Identification of an active LTR retrotransposon in rice.
Transposable elements are ubiquitous components of plant genomes. When active, these mobile elements can induce changes in the genome at both the structural and functional levels. Availability of the complete genome sequence for several model plant species provides the opportunity to study TEs in plants at an unprecedented scale. In the case of rice, annotation of the genomic sequence of the variety Nipponbare has revealed that TE-related sequences form more than 25% of its genome. However, most of the elements found are inactive, either because of structural alterations or because they are the target of various silencing pathways. In this paper, we propose a new post-genomic strategy aimed at identifying active TEs. Our approach relies on transcript profiling of TE-related sequences using a tiling microarray. We applied it to a particular class of TEs, the LTR retrotransposons. A transcript profiling assay of rice calli led to identification of a new transpositionally active family, named Lullaby. We provide a complete structural description of this element. We also show that it has recently been active in planta in rice, and discuss its phylogenetic relationships with Tos17, the only other active LTR retrotransposon described so far in the species.
Picault
Nathalie
N
Laboratoire Génome et Développement des Plantes, UMR CNRS/IRD/UPVD, Université de Perpignan Via Domitia, Perpignan cedex, France. nathalie.picault@univ-perp.fr
Chaparro
Christian
C
Piegu
Benoit
B
Stenger
Willfried
W
Formey
Damien
D
Llauro
Cristel
C
Descombin
Julie
J
Sabot
Francois
F
Lasserre
Eric
E
Meynard
Donaldo
D
Guiderdoni
Emmanuel
E
Panaud
Olivier
O
D018744:DNA, Plant / Q000235:genetics; D020869:Gene Expression Profiling; D018745:Genome, Plant; D020411:Oligonucleotide Array Sequence Analysis; D012275:Oryza / Q000235:genetics*; D010802:Phylogeny; D018626:Retroelements; D017422:Sequence Analysis, DNA; D020079:Terminal Repeat Sequences
D018744:DNA, Plant; D018626:Retroelements