Minimally destructive sampling of type specimens of Pyropia (Bangiales, Rhodophyta) recovers complete plastid and mitochondrial genomes

Abstract

Plant species, including algae and fungi, are based on type specimens to which the name of a taxon is permanently attached. Applying a scientific name to any specimen therefore requires demonstrating correspondence between the type and that specimen. Traditionally, identifications are based on morpho-anatomical characters, but recently systematists are using DNA sequence data. These studies are flawed if the DNA is isolated from misidentified modern specimens. We propose a genome-based solution. Using 4 × 4 mm2 of material from type specimens, we assembled 14 plastid and 15 mitochondrial genomes attributed to the red algae Pyropia perforata, Py. fucicola, and Py. kanakaensis. The chloroplast genomes were fairly conserved, but the mitochondrial genomes differed significantly among populations in content and length. Complete genomes are attainable from 19th and early 20th century type specimens; this validates the effort and cost of their curation as well as supports the practice of the type method.

Genomic and phylogenetic analysis of Ceramium cimbricum (Ceramiales, Rhodophyta) from the Atlantic and Pacific Oceans supports the naming of a new invasive Pacific entity Ceramium sungminbooi sp. nov.

“…The intraspecific organellar genome variation exhibited between specimens of C. sungminbooi from Denmark and California, USA are similar to those reported for Pyropia perforata (J. Agardh) S.C.Lindstrom (Hughey et al 2014). They found that the lectotype of P. perforata from San Francisco, California differed from a specimen from La Jolla, California by 185 SNPs and 14 gaps, and another from San Juan Island, Washington by 75 SNPs and one gap for its plastid genome.…”

“…The genome libraries were constructed using the methods outlined by Hughey et al (2014). The DNA library was sequenced using Illumina (Illumina Inc., San Diego, CA, USA) 36 bp paired-end analysis with the manufacturer's protocol via the cBot and HiSeq 2000 by HTGC (http:// www.htseq.org/).…”

Identification of a new marine algal species Pyropia nitida sp. nov. (Bangiales: Rhodophyta) from Monterey, California

“…The genome library was constructed using the methods outlined by Hughey et al (2014) and analyzed using Illumina 36 bp paired-end sequencing following the protocol of the manufacturer via the cBot and HiSeq 2000 by HTGC (http://www.htseq.org/). The reads were base called with Illumina's standard pipeline yielding 356 filtered reads of 11 483 length.…”

Mitochondrial and plastid genome analysis of the marine red alga Coeloseira compressa (Champiaceae, Rhodophyta)

“…The genomic library was constructed and sequenced by the High-Throughput Genomics Center (Seattle, Washington). The data were assembled using Velvet 1.2.08 (Zerbino & Birney 2008) on the Bio-Linux platform (Field et al 2006) using the assembly and annotation methods described by Hughey et al (2014). Alignment of the Florideophyte mitogenomes was completed using default settings in MAFFT (Katoh & Standley 2013).…”