Using Nextgen Sequencing to Investigate Genome Size Variation and Transposable Element Content

Abstract

Transposable element (TE) content explains a large part of Eukaryotic genome size variation. TE content is determined by transposition, removal and host responses, but the efficiency of these forces is ultimately governed by genetic drift and natural selection. Contribution of TE families to genome size variation has been recently quantified using next generation sequencing (NGS) in two species pairs: Zea mays ssp. mays and Zea luxurians, Arabidopsis lyrata and A. thaliana. In both interspecific comparisons, genome-wide differences in TE content rather than the proliferation of a small subset of TE families was observed. We discuss three nonexclusive hypotheses to explain this pattern: selection for genome shrinkage, differential efficiency of epigenetic control, and a purely stochastic process of genome size evolution. Additional genome-wide assessments are needed to assess the extent to which selection shapes TE genomic content. To facilitate such studies, we discuss the use of NGS in “orphan” species.