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. 2010 Sep 16:10:205.
doi: 10.1186/1471-2229-10-205.

DNA barcoding of the Lemnaceae, a family of aquatic monocots

Wenqin Wang  1 , Yongrui Wu, Yiheng Yan, Marina Ermakova, Randall Kerstetter, Joachim Messing
Affiliations

DNA barcoding of the Lemnaceae, a family of aquatic monocots

Wenqin Wang et al. BMC Plant Biol. .

Abstract

Background: Members of the aquatic monocot family Lemnaceae (commonly called duckweeds) represent the smallest and fastest growing flowering plants. Their highly reduced morphology and infrequent flowering result in a dearth of characters for distinguishing between the nearly 38 species that exhibit these tiny, closely-related and often morphologically similar features within the same family of plants.

Results: We developed a simple and rapid DNA-based molecular identification system for the Lemnaceae based on sequence polymorphisms. We compared the barcoding potential of the seven plastid-markers proposed by the CBOL (Consortium for the Barcode of Life) plant-working group to discriminate species within the land plants in 97 accessions representing 31 species from the family of Lemnaceae. A Lemnaceae-specific set of PCR and sequencing primers were designed for four plastid coding genes (rpoB, rpoC1, rbcL and matK) and three noncoding spacers (atpF-atpH, psbK-psbI and trnH-psbA) based on the Lemna minor chloroplast genome sequence. We assessed the ease of amplification and sequencing for these markers, examined the extent of the barcoding gap between intra- and inter-specific variation by pairwise distances, evaluated successful identifications based on direct sequence comparison of the "best close match" and the construction of a phylogenetic tree.

Conclusions: Based on its reliable amplification, straightforward sequence alignment, and rates of DNA variation between species and within species, we propose that the atpF-atpH noncoding spacer could serve as a universal DNA barcoding marker for species-level identification of duckweeds.

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Figures

Figure 1
Figure 1
Google map of the worldwide collection of duckweeds for the current study. The distribution of duckweeds was made by GPS with corresponding latitude and longitude.
Figure 2
Figure 2
Relative distribution of all intra- and inter-specific divergence for single or combined markers. (A) rpoC1. (B) rpoB. (C) rbcL. (D) matK. (E) psbK-psbI. (F) trnH-psbA. (G) atpF-atpH. (H) atpF-atpH+ psbK-psbI. × axis is uncorrected p-distance with corresponding increment unit based on variation of each marker. Y axis is the number of occurrences. Barcoding gaps were evaluated with high significance (p < 0.0001) by Median and Mann-Whitney U tests for all markers. Blue bars indicate intraspecific distance and red bars are interspecific distance.
Figure 3
Figure 3
UPGMA tree based atpF-atpH sequences. The tree was drawn among 20 species with more than one ecotype except L. japonica.
See this image and copyright information in PMC

References

    1. Meyer CP, Paulay G. DNA barcoding: error rates based on comprehensive sampling. PLoS Biol. 2005;3(12):e422. doi: 10.1371/journal.pbio.0030422. - DOI - PMC - PubMed
    1. Hebert PDN, Cywinska A, Ball SL, deWaard JR. Biological identifications through DNA barcodes. Proceedings of the Royal Society of London Series B: Biological Sciences. 2003;270(1512):313–321. doi: 10.1098/rspb.2002.2218. - DOI - PMC - PubMed
    1. Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM. Identification of birds through DNA barcodes. PLoS Biol. 2004;2(10):e312. doi: 10.1371/journal.pbio.0020312. - DOI - PMC - PubMed
    1. Hubert N, Hanner R, Holm E, Mandrak NE, Taylor E, Burridge M, Watkinson D, Dumont P, Curry A, Bentzen P, Zhang J, April J, Bernatchez L. Identifying Canadian freshwater fishes through DNA barcodes. PLoS ONE. 2008;3(6):e2490. doi: 10.1371/journal.pone.0002490. - DOI - PMC - PubMed
    1. Kress WJ, Wurdack KJ, Zimmer EA, Weigt LA, Janzen DH. Use of DNA barcodes to identify flowering plants. Proceedings of the National Academy of Sciences of the United States of America. 2005;102(23):8369–8374. doi: 10.1073/pnas.0503123102. - DOI - PMC - PubMed

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