Additional file 1 of Choice of primer pairs and PCR polymerase affect the detection of fish eDNA
Creators: name: Min, Xingyue
name: Li, Feilong
name: Zhang, Xinfei
name: Guo, Fen
name: Zhang, Fan
name: Zhang, Yuan
Publisher: name: figshare
Year: 2024
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Evolutionary Biology
subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Science Policy
subject: Mental Health

description: Additional file 1: Figure S1. The proportion of eDNA sequences annotated (Success, blue box) and unassigned (Failure, grey box) into fish communities in 15 groups of three DNA polymerases and five primer pairs in surface water (a) and sediment samples (b). Prefixes T-, R- and P- in the abscissa are the Taq master polymerase, the Rapid Taq polymerase and the Phanta Flash polymerase, respectively. Figure S2. The proportional of fish eDNA sequences at the order level among three repeated samples in surface water samples. Prefixes T-, R- and P- in the abscissa are the Taq master polymerase, the Rapid Taq polymerase and the Phanta Flash polymerase, respectively. Figure S3. The proportional of fish eDNA sequences at the order level among three repeated samples in sediment samples. Prefixes T-, R- and P- in the abscissa are the Taq master polymerase, the Rapid Taq polymerase and the Phanta Flash polymerase, respectively. Table S1. Summary of 10 primer pairs in the mitochondrial 12 s rRNA gene region for fish eDNA biomonitoring retrieved from the literature and analyzed in this study, including primer name, target group, amplicon size, original references and primer sequences. Table S2. Summary of the reaction conditions for PCR assays on random groups of retrieved 10 primer pairs and 3 DNA polymerases, including the set time and temperature of the denaturation, annealing, and extension processes. All PCR assays run 35 cycles. Table S3. Results of successful PCR assays between primer pairs and DNA polymerase, namely, the agarose gel electrophoresis have specific bands and correct amplification size. The symbols “√” and “ × ” represent successful and failed PCR assays, respectively. Table S4. The number and proportion of eDNA sequences successfully annotated different taxonomic classifications of fish communities in surface water samples. Three replicates in each group are analyzed together, and percentages in parentheses are the After quality filtering/All sequences, Class seq/After quality filtering, Order-seq/After quality filtering and so on. Table S5. The number and proportion of eDNA sequences successfully annotated different taxonomic classifications of fish communities in sediment samples. Three replicates in each group are analyzed together, and percentages in parentheses are the After quality filtering/All sequences, Class seq/After quality filtering, Order-seq/After quality filtering and so on. Table S6. Comparison between historical records of common fish species in Dianchi Lake over the past decade and eDNA data in this current study. Blue shadows represent consistency between each other.