Annotation of natural transposable element (TE) insertions in genome data remains a challenge. To promote the feasibility of this task for individuals using a laptop computer, we created an optimized, multithreaded, and FlyBase-compatible transposable element mapper (release 0.1) which uses a similar algorithm to Linheiro and Bergman's "ngs_te_mappe" tool (Linheiro and Bergman, 2012). The TE mapper looks for split-reads on both ends of a potential transposon and uses an aligner to determine the identity of the transposon. To assess this new tool, we segmented each chromosome of the genomic sequence data available in FlyBase (version 6.34) into 150-base-pair-long fragments into one base pair increments, for 150x coverage, and ran our TE mapper on these synthetic "reads". We excluded all known natural transposons already annotated in r6.34, described in the FlyBase 'all transposons' file. The attached Table 1, "Novel Natural TE Insertions with Annotations", contains the insertion sites and annotations, and describes the position and annotation of 302 novel natural transposons not previously mapped or annotated in r6.34. Table 2, "New Annotations of Mapped natural TEs" describes natural transposon insertion sites that are mapped in FlyBase r6.34, but are incompletely annotated. This approach will improve the accessibility, efficiency, and accuracy of future efforts to map natural TE insertions from genome sequencing data. Attached Documents: Table 1: Novel Natural TE Insertions with Annotations (Rankin.2021.1.25-1.xlsx on FlyBase ftp site) Table 2: New Annotations of Mapped Natural TEs (Rankin.2021.1.25-2.xlsx on FlyBase ftp site) Reference R. S. Linheiro and C. M. Bergman, Whole genome resequencing reveals natural target site preferences of transposable elements in Drosophila melanogaster, PLOS One, 7(2):e30008 (2012) ----------------------------------------------------------------------- Sanath G. Govindarajan Phillips Exeter Academy and University of Texas at Austin Lutz Kockel Stanford University School of Medicine Seung K. Kim Stanford University School of Medicine Anne E. Rankin Phillips Exeter Academy
