Ultra-barcoding in cacao (Theobroma spp.; Malvaceae) using whole chloroplast genomes and nuclear ribosomal DNA
• Premise of study: To reliably identify lineages below the species level such as subspecies or varieties, we propose an extension to DNA‐barcoding using next‐generation sequencing to produce whole organellar genomes and substantial nuclear ribosomal sequence. Because this method uses much longer ve...
| Autores principales: | , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Wiley
2012
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/35851 |
| _version_ | 1855539525164466176 |
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| author | Nolan K. Sveinsson, S. Dempewolf, Hannes Ji Yong Yang Dapeng Zhang Engels, Johannes M.M. Cronk, Q.C.B. |
| author_browse | Cronk, Q.C.B. Dapeng Zhang Dempewolf, Hannes Engels, Johannes M.M. Ji Yong Yang Nolan K. Sveinsson, S. |
| author_facet | Nolan K. Sveinsson, S. Dempewolf, Hannes Ji Yong Yang Dapeng Zhang Engels, Johannes M.M. Cronk, Q.C.B. |
| author_sort | Nolan K. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | • Premise of study: To reliably identify lineages below the species level such as subspecies or varieties, we propose an extension to DNA‐barcoding using next‐generation sequencing to produce whole organellar genomes and substantial nuclear ribosomal sequence. Because this method uses much longer versions of the traditional DNA‐barcoding loci in the plastid and ribosomal DNA, we call our approach ultra‐barcoding (UBC).• Methods: We used high‐throughput next‐generation sequencing to scan the genome and generate reliable sequence of high copy number regions. Using this method, we examined whole plastid genomes as well as nearly 6000 bases of nuclear ribosomal DNA sequences for nine genotypes of Theobroma cacao and an individual of the related species T. grandiflorum, as well as an additional publicly available whole plastid genome of T. cacao.• Key results: All individuals of T. cacao examined were uniquely distinguished, and evidence of reticulation and gene flow was observed. Sequence variation was observed in some of the canonical barcoding regions between species, but other regions of the chloroplast were more variable both within species and between species, as were ribosomal spacers. Furthermore, no single region provides the level of data available using the complete plastid genome and rDNA.• Conclusions: Our data demonstrate that UBC is a viable, increasingly cost‐effective approach for reliably distinguishing varieties and even individual genotypes of T. cacao. This approach shows great promise for applications where very closely related or interbreeding taxa must be distinguished. |
| format | Journal Article |
| id | CGSpace35851 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2012 |
| publishDateRange | 2012 |
| publishDateSort | 2012 |
| publisher | Wiley |
| publisherStr | Wiley |
| record_format | dspace |
| spelling | CGSpace358512025-03-11T12:14:31Z Ultra-barcoding in cacao (Theobroma spp.; Malvaceae) using whole chloroplast genomes and nuclear ribosomal DNA Nolan K. Sveinsson, S. Dempewolf, Hannes Ji Yong Yang Dapeng Zhang Engels, Johannes M.M. Cronk, Q.C.B. chloroplasts dna evolution gossypium theobroma cacao • Premise of study: To reliably identify lineages below the species level such as subspecies or varieties, we propose an extension to DNA‐barcoding using next‐generation sequencing to produce whole organellar genomes and substantial nuclear ribosomal sequence. Because this method uses much longer versions of the traditional DNA‐barcoding loci in the plastid and ribosomal DNA, we call our approach ultra‐barcoding (UBC).• Methods: We used high‐throughput next‐generation sequencing to scan the genome and generate reliable sequence of high copy number regions. Using this method, we examined whole plastid genomes as well as nearly 6000 bases of nuclear ribosomal DNA sequences for nine genotypes of Theobroma cacao and an individual of the related species T. grandiflorum, as well as an additional publicly available whole plastid genome of T. cacao.• Key results: All individuals of T. cacao examined were uniquely distinguished, and evidence of reticulation and gene flow was observed. Sequence variation was observed in some of the canonical barcoding regions between species, but other regions of the chloroplast were more variable both within species and between species, as were ribosomal spacers. Furthermore, no single region provides the level of data available using the complete plastid genome and rDNA.• Conclusions: Our data demonstrate that UBC is a viable, increasingly cost‐effective approach for reliably distinguishing varieties and even individual genotypes of T. cacao. This approach shows great promise for applications where very closely related or interbreeding taxa must be distinguished. 2012-02 2014-06-10T09:06:31Z 2014-06-10T09:06:31Z Journal Article https://hdl.handle.net/10568/35851 en Limited Access Wiley Nolan K.; Sveinsson, S.; Dempewolf, H.; Ji Yong Yang; Dapeng Zhang; Engels, J.M.M.; Cronk, Q. -2012-Ultra-barcoding in cacao (Theobroma spp.; Malvaceae) using whole chloroplast genomes and nuclear ribosomal DNA-American Journal of Botany 99(2)-p. 320-329 |
| spellingShingle | chloroplasts dna evolution gossypium theobroma cacao Nolan K. Sveinsson, S. Dempewolf, Hannes Ji Yong Yang Dapeng Zhang Engels, Johannes M.M. Cronk, Q.C.B. Ultra-barcoding in cacao (Theobroma spp.; Malvaceae) using whole chloroplast genomes and nuclear ribosomal DNA |
| title | Ultra-barcoding in cacao (Theobroma spp.; Malvaceae) using whole chloroplast genomes and nuclear ribosomal DNA |
| title_full | Ultra-barcoding in cacao (Theobroma spp.; Malvaceae) using whole chloroplast genomes and nuclear ribosomal DNA |
| title_fullStr | Ultra-barcoding in cacao (Theobroma spp.; Malvaceae) using whole chloroplast genomes and nuclear ribosomal DNA |
| title_full_unstemmed | Ultra-barcoding in cacao (Theobroma spp.; Malvaceae) using whole chloroplast genomes and nuclear ribosomal DNA |
| title_short | Ultra-barcoding in cacao (Theobroma spp.; Malvaceae) using whole chloroplast genomes and nuclear ribosomal DNA |
| title_sort | ultra barcoding in cacao theobroma spp malvaceae using whole chloroplast genomes and nuclear ribosomal dna |
| topic | chloroplasts dna evolution gossypium theobroma cacao |
| url | https://hdl.handle.net/10568/35851 |
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