Elementos transponíveis - nenhuma "narrativa coerente" da evolução dos genomas de vertebrados

sábado, fevereiro 04, 2017

Evolution and Diversity of Transposable Elements in Vertebrate Genomes 

Cibele G Sotero-Caio Roy N Platt, II Alexander Suh David A Ray

Genome Biol Evol (2017) evw264. DOI: https://doi.org/10.1093/gbe/evw264

Published: 01 February 2017 

Article history

Received: 15 March 2016 Revision Received: 13 July 2016 Revision Received: 19 October 2016 Accepted: 02 November 2016


Transposable elements (TEs) are selfish genetic elements that mobilize in genomes via transposition or retrotransposition and often make up large fractions of vertebrate genomes. Here, we review the current understanding of vertebrate TE diversity and evolution in the context of recent advances in genome sequencing and assembly techniques. TEs make up 4-60% of assembled vertebrate genomes, and deeply branching lineages such as ray-finned fishes and amphibians generally exhibit a higher TE diversity than the more recent radiations of birds and mammals. Furthermore, the list of taxa with exceptional TE landscapes is growing. We emphasize that the current bottleneck in genome analyses lies in the proper annotation of TEs, and provide examples where superficial analyses led to misleading conclusions about genome evolution. Finally, recent advances in long-read sequencing will soon permit access to TE-rich genomic regions that previously resisted assembly including the gigantic, TE-rich genomes of salamanders and lungfishes.

vertebrate, transposable element, transposons, retrotransposons

Issue Section: Invited Review

Author notes

‡ These authors contributed equally to the manuscript.

© The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

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"At the most basic level of inquiry, the percent of a genome derived from TEs, vertebrate genomes can vary from 6 to 60%. If one takes into account aspects of TE diversity, accumulation histories, and even variation in repeat annotations themselves, it becomes difficult to build a coherent narrative that adequately explains repeat variation across vertebrates. Generally, higher levels of TE diversity correlate with the age of vertebrate lineages; lineages that have existed for longer periods, such as fishes, and deep-branching tetrapods tend to have higher TE diversity than more recent radiations, such as birds and mammals. However, as the number of vertebrate genome assemblies increases, exceptions to this pattern will become more common. Known outliers within each vertebrate lineage include the lungfish with a genome dominated by two types of non-LTR retrotransposons, and the western clawed frog whose TE content is highly biased towards DNA transposons. Woodpeckers contain almost half a million more TE copies than other birds. Among mammals, vespertilionid bats is the sole lineage exhibiting DNA transposon activity. Indeed, our view of what is ‘normal’ for broad lineage such as mammals or birds continues to expand and our understanding of TEs and their role in vertebrate genome evolution benefits greatly from understanding both general trends and outliers. Identification of the contribution of TEs to the uniqueness of each genome will be key to unravelling the impact of genome architecture on organismal evolution.