Metabarcoding options to study eukaryotic endoparasites of birds
Résumé
There is growing interest in the study of avian endoparasite communities, and me-
tabarcoding is a promising approach to complement more conventional or targeted
methods. In the case of eukaryotic endoparasites, phylogenetic diversity is extreme,
with parasites from 4 kingdoms and 11 phyla documented in birds. We addressed this
challenge by comparing different primer sets across 16 samples from 5 bird species.
Samples consisted of blood, feces, and controlled mixes with known proportions of
bird and nematode DNA. Illumina sequencing revealed that a 28S primer set used in
combination with a custom blocking primer allowed detection of various plasmodiid
parasites and filarioid nematodes in the blood, coccidia in the feces, as well as two
potentially pathogenic fungal groups. When tested on the controlled DNA mixes,
these primers also increased the proportion of nematode DNA by over an order of
magnitude. An 18S primer set, originally designed to exclude metazoan sequences,
was the most effective at reducing the relative number of avian DNA sequences and
was the only one to detect Trypanosoma in the blood. Expectedly, however, it did not
allow nematode detection and also failed to detect avian malaria parasites. This study
shows that a 28S set including a blocking primer allows detection of several major
and very diverse bird parasite clades, while reliable amplification of all major parasite
groups may require a combination of markers. It helps clarify options for bird parasite
metabarcoding, according to priorities in terms of the endoparasite clades and the
ecological questions researchers wish to focus on.
Domaines
Parasitologie
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Licence : CC BY - Paternité