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

Abstract

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.

A chromosome-level genome assembly for the Pacific oyster (Crassostrea gigas)

“…In maize, Helitrons have significantly influenced genome evolution, leading to genome variation among lines [73] and to a notable diversification of transcripts via exon shuffling of thousands of genes [74]. To refine the annotation of Pacific oyster Helitrons , a structure-based search [75] was performed in addition to the homology based approach described above. The localization of these elements was heterogeneous across the Pacific oyster chromosomes, with LG5 and LG8 showing a higher density of elements (>1SD above the average across chromosomes) (Figure S9).…”

The genome of Draba nivalis shows signatures of adaptation to the extreme environmental stresses of the Arctic

“…Consistent with A. alpina , A. lyrata , and A. thaliana , LTR‐RT density increases in pericentromeric regions of each chromosome, TIR density decreases in pericentromeric regions, and Helitron density is stable along chromosomes. Abundance of LTR‐RT Copia and Gypsy elements is similar to that of A. alpina (Choudhury et al., 2017), whereas TIR‐CACTA elements and Helitrons seem to be particularly abundant in D. nivalis (Hu et al., 2019). Nucleotide divergence among LTR‐RTs identifies several Copia and Gypsy LTR‐RTs showing recent transposition bursts across the genome of D. nivalis .…”

slim shadyis a novel allele of PHYTOCHROME B present in the T-DNA line SALK_015201

“…et al, Yoshida et al, 2018;David et al, 2019) and are thought to be an unintended consequence of the T-DNA integration process (Tax and Vernon, 2001;Castle et al, 1993;Negruk et al, 1996;Nacry et al, 1998;Laufs et al, 1999). Previously a whole genome sequence was performed for SALK_015201 (Hu et al, 2019). Remapping and variant call analysis of these genomic sequences identified a single base pair deletion of a T nucleotide in the PHYTOCHROME B gene (AT2G18790) at position Chr2:8144002, which corresponds to position 3,370 in the PHYB cDNA ( Figure 4A; Supplemental Figure 7).…”

“…A long hypocotyl phenotype in SALK_015201 lines had been previously reported (Petrov et al, 2013) but a second T-DNA allele in IRR had a wild-type phenotype, prompting us to reconsider the genetic lesion responsible for the long hypocotyl phenotype. Analysis of whole genome sequence data available for this SALK line (Hu et al, 2019) identified a single base pair deletion within the coding sequence of PHYB. Transcriptomic comparison of SALK_015201 and wild type seedlings with and without auxin determined that genes associated with the BAP regulatory module (Bouré et al, 2019) were altered in this T-DNA background.…”