Improving our Knowledge of Transposable
Element Content and the Future of
TE Research
Tyler A. Elliott and T. Ryan Gregory
@TransposableMan
@TRyanGregory
References
Elliott, T.A., Gregory, T.R. 2015. Do larger genomes contain more diverse transposable elements? BMC Evol Biol. 15:69
Hoen, D.R. et al. 2015. A call for benchmarking transposable element annotation methods. Mob DNA. 6:13
Piégu B. et al. 2015. A survey of transposable element classification systems – a call for a fundamental update to meet the challenge of
their diversity and complexity. Mol Phy Evol. 86: 90-109
Dotto, B.R. et al. 2015. HTT-DB – Horizontally transferred transposable element database. Bioinf. 31:2915-2917
Jurka, J. et al. 2005. Repbase Update, a database of eukaryotic repetitive elements. Cyt Gen Res. 110:462-467
Vassetzky, N.S., Kramerov, D.A. 2013. SINEBase: A database and tool for SINE analysis Nucl Acid Res. 41:D83-D89
Wicker, T. et al. 2007. A unified classification system for eukaryotic transposable elements Nat Rev Genet. 8:973-982
Dai, L. et al. 2003. Database for mobile group II introns. Nucl Acid Res. 31:424-426
Siguier, P. et al. 2006. ISFinder: The reference center for bacterial insertion sequences. Nucl Acid Res. 34:D32-D36
TE Content
Elliott and Gregory, 2015 (BMC Evol Bio)
• 54.26% of published genome sequences do not assign TEs
down to superfamily level, 25% have little or no reporting of
TE content
Hoen et al., 2015 (Mob DNA)
• Lack of a benchmark for annotation of TEs in genomes
• Soliciting community for suggestions
TE Classification
Piégu et al., 2015 (Mol Phy and Evol)
• Classification should reflect common ancestry and include
elements in prokaryotes
• Lack of communication between various groups of researchers and
organizations/databases
• Call for the formation of a committee for TE taxonomy
TE Resources
• Numerous databases with useful features and tools
• Varying levels of support for each
• Little to no interconnectivity
The Future of TE Research
• Need for discussion amongst the community to determine interest and those willing to commit time and resources
• Re-annotation of genomes using standard methods and annotation of black box genomes, curated data should be freely available to all
• Expand support of databases and integration, sharing of data
• Perhaps time has come for the formation of a society or organization for researchers working on mobile genetic elements
• Provide centralized entity which can enforce standards of annotation, classification, storage and curation of TE information
Overview
• The study of TEs and mobile DNA in general is at a crossroads in regard to how we annotate, classify , store and curate information
• Our knowledge of TE content in genomes needs improvement, and a standardized way of annotating TE across genomes is needed
• The classification of TEs needs revision, to better encompass the diversity of more types of mobile DNA from all life and to reflect
common ancestry
• Useful databases and resources exist online but they often operate in isolation, with little support and interconnectivity
• The community would benefit from unifying to discuss these issues and propose a means forward, such as eventually forming the first
international society of mobile DNA researchers as a means to propose and enforce standards
Department of Integrative Biology, University of Guelph, Ontario, Canada
tyleraelliott@gmail.com
rgregory@uoguelph.ca