Virus diversity in metagenomes of a lichen symbiosis (Umbilicaria phaea): complete viral genomes, putative hosts and elevational distributions

Abstract

Summary Viruses can play critical roles in symbioses by initiating horizontal gene transfer, affecting host phenotypes, or expanding their host's ecological niche. However, knowledge of viral diversity and distribution in symbiotic organisms remains elusive. Here we use deep‐sequenced metagenomic DNA (PacBio Sequel II; two individuals), paired with a population genomics approach (Pool‐seq; 11 populations, 550 individuals) to understand viral distributions in the lichen Umbilicaria phaea. We assess (i) viral diversity in lichen thalli, (ii) putative viral hosts (fungi, algae, bacteria) and (iii) viral distributions along two replicated elevation gradients. We identified five novel viruses, showing 28%–40% amino acid identity to known viruses. They tentatively belong to the families Caulimoviridae, Myoviridae, Podoviridae and Siphoviridae. Our analysis suggests that the Caulimovirus is associated with green algal photobionts (Trebouxia) of the lichen, and the remaining viruses with bacterial hosts. We did not detect viral sequences in the mycobiont. Caulimovirus abundance decreased with increasing elevation, a pattern reflected by a specific algal lineage hosting this virus. Bacteriophages showed population‐specific patterns. Our work provides the first comprehensive insights into viruses associated with a lichen holobiont and suggests an interplay of viral hosts and environment in structuring viral distributions.

Protein kinase gene declines linearly with elevation: a shared genomic feature across species and continents in lichenized fungi suggests role in climate adaptation

“…We reconstructed metagenomic sequences from a low-elevation and a high-elevation specimen of U. pustulata and U. phaea . Sequence output and quality for U. pustulata were summarized in Singh et al 2022, for U phaea in Merges et al 2021 and in Table S1.…”

“…We largely followed the pipeline described in Merges et al (2021). In summary, we generated HiFi reads from the Pacbio Sequel II run using the PacBio tool CCS v5.0.0 with default parameters (https://ccs.how).…”

“…Lichen thalli were thoroughly washed with sterile water and checked under the stereomicroscope for the presence of possible contamination or other lichen thalli. DNA was extracted from all of the samples using a cetyltrimethylammonium bromide (CTAB)-based method (Mayjonade et al, 2016) as presented in Merges et al (2021).…”

A Candidate Gene Cluster for the Bioactive Natural Product Gyrophoric Acid in Lichen-Forming Fungi

“…Lichen thalli were thoroughly washed with sterile water and checked under the stereomicroscope for the presence of possible contamination and other lichen thalli. DNA was extracted from all of the samples using a cetyltrimethylammonium bromide (CTAB)-based method ( 41 ) as presented in reference 42 .…”

Phylogenomics reveals the evolutionary origins of lichenization in chlorophyte algae

“…SMRTbell libraries were constructed for samples passing quality control ( SI Appendix , Table S2) according to the manufacturer’s instructions of the SMRTbell Express Prep kit v2.0 following the Low DNA Input Protocol (Pacific Biosciences, Menlo Park, CA) as described in 61 . Genomic DNA was sheared to 20-kb fragments using Megaruptor 2 (Diagenode, Belgium) and then bead-size selected with AMPure PB beads (Pacific Biosciences) to remove <3-kb SMRTbell templates.…”