Dramatic amplification of a rice transposable element during recent domestication

Abstract

Despite the prevalence of transposable elements in the genomes of higher eukaryotes, what is virtually unknown is how they amplify to very high copy numbers without killing their host. Here, we report the discovery of rice strains where a miniature invertedrepeat transposable element (mPing) has amplified from Ϸ50 to Ϸ1,000 copies in four rice strains. We characterized 280 of the insertions and found that 70% were within 5 kb of coding regions but that insertions into exons and introns were significantly underrepresented. Further analyses of gene expression and transposable-element activity demonstrate that the ability of mPing to attain high copy numbers is because of three factors: (i) the rapid selection against detrimental insertions, (ii) the neutral or minimal effect of the remaining insertions on gene transcription, and (iii) the continued mobility of mPing elements in strains that already have >1,000 copies. The rapid increase in mPing copy number documented in this study represents a potentially valuable source of population diversity in self-fertilizing plants like rice. genome evolution ͉ miniature inverted-repeat transposable element ͉ transposon

Demography and weak selection drive patterns of transposable element diversity in natural populations of Arabidopsis lyrata

“…Second, previous studies have demonstrated convincingly that there is selection against TEs. For example, a recent study of rice TEs found that insertions into gene regions are lost rapidly because of strong selection against the interruption of gene function (55). These highly deleterious events are not expected to rise to appreciable population frequencies and are thus unlikely to have been included in our sample.…”

Whole-genome sequencing and intensive analysis of the undomesticated soybean ( Glycine soja Sieb. and Zucc.) genome

“…S3). It has been shown that the genomes of domesticated species can be expanded by dramatic amplification of TEs (39). Furthermore, retrotransposon insertions have been reported to collapse or silence genes, as exemplified by phenotypic changes in tomato fruit shape (40).…”

Evolutionary fate of rhizome-specific genes in a non-rhizomatous Sorghum genotype

“…Three RT-enriched genes did show significant differences in numbers of gene copies, suggesting gene amplification following speciation. Naito et al (2006) reported dramatic amplification of a rice-transposable element designed as mPing during domestication, suggesting that the rapid increase represents a potentially valuable source of population diversity. Although the nature of the three genes that are rapidly evolving in copy number is not yet clear, ongoing analysis of the 289 family members of RT/RMI19 in the recently completed genome sequence of S. bicolor might provide clues to shed further light on genome evolution following speciation.…”