Bioinformatics and genomic analysis of transposable elements in eukaryotic genomes

Abstract

A major portion of most eukaryotic genomes are transposable elements (TEs). During evolution, TEs have introduced profound changes to genome size, structure, and function. As integral parts of genomes, the dynamic presence of TEs will continue to be a major force in reshaping genomes. Early computational analyses of TEs in genome sequences focused on filtering out "junk" sequences to facilitate gene annotation. When the high abundance and diversity of TEs in eukaryotic genomes were recognized, these early efforts transformed into the systematic genome-wide categorization and classification of TEs. The availability of genomic sequence data reversed the classical genetic approaches to discovering new TE families and superfamilies. Curated TE databases and their accurate annotation of genome sequences in turn facilitated the studies on TEs in a number of frontiers including: (1) TE-mediated changes of genome size and structure, (2) the influence of TEs on genome and gene functions, (3) TE regulation by host, (4) the evolution of TEs and their population dynamics, and (5) genomic scale studies of TE activity. Bioinformatics and genomic approaches have become an integral part of large-scale studies on TEs to extract information with pure in silico analyses or to assist wet lab experimental studies. The current revolution in genome sequencing technology facilitates further progress in the existing frontiers of research and emergence of new initiatives. The rapid generation of large-sequence datasets at record low costs on a routine basis is challenging the computing industry on storage capacity and manipulation speed and the bioinformatics community for improvement in algorithms and their implementations.

Genome size evolution: patterns, mechanisms, and methodological advances

“…Repetitive noncoding DNA sequences, especially transposable elements, are considered to be one of the largest contributors to genome size variation. It is, therefore, fitting that several papers in this collection explore the role of transposable elements in genome evolution (Ågren and Wright 2011;Hertweck 2013;Janicki et al 2011;Lee et al 2013). In addition, Fattash et al (2013) review the current knowledge regarding miniature inverted repeat transposable elements (MITEs), and discuss computational advances in the discovery and analysis of MITEs.…”

Genome-Wide Analysis ofStowaway-Like MITEs in Wheat Reveals High Sequence Conservation, Gene Association, and Genomic Diversification

“…Overall, 18,217 MITE insertions were retrieved in silico, using the MITE analysis kit (MAK) software (kindly provided by Guojun Yang, University of Toronto; Yang and Hall, 2003;Janicki et al, 2011). The publicly available sequence of each of the 18 MITEs was used as a query in the MAK program to perform BLASTN against the draft 454-pyrosequencing database.…”

Évolution de la taille des génomes : les modèles, les mécanismes et les avancées méthodologiques

“…Une seconde série d'articles explore les nombreux mécanismes qui contribuent à la diversité de la taille des génomes Les séquences d'ADN répétitives et non-codantes, particulièrement les éléments transposables, sont considérées comme l'un des plus grands contributeurs à la variation de la taille des génomes Il convient donc que plusieurs des articles de cette collection explorent le rôle des éléments transposables dans l'évolution des génomes (Ågren et Wright 2011;Hertweck 2013;Janicki et al 2011;Lee et al 2013). De plus, Fattash et al (2013) passent en revue l'état des connaissances en ce qui a trait aux éléments transposables inversés répétés miniatures (MITE) et discutent des avancées en bioinformatique pour l'identification et l'analyse des MITE D'autres mécanismes pouvant expliquer les changements de la taille des génomes, souvent moins fréquemment considérés, sont également considérés Le commentaire de Hilliker et Taylor-Kamall (2013) apporte un éclai-rage sur la fonction génique de l'hétérochromatine et comment elle pourrait être liée à la variation de la taille du génome.…”