Fig 1.
Comparison between DNA concentrations obtained by different DNA extraction procedures from free-living and cultured nematodes.
Upper panel: comparison of DNA concentrations obtained using NaOH and QIAGEN kit extraction procedures from cultured nematodes (i.e. Plectus sp., Diplolaimelloides oschei and Pellioditis marina). Lower panel: comparison of DNA concentrations obtained using NaOH procedure, QIAGEN and MoBio kits from coastal and deep-sea nematodes. Mean (n = 5) and standard deviations are shown. The MoBio kit has not been used on cultured nematodes since they were not extracted from the sediment.
Table 1.
List of samples analysed by using Sanger, Roche 454 and Illumina MiSeq sequencing.
Table 2.
Results of clustering analysis carried out with OCTUPUS and Mothur pipelines.
Fig 2.
Eukaryotic taxa identified by metagenetic analysis of the nematode assemblage (10 individuals) collected in the NW Mediterranean Sea.
Reported are the relative contribution of eukaryotic taxa obtained at 97% and 99% clustering thresholds using the OCTUPUS pipeline and AmpliconNoise plus Mothur programs. The contributions are calculated from non-chimeric Operational Clustered Taxonomic Units (OCTUs) representing forward sequencing reads from 18S rRNA gene. The contributions of the most important components (expressed as percentage) are reported.
Fig 3.
Relative proportion of OCTUs belonging to different nematode species within the nematode assemblage (10 individuals) collected in the NW Mediterranean Sea.
Reported are the relative contribution of the different nematode genera obtained at 97% and 99% clustering thresholds using the OCTUPUS pipeline and AmpliconNoise plus Mothur programs. The contributions are calculated from non-chimeric OCTUs representing forward sequencing reads from 18S rRNA gene.
Table 3.
Comparison between molecular and morphological identification.
Fig 4.
Eukaryotic taxa identified by metagenetic analysis of the nematode assemblage (100 individuals) collected in the Central Mediterranean Sea.
Reported are the relative contribution of eukaryotic taxa obtained at 97% and 99% clustering thresholds using the OCTUPUS pipeline and AmpliconNoise plus Mothur programs. The contributions are calculated from non-chimeric Operational Clustered Taxonomic Units (OCTUs) representing forward sequencing reads from 18S rRNA gene. The contributions of the most important components (expressed as percentages) are reported.
Fig 5.
Relative proportion of OCTUs belonging to different nematode species within the nematode assemblage (100 individuals) collected in the Central Mediterranean Sea.
Reported are the relative contribution of the different nematode species obtained at 97% and 99% clustering thresholds using the OCTUPUS pipeline and AmpliconNoise plus Mothur programs. The contributions are calculated from non-chimeric OCTUs representing forward sequencing reads from 18S rRNA gene.
Table 4.
Results of intra-genomic variability analysis.