Background Lichens, encompassing 20,000 known species, are symbioses between specialized fungi (mycobionts), mostly ascomycetes, and unicellular green algae or cyanobacteria (photobionts). Here we describe the first parallel genomic analysis of the mycobiont Cladonia grayi and of its green algal photobiont Asterochloris glomerata . We focus on genes/predicted proteins of potential symbiotic significance, sought by surveying proteins differentially activated during early stages of mycobiont and photobiont interaction in coculture, expanded or contracted protein families, and proteins with differential rates of evolution. Results A) In coculture, the fungus upregulated small secreted proteins, membrane transport proteins, signal transduction components, extracellular hydrolases and, notably, a ribitol transporter and an ammonium transporter, and the alga activated DNA metabolism, signal transduction, and expression of flagellar components. B) Expanded fungal protein families include heterokaryon incompatibility proteins, polyketide synthases, and a unique set of G-protein α subunit paralogs. Expanded algal protein families include carbohydrate active enzymes and a specific subclass of cytoplasmic carbonic anhydrases. The alga also appears to have acquired by horizontal gene transfer from prokaryotes novel archaeal ATPases and Desiccation-Related Proteins. Expanded in both symbionts are signal transduction components, ankyrin domain proteins and transcription factors involved in chromatin remodeling and stress responses. The fungal transportome is contracted, as are algal nitrate assimilation genes. C) In the mycobiont, slow-evolving proteins were enriched for components involved in protein translation, translocation and sorting. Conclusions The surveyed genes affect stress resistance, signaling, genome reprogramming, nutritional and structural interactions. The alga carries many genes likely transferred horizontally through viruses, yet we found no evidence of inter-symbiont gene transfer. The presence in the photobiont of meiosis-specific genes supports the notion that sexual reproduction occurs in Asterochloris while they are free-living, a phenomenon with implications for the adaptability of lichens and the persistent autonomy of the symbionts. The diversity of the genes affecting the symbiosis suggests that lichens evolved by accretion of many scattered regulatory and structural changes rather than through introduction of a few key innovations. This predicts that paths to lichenization were variable in different phyla, which is consistent with the emerging consensus that ascolichens could have had a few independent origins. Electronic supplementary material The online version of this article (10.1186/s12864-019-5629-x) contains supplementary material, which is available to authorized users.

A s new environments are explored and technological innovations improve tools for the characterization of microbial biodiversity, insights into bacterial and archaeal diversity are continually emerging 1,2 , including improved understanding of physiological capacity, ecology and evolution of organisms across the tree of life. These advances are based on both cultivation strategies 3,4 and cultivation-independent methods that directly access diversity using single-cell 5,6 or metagenomic sequencing 7-9 (Box 1). Though our ability to culture fastidious microorganisms is improving, success seems to vary depending on the environment. For example, the microbial diversity of host-associated systems such as the human microbiome 11,12 may be more amenable to cultivation compared to some environments such as soil. At present, it seems clear that most archaeal and bacterial diversity remains yet to be cultured 10,13. The reasons are many, but as demonstrated recently by the cultivation of a member of the Asgard archaea 14 , syntrophic interactions, slow growth and media optimization can present formidable challenges. Rules of prokaryotic nomenclature and current challenges Describing biodiversity and identifying organisms are the scientific goals of taxonomy. Taxonomy integrates classification and nomenclature to describe biological diversity. Classification circumscribes and ranks taxa, and nomenclature is the process of assigning names. The commonly used Linnaean nomenclatural system focuses on the recognition of species as the basic unit, which are included in taxa of successively higher ranks (genus, family, order, class and phylum). There is some flexibility on how to circumscribe microbial species using phylogenetic, genotypic and phenotypic data. Once a species is delineated, rules of nomenclature given in the International Code of Nomenclature of Prokaryotes (ICNP or 'the Code' 14 ; see Box 2) guide the creation and assignment of names. This is true of all codes of nomenclature that currently exist-prokaryotes, viruses, animals, algae, fungi and plants-in addition to separate codes for cultivated plants and plant associations. Roadmap for naming uncultivated Archaea and Bacteria The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as 'type material', thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we b...

Genomics and metabolomics are widely used to explore specialized metabolite diversity. The Paired Omics Data Platform is a community initiative to systematically document links between metabolome and (meta)genome data, aiding identification of natural product biosynthetic origins and metabolite structures.