Long-read-based genome assembly reveals numerous endogenous viral elements in the green algal bacterivore <i>Cymbomonas tetramitiformis</i>

Additional data for the paper Gyaltshen, Rozenberg et al (2023) Long-read-based genome assembly reveals numerous endogenous viral elements in the green algal bacterivore Cymbomonas tetramitiformis, Genome Biol Evol 15(11):evad194. doi:10.1093/gbe/evad194. The files are as follows: Genome annotationInferno_Rfam.tblout - results of ncRNA predictiontRNA-ScanSE.tab - tRNA predictionsbraker_fixed.faa - protein sequencesbraker_fixed.gff - corrected gff gene annotationsbraker_original.gtf - original braker gene annotationseggnog.emapper.annotations - eggnog functional annotationsinterproscan.xml - interproscan functional annotations (xml)interproscan.tsv - interproscan functional annotations (tsv)RED.bed - genome masking (unmodified RED masking)masking.bed - genome masking (RED masking [subtracting regions of gene homologs in other prasinophytes] and viral elements)Viruses All_MCP_sequences.zip - all PLV and NCLDV MCP protein sequencesViruses_mcl_genes.tsv - clustering and function predictions for genes from selected viral elements using remote homologyViruses_phylogeny_AG_03_multigene.jtree - multigene phylogeny of AG_03 and related viruses, in jtree formatViruses_phylogeny_PLVs_MCP.jtree - PLV phylogeny based on MCP, in jtree formatViruses_phylogeny_AG_03_multigene.jtreeViruses_phylogeny_AG_03_multigene.zipViruses_phylogeny_PLVs_MCP.jtreeViruses_phylogeny_PLVs_MCP.zipViruses_locations_including_fragments.bedViruses_representatives.zipjcf7180000139292_CtGEV.gbk - annotation of scaffold jcf7180000139292 (CtGEV with a PLVB insert) in Genbank formatjcf7180000174485_CHeCME.gbk - annotation of scaffold jcf7180000174485 (a CHeCME representative flanked by two near-identical RT genes) in Genbank formatBacteria.zip - bacterial scaffoldsBusco.zip - busco resultsCymbomonas_tetramitiformis_genome.gbf - annotated genome in Genbank formatCymbomonas_tetramitiformis_genome.faa - protein sequences in fasta format