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Background   Helitron  is a rolling-circle DNA transposon; it plays an important role in plant evolution. However,  Helitron  distribution and contribution to evolution at the family level have not been previously investigated.    Results  We developed the software easy-to-annotate  Helitron  (EAHelitron), a Unix-like command line, and used it to identify  Helitrons  in a wide range of 53 plant genomes (including 13 Brassicaceae species). We determined  Helitron  density (abundance/Mb) and visualized and examined  Helitron  distribution patterns. We identified more than 104,653  Helitrons , including many new  Helitron s not predicted by other software. Whole genome  Helitron  density is independent from genome size and shows stability at the species level. Using linear discriminant analysis, de novo genomes (next-generation sequencing) were successfully classified into  Arabidopsis thaliana  groups. For most Brassicaceae species,  Helitron  density negatively correlated with gene density, and  Helitron  distribution patterns were similar to those of  A. thaliana . They preferentially inserted into sequence around the centromere and intergenic region. We also associated 13  Helitron  polymorphism loci with flowering-time phenotypes in 18  A. thaliana  ecotypes.    Conclusion  EAHelitron is a fast and efficient tool to identify new  Helitrons . Whole genome  Helitron  density can be an informative character for plant classification.  Helitron  insertion polymorphism could be used in association analysis.    Electronic supplementary material  The online version of this article (10.1186/s12859-019-2945-8) contains supplementary material, which is available to authorized users.

Helitron distribution in Brassicaceae and whole Genome Helitron density as a character for distinguishing plant species