Abstract
BackgroundAs a newly identified category of DNA transposon, helitrons have been found in a large number of eukaryotes genomes. Helitrons have contributed significantly to the intra-specific genome diversity in maize. Although many characteristics of helitrons in the maize genome have been well documented, the sequence of an intact autonomous helitrons has not been identified in maize. In addition, the process of gene fragment capturing during the transposition of helitrons has not been characterized.ResultsThe whole genome sequences of maize inbred line B73 were analyzed, 1,649 helitron-like transposons including 1,515 helAs and 134 helBs were identified. ZmhelA1, ZmhelB1 and ZmhelB2 all encode an open reading frame (ORF) with intact replication initiator (Rep) motif and a DNA helicase (Hel) domain, which are similar to previously reported autonomous helitrons in other organisms. The putative autonomous ZmhelB1 and ZmhelB2 contain an extra replication factor-a protein1 (RPA1) transposase (RPA-TPase) including three single strand DNA-binding domains (DBD)-A/-B/-C in the ORF. Over ninety percent of maize helitrons identified have captured gene fragments. HelAs and helBs carry 4,645 and 249 gene fragments, which yield 2,507 and 187 different genes respectively. Many helitrons contain mutilple terminal sequences, but only one 3'-terminal sequence had an intact "CTAG" motif. There were no significant differences in the 5'-termini sequence between the veritas terminal sequence and the pseudo sequence. Helitrons not only can capture fragments, but were also shown to lose internal sequences during the course of transposing.ConclusionsThree putative autonomous elements were identified, which encoded an intact Rep motif and a DNA helicase domain, suggesting that autonomous helitrons may exist in modern maize. The results indicate that gene fragments captured during the transposition of many helitrons happen in a stepwise way, with multiple gene fragments within one helitron resulting from several sequential transpositions. In addition, we have proposed a potential mechanism regarding how helitrons with multiple termini are generated.
Highlights
As a newly identified category of DNA transposon, helitrons have been found in a large number of eukaryotes genomes
Gene capturing of helitrons can happen in a stepwise mode through sequential transpositions
Three putative autonomous helitrons were discovered in maize with intact replication initiator (Rep) motif and a DNA helicase (Hel) domain, similar to those identified in other species
Summary
As a newly identified category of DNA transposon, helitrons have been found in a large number of eukaryotes genomes. Helitrons have contributed significantly to the intra-specific genome diversity in maize. A new category of DNA TEs, have recently been uncovered by the computational analysis of genomic sequences of A. thaliana, O. sativa and C. elegans [3]. It was estimated that there might be tens of thousands elements in maize inbred line B73 [13,14]. They could capture gene fragments and move around the genome, which leads to gene diversity between the maize inbred lines [15]. Helitrons have contributed the remarkable variation of haplotype in the Bz (bronze) genomic locus among different maize inbred lines [16,17]. Two helitrons containing hundreds of copies in maize inbred line B73 have been identified [13]
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