Hypervariable 3′ UTR region of plant LTR-retrotransposons as a source of novel satellite repeats

• Published in: Gene Vol. 448; no. 2; pp. 198 - 206
• Main Authors: Macas, Jiří, Koblížková, Andrea, Navrátilová, Alice, Neumann, Pavel
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 15.12.2009
• Subjects: 3' Untranslated Regions - genetics; Bioinformatics; Cloning, Molecular; Computational identification; Data processing; DNA, Satellite - genetics; Evolution; Fluorescence in situ hybridization; Gene Amplification - physiology; Genes, Plant; Genetic Variation - physiology; Genome, Plant; Genomes; genomics; Nucleotide sequence; Phylogeny; Pisum sativum; Pisum sativum - genetics; Retroelements - genetics; Retrotransposons; Satellite DNA; Satellite DNA evolution; Tandem repeats; Terminal Repeat Sequences - genetics; Transposable elements; PBS; Tandem repeats; ORF; RT; UTR; Pisum sativum; FISH; LTR; Computational identification; Transposable elements; Satellite DNA evolution
• ISSN: 0378-1119; 1879-0038
• DOI: 10.1016/j.gene.2009.06.014

The repetitive sequence PisTR-A has an unusual organization in the pea ( Pisum sativum) genome, being present both as short dispersed repeats as well as long arrays of tandemly arranged satellite DNA. Cloning, sequencing and FISH analysis of both PisTR-A variants revealed that the former occurs in the genome embedded within the sequence of Ty3/gypsy-like Ogre elements, whereas the latter forms homogenized arrays of satellite repeats at several genomic loci. The Ogre elements carry the PisTR-A sequences in their 3′ untranslated region (UTR) separating the gag-pol region from the 3′ LTR. This region was found to be highly variable among pea Ogre elements, and includes a number of other tandem repeats along with or instead of PisTR-A. Bioinformatic analysis of LTR-retrotransposons mined from available plant genomic sequence data revealed that the frequent occurrence of variable tandem repeats within 3′ UTRs is a typical feature of the Tat lineage of plant retrotransposons. Comparison of these repeats to known plant satellite sequences uncovered two other instances of satellites with sequence similarity to a Tat-like retrotransposon 3′ UTR regions. These observations suggest that some retrotransposons may significantly contribute to satellite DNA evolution by generating a library of short repeat arrays that can subsequently be dispersed through the genome and eventually further amplified and homogenized into novel satellite repeats.