Phylogenomics of the Carrot Genus (Daucus, Apiaceae)
•Premise of the study: We explored the utility of multiple nuclear orthologs for the taxonomic resolution of wild and cultivated carrot, Daucus species. •Methods: We studied the phylogeny of 92 accessions of 13 species and two subspecies of Daucus and 15 accessions of related genera (107 accessions...
| Autores principales: | , , , , |
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| Formato: | Artículo |
| Lenguaje: | Inglés |
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John Wiley & Sons
2020
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| Acceso en línea: | https://repositorio.inia.gob.pe/handle/20.500.12955/1135 https://doi.org/10.3732/ajb.1400106 |
| _version_ | 1855490444822052864 |
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| author | Arbizu Berrocal, Carlos Irvin Ruess, Holly Senalik, Douglas Simon, Philipp W. Spooner, David M. |
| author_browse | Arbizu Berrocal, Carlos Irvin Ruess, Holly Senalik, Douglas Simon, Philipp W. Spooner, David M. |
| author_facet | Arbizu Berrocal, Carlos Irvin Ruess, Holly Senalik, Douglas Simon, Philipp W. Spooner, David M. |
| author_sort | Arbizu Berrocal, Carlos Irvin |
| collection | Repositorio INIA |
| description | •Premise of the study: We explored the utility of multiple nuclear orthologs for the taxonomic resolution of wild and cultivated carrot, Daucus species.
•Methods: We studied the phylogeny of 92 accessions of 13 species and two subspecies of Daucus and 15 accessions of related genera (107 accessions total) with DNA sequences of 94 nuclear orthologs. Reiterative analyses examined data of both alleles using ambiguity codes or a single allele with the highest coverage, trimmed vs. untrimmed homopolymers; pure exonic vs. pure intronic data; the use of all 94 markers vs. a reduced subset of markers; and analysis of a concatenated data set vs. a coalescent (species tree) approach.
•Key results: Our maximum parsimony and maximum likelihood trees were highly resolved, with 100% bootstrap support for most of the external and many of the internal clades. They resolved multiple accessions of many different species as monophyletic with strong support, but failed to support other species. The single allele analysis gave slightly better topological resolution; trimming homopolymers failed to increase taxonomic resolution; the exonic data had a smaller proportion of parsimony‐informative characters. Similar results demonstrating the same dominant topology can be obtained with many fewer markers. A Bayesian concordance analysis provided an overall similar phylogeny, but the coalescent analysis provided drastic changes in topology to all the above.
•Conclusions: Our research highlights some difficult species groups in Daucus and misidentifications in germplasm collections. It highlights a useful subset of markers and approaches for future studies of dominant topologies in Daucus. |
| format | Artículo |
| id | INIA1135 |
| institution | Institucional Nacional de Innovación Agraria |
| language | Inglés |
| publishDate | 2020 |
| publishDateRange | 2020 |
| publishDateSort | 2020 |
| publisher | John Wiley & Sons |
| publisherStr | John Wiley & Sons |
| record_format | dspace |
| spelling | INIA11352022-11-21T20:34:42Z Phylogenomics of the Carrot Genus (Daucus, Apiaceae) Arbizu Berrocal, Carlos Irvin Ruess, Holly Senalik, Douglas Simon, Philipp W. Spooner, David M. Apiaceae Carrot Daucus Germplasm Next-generation suquencing Phylogenomics Biotecnología agrícola, Biotecnología alimentaria •Premise of the study: We explored the utility of multiple nuclear orthologs for the taxonomic resolution of wild and cultivated carrot, Daucus species. •Methods: We studied the phylogeny of 92 accessions of 13 species and two subspecies of Daucus and 15 accessions of related genera (107 accessions total) with DNA sequences of 94 nuclear orthologs. Reiterative analyses examined data of both alleles using ambiguity codes or a single allele with the highest coverage, trimmed vs. untrimmed homopolymers; pure exonic vs. pure intronic data; the use of all 94 markers vs. a reduced subset of markers; and analysis of a concatenated data set vs. a coalescent (species tree) approach. •Key results: Our maximum parsimony and maximum likelihood trees were highly resolved, with 100% bootstrap support for most of the external and many of the internal clades. They resolved multiple accessions of many different species as monophyletic with strong support, but failed to support other species. The single allele analysis gave slightly better topological resolution; trimming homopolymers failed to increase taxonomic resolution; the exonic data had a smaller proportion of parsimony‐informative characters. Similar results demonstrating the same dominant topology can be obtained with many fewer markers. A Bayesian concordance analysis provided an overall similar phylogeny, but the coalescent analysis provided drastic changes in topology to all the above. •Conclusions: Our research highlights some difficult species groups in Daucus and misidentifications in germplasm collections. It highlights a useful subset of markers and approaches for future studies of dominant topologies in Daucus. INTRODUCTION. MATERIALS AND METHODS. RESULTS. DISCUSSION. LITERATURE CITED. 2020-09-11T04:30:35Z 2020-09-11T04:30:35Z 2014-10-01 info:eu-repo/semantics/article Arbizu, C.; Ruess, H.; Senalik, D.; Simon, P.; Spooner, D. (2014). PHYLOGENOMICS OF THE CARROT GENUS (DAUCUS, APIACEAE). American Journal of Botany 101 ( 10 ): 1666 – 1685. doi: 10.3732/ajb.1400106 https://repositorio.inia.gob.pe/handle/20.500.12955/1135 American Journal of Botany https://doi.org/10.3732/ajb.1400106 eng American Journal of Botany 101 ( 10 ): 1666 – 1685 , 2014 https://doi.org/10.3732/ajb.1400106 info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/ application/pdf application/pdf Estados Unidos John Wiley & Sons Estados Unidos Instituto Nacional de Innovación Agraria Repositorio Institucional - INIA |
| spellingShingle | Apiaceae Carrot Daucus Germplasm Next-generation suquencing Phylogenomics Biotecnología agrícola, Biotecnología alimentaria Arbizu Berrocal, Carlos Irvin Ruess, Holly Senalik, Douglas Simon, Philipp W. Spooner, David M. Phylogenomics of the Carrot Genus (Daucus, Apiaceae) |
| title | Phylogenomics of the Carrot Genus (Daucus, Apiaceae) |
| title_full | Phylogenomics of the Carrot Genus (Daucus, Apiaceae) |
| title_fullStr | Phylogenomics of the Carrot Genus (Daucus, Apiaceae) |
| title_full_unstemmed | Phylogenomics of the Carrot Genus (Daucus, Apiaceae) |
| title_short | Phylogenomics of the Carrot Genus (Daucus, Apiaceae) |
| title_sort | phylogenomics of the carrot genus daucus apiaceae |
| topic | Apiaceae Carrot Daucus Germplasm Next-generation suquencing Phylogenomics Biotecnología agrícola, Biotecnología alimentaria |
| url | https://repositorio.inia.gob.pe/handle/20.500.12955/1135 https://doi.org/10.3732/ajb.1400106 |
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