Estimating the Nucleotide Diversity in <i>Ceratodon purpureus</i> (Ditrichaceae) from 218 Conserved Exon-Primed, Intron-Spanning Nuclear Loci

• Main Authors: Stuart F. McDaniel, Marijke J. van Baren, Kelly S. Jones, Adam C. Payton, Ralph S. Quatrano
• Format: Article
• Language: English
• Published: Wiley 2013-04-01
• Series: Applications in Plant Sciences
• Subjects: chromosomal inversion; expressed sequence tag (EST); phylogeography; Physcomitrella patens; sex-linked loci
• Online Access: http://www.bioone.org/doi/full/10.3732/apps.1200387
• ISSN: 2168-0450

Premise of the study: We developed and tested primers for 218 nuclear loci for studying population genetics, phylogeography, and genome evolution in bryophytes. Methods and Results: We aligned expressed sequence tags (ESTs) from <i>Ceratodon purpureus</i> to the <i>Physcomitrella patens</i> genome sequence, and designed primers that are homologous to conserved exons but span introns in the <i>P. patens</i> genome. We tested these primers on four isolates from New York, USA; Otavalo, Ecuador; and two laboratory isolates from Austria (WT4 and GG1). The median genome-wide nucleotide diversity was 0.008 substitutions/site, but the range was large (0–0.14), illustrating the among-locus heterogeneity in the species. Conclusions: These loci provide a valuable resource for finely resolved, genome-wide population genetic and species-level phylogenetic analyses of <i>C. purpureus</i> and its relatives.