Sequencing of cDNA clones and analysis of the expressed sequence tags (ESTs) of tea plant [Camellia sinensis (L.) O. Kuntze] young shoots

2005 ◽  
Vol 2 (2) ◽  
pp. 137-141
Author(s):  
Zhao Li-Ping ◽  
Gao Qi-Kang ◽  
Chen Liang
Keyword(s):  
Cdna Library ◽  
Camellia Sinensis ◽  
Expressed Sequence Tags ◽  
Tea Plant ◽  
Cdna Libraries ◽  
Functional Genes ◽  
Cdna Clones ◽  
Est Sequencing ◽  
Plant Ests ◽  
Expressed Sequence

AbstractThe construction of two cDNA libraries from young shoots of tea plant [Camellia sinensis cv. Longjing 43 and Anji Baicha], the sequencing of Longjing 43 cDNA clones and the analysis of expressed sequence tags (ESTs) are reported. Totally, 4320 clones from the cDNA library of Longjing 43 were sequenced, and 2963 useful sequences were obtained, corresponding to 68.6% of clones. A total of 416 clones shorter than 150 bp and 863 repeated clones were excluded, the first 1684 valid tea plant ESTs were generated. Most of the ESTs were between 300 and 700 bp, with an average of 478 bp. Six hundred and seven ESTs with known function or putative function were identified by BlastN searches against the National Center of Biotechnology Institute (NCBI) non-redundant nucleotide databases, corresponding to more than 130 functional genes in the tea plant. The rest, 1077 ESTs, were novel gene partial or full sequences. The results indicated that EST sequencing was a rapid and effective approach to identification of novel functional genes for tea plant.

Construction of cDNA library and preliminary analysis of expressed sequence tags from tea plant [Camellia sinensis (L) O. Kuntze]

Gene ◽  
2012 ◽  
Vol 506 (1) ◽  
pp. 202-206 ◽  
Author(s):  
Munmi Phukon ◽  
Richa Namdev ◽  
Diganta Deka ◽  
Mahendra K. Modi ◽  
Priyabrata Sen
Keyword(s):  
Cdna Library ◽  
Camellia Sinensis ◽  
Expressed Sequence Tags ◽  
Preliminary Analysis ◽  
Tea Plant ◽  
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 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.

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.

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