Shotgun sequencing decades-old lichen specimens to resolve
phylogenomic placement of type material
1
Department of Biology, Brigham Young University, 4102 Life Science
Building, Provo, UT 84602, USA
2
M. L. Bean Life Science Museum, Brigham Young University, 4102
Life Science Building, Provo, UT 84602, USA
3
Biology Department, Boise State University, 1910 West University
Drive, Boise, ID 83725, USA
Publication date: 2019-12-16
Plant and Fungal Systematics 2019; 64(2): 237–247
KEYWORDS
ABSTRACT
Natural history collections, including name-bearing type specimens, are
an important source of genetic information. These data can be critical for appropriate taxonomic
revisions in cases where the phylogenetic position of name-bearing type specimens
needs to be identified, including morphologically cryptic lichen-forming fungal species.
Here, we use high-throughput metagenomic shotgun sequencing to generate genome-scale
data from decades-old (i.e., more than 30 years old) isotype specimens representing three
vagrant taxa in the lichen-forming fungal genus Rhizoplaca, including one species and
two subspecies. We also use data from high-throughput metagenomic shotgun sequencing
to infer the phylogenetic position of an enigmatic collection, originally identified
as R. haydenii, that failed to yield genetic data via Sanger sequencing. We were able to
construct a 1.64 Mb alignment from over 1200 single-copy nuclear gene regions for the
Rhizoplaca specimens. Phylogenomic reconstructions recovered an isotype representing
Rhizoplaca haydenii subsp. arbuscula within a clade comprising other specimens identified
as Rhizoplaca haydenii subsp. arbuscula, while an isotype of R. idahoensis was recovered
within a clade with substantial phylogenetic substructure comprising Rhizoplaca haydenii
subsp. haydenii and other specimens. Based on these data and morphological differences,
Rhizoplaca haydenii subsp. arbuscula is elevated to specific rank as Rhizoplaca arbuscula.
For the enigmatic collection, we were able to assemble the nearly complete nrDNA cistron
and over 50 Mb of the mitochondrial genome. Using these data, we identified this specimen
as a morphologically deviant form representing Xanthoparmelia aff. subcumberlandia.
This study highlights the power of high-throughput metagenomic shotgun sequencing in
generating larger and more comprehensive genetic data from taxonomically important
herbarium specimens.
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