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Background  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. 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.    Results  The 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.    Conclusions  Three 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.

Structural characterization of helitrons and their stepwise capturing of gene fragments in the maize genome