file	bytes	sha256	description	download_status
01_reference/OSU_TarKok_3.0_nuclear.final.fa	1212760619	5571cb7b0540846d441eb2c76ae39a6ce273479a95bb86b2c75eeb8fa7705ba9	Nuclear reference genome: 658 sequences, 1,192,836,847 bp.	Zenodo deposition pending
01_reference/OSU_TarKok_3.0_nuclear.softmasked.fa	1212760619	e62c2342c721c1248d14783d604cdf362271b2eea0025dd16e94c685a85a6585	Softmasked nuclear reference genome: 658 sequences, 1,192,836,847 bp; lowercase bases mark repeats (924,495,754 bp; 77.504%).	Zenodo deposition pending
02_structural/OSU_TarKok_3.0_nuclear.BRAKER3.gff3	52533287	de6d1034408c268124b30f944405930cf59bda5eebc555bb2b185e1f50861cc4	BRAKER3 protein-coding gene models: 34,637 genes and 39,326 transcripts. GFF3 coordinates are 1-based and inclusive.	Zenodo deposition pending
02_structural/OSU_TarKok_3.0_nuclear.UTR_augmented.gff3	85631525	c6cb238792bcaef28f72d102944133288401d1d3bf0172856a4d76a782d8c59d	Nuclear gene models with exons and untranslated regions (UTRs). GFF3 coordinates are 1-based and inclusive.	Zenodo deposition pending
02_structural/OSU_TarKok_3.0_nuclear.cds.fa	43712600	47820435143755a97c986dafd79e04e6d6ca2e94572b37beb51b74ec26f39acb	Coding DNA sequences (CDS) for 39,326 nuclear transcripts; FASTA identifiers are transcript IDs.	Zenodo deposition pending
02_structural/OSU_TarKok_3.0_nuclear.longest_valid_per_gene.aa	12922163	d583fc3fe7a25c514d1ed37b68a2438ffe60796a4d2880c886a1d0b3aaa84ce1	One representative protein sequence per nuclear gene: 34,637 proteins; FASTA identifiers are transcript IDs.	Zenodo deposition pending
02_structural/OSU_TarKok_3.0_nuclear.proteins.all_isoforms.fa	14864353	5b4b6890b3bce3f150ba2c64f89a45037500ed6cfc5d5bb938ec81b4975f0949	Protein sequences for all 39,326 nuclear transcript isoforms; FASTA identifiers are transcript IDs.	Zenodo deposition pending
02_structural/gene_transcript_representative_map.tsv	1727766	0a8ef2ff5f98b229cb917677ef7d0929c1f323dac347a4ecb17182883a0bb81c	Gene-to-transcript mapping with genomic coordinates and strand; representative_protein=1 marks the selected protein for each gene.	Zenodo deposition pending
03_functional/OSU_TarKok_3.0_nuclear.functional_annotation.tsv	487981456	e53a866da1d8eb8728841ff314e6ba6d08f1ee4971959bf30c35e20a1a0a7eb3	Integrated functional annotations for 39,326 nuclear proteins. protein_id matches the protein FASTA; empty cells indicate no reported annotation; multiple plantiSMASH clusters are separated by semicolons.	Zenodo deposition pending
03_functional/eggnog/OSU_TarKok_3.0_nuclear.emapper.annotations.tsv	21612193	c0e6941068db052fe3cf5889625ffac32749dcd232461d5e018f5554c7167f4f	eggNOG-mapper functional and orthology annotations for 35,307 proteins, including GO, KEGG, COG and Pfam assignments; query matches the protein FASTA.	Zenodo deposition pending
03_functional/iTAK/TF_TR.representative_per_gene.tsv	63498	750718761f0683a3da72a966f30b58840197468634239900b2ca2e7ac273c415	iTAK transcription factor (TF) and transcriptional regulator (TR) families for 2,255 representative proteins (1,826 TF and 429 TR).	Zenodo deposition pending
03_functional/iTAK/shiu_classification.nuclear.tsv	35553	a849f922e94e7bea62df46e04b0ba9c3e304710a82edfe9d5daa67d2636ab0d6	iTAK kinase-family assignments for 1,409 nuclear proteins; protein_id matches the protein FASTA.	Zenodo deposition pending
03_functional/iTAK/tf_classification.nuclear.tsv	75312	16acd03fd824c486bc86d341af4c95cc812fa9004b2e27c90372022c642c5015	iTAK transcription factor (TF) and transcriptional regulator (TR) families for 2,677 nuclear protein isoforms.	Zenodo deposition pending
03_functional/interproscan/OSU_TarKok_3.0_nuclear.interproscan.tsv	1890298296	b4adc7cb23b6f9d3135782ec38746694e1c419fdf1f66a9f9a0c773642e0d2aa	InterProScan domain and signature matches (348,553 rows). Headerless columns: protein_id, MD5, length, analysis, signature_accession, signature_description, start, end, score, status, date; optional columns: InterPro_accession, InterPro_description, GO, pathways. Match coordinates are 1-based and inclusive.	Zenodo deposition pending
03_functional/tracks/dbcan.nuclear.tsv	529266	e76101cba4be525c5fc2247d182e46bb3730eaa376295c318df37b2e4d8c3756	dbCAN carbohydrate-active enzyme families, subfamilies and number of supporting tools per protein; empty cells indicate no reported annotation.	Zenodo deposition pending
03_functional/tracks/kofamscan.nuclear.tsv	1344301	7e3436a44a10c31a0298afd9f32b074fded32e460cda505e3052c1d0ce2d3802	KofamScan KEGG Orthology (KO) assignments, thresholds, scores and definitions per protein; empty cells indicate no reported annotation.	Zenodo deposition pending
03_functional/tracks/targetp2_localization.nuclear.tsv	564993	5ac54a3ccb6d439172474a6a43e3eaa017447f5f73e322d836f5ab8424b6653d	TargetP 2 targeting-peptide predictions for 39,326 proteins: SP, signal peptide; mTP, mitochondrial; cTP, chloroplast; luTP, thylakoid lumen; noTP, no targeting peptide predicted.	Zenodo deposition pending
04_ncRNA/OSU_TarKok_3.0_nuclear.ncRNA.gff3	2717875	cedfcb77ebf7273f82c09112a7f07aaee76245b1db244a2ccc47fb4f9d92fbbd	Combined nuclear non-coding RNA predictions (18,630 records), including rRNA, tRNA and other ncRNAs. GFF3 coordinates are 1-based and inclusive.	Zenodo deposition pending
04_ncRNA/OSU_TarKok_3.0_nuclear.ncRNA.tsv	2717942	0172f583af7347e93a1448b5e4ea1c2a48409d41bbc67dd047513e6ad23adb0e	Tabular nuclear non-coding RNA predictions (18,630 records), with genomic coordinates, RNA classes and prediction attributes; coordinates are 1-based and inclusive.	Zenodo deposition pending
05_repeats_TE/OSU_TarKok_3.0_nuclear.EDTA.TEanno.gff3	159187730	dc7e3f5f00523acdd77ebda44324eeca4716171dadb5ec450591ee3accb8978f	Genome-wide EDTA transposable-element annotations in GFF3; coordinates are 1-based and inclusive.	Zenodo deposition pending
05_repeats_TE/OSU_TarKok_3.0_nuclear.EDTA.intact.gff3	43673948	a6f79619d182573d96cbb08907d5235dc13a8ac048705efa9506d64b7530f953	Genome-wide EDTA annotations of intact transposable elements in GFF3; coordinates are 1-based and inclusive.	Zenodo deposition pending
05_repeats_TE/OSU_TarKok_3.0_nuclear.RepeatMasker.gff3	360988535	5c557656b6214bb3c35737775cfc7a66c71ca3407e3f90c6eadf8e7a7a5c2361	RepeatMasker nuclear repeat annotations in GFF3. Coordinates are 1-based and inclusive; repeat_group links fragments of the same repeat; Target gives valid repeat-consensus coordinates.	Zenodo deposition pending
06_plantiSMASH/OSU_TarKok_3.0_nuclear.plantismash.clusters.gff3	6168	087db6eb75b50548359c303e9a9203204337d1971e27ffb04642facead3c9965	Genomic intervals of 42 predicted plantiSMASH biosynthetic gene clusters. GFF3 coordinates are 1-based and inclusive.	Zenodo deposition pending
06_plantiSMASH/OSU_TarKok_3.0_nuclear.plantismash.clusters.tsv	2049	200a32f825089236fcd5ec7b97aa8263179e3504d7703a8305de40af40bb3002	Identifiers, genomic coordinates and types of 42 predicted plantiSMASH biosynthetic gene clusters; coordinates are 1-based and inclusive.	Zenodo deposition pending
06_plantiSMASH/OSU_TarKok_3.0_nuclear.plantismash.gene_membership.tsv	23344	c62b3b33f8d42f2ea94a2466499714fd9da896bf4a931436217f7f828f9c6897	Nuclear gene membership in predicted plantiSMASH biosynthetic gene clusters; one row per gene–cluster pair.	Zenodo deposition pending
07_chloroplast/OSU_TarKok_3.0_chloroplast.curated.gff3	74659	69ff9134cdc9d5ff836d07d57cc1e077b05224c76eb3be6c755dd7b2c9e6d31a	Curated chloroplast gene annotations in GFF3, including CDS, tRNA and rRNA features; coordinates are 1-based and inclusive. Multipart CDS and translation exceptions are retained.	Zenodo deposition pending
07_chloroplast/chloroplast.cds.fa	89969	04fcd82f9936540977fa92d3d09f16ad8fbf647d2d518d1882b52687ba358978	Chloroplast coding DNA sequences: 88 CDS records.	Zenodo deposition pending
07_chloroplast/chloroplast.genes_with_introns.fa	122172	8d8607821b80190af16879d289b7e1504449cecc990313f0ce649fb1d4e69941	Chloroplast gene sequences: 134 records, including introns where present.	Zenodo deposition pending
07_chloroplast/chloroplast.proteins.fa	36667	69a5419cfdeb09aee991b051c125344dda0744b2b5fdee4b16a09de189076257	Chloroplast protein sequences: 88 records.	Zenodo deposition pending
07_chloroplast/chloroplast.rRNA.fa	9978	9e8cf2bf4062e3f39fc62381033069d4ba6a7f1f70f71367376afa505d68d790	Chloroplast ribosomal RNA sequences: 8 records.	Zenodo deposition pending
07_chloroplast/chloroplast.tRNA.fa	6290	e007413011b2012307f2d774d910247743eaaee03426d4b1d2c8ff2d858e7dcd	Chloroplast transfer RNA sequences: 37 records.	Zenodo deposition pending
08_OrthoFinder/OSU_TarKok_3.0_nuclear.orthogroup_assignments.tsv	1228498	e27dd2c4d59d3c7b7ab1405b78aab92cda0f41c0d470a05402443b6cd0f5a95b	Orthogroup assignments for 34,637 OSU representative proteins and their gene IDs: 32,795 assigned and 1,842 unassigned.	Zenodo deposition pending
08_OrthoFinder/Orthogroups.GeneCount.tsv	989218	050507cc13e5e8a4e888ce143f7cc1e25ddc8d05c9294153e926d430733f048f	Gene counts for 33,849 orthogroups across eight proteomes; Total is the sum across proteomes. Proteome labels are defined in Orthogroups.tsv.README.txt.	Zenodo deposition pending
08_OrthoFinder/Orthogroups.tsv	4349978	3feebd8b30d199696bac31a97945a3244c372d6fe5b09e98b6a058c40340fe1c	Protein membership of 33,849 orthogroups across eight proteomes from seven species; multiple protein IDs are comma-separated. Proteomes: C_endivia=Cichorium endivia; C_intybus=Cichorium intybus; L_saligna=Lactuca saligna; L_sativa=Lactuca sativa; L_virosa=Lactuca virosa; T_mongolicum=Taraxacum mongolicum; Tks_OSU=Taraxacum kok-saghyz OSU; Tks_TK1151=Taraxacum kok-saghyz TK1151.	Zenodo deposition pending
08_OrthoFinder/Orthogroups_SingleCopyOrthologues.txt	49539	279bf2b293833fd1355cf767398e52559e1cb2bedc5223117a9daa081e9efe93	Identifiers of 4,954 orthogroups containing exactly one gene in each of the eight proteomes; membership is listed in Orthogroups.tsv.	Zenodo deposition pending
08_OrthoFinder/SpeciesTree_rooted_node_labels.txt	251	659c694b7390b5dbe94df305932ff9a78067818f889eeb687a9cd464de692f1d	Rooted phylogenetic tree of the eight proteomes in Newick format, with branch lengths and internal node labels. Proteome labels are defined in Orthogroups.tsv.README.txt.	Zenodo deposition pending
08_OrthoFinder/Tks_OSU__v__Tks_TK1151.tsv	902542	d01d3df85321e578d41689c08585f2f349dad5652da764357c19388b955c13d8	Orthology relationships between Taraxacum kok-saghyz OSU and TK1151 proteins: 21,706 rows, including 16,227 one-to-one relationships; comma-separated IDs represent multiple orthologues.	Zenodo deposition pending