The future of transposable element annotation and their classification in the light of functional genomics - what we can learn from the fables of Jean de la Fontaine?

Abstract

Transposable element (TE) science has been significantly influenced by the pioneering ideas of David Finnegan near the end of the last century, as well as by the classification systems that were subsequently developed. Today, whole genome TE annotation is mostly done using tools that were developed to aid gene annotation rather than to specifically study TEs. We argue that further progress in the TE field is impeded both by current TE classification schemes and by a failure to recognize that TE biology is fundamentally different from that of multicellular organisms. Novel genome wide TE annotation methods are helping to redefine our understanding of TE sequence origins and evolution. We briefly discuss some of these new methods as well as ideas for possible alternative classification schemes. Our hope is to encourage the formation of a society to organize a larger debate on these questions and to promote the adoption of standards for annotation and an improved TE classification. KEYWORDS genome; mobile genetic element; ontology; repeat; taxonomy Jean de la Fontaine, the most famous of the French poets of the seventeenth century, is well known for his fables involving animal protagonists that examine the organization of human society. Among these the "Wolf and Lamb" 1 and the "Lion and Rat" 2 describe 2 views of human society that may be summarized respectively as "might makes right" and "even the smallest can help the greater." In scientific circles sometimes it is the most powerful members of the community that dictate the dominant ideas in the field, "might makes right," which is an efficient system but often comes at the expense of collegiality. Alternatively, some scientific communities emphasize input from all members, along the lines of the second fable, but this comes at a cost of time to allow for contradictory debates. Communities in this second category often form societies where elected representatives organize the flow of information within the community and set procedures for making scientific decisions on the future of the field. We argue that the field of eukaryotic transposable elements (TEs) is currently organized around several concepts that are championed by a minority and accepted without argument by a majority. These concepts include what the nature of a TE is, how TEs are identified in assembled genomes, and how they are classified taxonomically. Recent publications (see discussions in refs. 3,4 ) reflect these views and it is time for the TE community to reexamine the bases upon which its science is organized. We call for the emergence of an international society for the biology of TEs to address these questions by including all the voices in the community, it is time for the "Lion and Rat." A definition of TEsHaren et al.5 defined TEs as "discrete segments of DNA capable of moving from one locus to another in their host genome or between different genomes." Recently, we proposed that this definition needs to be broadened to "TEs are discrete segments of DNA capable of moving withi...

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