Abstract
Recent comprehensive sequence analysis of the maize genome now permits detailed discovery and description of all transposable elements (TEs) in this complex nuclear environment. Reiteratively optimized structural and homology criteria were used in the computer-assisted search for retroelements, TEs that transpose by reverse transcription of an RNA intermediate, with the final results verified by manual inspection. Retroelements were found to occupy the majority (>75%) of the nuclear genome in maize inbred B73. Unprecedented genetic diversity was discovered in the long terminal repeat (LTR) retrotransposon class of retroelements, with >400 families (>350 newly discovered) contributing >31,000 intact elements. The two other classes of retroelements, SINEs (four families) and LINEs (at least 30 families), were observed to contribute 1,991 and ∼35,000 copies, respectively, or a combined ∼1% of the B73 nuclear genome. With regard to fully intact elements, median copy numbers for all retroelement families in maize was 2 because >250 LTR retrotransposon families contained only one or two intact members that could be detected in the B73 draft sequence. The majority, perhaps all, of the investigated retroelement families exhibited non-random dispersal across the maize genome, with LINEs, SINEs, and many low-copy-number LTR retrotransposons exhibiting a bias for accumulation in gene-rich regions. In contrast, most (but not all) medium- and high-copy-number LTR retrotransposons were found to preferentially accumulate in gene-poor regions like pericentromeric heterochromatin, while a few high-copy-number families exhibited the opposite bias. Regions of the genome with the highest LTR retrotransposon density contained the lowest LTR retrotransposon diversity. These results indicate that the maize genome provides a great number of different niches for the survival and procreation of a great variety of retroelements that have evolved to differentially occupy and exploit this genomic diversity.
Highlights
Transposable elements (TEs) were first discovered in maize (Zea mays) [1], but have subsequently been found in almost every organism investigated, from archaea and eubacteria to animals, plants, fungi and protists [2]
TEs are a major component of all studied plant genomes, and are the most significant contributors to genome structure and evolution in almost all eukaryotes that have been investigated, their properties and reasons for existence are not well understood in any eukaryotic genome
Most of these element families are present in low copy numbers and had been missed by previous searches that relied on a high-copynumber criterion
Summary
Transposable elements (TEs) were first discovered in maize (Zea mays) [1], but have subsequently been found in almost every organism investigated, from archaea and eubacteria to animals, plants, fungi and protists [2]. There are some class II TEs, for instance IS91 of bacteria and Helitrons in eukaryotes, that are believed to transpose through a rolling-circle DNA replication process that does not involve element excision [3,4]. A particular type of class I element, the long terminal repeat (LTR) retrotransposons, has been observed to be the major TE, accounting for .80% of the nuclear DNA in many angiosperms [5]. The other two types of class I elements, LINEs and SINEs, have been observed in all carefully annotated flowering plant genomes, but their copy numbers and overall contributions to genome composition have not usually been large. In lily (Lilium speciosum) and grapevine (Vitis vinifera), LINEs appear to be more numerous and/or active than in most plant species investigated [6,7]
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