{"id":"https://openalex.org/W4412066705","doi":"https://doi.org/10.3389/fbinf.2025.1625145","title":"Comparative transcriptome analysis of different tissues of Hylomecon japonica provides new insights into the biosynthesis pathway of triterpenoid saponins","display_name":"Comparative transcriptome analysis of different tissues of Hylomecon japonica provides new insights into the biosynthesis pathway of triterpenoid saponins","publication_year":2025,"publication_date":"2025-07-07","ids":{"openalex":"https://openalex.org/W4412066705","doi":"https://doi.org/10.3389/fbinf.2025.1625145","pmid":"https://pubmed.ncbi.nlm.nih.gov/40693151"},"language":"en","primary_location":{"id":"doi:10.3389/fbinf.2025.1625145","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1625145","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1625145/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1625145/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100534164","display_name":"Bing He","orcid":"https://orcid.org/0000-0003-0872-6466"},"institutions":[{"id":"https://openalex.org/I253932293","display_name":"Anhui University of Traditional Chinese Medicine","ror":"https://ror.org/0139j4p80","country_code":"CN","type":"education","lineage":["https://openalex.org/I253932293"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bing He","raw_affiliation_strings":["College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China"],"affiliations":[{"raw_affiliation_string":"College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China","institution_ids":["https://openalex.org/I253932293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100771221","display_name":"Teng Xu","orcid":"https://orcid.org/0000-0001-8925-256X"},"institutions":[{"id":"https://openalex.org/I253932293","display_name":"Anhui University of Traditional Chinese Medicine","ror":"https://ror.org/0139j4p80","country_code":"CN","type":"education","lineage":["https://openalex.org/I253932293"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Teng Xu","raw_affiliation_strings":["College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China"],"affiliations":[{"raw_affiliation_string":"College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China","institution_ids":["https://openalex.org/I253932293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102128274","display_name":"Shaowei Xu","orcid":null},"institutions":[{"id":"https://openalex.org/I253932293","display_name":"Anhui University of Traditional Chinese Medicine","ror":"https://ror.org/0139j4p80","country_code":"CN","type":"education","lineage":["https://openalex.org/I253932293"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shaowei Xu","raw_affiliation_strings":["College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China"],"affiliations":[{"raw_affiliation_string":"College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China","institution_ids":["https://openalex.org/I253932293"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Huqiang Fang","orcid":null},"institutions":[{"id":"https://openalex.org/I253932293","display_name":"Anhui University of Traditional Chinese Medicine","ror":"https://ror.org/0139j4p80","country_code":"CN","type":"education","lineage":["https://openalex.org/I253932293"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Huqiang Fang","raw_affiliation_strings":["College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China"],"affiliations":[{"raw_affiliation_string":"College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China","institution_ids":["https://openalex.org/I253932293"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012192305","display_name":"Qingshan Yang","orcid":"https://orcid.org/0000-0002-3925-0344"},"institutions":[{"id":"https://openalex.org/I253932293","display_name":"Anhui University of Traditional Chinese Medicine","ror":"https://ror.org/0139j4p80","country_code":"CN","type":"education","lineage":["https://openalex.org/I253932293"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Qingshan Yang","raw_affiliation_strings":["College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China","Key Laboratory of Xin'an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, China"],"affiliations":[{"raw_affiliation_string":"College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China","institution_ids":["https://openalex.org/I253932293"]},{"raw_affiliation_string":"Key Laboratory of Xin'an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, China","institution_ids":["https://openalex.org/I253932293"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5012192305"],"corresponding_institution_ids":["https://openalex.org/I253932293"],"apc_list":{"value":1900,"currency":"USD","value_usd":1900},"apc_paid":{"value":1900,"currency":"USD","value_usd":1900},"fwci":1.4487,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.82270116,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":"5","issue":null,"first_page":"1625145","last_page":"1625145"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11882","display_name":"Plant biochemistry and biosynthesis","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11882","display_name":"Plant biochemistry and biosynthesis","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11385","display_name":"Natural product bioactivities and synthesis","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10445","display_name":"Antioxidant Activity and Oxidative Stress","score":0.9897000193595886,"subfield":{"id":"https://openalex.org/subfields/2704","display_name":"Biochemistry"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.7957435250282288},{"id":"https://openalex.org/keywords/triterpenoid","display_name":"Triterpenoid","score":0.6075423955917358},{"id":"https://openalex.org/keywords/japonica","display_name":"Japonica","score":0.5204713344573975},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.48923230171203613},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.45248299837112427},{"id":"https://openalex.org/keywords/biosynthesis","display_name":"Biosynthesis","score":0.42195582389831543},{"id":"https://openalex.org/keywords/traditional-medicine","display_name":"Traditional medicine","score":0.33605313301086426},{"id":"https://openalex.org/keywords/botany","display_name":"Botany","score":0.27074170112609863},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1561412215232849},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.14576169848442078},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.13940033316612244},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1316356360912323}],"concepts":[{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.7957435250282288},{"id":"https://openalex.org/C107585567","wikidata":"https://www.wikidata.org/wiki/Q2915788","display_name":"Triterpenoid","level":2,"score":0.6075423955917358},{"id":"https://openalex.org/C2779409272","wikidata":"https://www.wikidata.org/wiki/Q1757789","display_name":"Japonica","level":2,"score":0.5204713344573975},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.48923230171203613},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.45248299837112427},{"id":"https://openalex.org/C553450214","wikidata":"https://www.wikidata.org/wiki/Q851162","display_name":"Biosynthesis","level":3,"score":0.42195582389831543},{"id":"https://openalex.org/C556039675","wikidata":"https://www.wikidata.org/wiki/Q771035","display_name":"Traditional medicine","level":1,"score":0.33605313301086426},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.27074170112609863},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1561412215232849},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.14576169848442078},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.13940033316612244},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1316356360912323}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.3389/fbinf.2025.1625145","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1625145","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1625145/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40693151","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40693151","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:c667943125b644ea96f52ebe027579e0","is_oa":true,"landing_page_url":"https://doaj.org/article/c667943125b644ea96f52ebe027579e0","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Frontiers in Bioinformatics, Vol 5 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12277290","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12277290","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Front Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3389/fbinf.2025.1625145","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1625145","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1625145/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4412066705.pdf"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W160595635","https://openalex.org/W1531569394","https://openalex.org/W1971707621","https://openalex.org/W1981445309","https://openalex.org/W1996423252","https://openalex.org/W1999574084","https://openalex.org/W2011657487","https://openalex.org/W2016029656","https://openalex.org/W2055043387","https://openalex.org/W2069458148","https://openalex.org/W2104906546","https://openalex.org/W2117608012","https://openalex.org/W2132632499","https://openalex.org/W2160310346","https://openalex.org/W2164154943","https://openalex.org/W2170551349","https://openalex.org/W2170747616","https://openalex.org/W2345895128","https://openalex.org/W2370639510","https://openalex.org/W2374993646","https://openalex.org/W2397924882","https://openalex.org/W2557315836","https://openalex.org/W2561757389","https://openalex.org/W2765245881","https://openalex.org/W2947101114","https://openalex.org/W3163347958","https://openalex.org/W4323653322","https://openalex.org/W4362459589","https://openalex.org/W4367316530","https://openalex.org/W4388923745","https://openalex.org/W4403609394","https://openalex.org/W6711963686"],"related_works":["https://openalex.org/W2356518103","https://openalex.org/W2052858527","https://openalex.org/W2170903871","https://openalex.org/W2392810065","https://openalex.org/W2399513595","https://openalex.org/W2374363391","https://openalex.org/W2391401111","https://openalex.org/W3133982388","https://openalex.org/W3203613594","https://openalex.org/W3134544077"],"abstract_inverted_index":{"Triterpenoid":[0],"saponins":[1,32],"are":[2],"one":[3],"of":[4,8,12,30,46,51,55,58,79,93,105,121,130,136,143],"the":[5,27,44,76,91,118,131,140],"main":[6],"activities":[7,18],"roots":[9],"and":[10,23,49,95,100,133],"rhizomes":[11],"<i>Hylomecon":[13],"japonica</i>,":[14,35,123],"with":[15],"various":[16],"pharmacological":[17],"such":[19],"as":[20],"antibacterial,":[21],"anticancer,":[22],"anti-inflammatory.":[24],"To":[25],"elucidate":[26],"biosynthesis":[28,77,111,141],"pathway":[29,78,142],"triterpenoid":[31,80,109,144],"in":[33,75,90,97,108,139],"<i>H.":[34,52,122],"DNA":[36],"nanoball":[37],"sequencing":[38],"technology":[39],"was":[40,112],"used":[41],"to":[42,87],"analyze":[43],"transcriptome":[45,119],"leaves,":[47],"roots,":[48],"stems":[50],"japonica</i>.":[53],"Out":[54],"a":[56,101],"total":[57],"99,404":[59],"unigenes,":[60],"78,989":[61],"unigenes":[62,70],"were":[63,85],"annotated":[64],"by":[65],"seven":[66],"major":[67],"databases;":[68],"49":[69],"encoded":[71],"11":[72],"key":[73,137],"enzymes":[74,138],"saponins.":[81,145],"Nine":[82],"transcription":[83],"factors":[84],"found":[86],"be":[88],"involved":[89],"metabolism":[92],"terpenoids":[94],"polyketides":[96],"<i>H</i>.":[98],"<i>japonica</i>":[99],"spatial":[102],"structure":[103],"model":[104],"squalene":[106],"synthase":[107],"saponin":[110],"established.":[113],"This":[114],"study":[115],"greatly":[116],"enriched":[117],"data":[120],"which":[124],"is":[125],"helpful":[126],"for":[127],"further":[128],"analysis":[129],"functions":[132],"regulatory":[134],"mechanisms":[135]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
