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Expressed sequence tags-based identification of genes in the biocontrol agent <Emphasis Type="Italic">Chaetomium cupreum</Emphasis> 总被引:2,自引:0,他引:2
Chaetomium cupreum has a potential as biocontrol agent against a range of plant pathogens on the basis of production of antifungal metabolites,
mycoparasitism, competition for space and nutrients, or various combinations of these. To explore genes expressed in C. cupreum, a cDNA library was constructed from mycelium and 3,066 expressed sequence tags (ESTs) were generated. Clusters analysis
enabled the identification of 1,471 unigenes with 392 contigs and 1,079 singleton sequences. Putative functions were assigned
to 874 unigenes that exhibited strong similarity to genes/ESTs in public databases putatively containing genes involved in
cellular component, molecular function, and biological process. Other 597 ESTs representing novel genes showed no significant
similarity to public database resource of NCBI. A proportion of genes was identified related to degradation of pathogen cell
wall, antifungal metabolite production, as was estimated in the biocontrol fungus. The paper described is a first step towards
the knowledge of the C. cupreum genome. The results present the useful application of EST analysis on C. cupreum and provide a preliminary indication of gene expression putatively involved in biocontrol. 相似文献
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Lee SH Kim BG Kim KJ Lee JS Yun DW Hahn JH Kim GH Lee KH Suh DS Kwon ST Lee CS Yoo YB 《Fungal genetics and biology : FG & B》2002,35(2):115-134
To characterize genes involved in fruit body development, two complementary DNA (cDNA) libraries were constructed from RNA isolated from liquid-cultured mycelia and fruit bodies of Pleurotus ostreatus. Using single-pass sequencing of cDNA clones, 952 and 1069 expressed sequence tags (ESTs) were generated from liquid-cultured mycelia and fruit body cDNA library, respectively. A BLASTX search revealed that 390 of the liquid-cultured mycelia ESTs (41%) and 531 of the fruit body ESTs (50%) showed significant similarity to protein sequences described in the nonredudant database (E values < or =1 x 10(-5)). When liquid-cultured mycelia and fruit body ESTs were compared by the SeqMan II program, among the total of 2021 ESTs, 1256 ESTs were unigenes, and 66 unigenes (5.3%) were commonly expressed during both stages. The functional catalogs of the ESTs were made by comparison with functionally identified Saccharomyces cerevisiae genes. Liquid-cultured mycelium ESTs were compared with fruit body ESTs and changes of the expressed genes during fruit body development were analyzed. 相似文献
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Uribe P Fuentes D Valdés J Shmaryahu A Zúñiga A Holmes D Valenzuela PD 《Marine biotechnology (New York, N.Y.)》2008,10(6):692-700
Dinoflagellates of the genus Alexandrium are photosynthetic microalgae that have an extreme importance due to the impact of some toxic species on shellfish aquaculture
industry. Alexandrium catenella is the species responsible for the production of paralytic shellfish poisoning in Chile and other geographical areas. We
have constructed a cDNA library from midexponential cells of A. catenella grown in culture free of associated bacteria and sequenced 10,850 expressed sequence tags (ESTs) that were assembled into
1,021 contigs and 5,475 singletons for a total of 6,496 unigenes. Approximately 41.6% of the unigenes showed similarity to
genes with predicted function. A significant number of unigenes showed similarity with genes from other dinoflagellates, plants,
and other protists. Among the identified genes, the most expressed correspond to those coding for proteins of luminescence,
carbohydrate metabolism, and photosynthesis. The sequences of 9,847 ESTs have been deposited in Gene Bank (accession numbers
EX 454357–464203). 相似文献
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Xiangying Meng Yaqing Chang Xuemei Qiu Xiuli Wang 《Comparative biochemistry and physiology. Part D, Genomics & proteomics》2010,5(4):288-294
A normalized cDNA library was constructed from the adductor muscle of M. yessoensis and acquired 4595 high quality expressed sequence tags (ESTs). After clustering and assembly of the ESTs, 3061 unigenes containing 654 contigs and 2407 singletons were identified. The contig length ranged from 266 bp to 2364 bp and the average length of these contigs was 544 bp. Blastx nonredundant protein database analysis showed that 1522 unigenes had significant homology to known genes (E value ≤ 10? 5). By comparing to Clusters of Orthologous Groups (COG) categories, 460 unigenes were annotated (E value ≤ 10? 10). Using Kyoto Encyclopedia of Genes and Genomes (KEGG), 345 of 3061 unigenes were assigned into 103 pathways (E value ≤ 10? 5). For InterProScan searches, 1237 unigenes were annotated containing 727 different types of protein domains. 941 of the 1237 unigenes were annotated for Gene Ontology (GO) classification using Uniprot2GO associations in any category (biological, cellular, and molecular). By sequences comparability and analysis of Blastx NCBI nonredundant protein database and KEGG, 66 unigenes were identified that may be involved in genetic information processing based on the known knowledge. The study provides a material basis as useful information for the genomic analysis of shellfish. 相似文献
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Wang XC Guo L Shangguan LF Wang C Yang G Qu SC Fang JG 《Molecular biology reports》2012,39(6):6825-6834
A total of 6,230 EST sequences were produced from 7,561 clones in a cDNA library generated from grapevine (Vitis vinifera cv. ‘Summer Black’) flower and fruit tissues in this study. After cluster and assembly analysis of the datasets, 3,582 unigenes
(GenBank accession numbers GW836604–GW840185) were established, among which 381 were new grapevine EST sequences. Out of the
381 new ESTs, 289 could be mapped on the 19 grapevine chromosomes. 913 unique ESTs with known or putative functions were assigned
to 11 putative cellular roles. 540 potentially workable grapevine EST-SSRs were developed from 3,582 unigenes and about 42.6%
of these unigenes were identified as true-to-type SSR loci and could amplify polymorphic bands from 22 individual plants of
V. vinifera L, indicating that grapevine EST datasets are a valuable source for the development of functional simple sequence repeat
(SSR) markers. 相似文献
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Chinese sturgeon Acipenser sinensis belongs to the family Acipenseridae, an ancient species of actinopterygian fishes. In order to advance molecular research on its reproduction, ontogenetic development, we were seeking for genomic information in the NCBI expressed sequence tag (EST database). We found 3384 indentified cDNA sequences which were assembled into 861 unigenes. Blast analysis revealed 301 unigenes shared high similarity with genes in the public databases, and these were classified into three groups: 202 known genes, 81 putative genes and 8 unknown genes. The remainder (560 genes) had no significant match to any protein sequence. Further, 255 unigenes and 333 unmatched unigenes were annotated with Gene Ontology (GO), which could be classified into cellular component, molecular function, and biological process. Among the known genes, the hormone genes pomc A (proopiomelanocortin), pomc B, GtH alpha I subunit (gonadotropin hormone), GtH alpha II subunit and GH (growth hormone) were present in this library. Comparison of the Chinese sturgeon proteins (GH, GtH alpha subunit and POMC) to proteins of other species showed higher levels of homology among sturgeon species. We performed five hormone related genes including GnRHRI (gonadotropin-releasing hormone receptor I), cpH (carboxypeptidase H), ppiB (peptidylprolyl isomerase B), stmn3 (stathmin-like 3), 7B2 (neuroendocrine protein 7B2), and four novel genes (contig 192, 177, 170 and 168) a semi-quantitative RT-PCR on different tissues from Chinese sturgeon. 相似文献
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Nakagawa T Nakatsuka A Yano K Yasugahira S Nakamura R Sun N Itai A Suzuki T Itamura H 《Plant cell reports》2008,27(5):931-938
Persimmon (Diospyros kaki Thunb.) is an important fruit in Asian countries, where it is eaten as a fresh fruit and is also used for many other purposes.
To understand the molecular mechanism of fruit development and ripening in persimmon, we generated a total of 9,952 expressed
sequence tags (ESTs) from randomly selected clones of two different cDNA libraries. One cDNA library was derived from fruit
of “Saijo” persimmon at an early stage of development, and the other from ripening fruit. These ESTs were clustered into 6,700
non-redundant sequences. Of the 6,700 non-redundant sequences evaluated, the deduced amino acid sequences of 4,356 (65%) showed
significant homology to known proteins, and 2,344 (35%) showed no significant similarity to any known proteins in Arabidopsis databases. We report comparison of genes identified in the two cDNA libraries and describe some putative genes involved in
proanthocyanidin and carotenoid synthesis. This study provides the first global overview of a set of genes that are expressed
during fruit development and ripening in persimmon. 相似文献
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Characterization of soybean genomic features by analysis of its expressed sequence tags 总被引:10,自引:0,他引:10
Tian AG Wang J Cui P Han YJ Xu H Cong LJ Huang XG Wang XL Jiao YZ Wang BJ Wang YJ Zhang JS Chen SY 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2004,108(5):903-913
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Sha AH Li C Yan XH Shan ZH Zhou XA Jiang ML Mao H Chen B Wan X Wei WH 《Molecular biology reports》2012,39(3):2867-2874
Although GenBank has now covered over 1,400,000 expressed sequence tags (ESTs) from soybean, most ESTs available to the public
have been derived from tissues or environmental conditions rather than developing seeds. It is absolutely necessary for annotating
the molecular mechanisms of soybean seed development to analyze completely the gene expression profiles of its immature seed
at various stages. Here we have constructed a full-length-enriched cDNA library comprised of a total of 45,408 cDNA clones
which cover various stages of soybean seed development. Furthermore, we have sequenced from 5′ ends of these clones, 36,656
ESTs were obtained in the present study. These EST sequences could be categorized into 27,982 unigenes, including 22,867 contigs
and 5,115 singletons, among which 27,931 could be mapped onto soybean 20 chromosome sequences. Comparative genomic analysis
with other plants has revealed that these unigenes include lots of candidate genes specific to dicot, legume and soybean.
Approximately 1,789 of these unigenes currently show no homology to known soybean sequences, suggesting that many represent
mRNAs specifically expressed in seeds. Novel abundant genes involved in the oil synthesis have been found in this study, may
serve as a valuable resource for soybean seed improvement. 相似文献