title: Potential use of low-copy nuclear genes in DNA barcoding: a comparison with plastid genes in two Hawaiian plant radiations.
abstract: BACKGROUND
  DNA barcoding of land plants has relied traditionally on a small number of markers from the plastid genome. In contrast, low-copy nuclear genes have received little attention as DNA barcodes because of the absence of universal primers for PCR amplification.
  
  
  RESULTS
  From pooled-species 454 transcriptome data we identified two variable intron-less nuclear loci for each of two species-rich genera of the Hawaiian flora: Clermontia (Campanulaceae) and Cyrtandra (Gesneriaceae) and compared their utility as DNA barcodes with that of plastid genes. We found that nuclear genes showed an overall greater variability, but also displayed a high level of heterozygosity, intraspecific variation, and retention of ancient alleles. Thus, nuclear genes displayed fewer species-diagnostic haplotypes compared to plastid genes and no interspecies gaps.
  
  
  CONCLUSIONS
  The apparently greater coalescence times of nuclear genes are likely to limit their utility as barcodes, as only a small proportion of their alleles were fixed and unique to individual species. In both groups, species-diagnostic markers from either genome were scarce on the youngest island; a minimum age of ca. two million years may be needed for a species flock to be barcoded. For young plant groups, nuclear genes may not be a superior alternative to slowly evolving plastid genes.
authors: Tropical Conservation Biology and Environmental Science, University of Hawai'i at Hilo, 200 West Kawili Street, Hilo, HI 96720, USA. pillon@hawaii.edu
authors: Yohan
authors: Y
authors: Pillon
authors: Jennifer
authors: J
authors: Johansen
authors: Tomoko
authors: T
authors: Sakishima
authors: Srikar
authors: S
authors: Chamala
authors: W Brad
authors: WB
authors: Barbazuk
authors: Eric H
authors: EH
authors: Roalson
authors: Donald K
authors: DK
authors: Price
authors: Elizabeth A
authors: EA
authors: Stacy
mesh_terms: D029422:Campanulaceae / Q000145:classification* / Q000235:genetics; D002467:Cell Nucleus / Q000235:genetics; D058893:DNA Barcoding, Taxonomic; D018744:DNA, Plant / Q000235:genetics; D006239:Haplotypes; D006254:Hawaii; D019684:Magnoliopsida / Q000145:classification* / Q000235:genetics; D058974:Phylogeography; D018087:Plastids / Q000235:genetics*
chemical_list: D018744:DNA, Plant
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