Identification and analysis of ingi-related retroposons in the trypanosomatid genomes

Frédéric Bringaud, Matthew Rogers, Elodie Ghedin

Research output: Contribution to journalArticle

Abstract

Transposable elements (TE), defined as discrete pieces of DNA that can move from one site to another site in genomes, represent significant components of eukaryotic genomes, including trypanosomatids. Up to 5% of the trypanosomatid genome content is composed of retroposons of the ingi clade, further divided into subclades and subfamilies ranging from short extinct truncated elements (SIDER) to long active elements (ingi). Important differences in ingi-related retroposon content have been reported between trypanosomatid species. For instance, Leishmania spp. have expanded and recycled a whole SIDER family to fulfill an important biological pathway, i.e., regulation of gene expression, while trypanosome genomes are primarily composed of active elements. Here, we present an overview of the computational methods used to identify, annotate, and analyze ingi-related retroposons for providing a comprehensive picture of all these TE families in newly available trypanosomatid genome sequences.

Original languageEnglish (US)
Pages (from-to)109-122
Number of pages14
JournalMethods in Molecular Biology
Volume1201
DOIs
StatePublished - Jan 1 2015

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Keywords

  • (Sub)family
  • Annotation
  • Classification
  • Computational methods
  • Consensus sequence
  • Evolution
  • Identification
  • Ingi-related retroposon
  • Transposable element
  • Trypanosomatid

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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