The paleontology of intergene retrotransposons of maize

Abstract

Retrotransposons, transposable elements related to animal retroviruses, are found in all eukaryotes investigated and make up the majority of many plant genomes. Their ubiquity points to their importance, especially in their contribution to the large-scale structure of complex genomes. The nature and frequency of retro-element appearance, activation and amplification are poorly understood in all higher eukaryotes. Here we employ a novel approach to determine the insertion dates for 17 of 23 retrotransposons found near the maize adh1 gene, and two others from unlinked sites in the maize genome, by comparison of long terminal repeat (LTR) divergences with the sequence divergence between adh1 in maize and sorghum. All retrotransposons examined have inserted within the last six million years, most in the last three million years. The structure of the adh1 region appears to be standard relative to the other gene-containing regions of the maize genome, thus suggesting that retrotransposon insertions have increased the size of the maize genome from approximately 1200 Mb to 2400 Mb in the last three million years. Furthermore, the results indicate an increased mutation rate in retrotransposons compared with genes.

Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species

“…We estimated the times of insertion for Gypsy and Copia elements using the method described by SanMiguel et al 25 ( Fig. 2e and Supplementary Fig.…”

The wheat powdery mildew genome shows the unique evolution of an obligate biotroph

“…The error estimate of 2.29 × 10 −9 for the substitution rate was then applied to the calculated divergence time. The Kimura two-parameter criterion was applied to weight the transition-totransversion ratio as previously described 41 .…”

Abundance, Distribution, and Transcriptional Activity of Repetitive Elements in the Maize Genome

“…Opie (and the cross-hybridizing Ji family) and Huck have inserted multiple times from 0.2 to 5 million years ago , allowing for significant diversification since the time of insertion. Zeon-1 appears to triple in copy number under lower stringency, and SanMiguel et al (1998) have estimated that that is the oldest of the elements that we assayed. The data suggest that Huck is extremely abundant in the genome when the LTR region of this element was used as a probe.…”