ARS | Publication request: A novel class of miniature inverted repeat transposable elements (MITEs) that contain hitchhiking (GTCY)n microsatellites

Submitted to: Insect Molecular Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: July 9, 2010
Publication Date: January 20, 2011
Citation: Coates, B.S., Kroemer, J.A., Sumerford, D.V., Hellmich II, R.L. 2011. A novel class of miniature inverted repeat transposable elements (MITEs) that contain hitchhiking (GTCY)n microsatellites. Insect Molecular Biology. 20(1):15-27.

Interpretive Summary: The control of yield-reducing caterpillar pests of U.S. crops costs growers millions of dollars each year. Our understanding of the biological processes that impact control of insect pests of corn has been enhanced by the development of genetic markers. Microsatellite DNA is a useful genetic tool, but has limitations for the study of caterpillar pests. The current research determined microsatellite movement within moth genomes limits their utility as genetic markers. Knowledge from our results provides new avenues for genetic-marker development that will aid scientists from the U.S. and Europe in their evaluation of insect movement and insect resistance management strategies.

Technical Abstract: The insertion of transposable elements results in the modification of genome structure and gene expression, and also facilitates the propagation of derived internal sequences. We show that (GTCY)n microsatellite loci within genomes of Lepidoptera are mobile and multilocus due to hitchhiking within a family of miniature inverted repeat transposable elements (MITEs). The MITEs have conserved secondary structures that flank (GTCY)n microsatellite loci including a 5' subterminal inverted repeat (SIR; GGGTTCCGTA), a complementary 3' SIR (TACGAAGCC), a 5' inverted repeat (IR) downstream and complementary to the 5' SIR, and a 3' stem loop structure. Dinucleotide TT target site duplications are created upon MITE insertion at consensus WTTTT target sites within the genomes of 12 lepidopteran species. The MITEs are part of the second described class of microsatellite-associated interspersed nuclear elements within lepidopteran genomes (herein named MINE-2a), and result in the integration of highly related (GTCY)n microsatellites at multiple independently segregating loci via transposition. Annotation of the Bombyx mori whole genome sequence and Heliconius bacterial artificial chromosome sequences indicate diverged MINE-2a element sequences are devoid of tandem (GTCY) repeats, but instead contain cryptically simple sequences or new classes of (CT)n and (GACA)n microsatellites. Genesis and subsequent mobility of tandem repeats within MINE-2a family members result in multiple microsatellite loci within a genome that share similar flanking DNA sequence that is attributed to conserved MITE-like secondary structures. Ubiquitous presence of MINE-2a members within the lepidopteran lineage may contribute to difficulties in developing microsatellite loci into single locus genetic markers.