SI Tables from Horizontal transfer and subsequent explosive expansion of a DNA transposon in sea kraits (Laticauda)

Table 1 - Laticauda colubrina and Laticauda laticaudata genes with Harbinger-Snek insertions into or overlapping open reading frames, and any noticeable effects on insertion noted from transcript data. Gene coordinates predicted with Liftoff [40] using the RefSeq Notechis scutatus assembly and gene annotation as reference. Repeat annotation performed with RepeatMasker [39] using a custom repeat library (see Methods). Intersect performed using BEDTools [54]. Transcripts mapped to the genome assembly using STAR [44] and viewed in IGV [45]. Table 2 - Biological processes with an over/under-representation of Harbinger-Snek insertions into Laticauda colubrina genes. Representation test performed using PANTHER [43]. Gene coordinates predicted with Liftoff [40] using the RefSeq Notechis scutatus assembly and gene annotation as reference. Repeat annotation performed with RepeatMasker [39] using a custom repeat library (see Methods). Intersect performed using plyranges [42]. Table 3 - Molecular functions with an over/under-representation of Harbinger-Snek insertions into Laticauda colubrina genes. Representation test performed using PANTHER [43]. Gene coordinates predicted with Liftoff [40] using the RefSeq Notechis scutatus assembly and gene annotation as reference. Repeat annotation performed with RepeatMasker [39] using a custom repeat library (see Methods). Intersect performed using plyranges [42]. Table 4 - Biological processes with an over/under-representation of Harbinger-Snek insertions into potential regulatory regions of Laticauda colubrina genes. Representation test performed using PANTHER [43]. Gene coordinates predicted with Liftoff [40] using the RefSeq Notechis scutatus assembly and gene annotation as reference. Repeat annotation performed with RepeatMasker [39] using a custom repeat library (see Methods). Intersect performed using plyranges [42]. Table 5 - Molecular functions with an over/under-representation of Harbinger-Snek insertions into potential regulatory regions of Laticauda colubrina genes. Representation test performed using PANTHER [43]. Gene coordinates predicted with Liftoff [40] using the RefSeq Notechis scutatus assembly and gene annotation as reference. Repeat annotation performed with RepeatMasker [39] using a custom repeat library (see Methods). Intersect performed using plyranges [42]. Table 6 - Latin species names and versions of all public genomes used. All were downloaded from RefSeq [41] when available, else from GenBank [55].