English (United Kingdom)

https://curated-unify.zendy.io/wp-json/zendy-region/v1/featured_content/oa?rat=en

https://curated-unify.zendy.io/wp-json/zendy-region/v1/highlighted_journal/

Global: Zendy Plus annual

Presents the access of premium content as premium feature

Premium Content

Presents the keyphrase highlighting as premium feature

Keyphrase Highlighting

Presents the summarisation as premium feature

Summarisation

Insights

Presents the pdf analysis as premium feature

PDF Analysis

Presents the zaia usage as premium feature

ZAIA

Global: Zendy Tools annual

Global: Zendy Free Plan

Global: Zendy Tools monthly

Global: Zendy Plus monthly

Background   Helitrons  represent a new class of transposable elements recently uncovered in plants and animals. One remarkable feature of  Helitrons  is their ability to capture gene sequences, which makes them of considerable potential evolutionary importance. However, because  Helitrons  lack the typical structural features of other DNA transposable elements, identifying them is a challenge. Currently, most researchers identify  Helitrons  manually by comparing sequences. With the maize whole genome sequencing project underway, an automated computational  Helitron  searching tool is needed. The characterization of  Helitron  activities in maize needs to be addressed in order to better understand the impact of  Helitrons  on the organization of the genome.    Results  We developed and implemented a heuristic searching algorithm in PERL for identifying  Helitrons . Our HelitronFinder program will (i) take FASTA-formatted DNA sequences as input and identify the hairpin looping patterns, and (ii) exploit the consensus 5' and 3' end sequences of known  Helitrons  to identify putative ends. We randomly selected five predicted  Helitrons  from the program's high quality output for molecular verification. Four out of the five predicted  Helitrons  were confirmed by PCR assays and DNA sequencing in different maize inbred lines. The HelitronFinder program identified two head-to-head dissimilar  Helitrons  in a maize BAC sequence.    Conclusion  We have identified 140 new  Helitron  candidates in maize with our computational tool HelitronFinder by searching maize DNA sequences currently available in GenBank. Four out of five candidates were confirmed to be real by empirical methods, thus validating the predictions of HelitronFinder. Additional points to emerge from our study are that  Helitrons  do not always insert at an AT dinucleotide in the host sequences, that they can insert immediately adjacent to an existing  Helitron , and that their movement may cause changes in the flanking region, such as deletions.

Computational prediction and molecular confirmation of Helitron transposons in the maize genome