Environmental DNA (eDNA) Metabarcoding in the Fish Market and Nearby Seafood Restaurants in Taiwan Reveals the Underestimation of Fish Species Diversity in Seafood
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Sample Collection
2.2. DNA Extraction
2.3. DNA Library Preparation
2.4. Data Process
2.5. Taxonomic Assignment
2.6. Statistical Analysis
3. Results
3.1. Identification and Classification of Fish Species from eDNA Samplings
3.2. Seafood and Its Species Composition
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Primer Sets | Sequence | Reference |
---|---|---|
12S | Miya et al. 2015 [25] | |
MiFish-U-F | GTCGGTAAAACTCGTGCCAGC | |
MiFish-U-R | CATAGTGGGGTATCTAATCCCAGTTTG | |
MiFish-E-F | GTTGGTAAATCTCGTGCCAGC | |
MiFish-E-R | CATAGTGGGGTATCTAATCCTAGTTTG | |
ND5 | Miya et al. 2015 [25] | |
MiFish-tuna-ND5-F | ATGTCCTTCCTCCTTATCGGCTG | |
MiFish-tuna-ND5-R | TTGCCAGTGGCAGCTACGATC | |
COI | Shokralla et al. 2015 [26] | |
Fish-miniA-F | ACIAAICAIAAAGAYATYGGC | |
Fish-miniA-R | AARAAAATYATAACRAAIGCRTGIGC | |
Fish-miniC-F | ACYAAICAYAAAGAYATIGGCAC | |
Fish-miniC-R | GAARATCATAATGAAGGCATGIGC | |
Fish-miniE-F | ACYAAICAYAAAGAYATIGGCAC | |
Fish-miniE-R | CTTATRTTRTTTATICGIGGRAAIGC | |
FishF1 | TCAACCAACCACAAAGACATTGGCAC | Becker et al. 2011 [27] |
FishF2 | TCGACTAATCATAAAGATATCGGCAC | |
FishR1 | TAGACTTCTGGGTGGCCAAAGAATCA | |
FishR2 | ACTTCAGGGTGACCGAAGAATCAGAA | |
Shark-COI-MINI-R | AAGATTACAAAAGCGTGGGC | Zahn et al. 2020 [28] |
Shark-MiniV1-R | AAGATTATTACAAAAGCRTGRGC | |
Shark-MiniV2-R | AAGATTATTACRAADGCRTGRGC |
Items | Reads | 12S | COI | ND5 | All |
---|---|---|---|---|---|
December-I | 6,995,762 | 64 | 52 | 15 | 81 * |
December-II | 10,194,137 | 39 | 44 | 11 | 56 * |
January-I | 22,323,200 | 103 | 68 | 17 | 126 * |
January-II | 11,021,896 | 44 | 52 | 14 | 60 * |
All | 50,534,995 | 112 * | 88 * | 18 * | 153 * |
Class | Order | Family | Species | Class | Order | Family | Species |
---|---|---|---|---|---|---|---|
Actinopterygii | Actinopterygii | ||||||
Anguilliformes | Congridae | 2 | Perciformes | Haemulidae | 2 | ||
Muraenidae | 12 | Istiophoridae | 5 | ||||
Beloniformes | Scomberesocidae | 1 | Kyphosidae | 1 | |||
Clupeiformes | Engraulidae | 1 | Labridae | 2 | |||
Gadiformes | Gadidae | 3 | Lutjanidae | 8 | |||
Mugiliformes | Mugilidae | 4 | Malacanthidae | 1 | |||
Ophidiiformes | Ophidiidae | 1 | Mullidae | 2 | |||
Pleuronectiformes | Cynoglossidae | 1 | Nemipteridae | 1 | |||
Paralichthyidae | 1 | Nomeidae | 1 | ||||
Salmoniformes | Salmonidae | 1 | Pempheridae | 1 | |||
Scorpaeniformes | Scorpaenidae | 2 | Pomacentridae | 7 | |||
Siluriformes | Loricariidae | 2 | Scombridae | 12 | |||
Tetraodontiformes | Diodontidae | 1 | Serranidae | 12 | |||
Monacanthidae | 3 | Siganidae | 1 | ||||
Tetraodontidae | 1 | Sparidae | 3 | ||||
Perciformes | Acropomatidae | 2 | Stromateidae | 3 | |||
Apogonidae | 2 | Trichiuridae | 5 | ||||
Bramidae | 1 | Xiphiidae | 1 | ||||
Caesionidae | 3 | Chondrichthyes | |||||
Carangidae | 11 | Carcharhiniformes | Carcharhinidae | 7 | |||
Centrolophidae | 3 | Sphyrnidae | 2 | ||||
Channichthyidae | 1 | Triakidae | 5 | ||||
Coryphaenidae | 1 | Lamniformes | Alopiidae | 2 | |||
Emmelichthyidae | 1 | Myliobatiformes | Dasyatidae | 5 | |||
Gempylidae | 2 | Urolophidae | 1 |
Order | Family | Scientific Name | 12S | COI | December-I | December-II | January-I | January-II | Status |
---|---|---|---|---|---|---|---|---|---|
Carcharhiniformes | Carcharhinidae | Carcharhinus brevipinna | 1 | 0 | 0 | 1 | 0 | 1 | VU |
Carcharhinus falciformis | 1 | 0 | 0 | 1 | 0 | 0 | VU | ||
Carcharhinus macloti | 1 | 0 | 0 | 1 | 0 | 0 | NT | ||
Carcharhinus obscurus | 1 | 1 | 0 | 1 | 1 | 1 | EN | ||
Carcharhinus sealei | 0 | 1 | 1 | 1 | 1 | 1 | NT | ||
Carcharhinus sorrah | 1 | 0 | 0 | 1 | 0 | 0 | NT | ||
Prionace glauca | 1 | 1 | 0 | 1 | 1 | 1 | NT | ||
Sphyrnidae | Sphyrna lewini | 1 | 0 | 0 | 1 | 0 | 0 | CR | |
Sphyrna zygaena | 1 | 1 | 1 | 1 | 1 | 1 | VU | ||
Triakidae | Galeorhinus galeus | 0 | 1 | 1 | 0 | 1 | 0 | CR | |
Hemitriakis japanica | 0 | 1 | 1 | 0 | 1 | 0 | EN | ||
Mustelus asterias | 0 | 1 | 1 | 0 | 1 | 0 | NT | ||
Mustelus griseus | 0 | 1 | 1 | 1 | 0 | 0 | EN | ||
Mustelus manazo | 0 | 1 | 1 | 1 | 0 | 0 | EN | ||
Lamniformes | Alopiidae | Alopias pelagicus | 1 | 1 | 1 | 1 | 1 | 1 | EN |
Alopias superciliosus | 1 | 1 | 1 | 1 | 1 | 1 | VU | ||
Myliobatiformes | Dasyatidae | Himantura leoparda | 0 | 1 | 0 | 1 | 1 | 1 | VU |
Maculabatis gerrardi | 1 | 1 | 1 | 1 | 1 | 1 | EN | ||
Maculabatis pastinacoides | 1 | 1 | 0 | 0 | 1 | 0 | EN | ||
Pastinachus gracilicaudus | 0 | 1 | 0 | 1 | 1 | 1 | EN | ||
Pateobatis jenkinsii | 0 | 1 | 0 | 0 | 1 | 1 | VU | ||
Urolophidae | Urolophus aurantiacus | 1 | 0 | 0 | 1 | 0 | 0 | VU |
Order | Family | Scientific Name | 12S | COI | December-I | December-II | January-I | January-II | Status |
---|---|---|---|---|---|---|---|---|---|
Anguilliformes | Congridae | Bathycongrus retrotinctus | 1 | 0 | 0 | 1 | 0 | 0 | R |
Gnathophis nystromi | 0 | 1 | 0 | 1 | 0 | 1 | R | ||
Muraenidae | Gymnothorax flavimarginatus | 1 | 1 | 1 | 1 | 1 | 1 | E | |
Gymnothorax isingteena | 1 | 1 | 1 | 1 | 1 | 0 | U | ||
Gymnothorax javanicus | 1 | 0 | 1 | 0 | 0 | 0 | E | ||
Gymnothorax prionodon | 1 | 0 | 0 | 1 | 0 | 0 | E | ||
Gymnothorax margaritophorus | 1 | 0 | 0 | 1 | 0 | 0 | E | ||
Gymnothorax niphostigmus | 1 | 0 | 0 | 1 | 0 | 0 | T | ||
Gymnothorax reevesii | 1 | 1 | 1 | 1 | 1 | 0 | E | ||
Gymnothorax reticularis | 1 | 0 | 0 | 1 | 1 | 1 | U | ||
Gymnothorax thyrsoideus | 1 | 0 | 0 | 1 | 1 | 1 | E | ||
Gymnothorax undulatus | 1 | 1 | 1 | 1 | 1 | 0 | E | ||
Enchelycore anatina | 1 | 0 | 0 | 1 | 0 | 0 | U | ||
Strophidon sathete | 1 | 0 | 1 | 1 | 1 | 1 | R |
Order | Family | Scientific Name | 12S | COI | December-I | December-II | January-I | January-II | Status |
---|---|---|---|---|---|---|---|---|---|
Perciformes | Serranidae | Aethaloperca rogaa | 1 | 1 | 1 | 1 | 1 | 0 | W |
Cephalopholis boenak | 1 | 0 | 1 | 1 | 1 | 0 | W | ||
Cephalopholis sexmaculata | 1 | 0 | 1 | 1 | 1 | 0 | W | ||
Epinephelus awoara | 1 | 1 | 1 | 0 | 0 | 1 | W | ||
Epinephelus coioides | 1 | 1 | 1 | 1 | 1 | 0 | C | ||
Epinephelus fasciatomaculosus | 1 | 0 | 0 | 1 | 0 | 0 | W | ||
Epinephelus fuscoguttatus | 1 | 1 | 1 | 1 | 1 | 1 | C | ||
Epinephelus lanceolatus | 1 | 0 | 0 | 1 | 0 | 0 | C | ||
Epinephelus bruneus | 1 | 0 | 1 | 1 | 0 | 1 | C | ||
Epinephelus quoyanus | 1 | 0 | 1 | 1 | 0 | 0 | W | ||
Epinephelus tukula | 1 | 0 | 0 | 1 | 0 | 0 | C | ||
Variola louti | 1 | 0 | 0 | 1 | 0 | 0 | W |
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Lee, H.-T.; Liao, C.-H.; Hsu, T.-H. Environmental DNA (eDNA) Metabarcoding in the Fish Market and Nearby Seafood Restaurants in Taiwan Reveals the Underestimation of Fish Species Diversity in Seafood. Biology 2021, 10, 1132. https://doi.org/10.3390/biology10111132
Lee H-T, Liao C-H, Hsu T-H. Environmental DNA (eDNA) Metabarcoding in the Fish Market and Nearby Seafood Restaurants in Taiwan Reveals the Underestimation of Fish Species Diversity in Seafood. Biology. 2021; 10(11):1132. https://doi.org/10.3390/biology10111132
Chicago/Turabian StyleLee, Hung-Tai, Cheng-Hsin Liao, and Te-Hua Hsu. 2021. "Environmental DNA (eDNA) Metabarcoding in the Fish Market and Nearby Seafood Restaurants in Taiwan Reveals the Underestimation of Fish Species Diversity in Seafood" Biology 10, no. 11: 1132. https://doi.org/10.3390/biology10111132
APA StyleLee, H. -T., Liao, C. -H., & Hsu, T. -H. (2021). Environmental DNA (eDNA) Metabarcoding in the Fish Market and Nearby Seafood Restaurants in Taiwan Reveals the Underestimation of Fish Species Diversity in Seafood. Biology, 10(11), 1132. https://doi.org/10.3390/biology10111132