Identification and analysis of ingi-related retroposons in the trypanosomatid genomes.
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.
Centre de Résonance Magnétique des Systèmes Biologiques (RMSB), UMR 5536 CNRS, Université de Bordeaux, 146, rue Léo Saignat, 33076, Bordeaux, France, bringaud@rmsb.u-bordeaux2.fr.
Frédéric
F
Bringaud
Matthew
M
Rogers
Elodie
E
Ghedin
D000465:Algorithms; D004251:DNA Transposable Elements; D019143:Evolution, Molecular; D018503:Genome, Protozoan; D023281:Genomics / Q000379:methods*; D058977:Molecular Sequence Annotation / Q000379:methods*; D010802:Phylogeny; D018626:Retroelements / Q000235:genetics*; D012984:Software; D014351:Trypanosomatina / Q000235:genetics*
D004251:DNA Transposable Elements; D018626:Retroelements