{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T18:00:59Z","timestamp":1790877659388,"version":"4.1.0"},"reference-count":70,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2026,8,25]],"date-time":"2026-08-25T00:00:00Z","timestamp":1787616000000},"content-version":"am","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background and Aims<\/jats:title>\n                    <jats:p>Parasitic plants have evolved extreme adaptations, but the origins of these innovations remain poorly understood. Cassytha filiformis is a leafless stem hemiparasite representing an ancient angiosperm lineage with a pantropical distribution. Plastome studies revealed cryptic lineages in South China and Southeast Asia, but the nuclear genomic basis underlying adaptation remains unclear.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>We combined comparative transcriptomics, phylogenomics and phenotypic assays to investigate genome dynamics and cryptic divergence. We quantified transcriptomic divergence via orthologous gene family comparisons, detected gene duplications using Ks distributions and assessed functional enrichment of parasitism-related duplicates; germination and parasitic vigour were measured under greenhouse conditions.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Key Results<\/jats:title>\n                    <jats:p>Nuclear phylogenomic analyses showed that morphologically indistinguishable lineages diverged in the Late Miocene, significantly later than plastid-based estimates, indicating decoupled organellar and nuclear evolutionary rates. The lineages exhibited highly asymmetric transcriptomic divergence, with less than 30\u2005% of gene families forming a conserved core transcriptome. We identified a recent, lineage-specific duplication (Ks = 0.2\u20130.4), with the preferential retention of known parasitism-related genes in each lineage. Functional enrichment highlighted convergence in hormone signalling and regulatory pathways.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>This genomic divergence between lineages is mirrored by distinct but overlooked differences in life-history strategies: one lineage invests more in propagule establishment (higher germination), while the other prioritizes rapid host exploitation (greater parasitic vigour). Our study demonstrates that regulatory innovation and lineage-specific duplication underpin ecological divergence and parasitic adaptation in this ancient hemiparasitic lineage.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/aob\/mcag264","type":"journal-article","created":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T11:26:09Z","timestamp":1787570769000},"source":"Crossref","is-referenced-by-count":0,"title":["Genome duplication and regulatory innovation underpin contrasting life-history strategies in cryptic\n                    <i>Cassytha filiformis<\/i>\n                    lineages"],"prefix":"10.1093","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4009-7906","authenticated-orcid":false,"given":"Zhi-Fang","family":"Liu","sequence":"first","affiliation":[{"name":"Shandong Academy of Agricultural Sciences, Institute of Leisure Agriculture , Jinan 250100 ,","place":["China"]},{"name":"Shandong Engineering Research Center of Ecological Horticultural Plant Breeding, Shandong Academy of Agricultural Sciences , Jinan 250100 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alex D","family":"Twyford","sequence":"additional","affiliation":[{"name":"Ashworth Laboratories, Institute of Ecology and Evolution, The University of Edinburgh , Edinburgh EH9 3JR ,","place":["UK"]},{"name":"Royal Botanic Garden Edinburgh , Edinburgh EH3 5LR ,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wen","family":"Chen","sequence":"additional","affiliation":[{"name":"Guangxi Key Laboratory of Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences , Guilin, Guangxi 541006 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qi","family":"Wang","sequence":"additional","affiliation":[{"name":"Shandong Academy of Agricultural Sciences, Institute of Leisure Agriculture , Jinan 250100 ,","place":["China"]},{"name":"Shandong Engineering Research Center of Ecological Horticultural Plant Breeding, Shandong Academy of Agricultural Sciences , Jinan 250100 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter M","family":"Hollingsworth","sequence":"additional","affiliation":[{"name":"Royal Botanic Garden Edinburgh , Edinburgh EH3 5LR ,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiu-Qin","family":"Ci","sequence":"additional","affiliation":[{"name":"Plant Phylogenetics and Conservation Group, Center for Integrative Conservation & Yunnan Key Laboratory for Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences , Mengla, Yunnan 666303 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John G","family":"Conran","sequence":"additional","affiliation":[{"name":"Environment Institute, School of Biological Sciences, Adelaide University , North Terrace, Adelaide, SA 5000 ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zeljana","family":"Prijic","sequence":"additional","affiliation":[{"name":"Department for Research and Development in Agriculture of Medicinal Plants, Institute for Medicinal Plants Research \u2018Dr Josif Pancic\u2019 , Belgrade 11000 ,","place":["Republic of Serbia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jian","family":"Li","sequence":"additional","affiliation":[{"name":"Shandong Academy of Agricultural Sciences, Institute of Leisure Agriculture , Jinan 250100 ,","place":["China"]},{"name":"Shandong Engineering Research Center of Ecological Horticultural Plant Breeding, Shandong Academy of Agricultural Sciences , Jinan 250100 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chen-Jing","family":"Han","sequence":"additional","affiliation":[{"name":"Shandong Academy of Agricultural Sciences, Institute of Leisure Agriculture , Jinan 250100 ,","place":["China"]},{"name":"Shandong Engineering Research Center of Ecological Horticultural Plant Breeding, Shandong Academy of Agricultural Sciences , Jinan 250100 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li-Na","family":"Dong","sequence":"additional","affiliation":[{"name":"Guangxi Key Laboratory of Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences , Guilin, Guangxi 541006 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jie","family":"Li","sequence":"additional","affiliation":[{"name":"Plant Phylogenetics and Conservation Group, Center for Integrative Conservation & Yunnan Key Laboratory for Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences , 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