Open Access Open Badges Research article

Potential use of low-copy nuclear genes in DNA barcoding: a comparison with plastid genes in two Hawaiian plant radiations

Yohan Pillon1*, Jennifer Johansen1, Tomoko Sakishima1, Srikar Chamala23, W Brad Barbazuk23, Eric H Roalson4, Donald K Price1 and Elizabeth A Stacy1

Author Affiliations

1 Tropical Conservation Biology and Environmental Science, University of Hawai‘i at Hilo, 200 West Kawili Street, Hilo, HI, 96720, USA

2 Department of Biology, University of Florida, Gainesville, FL, 32611, USA

3 Genetics Institute, University of Florida, Gainesville, FL, 32610, USA

4 School of Biological Sciences, Washington State University, 339 Abelson Hall, Pullman, WA, 99164-4236, USA

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BMC Evolutionary Biology 2013, 13:35  doi:10.1186/1471-2148-13-35

Published: 9 February 2013



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.


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.


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.

Adaptive radiation; Island biogeography; Lobeliads; Next-generation sequencing; Progression rule; Single-copy nuclear genes