 1896 singleton ESTs. Assignment of gene ontology terms (GOSlim/Plant) to the sequences revealed that 8101 assignments could be made with a total of 3863 molecular function assignments. Alignment to a set of 78 825 ESTs from other potato cDNA libraries derived from root, leaf, stolon, tuber, germinating eye, and callus tissues revealed 1476 sequences unique to abiotic stressed potato leaf and root tissue. Sequences present within the 5240 sequence set had similarity to genes known to be involved in abiotic stress responses in other plant species such as transcription factors, stress response genes, and signal transduction processes. In addition, we identified a number of genes unique to the abiotic stress library with unknown function, providing new candidate genes for investigation of abiotic stress responses in potato.Key words: potato, Solanacaeae, abiotic stress.

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

Australian Journal of Experimental Agriculture ◽

10.1071/ea03238 ◽

2004 ◽

Vol 44 (11) ◽

pp. 1127 ◽

Cited By ~ 33

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.

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Expressed sequence tags from normalized cDNA libraries prepared from gill and hypodermal tissues of the blue crab, Callinectes sapidus

Comparative Biochemistry and Physiology Part D Genomics and Proteomics ◽

10.1016/j.cbd.2005.10.004 ◽

2006 ◽

Vol 1 (2) ◽

pp. 200-208 ◽

Cited By ~ 8

Author(s):

Francie E. Coblentz ◽

David W. Towle ◽

Thomas H. Shafer

Keyword(s):

Blue Crab ◽

Expressed Sequence Tags ◽

Callinectes Sapidus ◽

Cdna Libraries ◽

Expressed Sequence

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EST Analysis for the Study of Cold Stress in Blueberry (Vaccinium spp.)

HortScience ◽

10.21273/hortsci.39.4.861d ◽

2004 ◽

Vol 39 (4) ◽

pp. 861D-862

Author(s):

Anik L. Dhanaraj* ◽

Janet P. Slovin ◽

Lisa J. Rowland

Keyword(s):

Cold Stress ◽

Expressed Sequence Tags ◽

The Other ◽

Cdna Libraries ◽

Functional Categories ◽

High Quality ◽

Est Analysis ◽

Woody Perennial ◽

Winter Conditions ◽

Expressed Sequence

To gain a better understanding of changes in gene expression associated with cold stress in the woody perennial blueberry (Vaccinium spp.), a genomics approach based on the analysis of expressed sequence tags (ESTs) was undertaken. Two cDNA libraries were constructed using RNA from cold acclimated (mid winter conditions when the plants are cold stressed) and non-acclimated (before they received any chilling) floral buds of the blueberry cultivar Bluecrop. About 600 5'-end ESTs were generated from each of the libraries. Putative functions were assigned to 57% of the cDNAs that yielded high quality sequences based on homology to other genes/ESTs from Genbank, and these were classified into 14 functional categories. From a contig analysis, which clustered sequences derived from the same or very similar genes, 430 and 483 unique transcripts were identified from the cold acclimated and non-acclimated libraries, respectively. Of the total unique transcripts, only 4.3% were shared between the libraries, suggesting marked differences in the genes expressed under the two conditions. The most highly abundant cDNAs that were picked many more times from one library than from the other were identified as representing potentially differentially expressed transcripts. Northern analyses were performed to examine expression of eight selected transcripts and seven of these were confirmed to be preferentially expressed under either cold acclimating or non-acclimating conditions. Only one of the seven transcripts, encoding a dehydrin, had been found previously to be up-regulated during cold stress of blueberry. This study demonstrates that analysis of ESTs is an effective strategy to identify candidate cold-responsive transcripts in blueberry.

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