My poster for the 2015 Mobile Genetic Elements Meeting, held at the MBL in Woods Hole MA

1. 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