| Title | Genome duplication and regulatory innovation underpin contrasting life-history strategies in cryptic Cassytha filiformis lineages |
| Author | Liu, Zhi-Fang |
| Publication | ANNALS OF BOTANY |
| Year | 2026 |
| Corresponding Author | Liu, ZF;Li, J |
| Abstract | Background and Aims 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.Methods 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.Key Results 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 % of gene families forming a conserved core transcriptome. We identified a recent, lineage-specific duplication (Ks = 0.2-0.4), with the preferential retention of known parasitism-related genes in each lineage. Functional enrichment highlighted convergence in hormone signalling and regulatory pathways.Conclusions 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. |
