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

Abstract

<p>Abstract</p> <p>Background</p> <p>As a newly identified category of DNA transposon, <it>helitrons </it>have been found in a large number of eukaryotes genomes. <it>Helitrons </it>have contributed significantly to the intra-specific genome diversity in maize. Although many characteristics of <it>helitrons </it>in the maize genome have been well documented, the sequence of an intact autonomous <it>helitrons </it>has not been identified in maize. In addition, the process of gene fragment capturing during the transposition of <it>helitrons </it>has not been characterized.</p> <p>Results</p> <p>The whole genome sequences of maize inbred line B73 were analyzed, 1,649 <it>helitron</it>-like transposons including 1,515 helAs and 134 helBs were identified. <it>ZmhelA1</it>, <it>ZmhelB1 </it>and <it>ZmhelB2 </it>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 <it>helitrons </it>in other organisms. The putative autonomous <it>ZmhelB1 </it>and <it>ZmhelB2 </it>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 <it>helitrons </it>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 <it>helitrons </it>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. <it>Helitrons </it>not only can capture fragments, but were also shown to lose internal sequences during the course of transposing.</p> <p>Conclusions</p> <p>Three putative autonomous elements were identified, which encoded an intact Rep motif and a DNA helicase domain, suggesting that autonomous <it>helitrons </it>may exist in modern maize. The results indicate that gene fragments captured during the transposition of many <it>helitrons </it>happen in a stepwise way, with multiple gene fragments within one <it>helitron </it>resulting from several sequential transpositions. In addition, we have proposed a potential mechanism regarding how <it>helitrons </it>with multiple termini are generated.</p