Abstract
BackgroundMembers 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.ResultsWe 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.ConclusionsBased 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.
Highlights
Members of the aquatic monocot family Lemnaceae represent the smallest and fastest growing flowering plants
The ecotypes selected encompass the worldwide geographical distribution of duckweeds originating from different climates and geographical regions, ranging from N60° to S42° latitude and 9 m to 1287 m in altitude (Additional file 1, Figure 1). 85 ecotypes from 19 species were used for statistical calculations and candidate barcode evaluations
It was not unexpected that the coding markers were conserved in PCR product length, while the noncoding spacers displayed more variability due to extensive insertions/deletions (Table 1). These results indicate that the selection of markers by the COBL plant-working group should provide a reasonable level of success for new untested plant families
Summary
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. The cost of DNA purification and sequencing has dropped considerably in recent years so that identification of individual species by DNA barcoding has become an independent, subtler method than solely morphological-based classification to distinguish closely related species, which defines the systematic relationships by analysis of genetic distance. The utility of each of these sequences for individual families of species within the plant kingdom is hardly predictable [11,12]
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