Article Dans Une Revue BMC Evolutionary Biology Année : 2013

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

Jennifer Johansen
  • Fonction : Auteur
Tomoko Sakishima
  • Fonction : Auteur
Srikar Chamala
  • Fonction : Auteur
Brad Barbazuk
  • Fonction : Auteur
Eric H Roalson
  • Fonction : Auteur
Donald K Price
  • Fonction : Auteur
Elizabeth A Stacy
  • Fonction : Auteur

Résumé

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.

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ird-05597453 , version 1 (20-04-2026)

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Yohan Pillon, Jennifer Johansen, Tomoko Sakishima, Srikar Chamala, Brad Barbazuk, et al.. Potential use of low-copy nuclear genes in DNA barcoding: a comparison with plastid genes in two Hawaiian plant radiations. BMC Evolutionary Biology, 2013, 13, pp.35. ⟨ird-05597453⟩
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