Giving IDs to turtles: SNP markers for assignment of individuals to lineages of the geographically structured Phrynops geoffroanus (Chelidae: Testudines)
We developed forensic nuclear SNPs for the side-necked turtle, Phrynops geoffroanus, using next-generation sequencing-based genotyping. We created a reduced-representation library for 23 individuals representing four previously identified lineages of P. geoffroanus using the ddRAD methodology for se...
| Autor principal: | Carvalho, Vinícius Tadeu de |
|---|---|
| Outros Autores: | Martínez, José Gregório, Hernández-Rangel, Sandra Marcela, Astolfi-Filho, Spártaco A.T., Vogt, Richard Carl, Farias, Izeni P., Hrbek, Tomas |
| Grau: | Artigo |
| Idioma: | English |
| Publicado em: |
Conservation Genetics Resources
2020
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| Acesso em linha: |
https://repositorio.inpa.gov.br/handle/1/17160 |
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oai:repositorio:1-17160 |
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| recordtype |
dspace |
| spelling |
oai:repositorio:1-17160 Giving IDs to turtles: SNP markers for assignment of individuals to lineages of the geographically structured Phrynops geoffroanus (Chelidae: Testudines) Carvalho, Vinícius Tadeu de Martínez, José Gregório Hernández-Rangel, Sandra Marcela Astolfi-Filho, Spártaco A.T. Vogt, Richard Carl Farias, Izeni P. Hrbek, Tomas We developed forensic nuclear SNPs for the side-necked turtle, Phrynops geoffroanus, using next-generation sequencing-based genotyping. We created a reduced-representation library for 23 individuals representing four previously identified lineages of P. geoffroanus using the ddRAD methodology for sequencing on the IonTorrent PGM. We analyzed the sequence data using the Stacks pipeline. We found 811 loci containing 1380 private SNPs. Of these, 473 were fixed in lineages 1, 2 and 3, or with frequency >0.91 in lineage 4. Seventy-three SNPs could be useful for forensics purpose (assignment of individuals to lineage of origin) using traditional PCR-based genotyping methods. © 2016, Springer Science+Business Media Dordrecht. 2020-06-15T21:39:30Z 2020-06-15T21:39:30Z 2017 Artigo https://repositorio.inpa.gov.br/handle/1/17160 10.1007/s12686-016-0626-8 en Volume 9, Número 1, Pags. 157-163 Restrito Conservation Genetics Resources |
| institution |
Instituto Nacional de Pesquisas da Amazônia - Repositório Institucional |
| collection |
INPA-RI |
| language |
English |
| description |
We developed forensic nuclear SNPs for the side-necked turtle, Phrynops geoffroanus, using next-generation sequencing-based genotyping. We created a reduced-representation library for 23 individuals representing four previously identified lineages of P. geoffroanus using the ddRAD methodology for sequencing on the IonTorrent PGM. We analyzed the sequence data using the Stacks pipeline. We found 811 loci containing 1380 private SNPs. Of these, 473 were fixed in lineages 1, 2 and 3, or with frequency >0.91 in lineage 4. Seventy-three SNPs could be useful for forensics purpose (assignment of individuals to lineage of origin) using traditional PCR-based genotyping methods. © 2016, Springer Science+Business Media Dordrecht. |
| format |
Artigo |
| author |
Carvalho, Vinícius Tadeu de |
| spellingShingle |
Carvalho, Vinícius Tadeu de Giving IDs to turtles: SNP markers for assignment of individuals to lineages of the geographically structured Phrynops geoffroanus (Chelidae: Testudines) |
| author2 |
Martínez, José Gregório Hernández-Rangel, Sandra Marcela Astolfi-Filho, Spártaco A.T. Vogt, Richard Carl Farias, Izeni P. Hrbek, Tomas |
| author2Str |
Martínez, José Gregório Hernández-Rangel, Sandra Marcela Astolfi-Filho, Spártaco A.T. Vogt, Richard Carl Farias, Izeni P. Hrbek, Tomas |
| title |
Giving IDs to turtles: SNP markers for assignment of individuals to lineages of the geographically structured Phrynops geoffroanus (Chelidae: Testudines) |
| title_short |
Giving IDs to turtles: SNP markers for assignment of individuals to lineages of the geographically structured Phrynops geoffroanus (Chelidae: Testudines) |
| title_full |
Giving IDs to turtles: SNP markers for assignment of individuals to lineages of the geographically structured Phrynops geoffroanus (Chelidae: Testudines) |
| title_fullStr |
Giving IDs to turtles: SNP markers for assignment of individuals to lineages of the geographically structured Phrynops geoffroanus (Chelidae: Testudines) |
| title_full_unstemmed |
Giving IDs to turtles: SNP markers for assignment of individuals to lineages of the geographically structured Phrynops geoffroanus (Chelidae: Testudines) |
| title_sort |
giving ids to turtles: snp markers for assignment of individuals to lineages of the geographically structured phrynops geoffroanus (chelidae: testudines) |
| publisher |
Conservation Genetics Resources |
| publishDate |
2020 |
| url |
https://repositorio.inpa.gov.br/handle/1/17160 |
| _version_ |
1787141775964504064 |
| score |
11.755432 |