When funding for Tetrahymena Genome Database (TGD) ended in 2006, no further updates were made to this important community resource and the main database was taken offline in 2008. We have restored and updated this important resource for use by the Tetrahymena research community. We have also retooled the TGD website (now TGD Wiki) to allow members of the community to directly update the information presented for each gene, including gene names, descriptions and Gene Ontology annotations, from a web browser. Maintenance of genome annotations by the authors generating and publishing primary data, rather than dedicated scientific curators, is a viable alternative for the upkeep of genomes, particularly for organisms with smaller research communities. By combining simple, intuitive displays with the powerful search functions made possible by its underlying relational database, TGD Wiki has been designed to maximize participation by bench scientists in the development of their community bioinformatics resource. DATABASE URL: http://ciliate.org.
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http://dx.doi.org/10.1093/database/bas007 | DOI Listing |
Ecol Lett
January 2025
Aquatic Ecology and Evolution, University of Konstanz, Konstanz, Germany.
Evolutionary change within community members and shifts in species composition via species sorting contribute to community and trait dynamics. However, we do not understand when and how both processes contribute to community dynamics. Here, we estimated the contributions of species sorting and evolution over time (60 days) in bacterial communities of 24 species under selection by a ciliate predator.
View Article and Find Full Text PDFNucleic Acids Res
January 2025
MOE Key Laboratory of Evolution & Marine Biodiversity and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
The ciliate Tetrahymena thermophila is a well-established unicellular model eukaryote, contributing significantly to foundational biological discoveries. Despite its acknowledged importance, current studies on Tetrahymena biology face challenges due to gene annotation inaccuracy, particularly the notable absence of untranslated regions (UTRs). To comprehensively annotate the Tetrahymena macronuclear genome, we collected extensive transcriptomic data spanning various cell stages.
View Article and Find Full Text PDFRNA Biol
January 2024
McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA.
BMC Biol
August 2024
Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou, 510631, China.
Background: Tubulins are major components of the eukaryotic cytoskeletons that are crucial in many cellular processes. Ciliated protists comprise one of the oldest eukaryotic lineages possessing cilia over their cell surface and assembling many diverse microtubular structures. As such, ciliates are excellent model organisms to clarify the origin and evolution of tubulins in the early stages of eukaryote evolution.
View Article and Find Full Text PDFGenome Biol Evol
August 2024
Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA.
Opportunistic pathogens are environmental microbes that are generally harmless and only occasionally cause disease. Unlike obligate pathogens, the growth and survival of opportunistic pathogens do not rely on host infection or transmission. Their versatile lifestyles make it challenging to decipher how and why virulence has evolved in opportunistic pathogens.
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