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BMC Evol Biol. 2013 Feb 9;13:35. doi: 10.1186/1471-2148-13-35.

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

Author information

1
Tropical Conservation Biology and Environmental Science, University of Hawai'i at Hilo, 200 West Kawili Street, Hilo, HI 96720, USA. pillon@hawaii.edu

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.

PMID:
23394592
PMCID:
PMC3605094
DOI:
10.1186/1471-2148-13-35
[Indexed for MEDLINE]
Free PMC Article

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