Tetrahymena is a genus of free-living ciliated protozoans that is widely distributed in freshwater environments around the world. Tetrahymena thermophila, best studied species in the genus, is well-established as a model eukaryote, elaborating typical eukaryotic components (eg, microtubules, membrane systems, chromatin) into a highly organized cell whose structural and functional complexity is comparable to, or exceeds that, of human and other metazoan cells. Importantly, Tetrahymena’s special elaborations of certain basic eukaryotic mechanisms have facilitated discoveries opening major new fields of fundamental research over the last five decades, including the discovery of dynein, the first microtubule motor, elucidation of the fundamental structure of telomeres, the discovery of catalytic RNA, the discovery and characterization of telomerase, the first demonstration that a transcription factor (GCN5p) acts by catalyzing a histone post-translational modification and the co-discovery that an RNAi-like process acts to target changes in chromatin function.
TetraFGD is a web-accessible functional genomics database of Tetrahymena thermophila. Currently, TetraFGD provides RNA-seq, MICROARRAY, GENE NETWORK and PHOSPHOPROTEOME data for T. thermophila using Gene ID or Gene description searches or Blast Sequences. TetraFGD will be extended to develop/collect other functional genomics data (e.g. proteome) and is intended to be a resource for all members of the scientific research community interested in Tetrahymena. As we develop TetraFGD, we would appreciate input from the community so that we can tailor it to meet your needs. Please feel free to send comments, suggestions, or questions to TetraFGD@ihb.ac.cn
Release of the complete MAC genomes of Tetrahymena thermophila and Tetrahymena shanghaiensis.
We assembled the complete genomes of two Tetrahymena species using a simple strategy incorporating the high coverage Nanopore data. It is the first time to get the complete MAC genome in ciliated protozoa. Get more details in the preprint: Wang G, Chai X, Zhang J, Yang W, Jiang C, Chen K, Miao W, Xiong J. A strategy for complete telomere-to-telomere assembly of ciliate macronuclear genome using ultra-high coverage Nanopore data. bioRxiv. 2020 Jan 1.
The Meiosis RNA-Seq data was added in the TetraFGD.
The phosphoproteomic data was added in the TetraFGD.
The RNA-Seq data at different stages were integrated into the TetraFGD Gbrowse.
The name of this database was changed to Tetrahymena Functional Genomics Database (TetraFGD), and a new version of the database was released. In addition to the microarray data, TetraFGD now contains the RNA-Seq and Gene Network data. In addition, the BLAST tool was applied in TetraFGD.
Gene functional annotation in the search result page was added to the TGED database.
Tetrahymena Gene Expression Database (TGED) was released.
- Wang G, Chai X, Zhang J, Yang W, Jiang C, Chen K, Miao W, Xiong J: A strategy for complete telomere-to-telomere assembly of ciliate macronuclear genome using ultra-high coverage Nanopore data. bioRxiv. 2020 Jan 1. doi: https://doi.org/10.1101/2020.01.08.898502
- Yan GX, Dang H, Tian M, Zhang J, Shodhan A, Ning YZ, Xiong J, Miao W: Cyc17, a meiosis-specific cyclin, is essential for anaphase initiation and chromosome segregation in Tetrahymena thermophila. Cell Cycle. 2016 May 18:0.
- Xu Q, Wang R, Ghanam AR, Yan G, Miao W, Song X: The key role of CYC2 during meiosis in Tetrahymena thermophila. Protein Cell. 2016 Apr;7(4):236-49.
- Tian M, Chen X, Xiong Q, Xiong J, Xiao C, Ge F, Yang F, Miao W: Phosphoproteomic analysis of protein phosphorylation networks in Tetrahymena thermophila, a model single-celled organism. Molecular & Cellular Proteomics 2014, 13, 503-519.
- Xiong J, Lu X, Zhou Z, Chang Y, Yuan D, Tian M, Wang L, Fu C, Orias E, Miao W: Transcriptome Analysis of the Model Protozoan, Tetrahymena thermop hila, Using Deep RNA Sequencing. PLoS One 2012, 7(2):e30630.
- Xiong J, Yuan D, Fillingham JS, Garg J, Lu X, Chang Y, Liu Y, Fu C, Pearlman RE, Miao W: Gene Network Landscape of the Ciliate Tetrahymena thermophila. PLoS One 2011, 6(5):e20124.
- Xiong J, Lu X, Lu Y, Zeng H, Yuan D, Feng L, Chang Y, Bowen J, Gorovsky MA, Fu C, Miao W: Tetrahymena Gene Expression Database (TGED): A resource of microarray data and co-expressi on analyses for Tetrahymena. SCIENCE CHINA Life Sciences 2011, 54(1):65-67.
- Miao W, Xiong J, Bowen J, Wang W, Liu YF, Braguinets O, Grigull J, Pearlman RE, Orias E, Gorovsky MA: Microarray Analyses of Gene Expression during the Tetrahymena thermophila Life Cycle. Plos One 2009, 4(2).