Stowaway miniature inverted repeat transposable elements 2019

18,518 DcSto insertion sites were identified across 31 genomes of D. carota. To identify insertion sites of 14 DcSto families we used RelocaTE with consensus sequences representing DcSto families. RelocaTE allowed identification of TE insertions from unassembled short reads.

This analysis consists of those stowaway annotations from the referenced publication present in Additional file 1: "DcSto annotation: contains gff3 annotations of 18.5 K DcSto insertions identified in 31 carrot genomes". In the gff3 file, for each insertion the ‘start position’ referred to the second nucleotide (A) of the target site (TA), while the ‘end position’ referred to the first nucleotide of the DcSto element, in the case of insertions present in the reference genome DH1, or to the first nucleotide following the target site, in the case of insertions not mapped to DH1. For each insertion, a note containing information about its genomic position was given, as well as the LOC number of the adjacent gene, when the DcSto copy was inserted in a genic region (less than 2 kb from the gene). The ID field contained information about the DcSto family to which the copy was attributed, and comma separated codes of accessions carrying the insertion.

Data from this analysis can be viewed in JBrowse here.