Supplementary Data for "Active and unusually expanded PIF/Harbinger transposable elements in the Caenorhabditis inopinata genome"

Figure 2A Harbinger-1M_cIno_258_elements.fa - Sequences of Harbinger-1M_cIno-like TEs (n = 258). Figure 4A Harbinger-1M_cIno_clustering_consensus.fa - Consensus sequences for the 74 clusters obtained by clustering the 252 Harbinger-1M_cIno elements lacking a DDE domain. Harbinger-1M_cIno_clusters_prefix*.fa - Sequences of Harbinger-1M_cIno TEs belonging to clusters containing n ≥ 10 sequences and used for K2P calculations. Harbinger-1M_cIno_clusters_prefix*.k2p.allpairs.tsv - Output files containing the K2P calculation results for Harbinger-1M_cIno clusters containing n ≥ 10 sequences. Figure 4B blastN_Ci-PIFHarbinger_257_elements.blastN.renumbered.out.csv - BLASTN results for the other 257 elements queried against Ci_Harb_258. This file can be used as the input for Figure4B_blast_hits.R. Figure4B_blast_hits.R - R script used to generate Figure 4B. Figure 5A DDE_Tnp_phylo_set.fa - Input sequences used to construct the DDE transposase phylogenetic tree. DDE_Tnp_phylo_set.treefile - Phylogenetic tree file for the DDE transposases. Figure 6A Harbinger-2M_cIno_1376_elements.fa - Sequences of Harbinger-2M_cIno-like TEs (n = 1,376). Figure 6E Harbinger-2M_cIno_clustering_consensus.fa - Consensus sequences for the 79 clusters obtained by clustering the 1,376 Harbinger-2M_cIno elements. Harbinger-2M_cIno_clusters_prefix*.fa - Sequences of Harbinger-2M_cIno TEs belonging to clusters containing n ≥ 10 sequences and used for K2P calculations. Harbinger-2M_cIno_clusters_prefix*.k2p.allpairs.tsv - Output files containing the K2P calculation results for Harbinger-2M_cIno clusters containing n ≥ 10 sequences. Supplementary Fig. 5A MADF_phylo_set.fa - Input sequences used to construct the MADF phylogenetic tree. MADF_phylo_set.treefile - Phylogenetic tree file for MADF domains. Supplementary Fig. 5C Cino_Turmoil1_Turmoil2_MADF_domain.combined.aa.fa.aln.trim.phylip - File containing the Kimura protein distance matrix calculated from the amino acid sequences of MADF domains from Harbinger-1M_cIno and Harbinger-2M_cIno. This file can be used as the input for MADF_domain_diversity_essential.R. MADF_domain_diversity_essential.R - R script used to compare MADF-domain divergence between Harbinger-1M_cIno and Harbinger-2M_cIno.