Publication Date:
2024-06-30
Description:
Traditional morphological methods for species identification are highly time consuming,
especially for small organisms, such as Foraminifera, a group of shell-building microbial
eukaryotes. To analyze large amounts of samples more efficiently, species identification
methods have extended to molecular tools in the last few decades. Although a wide
range of phyla have good markers available, for Foraminifera only one hypervariable
marker from the ribosomal region (18S) is widely used. Recently a new mitochondrial
marker cytochrome oxidase subunit 1 (COI) has been sequenced. Here we investigate
whether this marker has a higher potential for species identification compared to
the ribosomal marker. We explore the genetic variability of both the 18S and COI
markers in 22 benthic foraminiferal morphospecies (orders Miliolida and Rotaliida).
Using single-cell DNA, the genetic variability within specimens (intra) and between
specimens (inter) of each species was assessed using next-generation sequencing.
Amplification success rate was twice as high for COI (151/200 specimens) than
for 18S (73/200 specimens). The COI marker showed greatly decreased intra- and
inter-specimen variability compared to 18S in six out of seven selected species.
The 18S phylogenetic reconstruction fails to adequately cluster multiple species
together in contrast to COI. Additionally, the COI marker helped recognize misclassified
specimens difficult to morphologically identify to the species level. Integrative taxonomy,
combining morphological and molecular characteristics, provides a robust picture of the
foraminiferal species diversity. Finally, we suggest the use of a set of sequences (two or
more) to describe species showing intra-genomic variability additionally to using multiple
markers. Our findings highlight the potential of the newly discovered mitochondrial
marker for molecular species identification and metabarcoding purposes.
Keywords:
protist
;
high-throughput sequencing
;
metabarcoding
;
intra-genomic variation
;
benthic foraminifera
Repository Name:
National Museum of Natural History, Netherlands
Type:
info:eu-repo/semantics/article
Format:
application/pdf
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