Category Resource ID Resource name Species Accession BioProject File or subresource Source URL Original download URL Website use Reference ID Paper title Publication year DOI Paper URL Paper relationship Verification basis Limitations Historical catalogue ID Included runs Uniform-v4 runs Species verification Mirror URL Species code Evidence type Material or scope Evidence boundary Reference genome REF_TK1151 TK1151 / GWHBCHF00000000 Taraxacum kok-saghyz GWHBCHF00000000 PRJCA005187 Dna https://ngdc.cncb.ac.cn/gwh/Assembly/19732/show https://download.cncb.ac.cn/gwh/Plants/Taraxacum_kok-saghyz_Tao_Lin_GWHBCHF00000000/GWHBCHF00000000.genome.fasta.gz Primary reference, formal gene IDs, genome annotation and sequences, and uniform-model coordinates REF001 Extensive sequence divergence between the reference genomes of Taraxacum kok-saghyz and Taraxacum mongolicum 2022 10.1007/s11427-021-2033-2 https://doi.org/10.1007/s11427-021-2033-2 Original reference genome publication Official accession records and download listings checked on 2026-10-03 Repository API explicitly links accession to this DOI; use formal volume year, distinguish earlier online year. Direct files are repository-provided; no bulk genome download was required. Reference genome REF_TK1151 TK1151 / GWHBCHF00000000 Taraxacum kok-saghyz GWHBCHF00000000 PRJCA005187 Gff https://ngdc.cncb.ac.cn/gwh/Assembly/19732/show https://download.cncb.ac.cn/gwh/Plants/Taraxacum_kok-saghyz_Tao_Lin_GWHBCHF00000000/GWHBCHF00000000.gff.gz Primary reference, formal gene IDs, genome annotation and sequences, and uniform-model coordinates REF001 Extensive sequence divergence between the reference genomes of Taraxacum kok-saghyz and Taraxacum mongolicum 2022 10.1007/s11427-021-2033-2 https://doi.org/10.1007/s11427-021-2033-2 Original reference genome publication Official accession records and download listings checked on 2026-10-03 Repository API explicitly links accession to this DOI; use formal volume year, distinguish earlier online year. Direct files are repository-provided; no bulk genome download was required. Reference genome REF_TK1151 TK1151 / GWHBCHF00000000 Taraxacum kok-saghyz GWHBCHF00000000 PRJCA005187 Rna https://ngdc.cncb.ac.cn/gwh/Assembly/19732/show https://download.cncb.ac.cn/gwh/Plants/Taraxacum_kok-saghyz_Tao_Lin_GWHBCHF00000000/GWHBCHF00000000.RNA.fasta.gz Primary reference, formal gene IDs, genome annotation and sequences, and uniform-model coordinates REF001 Extensive sequence divergence between the reference genomes of Taraxacum kok-saghyz and Taraxacum mongolicum 2022 10.1007/s11427-021-2033-2 https://doi.org/10.1007/s11427-021-2033-2 Original reference genome publication Official accession records and download listings checked on 2026-10-03 Repository API explicitly links accession to this DOI; use formal volume year, distinguish earlier online year. Direct files are repository-provided; no bulk genome download was required. Reference genome REF_TK1151 TK1151 / GWHBCHF00000000 Taraxacum kok-saghyz GWHBCHF00000000 PRJCA005187 Cds https://ngdc.cncb.ac.cn/gwh/Assembly/19732/show https://download.cncb.ac.cn/gwh/Plants/Taraxacum_kok-saghyz_Tao_Lin_GWHBCHF00000000/GWHBCHF00000000.CDS.fasta.gz Primary reference, formal gene IDs, genome annotation and sequences, and uniform-model coordinates REF001 Extensive sequence divergence between the reference genomes of Taraxacum kok-saghyz and Taraxacum mongolicum 2022 10.1007/s11427-021-2033-2 https://doi.org/10.1007/s11427-021-2033-2 Original reference genome publication Official accession records and download listings checked on 2026-10-03 Repository API explicitly links accession to this DOI; use formal volume year, distinguish earlier online year. Direct files are repository-provided; no bulk genome download was required. Reference genome REF_TK1151 TK1151 / GWHBCHF00000000 Taraxacum kok-saghyz GWHBCHF00000000 PRJCA005187 Protein https://ngdc.cncb.ac.cn/gwh/Assembly/19732/show https://download.cncb.ac.cn/gwh/Plants/Taraxacum_kok-saghyz_Tao_Lin_GWHBCHF00000000/GWHBCHF00000000.Protein.faa.gz Primary reference, formal gene IDs, genome annotation and sequences, and uniform-model coordinates REF001 Extensive sequence divergence between the reference genomes of Taraxacum kok-saghyz and Taraxacum mongolicum 2022 10.1007/s11427-021-2033-2 https://doi.org/10.1007/s11427-021-2033-2 Original reference genome publication Official accession records and download listings checked on 2026-10-03 Repository API explicitly links accession to this DOI; use formal volume year, distinguish earlier online year. Direct files are repository-provided; no bulk genome download was required. Reference genome REF_TK1151 TK1151 / GWHBCHF00000000 Taraxacum kok-saghyz GWHBCHF00000000 PRJCA005187 Feature https://ngdc.cncb.ac.cn/gwh/Assembly/19732/show https://download.cncb.ac.cn/gwh/Plants/Taraxacum_kok-saghyz_Tao_Lin_GWHBCHF00000000/GWHBCHF00000000.feature.gz Primary reference, formal gene IDs, genome annotation and sequences, and uniform-model coordinates REF001 Extensive sequence divergence between the reference genomes of Taraxacum kok-saghyz and Taraxacum mongolicum 2022 10.1007/s11427-021-2033-2 https://doi.org/10.1007/s11427-021-2033-2 Original reference genome publication Official accession records and download listings checked on 2026-10-03 Repository API explicitly links accession to this DOI; use formal volume year, distinguish earlier online year. Direct files are repository-provided; no bulk genome download was required. Reference genome REF_OH1004 OH-1004 / OSU_TarKok_2.0 Taraxacum kok-saghyz GCA_047496595.1 PRJNA792143 GCA_047496595.1_OSU_TarKok_2.0_cds_from_genomic.fna.gz https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_047496595.1/ https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/047/496/595/GCA_047496595.1_OSU_TarKok_2.0/GCA_047496595.1_OSU_TarKok_2.0_cds_from_genomic.fna.gz Independent reference for historical expression and homology mapping No explicitly associated publication identified Original resource; no explicitly associated publication identified for OH-1004 Official accession records and download listings checked on 2026-10-03 USDA Ag Data Commons provides Ohio State University dataset citation and PRJNA792143, not a publication DOI. NCBI assembly directory exists with genome/GFF/CDS/protein/RNA and official md5checksums.txt. Do not attach a later paper merely using OSU_TarKok_2.0 (e.g. Gerbera paper dsag002). Year refers to dataset release, not a journal article. The dataset itself does not have a DOI; handle https://hdl.handle.net/10113/AF28516412. Reference genome REF_OH1004 OH-1004 / OSU_TarKok_2.0 Taraxacum kok-saghyz GCA_047496595.1 PRJNA792143 GCA_047496595.1_OSU_TarKok_2.0_genomic.fna.gz https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_047496595.1/ https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/047/496/595/GCA_047496595.1_OSU_TarKok_2.0/GCA_047496595.1_OSU_TarKok_2.0_genomic.fna.gz Independent reference for historical expression and homology mapping No explicitly associated publication identified Original resource; no explicitly associated publication identified for OH-1004 Official accession records and download listings checked on 2026-10-03 USDA Ag Data Commons provides Ohio State University dataset citation and PRJNA792143, not a publication DOI. NCBI assembly directory exists with genome/GFF/CDS/protein/RNA and official md5checksums.txt. Do not attach a later paper merely using OSU_TarKok_2.0 (e.g. Gerbera paper dsag002). Year refers to dataset release, not a journal article. The dataset itself does not have a DOI; handle https://hdl.handle.net/10113/AF28516412. Reference genome REF_OH1004 OH-1004 / OSU_TarKok_2.0 Taraxacum kok-saghyz GCA_047496595.1 PRJNA792143 GCA_047496595.1_OSU_TarKok_2.0_genomic.gff.gz https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_047496595.1/ https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/047/496/595/GCA_047496595.1_OSU_TarKok_2.0/GCA_047496595.1_OSU_TarKok_2.0_genomic.gff.gz Independent reference for historical expression and homology mapping No explicitly associated publication identified Original resource; no explicitly associated publication identified for OH-1004 Official accession records and download listings checked on 2026-10-03 USDA Ag Data Commons provides Ohio State University dataset citation and PRJNA792143, not a publication DOI. NCBI assembly directory exists with genome/GFF/CDS/protein/RNA and official md5checksums.txt. Do not attach a later paper merely using OSU_TarKok_2.0 (e.g. Gerbera paper dsag002). Year refers to dataset release, not a journal article. The dataset itself does not have a DOI; handle https://hdl.handle.net/10113/AF28516412. Reference genome REF_OH1004 OH-1004 / OSU_TarKok_2.0 Taraxacum kok-saghyz GCA_047496595.1 PRJNA792143 GCA_047496595.1_OSU_TarKok_2.0_protein.faa.gz https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_047496595.1/ https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/047/496/595/GCA_047496595.1_OSU_TarKok_2.0/GCA_047496595.1_OSU_TarKok_2.0_protein.faa.gz Independent reference for historical expression and homology mapping No explicitly associated publication identified Original resource; no explicitly associated publication identified for OH-1004 Official accession records and download listings checked on 2026-10-03 USDA Ag Data Commons provides Ohio State University dataset citation and PRJNA792143, not a publication DOI. NCBI assembly directory exists with genome/GFF/CDS/protein/RNA and official md5checksums.txt. Do not attach a later paper merely using OSU_TarKok_2.0 (e.g. Gerbera paper dsag002). Year refers to dataset release, not a journal article. The dataset itself does not have a DOI; handle https://hdl.handle.net/10113/AF28516412. Reference genome REF_OH1004 OH-1004 / OSU_TarKok_2.0 Taraxacum kok-saghyz GCA_047496595.1 PRJNA792143 GCA_047496595.1_OSU_TarKok_2.0_rna_from_genomic.fna.gz https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_047496595.1/ https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/047/496/595/GCA_047496595.1_OSU_TarKok_2.0/GCA_047496595.1_OSU_TarKok_2.0_rna_from_genomic.fna.gz Independent reference for historical expression and homology mapping No explicitly associated publication identified Original resource; no explicitly associated publication identified for OH-1004 Official accession records and download listings checked on 2026-10-03 USDA Ag Data Commons provides Ohio State University dataset citation and PRJNA792143, not a publication DOI. NCBI assembly directory exists with genome/GFF/CDS/protein/RNA and official md5checksums.txt. Do not attach a later paper merely using OSU_TarKok_2.0 (e.g. Gerbera paper dsag002). Year refers to dataset release, not a journal article. The dataset itself does not have a DOI; handle https://hdl.handle.net/10113/AF28516412. Reference genome REF_OH1004 OH-1004 / OSU_TarKok_2.0 Taraxacum kok-saghyz GCA_047496595.1 PRJNA792143 GCA_047496595.1_OSU_TarKok_2.0_translated_cds.faa.gz https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_047496595.1/ https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/047/496/595/GCA_047496595.1_OSU_TarKok_2.0/GCA_047496595.1_OSU_TarKok_2.0_translated_cds.faa.gz Independent reference for historical expression and homology mapping No explicitly associated publication identified Original resource; no explicitly associated publication identified for OH-1004 Official accession records and download listings checked on 2026-10-03 USDA Ag Data Commons provides Ohio State University dataset citation and PRJNA792143, not a publication DOI. NCBI assembly directory exists with genome/GFF/CDS/protein/RNA and official md5checksums.txt. Do not attach a later paper merely using OSU_TarKok_2.0 (e.g. Gerbera paper dsag002). Year refers to dataset release, not a journal article. The dataset itself does not have a DOI; handle https://hdl.handle.net/10113/AF28516412. Reference genome REF_OH1004 OH-1004 / OSU_TarKok_2.0 Taraxacum kok-saghyz GCA_047496595.1 PRJNA792143 md5checksums.txt https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_047496595.1/ https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/047/496/595/GCA_047496595.1_OSU_TarKok_2.0/md5checksums.txt Independent reference for historical expression and homology mapping No explicitly associated publication identified Original resource; no explicitly associated publication identified for OH-1004 Official accession records and download listings checked on 2026-10-03 USDA Ag Data Commons provides Ohio State University dataset citation and PRJNA792143, not a publication DOI. NCBI assembly directory exists with genome/GFF/CDS/protein/RNA and official md5checksums.txt. Do not attach a later paper merely using OSU_TarKok_2.0 (e.g. Gerbera paper dsag002). Year refers to dataset release, not a journal article. The dataset itself does not have a DOI; handle https://hdl.handle.net/10113/AF28516412. Reference genome REF_TKS_2017 TKS / GWHAAAA00000000 Taraxacum kok-saghyz GWHAAAA00000000 PRJCA000437 Dna https://ngdc.cncb.ac.cn/gwh/Assembly/1/show https://download.cncb.ac.cn/gwh/Plants/Taraxacum_kok-saghyz_TKS_GWHAAAA00000000/GWHAAAA00000000.genome.fasta.gz Historical gene-ID bridging and literature evidence; kept separate from current reference models REF002 Genome analysis of Taraxacum kok-saghyz Rodin provides new insights into rubber biosynthesis 2018 10.1093/nsr/nwx101 https://doi.org/10.1093/nsr/nwx101 Original reference genome publication Official accession records and download listings checked on 2026-10-03 Repository API explicitly links accession to this DOI; use formal volume year, distinguish earlier online year. Direct files are repository-provided; no bulk genome download was required. Reference genome REF_TKS_2017 TKS / GWHAAAA00000000 Taraxacum kok-saghyz GWHAAAA00000000 PRJCA000437 Gff https://ngdc.cncb.ac.cn/gwh/Assembly/1/show https://download.cncb.ac.cn/gwh/Plants/Taraxacum_kok-saghyz_TKS_GWHAAAA00000000/GWHAAAA00000000.gff.gz Historical gene-ID bridging and literature evidence; kept separate from current reference models REF002 Genome analysis of Taraxacum kok-saghyz Rodin provides new insights into rubber biosynthesis 2018 10.1093/nsr/nwx101 https://doi.org/10.1093/nsr/nwx101 Original reference genome publication Official accession records and download listings checked on 2026-10-03 Repository API explicitly links accession to this DOI; use formal volume year, distinguish earlier online year. Direct files are repository-provided; no bulk genome download was required. Reference genome REF_TKS_2017 TKS / GWHAAAA00000000 Taraxacum kok-saghyz GWHAAAA00000000 PRJCA000437 Rna https://ngdc.cncb.ac.cn/gwh/Assembly/1/show https://download.cncb.ac.cn/gwh/Plants/Taraxacum_kok-saghyz_TKS_GWHAAAA00000000/GWHAAAA00000000.RNA.fasta.gz Historical gene-ID bridging and literature evidence; kept separate from current reference models REF002 Genome analysis of Taraxacum kok-saghyz Rodin provides new insights into rubber biosynthesis 2018 10.1093/nsr/nwx101 https://doi.org/10.1093/nsr/nwx101 Original reference genome publication Official accession records and download listings checked on 2026-10-03 Repository API explicitly links accession to this DOI; use formal volume year, distinguish earlier online year. Direct files are repository-provided; no bulk genome download was required. Reference genome REF_TKS_2017 TKS / GWHAAAA00000000 Taraxacum kok-saghyz GWHAAAA00000000 PRJCA000437 Cds https://ngdc.cncb.ac.cn/gwh/Assembly/1/show https://download.cncb.ac.cn/gwh/Plants/Taraxacum_kok-saghyz_TKS_GWHAAAA00000000/GWHAAAA00000000.CDS.fasta.gz Historical gene-ID bridging and literature evidence; kept separate from current reference models REF002 Genome analysis of Taraxacum kok-saghyz Rodin provides new insights into rubber biosynthesis 2018 10.1093/nsr/nwx101 https://doi.org/10.1093/nsr/nwx101 Original reference genome publication Official accession records and download listings checked on 2026-10-03 Repository API explicitly links accession to this DOI; use formal volume year, distinguish earlier online year. Direct files are repository-provided; no bulk genome download was required. Reference genome REF_TKS_2017 TKS / GWHAAAA00000000 Taraxacum kok-saghyz GWHAAAA00000000 PRJCA000437 Protein https://ngdc.cncb.ac.cn/gwh/Assembly/1/show https://download.cncb.ac.cn/gwh/Plants/Taraxacum_kok-saghyz_TKS_GWHAAAA00000000/GWHAAAA00000000.Protein.faa.gz Historical gene-ID bridging and literature evidence; kept separate from current reference models REF002 Genome analysis of Taraxacum kok-saghyz Rodin provides new insights into rubber biosynthesis 2018 10.1093/nsr/nwx101 https://doi.org/10.1093/nsr/nwx101 Original reference genome publication Official accession records and download listings checked on 2026-10-03 Repository API explicitly links accession to this DOI; use formal volume year, distinguish earlier online year. Direct files are repository-provided; no bulk genome download was required. Reference genome REF_TKS_2017 TKS / GWHAAAA00000000 Taraxacum kok-saghyz GWHAAAA00000000 PRJCA000437 Feature https://ngdc.cncb.ac.cn/gwh/Assembly/1/show https://download.cncb.ac.cn/gwh/Plants/Taraxacum_kok-saghyz_TKS_GWHAAAA00000000/GWHAAAA00000000.feature.gz Historical gene-ID bridging and literature evidence; kept separate from current reference models REF002 Genome analysis of Taraxacum kok-saghyz Rodin provides new insights into rubber biosynthesis 2018 10.1093/nsr/nwx101 https://doi.org/10.1093/nsr/nwx101 Original reference genome publication Official accession records and download listings checked on 2026-10-03 Repository API explicitly links accession to this DOI; use formal volume year, distinguish earlier online year. Direct files are repository-provided; no bulk genome download was required. Transcriptome project PRJDB36270 Developing ovaries RNA-Seq of sexual and apomixis dandelion plants (PRJCA027669) https://www.ncbi.nlm.nih.gov/bioproject/PRJDB36270 https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJDB36270 No explicitly associated publication identified not_found_in_checked_primary_records NCBI explicitly cross-links NGDC PRJCA027669. NGDC retrieval failed with RemoteDisconnected; NCBI project contains no publication link. No paper assigned. PRJDB36270 9 9 Included runs verified as Taraxacum kok-saghyz; the umbrella PRJNA681093 project is Chrysanthemum, requiring run-level verification https://www.ebi.ac.uk/ena/browser/view/PRJDB36270 Transcriptome project PRJNA1262623 Taraxacum kok-saghyz Transcriptome or Gene expression https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1262623 https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA1262623 REF003 Geranyl Diphosphate Synthases GDS 1 and GDS7 Facilitate Natural Rubber Biosynthesis in Taraxacum kok-saghyz Roots 2025 10.3390/plants14192980 https://www.mdpi.com/2223-7747/14/19/2980 verified_article_reuse_accession_origin_not_established Article section 4.8 explicitly reuses PRJNA1262623 and cites a previous dataset. This establishes article use, not that the article originally generated all runs. PRJNA1262623 15 15 Included runs verified as Taraxacum kok-saghyz; the umbrella PRJNA681093 project is Chrysanthemum, requiring run-level verification https://www.ebi.ac.uk/ena/browser/view/PRJNA1262623 Transcriptome project PRJNA1490093 Transcriptome Analysis of Taraxacum kok-saghyz under Salt Stress https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1490093 https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA1490093 No explicitly associated publication identified not_found_in_checked_primary_records NCBI BioProject record checked on 2026-10-03. No publication assigned by topic alone. PRJNA1490093 15 15 Included runs verified as Taraxacum kok-saghyz; the umbrella PRJNA681093 project is Chrysanthemum, requiring run-level verification https://www.ebi.ac.uk/ena/browser/view/PRJNA1490093 Transcriptome project PRJNA361575 Taraxacum kok-saghyz Raw sequence reads https://www.ncbi.nlm.nih.gov/bioproject/PRJNA361575 https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA361575 REF004 Analysis of the first Taraxacum kok-saghyz transcriptome reveals potential rubber yield related SNPs 2017 10.1038/s41598-017-09034-2 https://pmc.ncbi.nlm.nih.gov/articles/PMC5577190/ verified_article_run_accession_to_bioproject Article explicitly lists SRR5181661-SRR5181665 and SRR5181667. NCBI SRA SRR5181661 belongs to PRJNA361575; linkage is run-level, not a title-only match. PRJNA361575 6 6 Included runs verified as Taraxacum kok-saghyz; the umbrella PRJNA681093 project is Chrysanthemum, requiring run-level verification https://www.ebi.ac.uk/ena/browser/view/PRJNA361575 Transcriptome project PRJNA413689 Identification of gene functions in different accessions. https://www.ncbi.nlm.nih.gov/bioproject/PRJNA413689 https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA413689 REF005 Comparative transcriptomics between high and low rubber producing Taraxacum kok-saghyz R. plants 2018 10.1186/s12864-018-5287-4 https://pmc.ncbi.nlm.nih.gov/articles/PMC6280347/ verified_bioproject_publication_and_article_accession NCBI BioProject lists this publication; article Data Availability explicitly states PRJNA413689. PRJNA413689 3 3 Included runs verified as Taraxacum kok-saghyz; the umbrella PRJNA681093 project is Chrysanthemum, requiring run-level verification https://www.ebi.ac.uk/ena/browser/view/PRJNA413689 Transcriptome project PRJNA539838 Transcriptome of Taraxacum kok-saghyz Rodin roots from different developmental stages https://www.ncbi.nlm.nih.gov/bioproject/PRJNA539838 https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA539838 REF006 Genome-Wide Identification and Characterization of the HMGR Gene Family in Taraxacum kok-saghyz Provide Insights into Its Regulation in Response to Ethylene and Methyl Jsamonate Treatments 2024 10.3390/plants13182646 https://pmc.ncbi.nlm.nih.gov/articles/PMC11435204/ verified_article_reuse_accession_origin_not_established Article section 4.6 explicitly reuses PRJNA539838. Original developmental-root RNA-seq publication remains unresolved; candidate original study recorded separately. PRJNA539838 16 16 Included runs verified as Taraxacum kok-saghyz; the umbrella PRJNA681093 project is Chrysanthemum, requiring run-level verification https://www.ebi.ac.uk/ena/browser/view/PRJNA539838 Transcriptome project PRJNA681093 Chrysanthemum lavandulifolium cultivar:G1 Nanopore sequencing data https://www.ncbi.nlm.nih.gov/bioproject/PRJNA681093 https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA681093 REF007 "The Chrysanthemum lavandulifolium genome and the molecular mechanism underlying diverse capitulum types" 2022 10.1093/hr/uhab022 https://academic.oup.com/hr/article/doi/10.1093/hr/uhab022/6510191 verified_bioproject_publication_and_article_accession Project primary organism is Chrysanthemum lavandulifolium; website-used run SRR15099898 is explicitly Taraxacum kok-saghyz and belongs to PRJNA681093, confirmed by NCBI SRA. Project includes Asteraceae comparative RNA-seq. Do not label all project runs as T. kok-saghyz. PRJNA681093 12 0 Included runs verified as Taraxacum kok-saghyz; the umbrella PRJNA681093 project is Chrysanthemum, requiring run-level verification https://www.ebi.ac.uk/ena/browser/view/PRJNA681093 Transcriptome project PRJNA745038 Taraxacum kok-saghyz Raw sequence reads https://www.ncbi.nlm.nih.gov/bioproject/PRJNA745038 https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA745038 REF008 Transcriptome analysis of Taraxacum kok-saghyz reveals the role of exogenous methyl jasmonate in regulating rubber biosynthesis and drought tolerance 2023 10.1016/j.gene.2023.147346 https://pubmed.ncbi.nlm.nih.gov/36898514/ candidate_article_metadata_verified_accession_link_not_verified Historical website manifest assigns this DOI, and NCBI project/abstract match MeJA laticifer study, but checked primary records do not expose an explicit accession-paper linkage. Publisher full text is access-limited. Do not present linkage as confirmed. PRJNA745038 9 9 Included runs verified as Taraxacum kok-saghyz; the umbrella PRJNA681093 project is Chrysanthemum, requiring run-level verification https://www.ebi.ac.uk/ena/browser/view/PRJNA745038 Transcriptome project PRJNA827459 Taraxacum kok-saghyz Transcriptome or Gene expression https://www.ncbi.nlm.nih.gov/bioproject/PRJNA827459 https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA827459 REF009 Metabolic and Transcriptomic Analyses Reveal the Effects of Ethephon on Taraxacum kok-saghyz Rodin 2022 10.3390/molecules27113548 https://pmc.ncbi.nlm.nih.gov/articles/PMC9182187/ verified_article_accession Article Data Availability explicitly links PRJNA827459; PMID checked in downloaded actual article. PRJNA827459 15 15 Included runs verified as Taraxacum kok-saghyz; the umbrella PRJNA681093 project is Chrysanthemum, requiring run-level verification https://www.ebi.ac.uk/ena/browser/view/PRJNA827459 Transcriptome project PRJNA918839 Taraxacum kok-saghyz latex RNA-seq by foliar application of lysophosphatidylethanolamine https://www.ncbi.nlm.nih.gov/bioproject/PRJNA918839 https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA918839 REF010 Enhanced natural rubber production in rubber dandelion Taraxacum kok-saghyz roots by foliar application of a natural lipid 2024 10.1016/j.indcrop.2023.117714 https://www.sciencedirect.com/science/article/pii/S0926669023014796 candidate_article_metadata_verified_accession_link_not_verified Publisher abstract and NCBI project both concern lysophosphatidylethanolamine-treated TKS latex; explicit PRJNA918839 linkage not found in accessible records. Title/DOI metadata verified; project-paper association remains candidate. PRJNA918839 6 6 Included runs verified as Taraxacum kok-saghyz; the umbrella PRJNA681093 project is Chrysanthemum, requiring run-level verification https://www.ebi.ac.uk/ena/browser/view/PRJNA918839 Transcriptome project PRJNA931633 Taraxacum kok-saghyz Raw sequence reads https://www.ncbi.nlm.nih.gov/bioproject/PRJNA931633 https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA931633 No explicitly associated publication identified not_found_in_checked_primary_records NCBI BioProject record checked on 2026-10-03. No publication assigned by topic alone. PRJNA931633 9 9 Included runs verified as Taraxacum kok-saghyz; the umbrella PRJNA681093 project is Chrysanthemum, requiring run-level verification https://www.ebi.ac.uk/ena/browser/view/PRJNA931633 Transcriptome project PRJNA985648 RNA-Seq of Taraxacum koksagyhz PEL-like overexpression line vs. near-isogenic line https://www.ncbi.nlm.nih.gov/bioproject/PRJNA985648 https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA985648 REF011 Overexpression of a pseudo-etiolated-in-light-like protein in Taraxacum koksaghyz leads to a pale green phenotype and enables transcriptome-based network analysis of photomorphogenesis and isoprenoid biosynthesis 2023 10.3389/fpls.2023.1228961 https://pmc.ncbi.nlm.nih.gov/articles/PMC10569127/ verified_article_accession Article Data Availability explicitly links PRJNA985648. PRJNA985648 2 2 Included runs verified as Taraxacum kok-saghyz; the umbrella PRJNA681093 project is Chrysanthemum, requiring run-level verification https://www.ebi.ac.uk/ena/browser/view/PRJNA985648 Transcriptome project PRJDB37370 The effects of MeOH on TKS growth and rubber production (KAP241469) https://www.ncbi.nlm.nih.gov/bioproject/PRJDB37370 https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJDB37370 No explicitly associated publication identified not_found_in_checked_primary_records Original local RunInfo BioProject field was blank. All four actual DRR records now explicitly link PRJDB37370/DRP016186. No invented BioProject. Sample labels must use verified MeOH/control records rather than previously inferred control labels. DRA_unassigned_DRR 4 4 Included runs verified as Taraxacum kok-saghyz; the umbrella PRJNA681093 project is Chrysanthemum, requiring run-level verification https://www.ebi.ac.uk/ena/browser/view/PRJDB37370 Other omics or author-supplied data PUB_TRANSCRIPTOME_PRJNA413689 Public RNA-seq project PRJNA413689 publisher_supplement_xlsx https://www.ncbi.nlm.nih.gov/bioproject/PRJNA413689 https://media.springernature.com/original/springer-static/esm/art%3A10.1186%2Fs12864-018-5287-4/MediaObjects/12864_2018_5287_MOESM1_ESM.xlsx Author-reported public resource, separate from website-computed results REF005 Comparative transcriptomics between high and low rubber producing Taraxacum kok-saghyz R. plants 2018 10.1186/s12864-018-5287-4 https://doi.org/10.1186/s12864-018-5287-4 Original data or author-supplied supplementary material publication Publisher Data Availability explicitly names PRJNA413689; TSA GFZW00000000 and TksCPT3 MG209739 are distinct related accessions. Other omics or author-supplied data PUB_TRANSCRIPTOME_S7 Author-reported contig-level HR/LR/Y11 RPKM matrix, original article Table S7 PMID30514210:Table S7 publisher_supplement_xlsx https://link.springer.com/article/10.1186/s12864-018-5287-4#MOESM1 https://media.springernature.com/original/springer-static/esm/art%3A10.1186%2Fs12864-018-5287-4/MediaObjects/12864_2018_5287_MOESM1_ESM.xlsx Import of author-supplied supplementary matrices with the original contig namespace retained; not formal gene-level quantification REF005 Comparative transcriptomics between high and low rubber producing Taraxacum kok-saghyz R. plants 2018 10.1186/s12864-018-5287-4 https://doi.org/10.1186/s12864-018-5287-4 Original data or author-supplied supplementary material publication Table S7 contains expression levels of assembled contigs; supplement workbook is publisher source; does not itself establish TK1151/OH-1004 gene ID correspondence. Other omics or author-supplied data PUB_TRANSCRIPTOME_S8 Author-reported differential expression results, original article Table S8 PMID30514210:Table S8 publisher_supplement_xlsx https://link.springer.com/article/10.1186/s12864-018-5287-4#MOESM1 https://media.springernature.com/original/springer-static/esm/art%3A10.1186%2Fs12864-018-5287-4/MediaObjects/12864_2018_5287_MOESM1_ESM.xlsx Import of author-supplied supplementary matrices with the original contig namespace retained; not formal gene-level quantification REF005 Comparative transcriptomics between high and low rubber producing Taraxacum kok-saghyz R. plants 2018 10.1186/s12864-018-5287-4 https://doi.org/10.1186/s12864-018-5287-4 Original data or author-supplied supplementary material publication Table S8 contains differential expression genes in original paper; original study results, not website rerun statistics. Other omics or author-supplied data PUB_PROTEOME_PXD011773 Author-processed MaxQuant outputs imported as proteomic evidence PXD011773 original_ftp https://www.ebi.ac.uk/pride/archive/projects/PXD011773 ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/05/PXD011773 Import of author-processed results; MaxQuant was not rerun by the website REF012 Comparative proteome and metabolome analyses of latex-exuding and non-exuding Taraxacum koksaghyz roots provide insights into laticifer biology 2020 10.1093/jxb/erz512 https://doi.org/10.1093/jxb/erz512 Original data or author-supplied supplementary material publication PRIDE API references DOI erz512 and PubMed 31740929 explicitly. Repository title differs from paper title. PRIDE processing protocol explicitly used MaxQuant 1.5.2.8 with Andromeda and dandelion Lin 2017 sequence database; this is the original study pipeline, not proof that website reran MaxQuant. Official FTP path recorded by ProteomeXchange; HTTPS archive directory HEAD access check returned 200. Other omics or author-supplied data PUB_PROTEOME_PXD011773 Author-processed MaxQuant outputs imported as proteomic evidence PXD011773 pride_repository https://www.ebi.ac.uk/pride/archive/projects/PXD011773 https://www.ebi.ac.uk/pride/archive/projects/PXD011773 Import of author-processed results; MaxQuant was not rerun by the website REF012 Comparative proteome and metabolome analyses of latex-exuding and non-exuding Taraxacum koksaghyz roots provide insights into laticifer biology 2020 10.1093/jxb/erz512 https://doi.org/10.1093/jxb/erz512 Original data or author-supplied supplementary material publication PRIDE API references DOI erz512 and PubMed 31740929 explicitly. Repository title differs from paper title. PRIDE processing protocol explicitly used MaxQuant 1.5.2.8 with Andromeda and dandelion Lin 2017 sequence database; this is the original study pipeline, not proof that website reran MaxQuant. Official FTP path recorded by ProteomeXchange; HTTPS archive directory HEAD access check returned 200. Other omics or author-supplied data PUB_WGR_CRA009020 Whole-genome resequencing raw reads from 129 samples CRA009020 publisher_supplement_xlsx https://ngdc.cncb.ac.cn/gsa/browse/CRA009020 https://media.springernature.com/original/springer-static/esm/art%3A10.1186%2Fs12864-022-09105-3/MediaObjects/12864_2022_9105_MOESM2_ESM.xlsx GSA raw reads realigned to two references for variant calling REF013 Construction of the first high-density SNP genetic map and identification of QTLs for the natural rubber content in Taraxacum kok-saghyz Rodin 2023 10.1186/s12864-022-09105-3 https://doi.org/10.1186/s12864-022-09105-3 Original data or author-supplied supplementary material publication Publisher data availability explicitly names CRA009020 for WGR raw reads. Population: 127 F1 offspring and two parents (166 and X51). GSA page fetch failed due transient proxy interruption; raw-run download links not invented. Other omics or author-supplied data PUB_VARIANTS_GVM000440 Author-deposited variants, separate from website realignment and variant calling GVM000440 publisher_supplement_xlsx https://ngdc.cncb.ac.cn/gvm/getProjectDetail?project=GVM000440 https://media.springernature.com/original/springer-static/esm/art%3A10.1186%2Fs12864-022-09105-3/MediaObjects/12864_2022_9105_MOESM2_ESM.xlsx Author-reported public resource, separate from website-computed results REF013 Construction of the first high-density SNP genetic map and identification of QTLs for the natural rubber content in Taraxacum kok-saghyz Rodin 2023 10.1186/s12864-022-09105-3 https://doi.org/10.1186/s12864-022-09105-3 Original data or author-supplied supplementary material publication Publisher Data Availability names GVM000440; current GVM repository supplies genotype CSV and diff_parent_SNP_info.xlsx links. Not an unrelated association panel. Other omics or author-supplied data PUB_VARIANTS_GVM000440 Author-deposited variants, separate from website realignment and variant calling GVM000440 SNP_matrix_final.genotype.csv https://ngdc.cncb.ac.cn/gvm/getProjectDetail?project=GVM000440 http://download.big.ac.cn/GVM/Taraxacum_kok-saghyz/GVM000440/SNP_matrix_final.genotype.csv Author-reported public resource, separate from website-computed results REF013 Construction of the first high-density SNP genetic map and identification of QTLs for the natural rubber content in Taraxacum kok-saghyz Rodin 2023 10.1186/s12864-022-09105-3 https://doi.org/10.1186/s12864-022-09105-3 Original data or author-supplied supplementary material publication Publisher Data Availability names GVM000440; current GVM repository supplies genotype CSV and diff_parent_SNP_info.xlsx links. Not an unrelated association panel. Other omics or author-supplied data PUB_VARIANTS_GVM000440 Author-deposited variants, separate from website realignment and variant calling GVM000440 diff_parent_SNP_info.xlsx https://ngdc.cncb.ac.cn/gvm/getProjectDetail?project=GVM000440 http://download.big.ac.cn/GVM/Taraxacum_kok-saghyz/GVM000440/diff_parent_SNP_info.xlsx Author-reported public resource, separate from website-computed results REF013 Construction of the first high-density SNP genetic map and identification of QTLs for the natural rubber content in Taraxacum kok-saghyz Rodin 2023 10.1186/s12864-022-09105-3 https://doi.org/10.1186/s12864-022-09105-3 Original data or author-supplied supplementary material publication Publisher Data Availability names GVM000440; current GVM repository supplies genotype CSV and diff_parent_SNP_info.xlsx links. Not an unrelated association panel. Other omics or author-supplied data PUB_QTL_PHENOTYPE_SUPPLEMENT Author-supplied phenotype and QTL supplementary tables 10.1186/s12864-022-09105-3:Additional file 2 publisher_supplement_xlsx https://link.springer.com/article/10.1186/s12864-022-09105-3#MOESM2 https://media.springernature.com/original/springer-static/esm/art%3A10.1186%2Fs12864-022-09105-3/MediaObjects/12864_2022_9105_MOESM2_ESM.xlsx Author-reported public resource, separate from website-computed results REF013 Construction of the first high-density SNP genetic map and identification of QTLs for the natural rubber content in Taraxacum kok-saghyz Rodin 2023 10.1186/s12864-022-09105-3 https://doi.org/10.1186/s12864-022-09105-3 Original data or author-supplied supplementary material publication Supplement publisher metadata describes resequencing, bin-marker coordinates, genotypes, QTL gene regions, QTL genetic effects and QTL genotypes. Per-individual phenotype availability has not been checked inside workbook; do not label this entire file a complete raw phenotype matrix. Other omics or author-supplied data OWN_TKS_TISSUE_FPKM_202609 In-house bred Zhaosu line: FPKM for 24 samples from eight tissues Not deposited in a public repository tissue_fpkm_original.xlsx (user-supplied original workbook) User-provided research data http://47.95.224.165/rubber/tissue-expression/files/matrix Import of the user-provided matrix with TK1151 ID checks; no public raw-read deposition claimed No explicitly associated publication identified Unpublished or no associated publication supplied The website provides the user-supplied workbook. No public upstream raw-read accession, associated publication, or processing-software version has been supplied Cross-species literature evidence HB_HRT1_ELIFE_2016 BAB71776.2;AB061234.3;LC057267 https://doi.org/10.7554/eLife.19022 REF041 Identification and reconstitution of the rubber biosynthetic machinery on rubber particles from Hevea brasiliensis 2016 10.7554/eLife.19022 https://doi.org/10.7554/eLife.19022 Evidence in the original species; not experimental validation in Taraxacum kok-saghyz DOI metadata verified; gene relationships retained from existing manual curation, without independently rechecking every experimental conclusion HB direct functional experiment Rubber particles Cross-species literature evidence HB_CPT_2003 AB061234.3;AB064661.2 https://doi.org/10.1046/j.1432-1033.2003.03863.x REF042 "Molecular cloning, expression and characterization of cDNA encoding cis ‐prenyltransferases from Hevea brasiliensis" 2003 10.1046/j.1432-1033.2003.03863.x https://doi.org/10.1046/j.1432-1033.2003.03863.x Evidence in the original species; not experimental validation in Taraxacum kok-saghyz DOI metadata verified; gene relationships retained from existing manual curation, without independently rechecking every experimental conclusion HB enzyme experiment Latex and recombinant enzyme Cross-species literature evidence HB_GEO_LATEX_2018 GSE101568;PRJNA394848;SRP112717 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE101568 No explicitly associated publication identified https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE101568 Evidence in the original species; not experimental validation in Taraxacum kok-saghyz DOI metadata verified; gene relationships retained from existing manual curation, without independently rechecking every experimental conclusion HB RNA-seq processed-result source 21 latex samples healthy and tapping panel dryness or ethephon conditions Cross-species literature evidence PA_CPT_CBP_2019 MF688933;MF688934;MF688936;MF688938;SRP107961 https://pmc.ncbi.nlm.nih.gov/articles/PMC6397875/ REF043 Molecular Studies of the Protein Complexes Involving Cis-Prenyltransferase in Guayule (Parthenium argentatum), an Alternative Rubber-Producing Plant 2019 10.3389/fpls.2019.00165 https://doi.org/10.3389/fpls.2019.00165 Evidence in the original species; not experimental validation in Taraxacum kok-saghyz DOI metadata verified; gene relationships retained from existing manual curation, without independently rechecking every experimental conclusion PA direct functional experiment PI478663 and heterologous systems Cross-species literature evidence PA_CPT_CBP_2022 MF688933;MF688934;MF688936;MF688938 https://pmc.ncbi.nlm.nih.gov/articles/PMC8904820/ REF044 Reconstitution of prenyltransferase activity on nanodiscs by components of the rubber synthesis machinery of the Para rubber tree and guayule 2022 10.1038/s41598-022-07564-y https://doi.org/10.1038/s41598-022-07564-y Evidence in the original species; not experimental validation in Taraxacum kok-saghyz DOI metadata verified; gene relationships retained from existing manual curation, without independently rechecking every experimental conclusion PA direct functional experiment Cell-free nanodisc reconstruction Cross-species literature evidence PA_AOS_2019 X78166.2 https://pmc.ncbi.nlm.nih.gov/articles/PMC6607968/ REF045 Downregulation of a CYP74 Rubber Particle Protein Increases Natural Rubber Production in Parthenium argentatum 2019 10.3389/fpls.2019.00760 https://doi.org/10.3389/fpls.2019.00760 Evidence in the original species; not experimental validation in Taraxacum kok-saghyz DOI metadata verified; gene relationships retained from existing manual curation, without independently rechecking every experimental conclusion PA direct genetic experiment AOS RNAi and overexpression plants Cross-species literature evidence PA_DROUGHT_2021 PRJNA400611 https://pmc.ncbi.nlm.nih.gov/articles/PMC8566568/ REF046 RNASeq analysis of drought-stressed guayule reveals the role of gene transcription for modulating rubber, resin, and carbohydrate synthesis 2021 10.1038/s41598-021-01026-7 https://doi.org/10.1038/s41598-021-01026-7 Evidence in the original species; not experimental validation in Taraxacum kok-saghyz DOI metadata verified; gene relationships retained from existing manual curation, without independently rechecking every experimental conclusion PA RNA-seq processed-result source AZ-3 field bark under well-watered and drought conditions Cross-species literature evidence PA_COLD_2019 PRJNA387289;GFTW000000000.1 https://pmc.ncbi.nlm.nih.gov/articles/PMC6373111/ REF047 Transcriptome analysis of rubber biosynthesis in guayule (Parthenium argentatum gray) 2019 10.1186/s12870-019-1669-2 https://doi.org/10.1186/s12870-019-1669-2 Evidence in the original species; not experimental validation in Taraxacum kok-saghyz DOI metadata verified; gene relationships retained from existing manual curation, without independently rechecking every experimental conclusion PA RNA-seq processed-result source Stem and leaf under summer or winter simulation Cross-species literature evidence PA_SRPP_PROMOTER_2025 PV754023.1 https://pmc.ncbi.nlm.nih.gov/articles/PMC12406399/ REF048 Characterization of Small Rubber Particle Protein 1 promoter from guayule (Parthenium argentatum) 2025 10.1186/s13104-025-07448-0 https://doi.org/10.1186/s13104-025-07448-0 Evidence in the original species; not experimental validation in Taraxacum kok-saghyz DOI metadata verified; gene relationships retained from existing manual curation, without independently rechecking every experimental conclusion PA promoter experiment SRPP1 promoter reporter assay Cross-species literature evidence TB_CPT_2012 JQ991925.1;JQ991926.1;JQ991927.1 https://doi.org/10.1104/pp.111.187880 REF049 Laticifer-Specific cis-Prenyltransferase Silencing Affects the Rubber, Triterpene, and Inulin Content of Taraxacum brevicorniculatum 2012 10.1104/pp.111.187880 https://doi.org/10.1104/pp.111.187880 Evidence in the original species; not experimental validation in Taraxacum kok-saghyz DOI metadata verified; gene relationships retained from existing manual curation, without independently rechecking every experimental conclusion TB laticifer-specific functional experiment RNAi laticifers with polymer and particle assays Cross-species literature evidence TB_SRPP_2018 JQ991928.1;JQ991929.1;JQ991930.1;JQ991931.1;JQ991932.1 https://doi.org/10.1111/tpj.13829 REF050 Small rubber particle proteins from Taraxacum brevicorniculatum promote stress tolerance and influence the size and distribution of lipid droplets and artificial poly(cis‐1,4‐isoprene) bodies 2018 10.1111/tpj.13829 https://doi.org/10.1111/tpj.13829 Evidence in the original species; not experimental validation in Taraxacum kok-saghyz DOI metadata verified; gene relationships retained from existing manual curation, without independently rechecking every experimental conclusion TB rubber-particle experiment Rubber-particle extraction and heterologous assays Cross-species literature evidence TB_NUCCORE KP763637.1;MF471639.1;KJ911908.1;KJ911910.1 https://www.ncbi.nlm.nih.gov/nuccore/JQ991925.1 No explicitly associated publication identified https://www.ncbi.nlm.nih.gov/nuccore/JQ991925.1 Evidence in the original species; not experimental validation in Taraxacum kok-saghyz DOI metadata verified; gene relationships retained from existing manual curation, without independently rechecking every experimental conclusion TB sequence records Public cDNA records Cross-species literature evidence EU_TRANS_1996 https://doi.org/10.1016/S0031-9422(96)00806-0 REF051 Structure and biosynthesis of trans-polyisoprene from Eucommia ulmoides 1997 10.1016/S0031-9422(96)00806-0 https://doi.org/10.1016/S0031-9422(96)00806-0 Evidence in the original species; not experimental validation in Taraxacum kok-saghyz DOI metadata verified; gene relationships retained from existing manual curation, without independently rechecking every experimental conclusion EU polymer chemistry experiment Eucommia gum Cross-species literature evidence EU_IPI_2012 AB041629.2 https://doi.org/10.1186/1472-6750-12-78 REF052 Overexpression of an isopentenyl diphosphate isomerase gene to enhance trans-polyisoprene production in Eucommia ulmoides Oliver 2012 10.1186/1472-6750-12-78 https://doi.org/10.1186/1472-6750-12-78 Evidence in the original species; not experimental validation in Taraxacum kok-saghyz DOI metadata verified; gene relationships retained from existing manual curation, without independently rechecking every experimental conclusion EU direct genetic experiment Transgenic roots Cross-species literature evidence EU_GENOME_2021 GCA_016647705.1;PRJNA599775 https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_016647705.1/ No explicitly associated publication identified https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_016647705.1/ Evidence in the original species; not experimental validation in Taraxacum kok-saghyz DOI metadata verified; gene relationships retained from existing manual curation, without independently rechecking every experimental conclusion EU genome annotation Weixian material leaf-derived reference