Fig 1.
Schematic diagram of parallel barcode recovery using a high throughput sequencing protocol.
Fig 2.
Composition of COI barcode sequence in NCBI Genbank.
COI sequences were downloaded from NCBI Genbank with keyword “COI”. (A): Growth trend of COI sequences. (B): Taxa composition of COI sequences. (C): Composition of zooplankton COI sequences.
Fig 3.
Zooplankton species in the indigenous barcode database of Lake Tai.
(A) A tree diagram of representative sequences for each species. Distance was measured as the number of base substitutions per site, based on the Kimura two-parameter (K2P) method. One thousand bootstrap trials were run using the neighbor-joining algorithm of the Mega 6.0 program. (B) Number of specimens of each species; red dot means that the species have barcode sequence in NCBI Genbank. (C) Intraspecific divergence based on the indigenous sequences. (D) COI sequences in NCBI Genbank. (E) Intraspecific divergence based on the NCBI Genbank sequences. (F) Similarity of indigenous DNA sequence against NCBI Genbank using Blastx. (G) Similarity of indigenous amino acid sequence against NCBI Genbank using Blastn. (H) Converge of indigenous DNA sequence against NCBI Genbank using Blastn.
Fig 4.
Taxonomic assignment of NGS data.
(A) Numbers of zooplankton OTUs and sequences in the NGS data. (B) Distribution of sequence similarity of OTUs against database (both indigenous and NCBI Genbank database). (C) Number of OTUs annotated by indigenous database and/or NCBI Genbank database. “Local” means the OTUs annotated by the indigenous database and “NCBI” means the OTUs annotated by NCBI Genbank. (D) Comparison of NGS data annotated by indigenous database and NCBI Genbank database. Only 24 species that have barcode sequence in NCBI Genbank were showed.
Fig 5.
Species identified by metabarcoding analysis.
The size of red dots indicated the frequency of each species that detected by morphology method (A) Reads number of each species in metabarcoding data. (B) The internal arcs indicate the species found in morphological analysis. The middle arcs indicate the species that have barcode sequences in indigenous species database. The external arcs indicate which species were detected by metabarcoding. Abundant (detected frequency > 1/2), moderate (detected frequency > 1/3) and rare (detected frequency < 1/3).
Fig 6.
Comparison of zooplankton identification in water samples between metabarcoding and morphology approaches.
(A) Species number. (B) Frequency detected. The R2 and p-value are indicated for each regression axis.