An Antarctic lichen isolate (Cladonia borealis) genome reveals potential adaptation to extreme environments

Abstract

Cladonia borealis is a lichen that inhabits Antarctica's harsh environment. We sequenced the whole genome of a C. borealis culture isolated from a specimen collected in Antarctica using long-read sequencing technology to identify specific genetic elements related to its potential environmental adaptation. The final genome assembly produced 48 scaffolds, the longest being 2.2 Mbp, a 1.6 Mbp N50 contig length, and a 36 Mbp total length. A total of 10,749 protein-coding genes were annotated, containing 33 biosynthetic gene clusters and 102 carbohydrate-active enzymes. A comparative genomics analysis was conducted on six Cladonia species, and the genome of C. borealis exhibited 45 expanded and 50 contracted gene families. We identified that C. borealis has more Copia transposable elements and expanded transporters (ABC transporters and magnesium transporters) compared to other Cladonia species. Our results suggest that these differences contribute to C. borealis' remarkable adaptability in the Antarctic environment. This study also provides a useful resource for the genomic analysis of lichens and genetic insights into the survival of species isolated from Antarctica.

Figure 1

Genome synteny and comparisons between six Cladonia species. (a) Circos plot showing conservation of synteny between C. borealis and C. metacorallifera. The synteny map represents 20 C. metacorallifera scaffolds (black) and 19 C. borealis scaffolds (red). (b) Venn diagram, created using the Orthovenn 2 web platform, showing the numbers of gene families shared among Cladonia species and unique to each species. (c) Maximum-likely hood tree, created using MegaX, based on the sequences of single-copy orthologous proteins The numbers of gene families that have expanded (red, +) and contracted (blue, −), as inferred using CAFÉ, are represented.

Figure 2

Secondary metabolite synthase gene clusters and CAZyme genes found in the six Cladonia species’ genomes. (a) Secondary metabolite clusters, including type I polyketide synthases (T1PKS), non-ribosomal peptide synthetases (NRPS), terpenes, hybrid, fungal-RiPP-like, and other clusters, in the Cladonia genomes. (b) Number of CAZyme genes, including auxiliary activities (AA), glycoside hydrolases (GH), and glycosyl transferases (GT) and combined two-gene domains comprising GH and GT (GH + GT) or carbohydrate-binding modules (CBM) and AA(AA + CBM) or GH (CBM + GH), in the Cladonia genomes. See Table 3 for species abbreviations.

Figure 3

Phylogenetic tree depicting the relationships among the ABC transporter proteins of the six Cladonia species. Most genes possessed three conserved motifs, while there are 1 and 14 genes with one and two motifs, respectively. Five genes did not possess the “LSGGQ” motif, with three genes belonging to C. borealis and the other two genes originating from C. grayi and C. uncialis. Each protein identifier contains the species abbreviation (see Table 3); “JMJ” represents C. borealis.

Figure 4

Phylogenetic tree depicting the relationships among the magnesium transporter proteins of the six Cladonia species. Except for five, all genes contained one conserved domain. These five exhibited three domains, with C. grayi being the only species not containing any genes with the three conserved motifs. Each protein identifier contains the species abbreviation (see Table 3); “JMJ” represents C. borealis.