StrucRadiation aimed to leverage the repeated edaphic adaptations of New Caledonian Diospyros species to explore the relationship between transposable element (TE) dynamics and ecological adaptation in the face of new environmental opportunities.
Our first objective was to produce a comprehensive multi-trait dataset that integrates genomic, transcriptomic, physiological and environmental data for Diospyros species pairs with contrasting edaphic preferences across the New Caledonian adaptive radiation. Apart from gathering molecular data, we focused in particular on soil and leaf chemistry, together with quantifications of photosynthetic parameters. In collaboration with local plant nurseries in New Caledonia, we established a common garden experiment including selected ultramafic and volcanic species pairs. This common garden provided the material for transcriptomic analysis, and remains an easily accessible source of genetic material for Diospyros species in New Caledonia for ongoing studies of the system.
We assayed gene expression profiles of leaf and root tissue from Diospyros species adapted to ultramafic or serpentine and volcanic soils, grown in the common garden. Our goal was to identify fixed gene expression differences related to edaphic adaptation. Screening differentially expressed genes between edaphically contrasting species pairs using known serpentine and ultramafic adaptation genes from the literature, we found significant overlap only for the ultramafic-calcareous species pair. Interestingly, the known gene found to be differentially expressed in this species pair, a putative cyclin transmembrane metal transporter, is likely involved in metal ion homeostasis. However, no unique differentially expressed genes were identified in the serpentine-volcanic species pair, highlighting the polygenic nature of edaphic adaptation - a topic that is the subject of further investigation.
We assembled high-quality genomes for five selected species from the radiation plus an outgroup using long read PacBio data. The assemblies have been further characterised with structural and functional gene annotations, as well as repeat content analyses, focusing on TEs and tandem repeats. By comparing genome assemblies for species with contrasting edaphic adaptation (volcanic versus ultramafic), we identified patterns of gene-transposable element proximity, revealing highly lineage specific patterns of TE activity. Leveraging soil chemistry analysis performed on soil collected in New Caledonia, we discovered that TE insertions in Diospyros species growing in challenging ultramafic soil were associated with genes involved in DNA and RNA metabolism, providing a list of candidate genes for further investigation in Diospyros.
The results obtained over the course of StrucRadiation are currently being prepared for publication, with preprints to be shared on platforms such as bioRxiv prior to submission to open-access peer-reviewed journals. One publication dealing with the involvement of phenotypic plasticity in edaphic adaptation that used bioinformatic pipelines produced in StrucRadiation is available in bioRxiv and is currently undergoing peer-review in a journal. All associated data and metadata will be made publicly available via repositories such as the European Nucleotide Archive and FigShare. EU funding through StrucRadiation will continue to be acknowledged in all publications and dissemination activities.
