Woudstra, Y. | bioRxiv Science

bioRxiv2023

Conifers concentrate large numbers of NLR immune receptor genes on one chromosome

Nucleotide-binding domain and Leucine-rich Repeat (NLR) immune receptor genes form a major line of defence in plants, acting in both pathogen recognition and resistance machinery activation. NLRs are reported to form large gene clusters in limber pine (Pinus flexilis) but it is unknown how widespread this genomic architecture may be among the extant species of conifers (Pinophyta). We used comparative genomic analyses to assess patterns in the abundance, diversity and genomic distribution of NLR genes. Chromosome-level whole genome assemblies and high-density linkage maps in the Pinaceae, Cupressaceae, Taxaceae and other gymnosperms were scanned for NLR genes using existing and customised pipelines. Discovered genes were mapped across chromosomes and linkage groups, and analysed phylogenetically for evolutionary history. Conifer genomes are characterised by dense clusters of NLR genes, highly localised on one chromosome. These clusters are rich in TNL-encoding genes, which seem to have formed through multiple tandem duplication events. In contrast to angiosperms and non-coniferous gymnosperms, genomic clustering of NLR genes is ubiquitous in conifers. NLR-dense genomic regions are likely to influence a large part of the plants resistance, informing our understanding of adaptation to biotic stress and the development of genetic resources through breeding. Plain language summaryNLR immune receptor genes are important in pest, disease and drought resistance of plants. In the giga-genomes of conifers, they concentrate on very small chromosomal regions. These regions act as important reservoirs for NLR diversity and can be used in breeding to improve the resilience of conifer trees.

genomics↗

bioRxiv2023

Some like it hot: adaptation to the urban heat island in common dandelion.

The Urban Heat Island Effect (UHIE) is a globally consistent pressure on species living in cities. Rapid adaptation to the UHIE may be necessary for urban wild flora to persist in cities, but experimental evidence is lacking. Here, we report the first evidence of genetic differentiation in a plant species in response to the UHIE. We collected seeds from common dandelion (Taraxacum officinale) individuals along an urban-rural gradient in the city of Amsterdam (The Netherlands). In common-environment greenhouse experiments, we assessed the effect of elevated temperatures on plant growth and the effect of vernalisation treatments on flowering phenology. We found that urban plants accumulate more biomass at higher temperatures and require shorter vernalisation to induce flowering compared to rural plants. Differentiation was also observed between different intra-urban subhabitats, with park plants displaying a higher vernalisation requirement than street plants. Our results show strong differentiation between urban and rural dandelions in temperature-dependent growth and phenology, consistent with adaptive divergence in response to the UHIE. Rapid adaptation to the UHIE may be a potential explanation for the widespread success of dandelions in urban environments. Summary statementThe urban heat island effect (UHIE) is the most prominent and globally consistent characteristic of environmental change due to urbanisation, severely impacting human populations in cities as well as the cohabiting wildlife. Despite the profoundly mitigating effect of vegetation on urban heat, evidence for plant adaptation to the UHIE has been lacking. Here we provide the first experimental evidence to date, demonstrating adaptation in urban dandelions in response to elevated temperatures, similar to the UHIE. We furthermore show an urban-rural differentiation in flowering response to shorter vernalisation times (cold winter period to activate the onset of flowering in early spring). Given the predominantly asexual apomictic mode of reproduction in dandelions, this evolution is likely the result of environmental filtering on a diverse population of clonal genotypes. We conclude that plant adaptation to the UHIE exists and recommend future studies to contrast our findings with those in outcrossing sexual plant systems. Studies of urban heat adaptation can bring impactful contributions to building climate change-resilient environments and plants should be an integral part of this research.

plant biology↗