Horizontal transposon transfer and its implications for the ancestral ecology of hydrophiine snakes
Authors/Creators
- 1. School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- 2. School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
- 3. Venom Supplies Pty Ltd., Tanunda, South Australia, Australia
- 4. School of Biological Sciences, University of East Anglia, Norwich Research Park, NR4 7TU, Norwich, United Kingdom
Description
Transposable elements (TEs), also known as jumping genes, are sequences able to move or copy themselves within a genome. As TEs move throughout genomes they often act as a source of genetic novelty, hence understanding TE evolution within lineages may help in understanding environmental adaptation. Studies into the TE content of lineages of mammals such as bats have uncovered horizontal transposon transfer (HTT) into these lineages, with squamates often also containing the same TEs. Despite the repeated finding of HTT into squamates, little comparative research has examined the evolution of TEs within squamates. Here we examine a diverse family of Australo-Melanesian snakes (Hydrophiinae) to examine if the previously identified, order-wide pattern of variable TE content and activity holds true on a smaller scale. Hydrophiinae diverged from Asian elapids ~15-25 Mya and have since rapidly diversified into six amphibious, ~60 marine and ~100 terrestrial species which fill a broad range of ecological niches. We find TE diversity and expansion differs between hydrophiines and their Asian relatives and identify multiple HTTs into Hydrophiinae, including three likely transferred into the ancestral hydrophiine from fish. These HTT events provide the first tangible evidence that Hydrophiinae reached Australia from Asia via a marine route.
Table S1. Genbank accession numbers, assembly names and binomial names of the 2314 metazoan genomes assemblies investigated as the potential sources of the horizontally transferred TEs.
Data S1. RepeatMasker output of elapid genomes and repeat library used for said masking. Genome assemblies annotated with RepeatMasker using a custom library of curated RepeatModeler2 libraries and previously described lepidosaur TEs from the Repbase RepeatMasker library.
Data S2. Filtered output of BLASTN 2.7.1+ (-task dc-megablast) searches of the 2314 metazoan genomes assemblies for HT candidates. Of the 2314 genomes searched, only 373 contained hits of significant quality (>70% pairwise identity, >50% coverage).
Data S3. Nucleotide multiple sequence alignments of each HT candidate and the curated consensus sequences identified in other species. Sequences were aligned using MAFFT v7.453 (--localpair).
Data S4. Phylogenies of each HT candidate and the curated consensus sequences identified in other species. Trees constructed using FastTree 2.1.1.1.