Disclosing the hidden nucleotide sequences: a journey into DNA barcoding of raptor species in public repositories

Wattanawan Jaito^#^{1

2}, Jumaporn Sonongbua^#^{1

3

4}, Thitipong Panthum^#^{1

4

5}, Pish Wattanadilokcahtkun¹, Nattakan Ariyaraphong^{1

5}, Thanyapat Thong¹, Worapong Singchat^{1

2

4

5}, Syed Farhan Ahmad^{1

5}, Ekaphan Kraichak^{1

6}, Narongrit Muangmai^{1

5

7}, Kyudong Han^{1

8

9}, Agostinho Antunes^{10

11}, Ratiwan Sitdhibutr¹², Akihiko Koga¹, Prateep Duengkae^{1

5}, Chaiyan Kasorndorkbua^{13

14}, Kornsorn Srikulnath^{15

16

17

18

19}

Affiliations

¹ Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
² Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
³ Faculty of Interdisciplinary Studies, Khon Kaen University, Nong Kom Ko, Mueang Nong Khai District, Nong Khai, 43000, Thailand.
⁴ Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand.
⁵ Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
⁶ Department of Botany, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand.
⁷ Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok, 10900, Thailand.
⁸ Department of Microbiology, Dankook University, Cheonan, 31116, Korea.
⁹ Bio-Medical Engineering Core Facility Research Center, Dankook University, Cheonan, 31116, Korea.
¹⁰ CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal.
¹¹ Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal.
¹² Raptor Rehabilitation Unit, Kasetsart University Veterinary Teaching Hospital Kamphaengsaen Campus, Nakhon Pathom, 73140, Thailand.
¹³ Raptor Rehabilitation Unit, Kasetsart University Veterinary Teaching Hospital Kamphaengsaen Campus, Nakhon Pathom, 73140, Thailand. chaiyan.k@ku.th.
¹⁴ Department of Pathology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, 10900, Thailand. chaiyan.k@ku.th.
¹⁵ Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand. kornsorn.s@ku.ac.th.
¹⁶ Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand. kornsorn.s@ku.ac.th.
¹⁷ Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand. kornsorn.s@ku.ac.th.
¹⁸ Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand. kornsorn.s@ku.ac.th.
¹⁹ Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand. kornsorn.s@ku.ac.th.

^# Contributed equally.

PMID: 37985545
DOI: 10.1007/s13258-023-01462-x

Disclosing the hidden nucleotide sequences: a journey into DNA barcoding of raptor species in public repositories

Wattanawan Jaito et al. Genes Genomics. 2024 Jan.

. 2024 Jan;46(1):95-112.

doi: 10.1007/s13258-023-01462-x. Epub 2023 Nov 20.

Authors

Affiliations

¹ Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
² Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
³ Faculty of Interdisciplinary Studies, Khon Kaen University, Nong Kom Ko, Mueang Nong Khai District, Nong Khai, 43000, Thailand.
⁴ Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand.
⁵ Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
⁶ Department of Botany, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand.
⁷ Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok, 10900, Thailand.
⁸ Department of Microbiology, Dankook University, Cheonan, 31116, Korea.
⁹ Bio-Medical Engineering Core Facility Research Center, Dankook University, Cheonan, 31116, Korea.
¹⁰ CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal.
¹¹ Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal.
¹² Raptor Rehabilitation Unit, Kasetsart University Veterinary Teaching Hospital Kamphaengsaen Campus, Nakhon Pathom, 73140, Thailand.
¹³ Raptor Rehabilitation Unit, Kasetsart University Veterinary Teaching Hospital Kamphaengsaen Campus, Nakhon Pathom, 73140, Thailand. chaiyan.k@ku.th.
¹⁴ Department of Pathology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, 10900, Thailand. chaiyan.k@ku.th.
¹⁵ Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand. kornsorn.s@ku.ac.th.
¹⁶ Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand. kornsorn.s@ku.ac.th.
¹⁷ Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand. kornsorn.s@ku.ac.th.
¹⁸ Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand. kornsorn.s@ku.ac.th.
¹⁹ Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand. kornsorn.s@ku.ac.th.

^# Contributed equally.

PMID: 37985545
DOI: 10.1007/s13258-023-01462-x

Abstract

Background: In nucleotide public repositories, studies discovered data errors which resulted in incorrect species identification of several accipitrid raptors considered for conservation. Mislabeling, particularly in cases of cryptic species complexes and closely related species, which were identified based on morphological characteristics, was discovered. Prioritizing accurate species labeling, morphological taxonomy, and voucher documentation is crucial to rectify spurious data.

Objective: Our study aimed to identify an effective DNA barcoding tool that accurately reflects the efficiency status of barcodes in raptor species (Accipitridae).

Methods: Barcode sequences, including 889 sequences from the mitochondrial cytochrome c oxidase I (COI) gene and 1052 sequences from cytochrome b (Cytb), from 150 raptor species within the Accipitridae family were analyzed.

Results: The highest percentage of intraspecific nearest neighbors from the nearest neighbor test was 88.05% for COI and 95.00% for Cytb, suggesting that the Cytb gene is a more suitable marker for accurately identifying raptor species and can serve as a standard region for DNA barcoding. In both datasets, a positive barcoding gap representing the difference between inter-and intra-specific sequence divergences was observed. For COI and Cytb, the cut-off score sequence divergences for species identification were 4.00% and 3.00%, respectively.

Conclusion: Greater accuracy was demonstrated for the Cytb gene, making it the preferred primary DNA barcoding marker for raptors.

Keywords: Accipitridae; Barcoding gap; Mislabeling data; Sequence divergence; Species delimitation.

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References

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Disclosing the hidden nucleotide sequences: a journey into DNA barcoding of raptor species in public repositories

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Disclosing the hidden nucleotide sequences: a journey into DNA barcoding of raptor species in public repositories

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