Beschrijving
IntroductionDNA metabarcoding has proven to be a cost- and time-effective alternative to morphological
identifications for environmental monitoring. However, when a community contains a high
phylogenetic diversity, it can be difficult to tailor PCR primers that effectively amplify a marker gene
from all species. This results in PCR amplification bias, which affects monitoring data quality derived
from metabarcoding. Several studies have proposed to use PCR-free approaches (i.e. shotgun
metagenomics) to circumvent this issue, but generally indicate two hurdles preventing the wide
applicability of this approach: 1) a lack of reference genomes for most species present in a given
environment, and 2) computational intensive pipelines for processing shotgun metagenomic data.
Here, we propose a strategy that tackles these two hurdles and apply it to classify shotgun
metagenomic reads from macrobenthos samples.
Methods
We selected 25 macrobenthos species from various phyla for low-coverage Illumina whole genome
sequencing. We build a k-mer index database directly from the sequencing reads, thus circumventing
tedious genome assembly. This database was then used to classify shotgun metagenomic reads from
macrobenthos samples using a very fast exact k-mer matching algorithm. The same samples were
simultaneously characterized by morphological identification and metabarcoding to compare results
obtained by different methods.
Results
We show that low-coverage genome sequencing allows us to build a database that equals the
classification potential of a database build with fully assembled reference genomes. We are able to
classify a large fraction of metagenomic reads from our samples (up to 96%). Results from shotgun
metagenomics algin better with biomass than those from metabarcoding due to the absence of PCR
amplification bias.
Conclusions
Our strategy provides an easy, fast, and accessible way to assess community composition in
metazoan bulk samples by shotgun metagenomics
Periode | 5-sep.-2024 |
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Titel evenement | International Barcode of Life Conference |
Soort evenement | Congres |
Locatie | Bélem, BraziliëTonen op kaart |
Mate van erkenning | Internationaal |