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Gene expression during Ustilago maydis diploid filamentous growth: EST library creation and analyses
Ustilago maydis is an important model system for the plant pathogenic smut and rust fungi. Critical to the continued development of this model is establishing genomic resources. We have constructed a cDNA library from a forced diploid culture of U. maydis growing as filaments and have generated 7455 ESTs that are assembled into 3074 contiguous sequences. This represents as much as 46% of the coding capacity predicted for U. maydis. BLAST searches with a similarity cutoff of E = 10(-5), allow us to annotate 59% of the contigs based upon matches in the NCBI nr and dbEST databases. These annotated sequences provide information on mature mRNAs that will aid with gene prediction in the U. maydis genome sequence. Functional categorization and comparative analyses of the sequences provides gene identities, expression information and a solid base for future research in this model fungal pathogen. 相似文献
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Fusarium culmorum is one of the most common and globally important causal agent of root and crown rot diseases of cereals. These
diseases cause grain yield loss and reduced grain quality in barley. In this study, we have analyzed an expressed sequence tag
(EST) database derived from F. culmorum infected barley root tissues available at the National Center for Biotechnology
Information (NCBI). The 2294 sequences were assembled into 1619 non-redundant sequences consisting of 359 contigs and 1260
singletons using the program CAP3. BLASTX analysis for these sequences was conducted in order to find similar sequences in all
databases. Gene Ontology search, enzyme search, KEGG mapping and InterProScan search were done using Blast2GO 3.0.7 tool.
By BLASTX analysis, 41.7%, 7.7%, 3.2% and 47.4% of ESTs were categorized as annotated, unannotated, not mapping and without
blast hits, respectively. BLASTX analysis revealed that the majority of top hits were barley proteins (43.5%). Based on Gene
Ontology classification, 38.3%, 31.3%, and 16% of ESTs were assigned to molecular function, biological process, and cellular
component GO terms, respectively. Most abundant GO terms were as follows: 157 sequences were related to response to stress
(biological process), 207 sequences were related to ion binding (molecular function), and 160 sequences were related to plastid
(cellular component). Furthermore, based on KEGG mapping, 369 sequences could be assigned to 264 enzymes and 83 different
KEGG pathways. According to Enzyme Commission (EC) distribution; 94 sequences were transferases (EC2) while 70 sequences
were hydrolases (EC3). 相似文献
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Zea mays DataBase (ZmDB) seeks to provide a comprehensive view of maize (corn) genetics by linking genomic sequence data with gene expression analysis and phenotypes of mutant plants. ZmDB originated in 1999 as the Web portal for a large project of maize gene discovery, sequencing and phenotypic analysis using a transposon tagging strategy and expressed sequence tag (EST) sequencing. Recently, ZmDB has broadened its scope to include all public maize ESTs, genome survey sequences (GSSs), and protein sequences. More than 170 000 ESTs are currently clustered into approximately 20 000 contigs and about an equal number of apparent singlets. These clusters are continuously updated and annotated with respect to potential encoded protein products. More than 100 000 GSSs are similarly assembled and annotated by spliced alignment with EST and protein sequences. The ZmDB interface provides quick access to analytical tools for further sequence analysis. Every sequence record is linked to several display options and similarity search tools, including services for multiple sequence alignment, protein domain determination and spliced alignment. Furthermore, ZmDB provides web-based ordering of materials generated in the project, including ESTs, ordered collections of genomic sequences tagged with the RescueMu transposon and microarrays of amplified ESTs. ZmDB can be accessed at http://zmdb.iastate.edu/. 相似文献
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Large-scale statistical analysis of secondary xylem ESTs in pine 总被引:3,自引:0,他引:3
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Peter Wenzl Haobing Li Jason Carling Meixue Zhou Harsh Raman Edie Paul Phillippa Hearnden Christina Maier Ling Xia Vanessa Caig Jaroslava Ovesná Mehmet Cakir David Poulsen Junping Wang Rosy Raman Kevin P Smith Gary J Muehlbauer Ken J Chalmers Andris Kleinhofs Eric Huttner Andrzej Kilian 《BMC genomics》2006,7(1):1-22
Background
Wheat is an excellent species to study freezing tolerance and other abiotic stresses. However, the sequence of the wheat genome has not been completely characterized due to its complexity and large size. To circumvent this obstacle and identify genes involved in cold acclimation and associated stresses, a large scale EST sequencing approach was undertaken by the Functional Genomics of Abiotic Stress (FGAS) project.Results
We generated 73,521 quality-filtered ESTs from eleven cDNA libraries constructed from wheat plants exposed to various abiotic stresses and at different developmental stages. In addition, 196,041 ESTs for which tracefiles were available from the National Science Foundation wheat EST sequencing program and DuPont were also quality-filtered and used in the analysis. Clustering of the combined ESTs with d2_cluster and TGICL yielded a few large clusters containing several thousand ESTs that were refractory to routine clustering techniques. To resolve this problem, the sequence proximity and "bridges" were identified by an e-value distance graph to manually break clusters into smaller groups. Assembly of the resolved ESTs generated a 75,488 unique sequence set (31,580 contigs and 43,908 singletons/singlets). Digital expression analyses indicated that the FGAS dataset is enriched in stress-regulated genes compared to the other public datasets. Over 43% of the unique sequence set was annotated and classified into functional categories according to Gene Ontology.Conclusion
We have annotated 29,556 different sequences, an almost 5-fold increase in annotated sequences compared to the available wheat public databases. Digital expression analysis combined with gene annotation helped in the identification of several pathways associated with abiotic stress. The genomic resources and knowledge developed by this project will contribute to a better understanding of the different mechanisms that govern stress tolerance in wheat and other cereals. 相似文献10.
EST sequencing and phylogenetic analysis of the model grass Brachypodium distachyon 总被引:10,自引:0,他引:10
Vogel JP Gu YQ Twigg P Lazo GR Laudencia-Chingcuanco D Hayden DM Donze TJ Vivian LA Stamova B Coleman-Derr D 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2006,113(2):186-195
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Takeshi Akao Motoaki Sano Osamu Yamada Terumi Akeno Kaoru Fujii Kuniyasu Goto Sumiko Ohashi-Kunihiro Kumiko Takase Makoto Yasukawa-Watanabe Kanako Yamaguchi Yoko Kurihara Jun-ichi Maruyama Praveen Rao Juvvadi Akimitsu Tanaka Yoji Hata Yasuji Koyama Shotaro Yamaguchi Noriyuki Kitamoto Katsuya Gomi Keietsu Abe Michio Takeuchi Tetsuo Kobayashi Hiroyuki Horiuchi Katsuhiko Kitamoto Yutaka Kashiwagi Masayuki Machida Osamu Akita 《DNA research》2007,14(2):47-57
We performed random sequencing of cDNAs from nine biologically or industrially important cultures of the industrially valuable fungus Aspergillus oryzae to obtain expressed sequence tags (ESTs). Consequently, 21 446 raw ESTs were accumulated and subsequently assembled to 7589 non-redundant consensus sequences (contigs). Among all contigs, 5491 (72.4%) were derived from only a particular culture. These included 4735 (62.4%) singletons, i.e. lone ESTs overlapping with no others. These data showed that consideration of culture grown under various conditions as cDNA sources enabled efficient collection of ESTs. BLAST searches against the public databases showed that 2953 (38.9%) of the EST contigs showed significant similarities to deposited sequences with known functions, 793 (10.5%) were similar to hypothetical proteins, and the remaining 3843 (50.6%) showed no significant similarity to sequences in the databases. Culture-specific contigs were extracted on the basis of the EST frequency normalized by the total number for each culture condition. In addition, contig sequences were compared with sequence sets in eukaryotic orthologous groups (KOGs), and classified into the KOG functional categories. 相似文献
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Transcriptome sequencing and comparative analysis of the gametophyte thalli of Pyropia tenera under normal and high temperature conditions 总被引:1,自引:0,他引:1
San Choi Mi Sook Hwang Sungoh Im Namju Kim Won-Joong Jeong Eun-Jeong Park Yong-Gun Gong Dong-Woog Choi 《Journal of applied phycology》2013,25(4):1237-1246