DOI: 10.5061/dryad.hdr7sqvts
title: Data from: Fungal and algal lichen symbionts show different transcriptional expression patterns in two climate zones

description: In the lichen symbiosis, the fungal and algal partners constitute a
 closely integrated system. The combination of fungal and algal partners
 changes along climate gradients in many species, and is expected to be
 adaptive. However, the functional mechanisms behind this
 symbiosis-mediated environmental adaptation are unknown. We investigate
 which transcriptional profiles are associated with specific fungal-algal
 symbiont pairings found in lichens from high-elevation (Lower
 Supratemperate) and low-elevation (Lower Mesomediterranean) sites at two
 extremes of a climatic gradient on Mt. Limbara, Sardinia. Using
 laboratory-acclimatized thalli, we find that lichen fungal and algal
 symbionts show variable expression profiles between high- and
 low-elevation individuals: circadian- and temperature-associated genes for
 fungi and light-responsive genes for algae show climate-specific patterns.
 High- and low-elevation individuals differentially express sugar
 transporters in both symbionts, pointing to symmetrical and
 climate-dependent sugar transport mechanisms between them. A light pulse
 treatment identified asymmetries between fungal and algal light response,
 with high- and low-elevation fungal symbionts but only low-elevation algal
 symbionts showing a response. Together, these results tie
 previously-observed genomic variation along climatic gradients in a lichen
 species to functional differences in transcription for the fungal and
 algal symbionts, contributing to our understanding of environmental
 specialization and niche-specific partner combinations in lichens.
description: Lichen thalli were sampled in the field (Sardinia, Italy) and
 dried before transport to Frankfurt, Germany. Dried individuals were split
 into two pieces (LL and DD) and then rehydrated within 3 days of field
 collection and allowed to acclimatize over 3 days in a plant growth
 chamber (12h light/12h dark cycles, 60 μmol photons
 m<sup>-2</sup> s<sup>-1</sup> at 16° C).
 After 3 days, samples were exposed to 24 h of total darkness
 before LL group was additionally exposed to 20 minutes of light (60 μmol
 photons m<sup>-2</sup> s<sup>-1</sup>). All
 samples were then harvested into liquid nitrogen. After
 tissue harvesting from lichen thalli (150 mg), RNA was extracted with TRI
 Reagent (Zymo Research Europe GmbH, Freiburg, DE) according to the
 manufacturer’s instructions. The extracted RNA was then sent to Novogene
 (Cambridge, UK) for library construction, quality control and 150 bp
 paired-end sequencing with NovaSeq. All sequence information can be found
 on the European Nucleotide Archive (ENA) under project accession number
 PRJEB72275.
description: # Fungal and algal lichen symbionts show different transcriptional
 expression patterns in two climate zones
 [https://doi.org/10.5061/dryad.hdr7sqvts](https://doi.org/10.5061/dryad.hdr7sqvts) ## Description of the data and file structure Data files included: 1. RNAseq_workflow.Rmd: R markdown file containing all code used to generate data, analyses, and figures used in the manuscript 2. Upust.final.file: final, joined Salmon-quantified RNA-seq data for fungal reads (mapped to Umbilicaria pustulata fungal mRNAs) 3. OTU5.final.file: final, joined Salmon-quantified RNA-seq data for algal reads (mapped to Trebouxia sp. pure culture mRNAs) 4. SampleTable.csv: sample information file (treatments, sites, and coordinates and elevation of sampling locations Categorical variables in SampleTable.csv include: **Clim**: "climate," the rough climate zone at the site where each sample was taken. Values: "warm" = "Lower Mesomediterranean" and "cold" = "Lower Supratemperate," both taken from the categorizations for Sardinia in Canu et al. (2015) Bioclimate map of Sardinia (Italy). Journal of Maps **11**: 711–718 **Rep**: "replicate number" **Treat**: "treatment," referring to the light pulse treatment. Values: "DD" = "dark-adapted controls," samples that did not undergo a light pulse; "LL" = "light pulse-treated," samples undergoing a 20-minute light pulse after dark adaptation. **Site**: the precise site from which each sample was taken, with a replicate number for the sites from the same location. Values: "PDN" = "Ponte Diana North," referring to sites to the north of Ponte Diana bridge on Lake Coghinas. "PDS" = "Ponte Diana South," equivalent sites south of the same bridge. "LP" = "Limbara peak," samples taken from the top of Mt. Limbara. **newSite**: Simplified site names, with the overall location only. Values: "PD" = "Ponte Diana," referring to sites arond Ponte Diana bridge on Lake Coghinas. "LP" = "Limbara peak," samples taken from the top of Mt. Limbara. 5. Upust_TBG_2345_GOs.txt: topGO-formatted GO annotations for fungal fraction of Umbilicaria pustulata 6. OTU5_geneID2GO.txt: topGO-formatted GO annotations for algal fraction of Umbilicaria pustulata (Trebouxia sp. genotype OTU5, also known as [Trebouxia sp. C0006](https://www.ncbi.nlm.nih.gov/datasets/taxonomy/2905655/)) 7. Upust_TBG_2345_scaffolds.fa: FASTA file with the genome scaffolds for Umbilicaria pustulata, used for generating the fungal fraction index file 8. Upust_TBG_2345_mrna.fa: FASTA file with the transcriptome (mRNA) for Umbilicaria pustulata, used for generating the fungal fraction index file 9. Upust_TBG_2345.gff: GFF file with genome annotations for Umbilicaria pustulata, used for generating the fungal fraction index file 10. OTU5_scaffolds.fa: FASTA file with the genome scaffolds for Trebouxia sp. genotype OTU5, used for generating the algal fraction index file 11. OTU5_mrna.fa: FASTA file with the transcriptome (mRNA) for Trebouxia sp. genotype OTU5, used for generating the algal fraction index file 12. OTU5.gff: GFF file with genome annotations for Trebouxia sp. genotype OTU5, used for generating the algal fraction index file Upust: Umbilicaria pustulata OTU5: Trebouxia sp. genotype OTU5, also known as [Trebouxia sp. C0006](https://www.ncbi.nlm.nih.gov/datasets/taxonomy/2905655/) Other information on experimental approaches and analyses can be found either in the manuscript file's Methods or in detail within the R markdown file. ## Code/software Software needed to view the R markdown file and analyze the final Salmon-generated files: * R version 4.2.3 (2023-03-15) or newer * R studio 2022.07.2 Build 576 or newer Software needed to perform the analyses that produced the two Salmon-quantified RNA-seq datasets are described in detail within the R markdown file. ## Access information Other publicly accessible locations of the data: * [https://www.ebi.ac.uk/ena/browser/view/PRJEB72275](https://www.ebi.ac.uk/ena/browser/view/PRJEB72275)