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DNA Barcoding of the Lemnaceae, a Family of Aquatic Monocots

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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.

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.

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