darn

Dark mAtteR iNvestigator: diving into the dark matter of your COI sequences

This project is maintained by hariszaf

Dark mAtteR iNvesigator (DARN)
understanding the unknown unknowns

On this page, we present the Krona plots returned by DARN regarding the analyses implemented for its corresponding publication.

A series of samples were investigated to establish the presence of bacterial and non-bacterial dark matter on COI data, in an attempt to represent the various feautures thay may affect such studies.

In the sections to follow, we present all the Krona plots of each case in a single plot, meaning that for all the different tests of a single case, all Kronas are embeded on a single plot and you may compare them by clicking on the up-left box where are listed.

Marine samples

Both bulk and eDNA marine samples were analysed. For a thorough description of the samples you may see the DARN manuscript and the corresponding supplementary files.

Ireland

Primer set: jgHCO2198 - jgLCO1490 and LoboF1 - LoboR1

A dataset of 57 marine, surface water eDNA samples (PRJEB45030) were analysed in 2 ways:

The ASVs returned in both cases, were used as input to run DARN.

Honduras

Primer set: mlCOIintF - jgHCO2198

Reef and mangrove data from Honduras were also analyzed in 2 ways:

DARN output is rather similar comparing one bioinformatics pipeline with the other, especially in the case of the reef samples.

The differences

Bulk Vs eDNA samples

Using samples from the same study (Obst et al. 2020) we compared the dark matter in bulk and environmental samples.

We also tested how our results change, when we set another d parameter value, meaning increasing or decreasing the number of ASVs returned from the same sample.

Finally, we compared how the dark matter changes when our samples have been preserved.

Primer set: mlCOIintF - jgHCO2198

The following Krona plots are coming from samples that

Unlike the previous Kronas, those presented here represent a single sample; not a complete dataset.

In all the cases to follow, Krona plots always stand for a single sample.

Freshwater samples

As already mentioned, each Krona represents a single sample.

Lakes in Norway

Here are the first two of them.

We know only that are coming from some vikings for the time being. We add more once we know! :)

Primer set: fwhF2 - EPTDr2

As already mentioned, each Krona represents a single sample.

Norway river sample

Last but not least, one riverine sample was analysed through PEMA and then used to run DARN.

Primer set: BF3 - BR2

As already mentioned, each Krona represents a single sample.