Lichen Cell Atlas: Tools for exploring photosymbiotic associations

Photosymbiotic associations are partnerships where one partner is photosynthetic, termed the photobiont. Such associations span the eukaryotic tree of life from fungi to metazoans. Certain fungi (lichens) have evolved to live as a symbiont dependent on energy from a photobiont. Lichens uniquely produce an anatomically complex structure through the symbiotic association between fungi and algae, which resembles neither symbiont independently but instead resembles a multicellular organism. Co-evolution of such symbioses is likely underpinned by molecular interactions which has previously been characterised using bulk sequencing approaches. However, bulk sequencing fails to capture diversity of individual symbionts preventing the exploration of functional differentiation and cell types found in symbiotic associations. Single-nucleus RNA sequencing (snRNAseq) provides a high-resolution tool to investigate symbiont cellular heterogeneity and further inform roles of symbionts, cell-cell communication, and complex tissue differentiation. Many questions and challenges remain when working with biodiverse data types including: how to define ‘cell types’ in biological systems that form through interaction of simple microbial symbionts? In this project, we present the first cell atlas for a lichen, Xanthoria parietina, using snRNAseq data and a computational framework for studying symbiotic partnerships at the single nuclear level. Functional clusters for fungal and algal symbionts corresponding to key biological functions including carbohydrate transport and photosynthesis were generated suggestive of ‘cell types’. As more cell atlases are generated for mutualistic symbiotic associations (e.g., corals), future cross-species comparisons will enable identification of potential functional conservation and new understanding of the evolution of symbioses across the eukaryotic tree of life.