Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2025.07.31.667835

Molecular evolution of terpene synthase underlying the diversification of isoprene emission in Fagaceae

Ikezaki, Y.·Kudo, S. N.·Nakata, T.·Koita, S.·Munakata, R.·Yazaki, K.·Torimaru, T.·Tomaru, N.·Isobe, S.·Hirakawa, H.·Kusumi, J.·Satake, A.
View original source ↗Export metadata ↓

Abstract

Plants emit a wide range of volatile organic compounds, among which isoprene is the most abundant and atmospherically influential. Although oak species are major contributors to isoprene emission, there is considerable variation in isoprene emission capacity within the Fagaceae family. To unravel the evolutionary origins of isoprene emission, we investigated the molecular evolution of terpene synthase (TPS) genes across eight species within the Fagaceae. We identified a Fagaceae-specific TPS-b subclade in which potential isoprene synthase (IspS) activity evolved independently in two gene lineages within subgenus Quercus. Ancestral sequence reconstruction revealed that the acquisition of a diagnostic amino acid residue for IspS function arose convergently in these lineages and was subject to positive selection, suggesting adaptive evolution. Ancestral-enzyme assays targeting the gene lineage with high gene expression revealed that the early protein primarily produced monoterpenes from geranyl diphosphate (GPP), whereas their descendants shifted substrate preference to dimethylallyl diphosphate (DMAPP), evolving into dedicated isoprene synthases. Our results indicate that IspS activity was not ancestral in Fagaceae, but evolved approximately 56 million years ago within the subgenus Quercus, and has been retained ever since. These findings emphasize the roles of enzyme structural innovation and regulatory shifts in the diversification of volatile terpenoid biosynthesis.

Source connections

Explore related subjects

evolutionary biologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Ikezaki, Y., Kudo, S. N., Nakata, T., Koita, S., Munakata, R., Yazaki, K., Torimaru, T., Tomaru, N., Isobe, S., Hirakawa, H., Kusumi, J., Satake, A.. 2025-07-31. Molecular evolution of terpene synthase underlying the diversification of isoprene emission in Fagaceae. https://doi.org/10.1101/2025.07.31.667835

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Evolutionary dynamics of RNA viruses during persistent infection in Drosophila melanogaster

Persistent viral infections provide an extended window for viral evolution, yet their intra-host trajectories across the host lifespan remain underexplored. Here, we tracked the longitudinal evolution of three single-stranded RNA (ssRNA) viruses (Drosophila A virus [DAV], Drosophila C virus [DCV], and Nora virus) and one double-stranded RNA (dsRNA) virus (Bloomfield virus) during persistent infection in Drosophila melanogaster. By analyzing viral populations across early, intermediate, and late infection stages, we mapped dynamic shifts in the viral quasispecies and the emergence of adaptive mutations. These data demonstrate that long-term persistence drives viral evolution in a viral species-specific manner. DAV evolution was defined by clonal interference, driven by the continuous turnover of competing haplotypes. Nora virus exhibited prolonged evolutionary stasis punctuated by a late-stage sweep, suggesting adaptation to the senescing host environment. In contrast, standard DCV populations were locked under strong purifying selection, where no adaptive mutations were detected. However, this constraint collapsed in high-titer DCV infections, triggering extensive mutational diversification. Distinct from the ssRNA dynamics, the multi-segmented dsRNA Bloomfield virus maintained higher sequence fidelity and a stable genomic formula. Ultimately, these results demonstrate that viral evolution during persistent infection is governed by the interplay between specific host-pathogen interactions and the physiological decline of the host.

evolutionary biology↗
bioRxiv2026

A new cell type facilitated live-bearing and multiple independent origins of placentation in fish

The origin of new organs has fascinated biologists since Darwin. Yet the molecular and evolutionary steps that give rise to new organs remain difficult to resolve, largely because most organs have ancient origins. The fish family Poeciliidae offers a rare exception. Within poeciliids, placentas have independently evolved at least nine times, including within the last ~10 million years. Here, we study the molecular and cellular drivers of five independent origins of a placenta, using pairs of sister species with and without a placenta. We identified a new maternal cell type that emerged in the common ancestor of poeciliids and likely enabled the family to transition from egg-laying to live-bearing through egg retention. This new cell type originated by partly co-opting the existing gene regulatory network of another ovarian cell type. Subsequently, this same new maternal cell type, together with the embryonic yolk sac, was repeatedly and independently co-opted to form a placenta in all five origins. The evolution of these placentas involved high levels of convergence at the pathway level (e.g., lipid metabolism and vesicle-mediated transport), although these functional changes relied primarily on distinct genes across species. Our analyses show how the evolution and modification of a new cell type enabled the evolution of live birth and placentation, providing the cellular and genetic foundations for the repeated evolution of a new organ.

evolutionary biology↗
bioRxiv2026

The extracellular morphology and behaviour of the last common ancestor of animals and choanoflagellates

Choanoflagellates, the closest known living relatives of animals, provide a powerful comparative system for investigating the evolution of extracellular morphology and cell behaviour on the animal stem lineage. Although all choanoflagellates share a conserved cellular architecture including a flagellum and collar of microvilli, they display a wide diversity of extracellular structures and behaviours throughout the life cycle. Their extracellular features, historically used for species identification, have long been suspected to reflect a mixture of evolutionary inheritance and ecological plasticity. Yet, the majority of choanoflagellate diversity remains undescribed, and the extent to which their extracellular traits map onto their phylogeny has remained unclear, impeding comparative reconstructions of the evolutionary history of extracellular structures with the earliest animals. Here, we integrate super-resolution fluorescence imaging, electron microscopy and transcriptomic analysis to characterize the extracellular structures and behaviours across both currently described lineages of choanoflagellates (Craspedida and Acanthoecida), by studying pairs of closely related species in conjunction with novel isolates representing previously unexplored clades. Our results reveal strong conservation of extracellular morphology between close relatives, whereas deeper evolutionary distances uncover unexpected innovations, such as sheath-like layers, bipartite thecae, crawling stages and atypical inverted division patterns. Furthermore, the inclusion of early-branching taxa sister to the loricates supports the hypothesis that the silicified extracellular lorica is a derived trait rather than an ancestral feature. Together, our findings suggest that the last choanoflagellate common ancestor possessed an organic non-silicified extracellular covering composed of one or more layers and that it was capable of both swimming and crawling behaviours, refining the cellular context from which animals evolved.

evolutionary biology↗