TY - JOUR
T1 - Identification and analysis of ingi-related retroposons in the trypanosomatid genomes
AU - Bringaud, Frédéric
AU - Rogers, Matthew
AU - Ghedin, Elodie
N1 - Publisher Copyright:
© Springer Science+Business Media New York 2015.
PY - 2015
Y1 - 2015
N2 - 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.
AB - 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.
KW - (Sub)family
KW - Annotation
KW - Classification
KW - Computational methods
KW - Consensus sequence
KW - Evolution
KW - Identification
KW - Ingi-related retroposon
KW - Transposable element
KW - Trypanosomatid
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U2 - 10.1007/978-1-4939-1438-8_6
DO - 10.1007/978-1-4939-1438-8_6
M3 - Article
C2 - 25388110
AN - SCOPUS:84921890129
SN - 1064-3745
VL - 1201
SP - 109
EP - 122
JO - Methods in Molecular Biology
JF - Methods in Molecular Biology
ER -