The V4 and V9 hypervariable regions of 18S rRNAs are both generally used for exploring the eukaryotic plankton diversity in oceans. The aim of this investigation is to compare the performance of these two barcode regions in the taxonomic characterization, at qualitative and quantitative level, of the eukaryotic microbiome from 30 metagenomic samples collected in the 2014 OSD summer campaign. Here, preliminary results show how the inferred biodiversity is strongly dependent on the specific marker used in the study. Probably this is due to: the biased sequence coverage in the reference database, with the V4 regions much more represented than the V9 region; the variable efficiency of primer annealing in the considered taxonomic range; and the different V4 and V9 amplicon length that undoubtedly affects their genetic discrimination power.
CHARACTERIZATION OF THE EUKARYOTIC MICROBIOME BY 18S RRNA METABARCODING DATA ANALYSIS AND ASSESSMENT OF THE RELATIVE RESOLUTION OF V4 AND V9 REGIONS
B Fosso;M Santamaria;C Manzari;A M D'Erchia;B Balech;G Pesole
2016
Abstract
The V4 and V9 hypervariable regions of 18S rRNAs are both generally used for exploring the eukaryotic plankton diversity in oceans. The aim of this investigation is to compare the performance of these two barcode regions in the taxonomic characterization, at qualitative and quantitative level, of the eukaryotic microbiome from 30 metagenomic samples collected in the 2014 OSD summer campaign. Here, preliminary results show how the inferred biodiversity is strongly dependent on the specific marker used in the study. Probably this is due to: the biased sequence coverage in the reference database, with the V4 regions much more represented than the V9 region; the variable efficiency of primer annealing in the considered taxonomic range; and the different V4 and V9 amplicon length that undoubtedly affects their genetic discrimination power.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
