Biology subjects

Strijk, J. S.

Publications and source records attributed to Strijk, J. S..

4 recordsLinked to original sources

bioRxiv2025

Stabilising selection and ecological trade-offs underpin coexistence in a tropical flora

Tropical forests harbour the majority of global plant biodiversity1,2, yet the genomic mechanisms governing the assembly and maintenance of these communities remain poorly understood. Here, we assembled draft genomes for 499 angiosperm species from a lowland rainforest in Singapore, representing 67% of its flora, and integrated these with plant traits and comprehensive forest census data. Across the community, most gene families evolve under stabilising selection, with copy numbers maintained near long-term optima that differ among ecological strategies. These niche-associated genomic attractor states provide a mechanism for convergent adaptation and species coexistence. Modelling stabilising selection also identified a strong trade-off between defence and growth, indicating that pathogen pressure constrains developmental diversification. Consistent with this, species-specific genome space was enriched for resistance genes and transposable elements. In contrast, genomic processes structuring present-day plant community composition differ from those driving deep-time convergence. Genomic comparisons across forest types revealed stronger selection on defence-related pathways in old-growth primary forests and on growth-related processes in regenerating secondary forests, while community-level genomic profiles showed expansions in gene families associated with rapid responses to environmental fluctuations. Stabilising selection therefore links population-level adaptation3,4 with long-term species diversification in the tropics. Niche similarity promotes long-term coexistence, whereas local community structure is shaped by more rapid ecological filtering driven by environmental change. Taken together, these two distinct evolutionary layers provide a genomic framework for understanding how hyperdiverse rainforest floras arise and persist.

genomics↗

bioRxiv2025

How much can reticulate evolution entangle plant systematics? Revisiting subfamilial classification of the Malvatheca clade (Malvaceae) on the basis of phylogenomics

Reticulate evolution (RE), involving hybridization and related processes, generates network-like rather than strictly bifurcating relationships among lineages and can obscure phylogenetic relationships. Detecting ancient hybridization is particularly challenging, as genomic signals may erode over time. The Malvatheca clade (Malvaceae), marked by multiple paleopolyploidy events since its estimated origin 66 my, offers a useful model for examining RE. Its three subfamilies--Bombacoideae (with high chromosome numbers, mostly trees), Malvoideae (lower chromosome numbers, mostly herbs), and the recently described Matisioideae--show unresolved relationships, with several taxa of uncertain placement. We conducted a phylogenomic analysis of 62 Malvatheca species via complete plastomes, 35S rDNA cistrons, and comparative repeatome data. All datasets consistently resolved three main clades: (i) Bombacoideae, (ii) Malvoideae, and (iii) a heterogeneous assemblage including most of the recently assigned Matisioideae and several incertae sedis taxa, suggesting a more complex evolutionary history and circumscription than previously recognized. Chromosome numbers were negatively correlated with repeatome diversity: Bombacoideae presented higher counts but lower repeat diversity, possibly reflecting slower repeat evolution associated with woody growth forms. In contrast, clade III showed marked heterogeneity in both chromosome number and repeat composition, which is consistent with a reticulate origin. Overall, our results show evidence of ancient hybridization and polyploidy, predominantly allopolyploidy, in shaping Malvatheca evolution. These results highlight that reticulation and genome dynamics, rather than taxonomic boundaries alone, are central to understanding the diversification of Malvatheca.

genomics↗

bioRxiv2019

Trochodendron aralioides, the first chromosome-level draft genome in Trochodendrales and a valuable resource for basal eudicot research

BackgroundThe wheel tree (Trochodendron aralioides) is one of only two species in the basal eudicot order Trochodendrales. Together with Tetracentron sinense, the family is unique in having secondary xylem without vessel elements, long considered to be a primitive character also found in Amborella and Winteraceae. Recent studies however have shown that Trochodendraceae belong to basal eudicots and demonstrate this represents an evolutionary reversal for the group. Trochodendron aralioides is widespread in cultivation and popular for use in gardens and parks.\n\nFindingsWe assembled the T. aralioides genome using a total of 679.56 Gb of clean reads that were generated using both PacBio and Illumina short-reads in combination with 10XGenomics and Hi-C data. Nineteen scaffolds corresponding to 19 chromosomes were assembled to a final size of 1.614 Gb with a scaffold N50 of 73.37 Mb in addition to 1,534 contigs. Repeat sequences accounted for 64.226% of the genome, and 35,328 protein-coding genes with an average of 5.09 exons per gene were annotated using de novo, RNA-seq, and homology-based approaches. According to a phylogenetic analysis of protein-coding genes, T. aralioides diverged in a basal position relatively to core eudicots, approximately 121.8-125.8 million years ago.\n\nConclusionsTrochodendron aralioides is the first chromosome-scale genome assembled in the order Trochodendrales. It represents the largest genome assembled to date in the basal eudicot grade, as well as the closest order relative to the core-eudicots, as the position of Buxales remains unresolved. This genome will support further studies of wood morphology and floral evolution, and will be an essential resource for understanding rapid changes that took place at the base of the Eudicot tree. Finally, it can serve as a valuable source to aid both the acceleration of genome-assisted improvement for cultivation and conservation efforts of the wheel tree.

genomics↗

bioRxiv2019

The soursop genome and comparative genomics of basalangiosperms provide new insights on evolutionaryincongruence

Deep relationships and the sequence of divergence among major lineages of angiosperms (magnoliids, monocots and eudicots) remain ambiguous and differ depending on analytical approaches and datasets used. Complete genomes potentially provide opportunities to resolve these uncertainties, but two recently published magnoliid genomes instead deliver further conflicting signals. To disentangle key angiosperm relationships, we report a high-quality draft genome for the soursop (Annona muricata, Annonaceae). We reconstructed phylogenomic trees and show that the soursop represents a genomic mosaic supporting different histories, with scaffolds almost exclusively supporting single topologies. However, coalescent methods and a majority of genes support magnoliids as sister to monocots and eudicots, where previous whole genome-based studies remained inconclusive. This result is clear and consistent with recent studies using plastomes. The soursop genome highlights the need for more early diverging angiosperm genomes and critical assessment of the suitability of such genomes for inferring evolutionary history.

evolutionary biology↗