Isolation and characterization of 30 STRs in Temminck’s ground pangolin (Smutsia temminckii) and potential for cross amplification in other African species

Zelda du Toit; Desiré L. Dalton; Morné du Plessis; Raymond Jansen; J. Paul Grobler; Antoinette Kotzé

doi:10.1007/s12041-020-1176-0

Isolation and characterization of 30 STRs in Temminck’s ground pangolin (Smutsia temminckii) and potential for cross amplification in other African species

Zelda du Toit, Desiré L. Dalton, Morné du Plessis, Raymond Jansen, J. Paul Grobler, Antoinette Kotzé

SHLS Life Sciences

Research output: Contribution to journal › Article › peer-review

3 Citations (Scopus)

Abstract

Temminck’s ground pangolin (Smutsia temminckii) is one of four species of pangolin, endemic to Africa. Two of the African pangolin species are listed as vulnerable and two are listed as endangered on the International Union for Conservation of Nature Red List of Threatened Species due to their ongoing exploitation for traditional medicine and bushmeat. In this study, we developed 30 species-specific short-tandem repeats (STRs) in Temminck’s ground pangolin using next-generation sequencing. The markers were also optimized for cross-amplification in other African species. All the markers amplified successfully in Temminck’s ground pangolin with allelic polymorphisms observed in 87% of the markers in giant pangolin (S. gigantea) whereas 60% of the markers were amplified polymorphic loci in both white-bellied pangolin (Phataginus tricuspis) and black-bellied pangolin (P. tetradactyla). Analysis of diversity estimates showed moderate levels of variability in Temminck’s ground pangolin (N_a = 5; H_o = 0.559), giant pangolin (N_a = 4.909; H_o = 0.514) and white-bellied pangolin (N_a = 2.686; H_o = 0.541) with lower values being observed in black-bellied pangolin (N_a = 3; H_o = 0.242). This study provides data of the first available STR markers which was amplified in all four African pangolin species that can now be used in conservation genetic and evolutionary aspects of population histories.

Original language	English
Article number	20
Journal	Journal of Genetics
Volume	99
DOIs	https://doi.org/10.1007/s12041-020-1176-0
Publication status	Published - 6 Mar 2020

Bibliographical note

Funding Information:
We are indebted to the following persons for collecting tissue and scale samples: Darren and Errol Pietersen; Gus van Dyk, Wouter Jordaan and Dylan Smith from Tswalu Kalahari Reserve, John Davies from the Kgalagadi Transfrontier Park, Maxwell Boakye from the African Pangolin Working Group and the Endangered Species Protection Division, Agriculture, Fisheries and Conservation Department, CITES Management Authority of Hong Kong. The National Zoological Garden (NZG) previously a national research facility under the National Research Foundation (NRF) and now under the South African National Biodiversity Institute (SANBI) funded all laboratory analyses. Zelda du Toit was supported as a doctoral candidate under the Professional Development Programme of the National Research Foundation (NRF) as part of NZG grant no 86125.

Funding Information:
We are indebted to the following persons for collecting tissue and scale samples: Darren and Errol Pietersen; Gus van Dyk, Wouter Jordaan and Dylan Smith from Tswalu Kalahari Reserve, John Davies from the Kgalagadi Transfrontier Park, Maxwell Boakye from the African Pangolin Working Group and the Endangered Species Protection Division, Agriculture, Fisheries and Conservation Department, CITES Management Authority of Hong Kong. The National Zoological Garden (NZG) previously a national research facility under the National Research Foundation (NRF) and now under the South African National Biodiversity Institute (SANBI) funded all laboratory analyses. Zelda du Toit was supported as a doctoral candidate under the Professional Development Programme of the National Research Foundation (NRF) as part of NZG grant no 86125.

Publisher Copyright:
© 2020, Indian Academy of Sciences.

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Cite this

@article{ed9b93079f734684a230f94ba63c0d6f,

title = "Isolation and characterization of 30 STRs in Temminck{\textquoteright}s ground pangolin (Smutsia temminckii) and potential for cross amplification in other African species",

abstract = "Temminck{\textquoteright}s ground pangolin (Smutsia temminckii) is one of four species of pangolin, endemic to Africa. Two of the African pangolin species are listed as vulnerable and two are listed as endangered on the International Union for Conservation of Nature Red List of Threatened Species due to their ongoing exploitation for traditional medicine and bushmeat. In this study, we developed 30 species-specific short-tandem repeats (STRs) in Temminck{\textquoteright}s ground pangolin using next-generation sequencing. The markers were also optimized for cross-amplification in other African species. All the markers amplified successfully in Temminck{\textquoteright}s ground pangolin with allelic polymorphisms observed in 87% of the markers in giant pangolin (S. gigantea) whereas 60% of the markers were amplified polymorphic loci in both white-bellied pangolin (Phataginus tricuspis) and black-bellied pangolin (P. tetradactyla). Analysis of diversity estimates showed moderate levels of variability in Temminck{\textquoteright}s ground pangolin (Na = 5; Ho = 0.559), giant pangolin (Na = 4.909; Ho = 0.514) and white-bellied pangolin (Na = 2.686; Ho = 0.541) with lower values being observed in black-bellied pangolin (Na = 3; Ho = 0.242). This study provides data of the first available STR markers which was amplified in all four African pangolin species that can now be used in conservation genetic and evolutionary aspects of population histories.",

author = "{du Toit}, Zelda and Dalton, {Desir{\'e} L.} and {du Plessis}, Morn{\'e} and Raymond Jansen and Grobler, {J. Paul} and Antoinette Kotz{\'e}",

note = "Funding Information: We are indebted to the following persons for collecting tissue and scale samples: Darren and Errol Pietersen; Gus van Dyk, Wouter Jordaan and Dylan Smith from Tswalu Kalahari Reserve, John Davies from the Kgalagadi Transfrontier Park, Maxwell Boakye from the African Pangolin Working Group and the Endangered Species Protection Division, Agriculture, Fisheries and Conservation Department, CITES Management Authority of Hong Kong. The National Zoological Garden (NZG) previously a national research facility under the National Research Foundation (NRF) and now under the South African National Biodiversity Institute (SANBI) funded all laboratory analyses. Zelda du Toit was supported as a doctoral candidate under the Professional Development Programme of the National Research Foundation (NRF) as part of NZG grant no 86125. Funding Information: We are indebted to the following persons for collecting tissue and scale samples: Darren and Errol Pietersen; Gus van Dyk, Wouter Jordaan and Dylan Smith from Tswalu Kalahari Reserve, John Davies from the Kgalagadi Transfrontier Park, Maxwell Boakye from the African Pangolin Working Group and the Endangered Species Protection Division, Agriculture, Fisheries and Conservation Department, CITES Management Authority of Hong Kong. The National Zoological Garden (NZG) previously a national research facility under the National Research Foundation (NRF) and now under the South African National Biodiversity Institute (SANBI) funded all laboratory analyses. Zelda du Toit was supported as a doctoral candidate under the Professional Development Programme of the National Research Foundation (NRF) as part of NZG grant no 86125. Publisher Copyright: {\textcopyright} 2020, Indian Academy of Sciences.",

year = "2020",

month = mar,

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doi = "10.1007/s12041-020-1176-0",

language = "English",

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T1 - Isolation and characterization of 30 STRs in Temminck’s ground pangolin (Smutsia temminckii) and potential for cross amplification in other African species

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AU - Dalton, Desiré L.

AU - du Plessis, Morné

AU - Jansen, Raymond

AU - Grobler, J. Paul

AU - Kotzé, Antoinette

N1 - Funding Information: We are indebted to the following persons for collecting tissue and scale samples: Darren and Errol Pietersen; Gus van Dyk, Wouter Jordaan and Dylan Smith from Tswalu Kalahari Reserve, John Davies from the Kgalagadi Transfrontier Park, Maxwell Boakye from the African Pangolin Working Group and the Endangered Species Protection Division, Agriculture, Fisheries and Conservation Department, CITES Management Authority of Hong Kong. The National Zoological Garden (NZG) previously a national research facility under the National Research Foundation (NRF) and now under the South African National Biodiversity Institute (SANBI) funded all laboratory analyses. Zelda du Toit was supported as a doctoral candidate under the Professional Development Programme of the National Research Foundation (NRF) as part of NZG grant no 86125. Funding Information: We are indebted to the following persons for collecting tissue and scale samples: Darren and Errol Pietersen; Gus van Dyk, Wouter Jordaan and Dylan Smith from Tswalu Kalahari Reserve, John Davies from the Kgalagadi Transfrontier Park, Maxwell Boakye from the African Pangolin Working Group and the Endangered Species Protection Division, Agriculture, Fisheries and Conservation Department, CITES Management Authority of Hong Kong. The National Zoological Garden (NZG) previously a national research facility under the National Research Foundation (NRF) and now under the South African National Biodiversity Institute (SANBI) funded all laboratory analyses. Zelda du Toit was supported as a doctoral candidate under the Professional Development Programme of the National Research Foundation (NRF) as part of NZG grant no 86125. Publisher Copyright: © 2020, Indian Academy of Sciences.

PY - 2020/3/6

Y1 - 2020/3/6

N2 - Temminck’s ground pangolin (Smutsia temminckii) is one of four species of pangolin, endemic to Africa. Two of the African pangolin species are listed as vulnerable and two are listed as endangered on the International Union for Conservation of Nature Red List of Threatened Species due to their ongoing exploitation for traditional medicine and bushmeat. In this study, we developed 30 species-specific short-tandem repeats (STRs) in Temminck’s ground pangolin using next-generation sequencing. The markers were also optimized for cross-amplification in other African species. All the markers amplified successfully in Temminck’s ground pangolin with allelic polymorphisms observed in 87% of the markers in giant pangolin (S. gigantea) whereas 60% of the markers were amplified polymorphic loci in both white-bellied pangolin (Phataginus tricuspis) and black-bellied pangolin (P. tetradactyla). Analysis of diversity estimates showed moderate levels of variability in Temminck’s ground pangolin (Na = 5; Ho = 0.559), giant pangolin (Na = 4.909; Ho = 0.514) and white-bellied pangolin (Na = 2.686; Ho = 0.541) with lower values being observed in black-bellied pangolin (Na = 3; Ho = 0.242). This study provides data of the first available STR markers which was amplified in all four African pangolin species that can now be used in conservation genetic and evolutionary aspects of population histories.

AB - Temminck’s ground pangolin (Smutsia temminckii) is one of four species of pangolin, endemic to Africa. Two of the African pangolin species are listed as vulnerable and two are listed as endangered on the International Union for Conservation of Nature Red List of Threatened Species due to their ongoing exploitation for traditional medicine and bushmeat. In this study, we developed 30 species-specific short-tandem repeats (STRs) in Temminck’s ground pangolin using next-generation sequencing. The markers were also optimized for cross-amplification in other African species. All the markers amplified successfully in Temminck’s ground pangolin with allelic polymorphisms observed in 87% of the markers in giant pangolin (S. gigantea) whereas 60% of the markers were amplified polymorphic loci in both white-bellied pangolin (Phataginus tricuspis) and black-bellied pangolin (P. tetradactyla). Analysis of diversity estimates showed moderate levels of variability in Temminck’s ground pangolin (Na = 5; Ho = 0.559), giant pangolin (Na = 4.909; Ho = 0.514) and white-bellied pangolin (Na = 2.686; Ho = 0.541) with lower values being observed in black-bellied pangolin (Na = 3; Ho = 0.242). This study provides data of the first available STR markers which was amplified in all four African pangolin species that can now be used in conservation genetic and evolutionary aspects of population histories.

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Isolation and characterization of 30 STRs in Temminck’s ground pangolin (Smutsia temminckii) and potential for cross amplification in other African species

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