Journal article
Potential use of low-copy nuclear genes in DNA barcoding: a comparison with plastid genes in two Hawaiian plant radiations
BMC evolutionary biology, Vol.13(1), pp.35-35
02/09/2013
Handle:
https://hdl.handle.net/2376/104898
PMCID: PMC3605094
PMID: 23394592
Abstract
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.
Metrics
6 Record Views
Details
- Title
- Potential use of low-copy nuclear genes in DNA barcoding: a comparison with plastid genes in two Hawaiian plant radiations
- Creators
- Yohan Pillon - Tropical Conservation Biology and Environmental Science, University of Hawai'i at Hilo, 200 West Kawili Street, Hilo, HI 96720, USA. pillon@hawaii.eduJennifer JohansenTomoko SakishimaSrikar ChamalaW Brad BarbazukEric H RoalsonDonald K PriceElizabeth A Stacy
- Publication Details
- BMC evolutionary biology, Vol.13(1), pp.35-35
- Academic Unit
- Biological Sciences, School of
- Publisher
- England
- Identifiers
- 99900546776901842
- Language
- English
- Resource Type
- Journal article