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

Abstract

Long terminal repeat (LTR) retrotransposons have been shown to make up much of the maize genome. Although these elements are known to be prevalent in plant genomes of a middle-to-large size, little information is available on the relative proportions composed by specific families of elements in a single genome. We sequenced a library of randomly sheared genomic DNA from maize to characterize this genome. BLAST analysis of these sequences demonstrated that the maize genome is composed of diverse sequences that represent numerous families of retrotransposons. The largest families contain the previously described elements Huck, Ji, and Opie. Approximately 5% of the sequences are predicted to encode proteins. The genomic abundance of 16 families of elements was estimated by hybridization to an array of 10,752 maize bacterial artificial chromosome (BAC) clones. Comparisons of the number of elements present on individual BACs indicated that retrotransposons are in general randomly distributed across the maize genome. A second library was constructed that was selected to contain sequences hypomethylated in the maize genome. Sequence analysis of this library indicated that retroelements abundant in the genome are poorly represented in hypomethylated regions. Fifty-six retroelement sequences corresponding to the integrase and reverse transcriptase domains were isolated from ∼407,000 maize expressed sequence tags (ESTs). Phylogenetic analysis of these and the genomic retroelement sequences indicated that elements most abundant in the genome are less abundant at the transcript level than are more rare retrotransposons. Additional phylogenies also demonstrated that rice and maize retrotransposon families are frequently more closely related to each other than to families within the same species. An analysis of the GC content of the maize genomic library and that of maize ESTs did not support recently published data that the gene space in maize is found within a narrow GC range, but does indicate that genic sequences have a higher GC content than intergenic sequences (52% vs. 47% GC).

Differential Methylation during Maize Leaf Growth Targets Developmentally Regulated Genes

“…However, the most prevalent maize TE, Huck, is found only once in our data set. Moreover, the average GC content of Huck elements is 60%, which is much higher than the average GC content of the maize repetitive fraction (48%) and the average genomic GC content (47%; Meyers et al, 2001). The Giepum TE, on the other hand, is more than eight times less present in the maize genome but eight times more present in our data set.…”

Computational Finishing of Large Sequence Contigs Reveals Interspersed Nested Repeats and Gene Islands in the rf1-Associated Region of Maize

“…LTR retrotransposons were examined for differing insertion patterns between repeat clusters. Of the three most abundant retrotransposons found in maize (Meyers et al, 2001), Huck, a Gypsy element, was found to be distributed evenly across the contigs and repeat clusters. Opie, a Copia element, was found nested almost exclusively in one location.…”

Transposable Element Insertion and Epigenetic Modification Cause the Multiallelic Variation in the Expression of FAE1 in Sinapis alba

“…Allelic differences in nucleotide sequences resulting from singlenucleotide polymorphisms (SNPs), indels (insertions or deletions), and transposable element (TE) insertions are primarily responsible for contrasting trait phenotypes. TEs represent a large proportion of the nuclear genomes in many plant species (Vicient et al, 1999;Meyers et al, 2001). They are classified into class I (RNA) and II (DNA) based on their different modes of mobility (Charlesworth et al, 1994).…”