Abstract
BackgroundHelitron 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.ResultsWe 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 Helitrons 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.ConclusionEAHelitron 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.
Highlights
Helitron is a rolling-circle DNA transposon; it plays an important role in plant evolution
All records of putative Helitrons were printed in FASTA format including the terminal ends, 3′ upstream and downstream sequences, possible full-length Helitron sequences, and a general feature format (GFF) annotation file (Fig. 1)
We investigated the evolutionary process of Helitrons in eight sibling genomes in Brassicaceae (Ath, Arabidopsis lyrata (Aly), Capsella rubella (Cru), Thellungiella parvula (Tpa), Brassica olerracea (Bol) v1, Bol v2, Brassica rapa (Bra), and Brassica napus (Bna)), and upstream 1kbp sequences of 3′ termini were chosen to search for conserved sequences showing highly similarity (Additional file 2: Table S6)
Summary
Helitron is a rolling-circle DNA transposon; it plays an important role in plant evolution. Helitrons transpose by rolling-circle replication (RCR) with only one strand cut and are important DNA transposons (Class II) in diverse eukaryotic genomes. They were discovered by data mining the Arabidopsis thaliana, Oryza sativa, and Caenorhabditis elegans genomes [3]. The family includes many important species, such as the model plant A. thaliana [7], the crop Brassica rapa [8], and Brassica oleracea (Cabbage) [9, 10] Many species in this family have sequenced genomes, which are useful for Helitron evolution research at family level.
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