Moschin, S. | bioRxiv Science

bioRxiv2025

Sequencing a botanical monument: a chromosome-level assembly of the 400-year-old Goethe's Palm (Chamaerops humilis L.) at the Botanical Garden of the University of Padua (Italy)

The rapid decline in global biodiversity highlights the urgent need for conservation efforts, with botanical gardens playing a crucial role in ex situ plant preservation. Monumental plants, such as the 400-year-old Goethes Palm (Chamaerops humilis L.) at the UNESCO Botanical Garden of the University of Padua (Italy), serve as vital flagship species with significant ecological and cultural value. In this study, we present the first high-quality, chromosome-level genome assembly of C. humilis, using PacBio HiFi and Arima Hi-C sequencing technologies. This genome is the most contiguous and complete within the Arecaceae family to date, with an exceptionally high repeat content of 88%, of which 63% is attributed to Long Terminal Repeat (LTR) elements. Comparative analysis of the transposable element (TE) landscape in palms suggests that the LTR expansion in C. humilis is likely the result of recent TE bursts. Furthermore, we provide the first comprehensive annotation of microRNAs (miRNAs) in the Arecaceae family, identifying, for the first time in palms, the miRNA family miR827, which plays a key role in nutrient regulation. Microsatellite analysis suggests that it probably belongs to the Western genetic lineage of C. humilis. These findings represent a significant advancement in the conservation genomics of this species, laying the groundwork for enhanced preservation strategies, with botanical gardens as pivotal actors in the fight to safeguard global biodiversity.

genomics↗

bioRxiv2023

The genome of the Wollemi pine, a critically endangered living fossil unchanged since the Cretaceous, reveals extensive ancient transposon activity.

We present the genome of the living fossil, Wollemia nobilis, a southern hemisphere conifer morphologically unchanged since the Cretaceous. Presumed extinct until rediscovery in 1994, the Wollemi pine is critically endangered with less than 60 wild adults threatened by intensifying bushfires in the Blue Mountains of Australia. The 12 Gb genome is among the most contiguous large plant genomes assembled, with extremely low heterozygosity and unusual abundance of DNA transposons. Reduced representation and genome re-sequencing of individuals confirms a relictual population since the last major glacial/drying period in Australia, 120 ky BP. Small RNA and methylome sequencing reveal conservation of ancient silencing mechanisms despite the presence of thousands of active and abundant transposons, including some transferred horizontally to conifers from arthropods in the Jurassic. A retrotransposon burst 8-6 my BP coincided with population decline, possibly as an adaptation enhancing epigenetic diversity. Wollemia, like other conifers, is susceptible to Phytophthora, and a suite of defense genes, similar to those in loblolly pine, are targeted for silencing by sRNAs in leaves. The genome provides insight into the earliest seed plants, while enabling conservation efforts.

genomics↗