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Bioinformatics and genomic analysis of transposable elements in eukaryotic genomes

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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.

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Abbreviations

LINE:

Long interspersed nuclear element

LTR:

Long terminal repeat

MAK:

MITE analysis toolkit

MITE:

Miniature inverted repeat transposable element

MULE:

Mutator-like element

SINE:

Short interspersed nuclear element

TE:

Transposable element

TESD:

Transposable element simulator dynamics

TIR:

Terminal inverted repeat

TSD:

Target site duplication

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Funding

This study was supported by National Sciences and Engineering Research Council (RGPIN371565 to G.Y.), Canadian Foundation for Innovation (24456 to G.Y.), Ontario Research Fund (24456 to G.Y.), and University of Toronto.

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Correspondence to Guojun Yang.

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Responsible Editor: T. Ryan Gregory and Jillian D. Bainard.

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Janicki, M., Rooke, R. & Yang, G. Bioinformatics and genomic analysis of transposable elements in eukaryotic genomes. Chromosome Res 19, 787–808 (2011). https://doi.org/10.1007/s10577-011-9230-7

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