The D3-D5 region of large subunit ribosomal DNA provides good resolution of German limnic and terrestrial nematode communities

in Nematology
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Reliable and well-developed DNA barcode databases are indispensable for the identification of microscopic life. However, effectiveness of molecular barcoding in identifying terrestrial specimens, and nematodes in particular, has received little attention. In this study, ca 600 ribosomal large subunit DNA fragments (D3-D5 region) were successfully amplified for 79 limnic and terrestrial nematode species sampled at 147 locations across Germany. Distinctive DNA motifs in the LSU region were identified in 80% of all species examined. For 13 supposedly single morphospecies, 2-7 LSU barcode groups were detected with a wide range of intraspecific variations (0.09-7.9%). This region seems to be more suitable for the assessment of limno-terrestrial nematode diversity than the frequently used mitochondrial gene COI, as amplification success of the latter fragment is low for several nematode species. Our reference database for nematodes may serve as a starting point for applied and fundamental studies for these ubiquitous, ecologically highly relevant, organisms.

The D3-D5 region of large subunit ribosomal DNA provides good resolution of German limnic and terrestrial nematode communities

in Nematology

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Figures

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    Sampling locations in Germany. Black stars indicate the sampling locations for limnic nematodes, and black dots those of terrestrial nematodes.

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    Intraspecific divergences for the large ribosomal subunit (LSU) based on pairwise divergences (%). Only species that exhibited a detectable intraspecific divergence are shown; species with no intraspecific variance (Tripyla setifera, Acrostichus nudicapitatus, Eumonhystera filiformis) are only shown as examples.

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    Intra- and interspecific variability for the LSU based on nucleotide p-distance (uncorrected, %). The frequencies of the pairwise differences for the 79 species included in the analysis are shown. Intraspecific variability is shown in grey, and interspecific variability in black.

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    Maximum likelihood tree for 79 nematode species, sampled and sequenced in this study, based on the LSU gene fragment. The analysis was run with a bootstrap value of 1000. The major clades are indicated by coloured boxes. Numbers at the branches represent support values for the nodes. Numbers in parentheses indicate the number of sequences for this species.

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    Maximum likelihood tree for 21 nematode species based on the SSU gene fragment. All sequences were generated in this study. The analysis was run with a bootstrap value of 1000. The major clades are indicated by coloured boxes. Numbers at the branches represent support values for the nodes.

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