Reconstruction of full-length LINE-1 progenitors from ancestral genomes (Supplementary Data)

<strong>Web Supplementary Files</strong> Web Supplementary File 1 - FASTA files containing full-length reconstruction input sequences<strong>: full_length_reconstruction_input_sequence_fastas.zip</strong> Web Supplementary File 2 - FASTA files containing Muscle alignments of the full-length reconstruction input sequences.<strong> full_length_reconstruction_input_sequence_alns.zip</strong> Web Supplementary File 3 - FASTA file of full-length reconstructed sequences:<strong> full_length_reconstructions.fa</strong> Web Supplementary File 4 - Table of full-length reconstruction statistics: <strong>full_length_reconstruction_stats.csv</strong> Web Supplementary File 5 - FASTA files containing ORF reconstruction input sequences:<strong> orf_fastas.zip</strong> Web Supplementary File 6 - FASTA files containing Macse alignments of the ORF reconstruction input sequences:<strong> ORF_reconstruction_input_sequence_alns.zip</strong> Web Supplementary File 7 - Table of ORF reconstruction statistics: <strong>ORF_reconstructions.fa</strong> Web Supplementary File 8 - Table of ORF reconstruction statistics: <strong>ORF_reconstruction_stats.csv</strong> Web Supplementary File 9 - Table of Composite Sequences: <strong>bestfl_selection_fixed_CS_seqs.csv</strong> Web Supplementary File 10 - Database of gold standards: <strong>L1_goldstandards.csv</strong> <strong>Data Underlying Figures</strong> RepeatMasker scans of hg38 and ancestral genomes:<strong> </strong><strong>anc_gen_RM_out_files.zip</strong> <strong>Figure 4</strong> 4A Source alignment of 54 composite sequences: <strong>220121_dropped12+L1ME3A_muscle.nt.afa</strong> Tree produced using the alignment and FastTree: <strong>220121_dropped12+L1ME3A.tree</strong> 4B Source alignment of 67 Dfam L1 subfamily 3’ end models: <strong>200123_dfam_3ends.fa.muscle.aln</strong> Tree produced using the alignment: <strong>200123_dfam_3ends.fa.muscle.aln.tree</strong> <strong>Figure 5</strong> KZFP-TE enrichment p-values (from Barazandeh <em>et al</em> 2018):<strong> TE_KZFP_enrichment_pvals.xlsx</strong> KZFP-TE top 500 peak overlap (from Barazandeh <em>et al</em> 2018): <strong>top500_peak_overlap.xlsx</strong> <strong>Figure 6</strong> RepeatMasker .out file for the Composite Sequence custom library queried against hg38: <strong>CS_RM_hg38.fa.out.gz</strong> <strong>Figure S2</strong> RepeatMasker scan .out file of hg38 (CG corrected Kimura Divergence values are in last column): <strong>hg38+KimDiv_RM.out</strong> RepeatMasker scan .out file of the Progressive Cactus eutherian ancestral genome (CG corrected Kimura Divergence values are in last column): <strong>Progressive_Cactus_Euth+KimDiv_RM.out</strong> RepeatMasker scan .out file of the Ancestors 1.1 eutherian ancestral genome (CG corrected Kimura Divergence values are in last column): <strong>Ancestors_Euth+KimDiv_RM.out</strong> <strong>Figure S5</strong> RepeatMasker scan .out files for Progressive Cactus simian and primate reconstructed ancestral genomes: <strong>progCactus_RM_outfiles.zip</strong> S5A FASTA files containing Cactus genome-derived reconstructed sequences equivalent to the L1MA2, L1MA4, and L1MD1-3 best full-length sequences: <strong>progCactus_reconstruction_bestFL_equivalents.zip</strong> S5B FASTA files containing Muscle alignments of Cactus genome-derived full-length reconstruction input sequences: <strong>progCactus_reconstruction_input_sequence_alns.zip</strong> <strong>Figure S6</strong> S6A Results of Conserved Domain scans of Cactus genome-derived full-length reconstructed sequences: <strong>CD_search_results_short_nms.txt</strong> S6B-D Character posterior probabilities of “best” full-length reconstructed sequences: <strong>best_fl_post_probs.zip</strong> <strong>Figure S7</strong> S7B-C Results of Conserved Domain scans of translated initial full-length reconstructed sequences: <strong>initial_recons_all_3frametrans_CD-search.txt</strong> Results of Conserved Domain scans of translated reconstructed ORFs: <strong>recons_ORF1-2_all_3frametrans_CD-search.csv</strong> <strong>Figure S15</strong> S15A Source alignment of 67 composite sequences: <strong>bestfl_selection_fixed_CS_seqs_muscle.nt.afa</strong> Tree produced using the alignment: <strong>bestfl_selection_fixed_CS_seqs_muscle.nt.afa.tree</strong> S15B-E Source Muscle alignments for phylogenetic trees of reconstructed sequence components: ORF2: <strong>ORF2_keep54_muscle.nt.afa</strong> 5’ UTR: <strong>5utr_keep54_muscle.nt.afa</strong> ORF1: <strong>ORF1_keep54_muscle.nt.afa</strong> 3’ UTR: <strong>3utr_keep54_muscle.nt.afa</strong> Trees produced using above alignments: ORF2: <strong>ORF2_keep54_muscle.nt.afa.tree</strong> 5’ UTR: <strong>5utr_keep54_muscle.nt.afa.tree</strong> ORF1: <strong>ORF1_keep54_muscle.nt.afa.tree</strong> 3’ UTR: <strong>3utr_keep54_muscle.nt.afa.tree</strong> <strong>Figure S17</strong> Unfiltered BLAST results of Composite Sequences queried against hg38: <strong>CS_hg38_blastn.csv.zip</strong> BED file of L1 instances annotated using BLAST pipeline: <strong>BLAST_L1_hits.bed</strong>