Genomic Resources for the First Federally Endangered Lichen: The Florida Perforate Cladonia (Cladonia perforata)

Abstract

Thirty years after its designation as a federally endangered species, the Florida Perforate Cladonia (FPC) remains imperiled in isolated populations in the Florida scrub in the southeastern USA. For threatened and endangered species, such as FPC, reference genomes provide critical insight into genomic diversity, local adaptations, landscape-level genetics, and phylogenomics. Using high-throughput sequencing, we assemble the first draft nuclear and mitochondrial genomes for the FPC mycobiont—Cladonia perforata. We also assess genetic diversity within and among populations in southeastern Florida using genome-scale data and investigate diversity across the entire nuclear ribosomal cistron, including the standard DNA barcoding marker for fungi. The draft nuclear genome spanned 33.6 Mb, and the complete, circular mitochondrial genome was 59 Kb. We also generated the first chloroplast genome, to our knowledge, for the photobiont genus associated with FPC, an undescribed Asterochloris species. We inferred the presence of multiple, distinct mycobiont parental genotypes (genets) occurring at local scales in southeastern Florida, and strikingly, no genets were shared among even the closest sample sites. All sampled thalli shared identical mitochondrial genomes, while the nuclear ribosomal cistron showed limited variability—highlighting the genetic resolution provided by nuclear genome-scale datasets. The genomic resources generated here provide critical resources for informed conservation efforts for the FPC.

Myrmecia, Not Asterochloris, Is the Main Photobiont of Cladonia subturgida (Cladoniaceae, Lecanoromycetes)

“…(1) Myrmecia has not been found in previous metabarcoding studies from other Cladonia species [88][89][90] and (2) the commonly used primers employed in this study allowed amplification of Myrmecia by Sanger sequencing in all the thalli of C. subturgida studied. This observation implies that the primers used in this study, as in prior Cladonia studies [34,41], effectively target the Myrmecia species.…”

Lichens as Bioindicators of Global Change Drivers

“…Another important facet of research in the field of lichens regards genomic resources, which serve as critical tools that inform conservation efforts aiming to protect threatened species. Leavitt et al [12] analyzed the reference genomes of the endangered soil lichen species Florida Perforate Cladonia within the Florida scrub in the southeastern USA. The authors used high-throughput sequencing to analyze the reference genomes, which play a crucial role in understanding the genomic diversity, local adaptations and landscape-level genetics of this species.…”