DOI: 10.5281/zenodo.15297793
title: Supplementary Datasets for "Phylogenetic relatedness rather than aquatic habitat fosters horizontal transfer of transposable elements in animals"

description: Dataset S1. Metadata on the 247 assemblies of the study.Information on species name, their GenBank IDs, their taxonomic group as defined in this study, their habitat, the busco database used to run Busco, their genome size, N50, the percentage of complete BUSCO genes we recovered, and statistics on their TE content.

Dataset S2. Phylogenetic tree of the 247 species in newick format.

Dataset S3. TE-TE hits clustered per clade.This table is the final output of script 12. Each line corresponds to one TE-TE hit. It only contains hits that passed the three filters in Figure S2. “copy1” and “copy2” indicate the names of the two copies invoved in the hit, while “ID.1” and “ID.2” corresponds to their numerical identifier. “TEconsensus.1” and “TEconsensus.2” are the name of the consensus from the TE library we used to run RepeatMasker. “superfamily” indicates the superfamily of both TE copies. “species.1” and “species.2” indicate the species names of the two host genomes. “divTime” is the additive divergence time between both species and “mrca” indicates their clade identifier as in the newick tree. “pID”, “length”, “qStart”, and “sEnd” are the output of the second similarity search (dc-megablast). dS and dN indicate the synonymous and the non-synonymous distance, reciprocally. “length.aa” indicates the length of the coding region. All hits of a same community get the same value in “community” and those of a same hit group get the same value in “hitGroup”. Thus, all TE copies involved in a same transfer can be recovered by selecting lines whose hit group value is the same. “independent” indicates whether this hit can be explained by another one (FALSE) or not (TRUE). “subclass” indicates whether this TE superfamily is a Class 1 (RNA) or Class 2 (DNA) TE. The number of independent events of horizontal transfers across the dataset conresponds to the number of unique values of hit groups for which "independent" equals true.

Dataset S4. TE-TE hits clustered per pair of species.Each line corresponds to one TE-TE hit. It only contains hits that passed the three filters in Figure S2. All columns are the same as in Dataset S3, except that “community” and “hitGroup” correspond to clustering per pair of species. Here, each count of hit groups between a pair of species is not affected by the other species composing the dataset. However, an event of horizontal transfer can be counted several times in different pairs of related species.

Dataset S5. Number of horizontal transfers we recovered in each pair of species.From Dataset S4, we counted the total number of horizontal transfers (column “n”) in which each pair of species is involved. It contains all pairs of species for which we could look for horizontal transfers, even those involved in no horizontal transfer. Species of a same species unit have the same “spClade”. Species alone in their species unit takes their own species name, otherwise it takes the mrca value of the last common ancestor of the species unit. “pairClade” indicates the pair of species unit corresponding to the pair of species.

Dataset S6. Total number and total predicted number of horizontal transfers.From Dataset S4, we counted the total number of horizontal transfers in which each species is involved, seperately for TE of Class 1 and 2. Predicted numbers result of the Bayesian modeling, in which  additive divergence time was fixed at 500 Myrs and habitat was assumed to be shared.

Dataset S7. Part of the TE library used for TE annotation.This library is the result of a de novo annotation of 245 of the 247 genomes of the current study (recovered with RepeatModeler v2), to which we added TEs recovered from Peccoud et al. (2017), Zhang et al. (2020), and Chebbi et al. (2019) for A. vulgare's TE. While the TE library we used in the present study also includes TE consensus from Repbase, downloaded in February 2022, they are not included in this supplemental dataset because sequences from Repbase cannot be freely shared. After removing TE consensus shorter than 300bp, not classified at the superfamily level, SINEs, satellites and tandem repeats, our final TE library includes 284,643 TE consensus, 223,414 of which are freely available in the present dataset.