Chromosome-scale scaffolding of the black raspberry (Rubus occidentalis L.) genome based on chromatin interaction data
Plant genomics: Improved genome for the black raspberry Assembly of a high-quality reference genome for the black raspberry plant will inform future crop improvements. Sequencing the genomes of widely-grown, profitable fruit crops can help researchers identify the DNA markers linked to desirable tra...
| Main Authors: | , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Oxford University Press
2018-02-01
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| Series: | Horticulture Research |
| Online Access: | https://doi.org/10.1038/s41438-017-0013-y |
| _version_ | 1828764718203928576 |
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| author | Rubina Jibran Helge Dzierzon Nahla Bassil Jill M. Bushakra Patrick P. Edger Shawn Sullivan Chad E. Finn Michael Dossett Kelly J. Vining Robert VanBuren Todd C. Mockler Ivan Liachko Kevin M. Davies Toshi M. Foster David Chagné |
| author_facet | Rubina Jibran Helge Dzierzon Nahla Bassil Jill M. Bushakra Patrick P. Edger Shawn Sullivan Chad E. Finn Michael Dossett Kelly J. Vining Robert VanBuren Todd C. Mockler Ivan Liachko Kevin M. Davies Toshi M. Foster David Chagné |
| author_sort | Rubina Jibran |
| collection | DOAJ |
| description | Plant genomics: Improved genome for the black raspberry Assembly of a high-quality reference genome for the black raspberry plant will inform future crop improvements. Sequencing the genomes of widely-grown, profitable fruit crops can help researchers identify the DNA markers linked to desirable traits, potentially improving crop health and yields. David Chagné at the New Zealand Institute for Plant and Food Research Limited and co-workers combined new techniques to significantly improve on an existing genome for the black raspberry (Rubus occidentalis L.). The researchers used Hi-C analysis to create a map identifying the interactions between chromatin fragments – macromolecules made from DNA, proteins and RNA – and the three-dimensional structure of chromosomes inside the cell nucleus. Then, they used a bioinformatics assembly method to construct the genome from this data. The new genome showed high accuracy when compared to another genome from the same family. |
| first_indexed | 2024-12-11T04:39:47Z |
| format | Article |
| id | doaj.art-6c3b796e2a574ad5a5a0095d23e92974 |
| institution | Directory Open Access Journal |
| issn | 2052-7276 |
| language | English |
| last_indexed | 2024-12-11T04:39:47Z |
| publishDate | 2018-02-01 |
| publisher | Oxford University Press |
| record_format | Article |
| series | Horticulture Research |
| spelling | doaj.art-6c3b796e2a574ad5a5a0095d23e929742022-12-22T01:20:39ZengOxford University PressHorticulture Research2052-72762018-02-015111110.1038/s41438-017-0013-yChromosome-scale scaffolding of the black raspberry (Rubus occidentalis L.) genome based on chromatin interaction dataRubina Jibran0Helge Dzierzon1Nahla Bassil2Jill M. Bushakra3Patrick P. Edger4Shawn Sullivan5Chad E. Finn6Michael Dossett7Kelly J. Vining8Robert VanBuren9Todd C. Mockler10Ivan Liachko11Kevin M. Davies12Toshi M. Foster13David Chagné14The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600USDA-ARS National Clonal Germplasm RepositoryUSDA-ARS National Clonal Germplasm RepositoryDepartment of Horticulture, Michigan State UniversityPhase GenomicsUSDA-ARS Horticultural Crops Research UnitB.C. Blueberry Council (in Partnership with Agriculture and Agri-Food Canada) Agassiz Food Research CentreB.C. Blueberry Council (in Partnership with Agriculture and Agri-Food Canada) Agassiz Food Research CentreDepartment of Horticulture, Michigan State UniversityThe Donald Danforth Plant Science CenterPhase GenomicsThe New Zealand Institute for Plant & Food Research LimitedThe New Zealand Institute for Plant & Food Research LimitedThe New Zealand Institute for Plant & Food Research LimitedPlant genomics: Improved genome for the black raspberry Assembly of a high-quality reference genome for the black raspberry plant will inform future crop improvements. Sequencing the genomes of widely-grown, profitable fruit crops can help researchers identify the DNA markers linked to desirable traits, potentially improving crop health and yields. David Chagné at the New Zealand Institute for Plant and Food Research Limited and co-workers combined new techniques to significantly improve on an existing genome for the black raspberry (Rubus occidentalis L.). The researchers used Hi-C analysis to create a map identifying the interactions between chromatin fragments – macromolecules made from DNA, proteins and RNA – and the three-dimensional structure of chromosomes inside the cell nucleus. Then, they used a bioinformatics assembly method to construct the genome from this data. The new genome showed high accuracy when compared to another genome from the same family.https://doi.org/10.1038/s41438-017-0013-y |
| spellingShingle | Rubina Jibran Helge Dzierzon Nahla Bassil Jill M. Bushakra Patrick P. Edger Shawn Sullivan Chad E. Finn Michael Dossett Kelly J. Vining Robert VanBuren Todd C. Mockler Ivan Liachko Kevin M. Davies Toshi M. Foster David Chagné Chromosome-scale scaffolding of the black raspberry (Rubus occidentalis L.) genome based on chromatin interaction data Horticulture Research |
| title | Chromosome-scale scaffolding of the black raspberry (Rubus occidentalis L.) genome based on chromatin interaction data |
| title_full | Chromosome-scale scaffolding of the black raspberry (Rubus occidentalis L.) genome based on chromatin interaction data |
| title_fullStr | Chromosome-scale scaffolding of the black raspberry (Rubus occidentalis L.) genome based on chromatin interaction data |
| title_full_unstemmed | Chromosome-scale scaffolding of the black raspberry (Rubus occidentalis L.) genome based on chromatin interaction data |
| title_short | Chromosome-scale scaffolding of the black raspberry (Rubus occidentalis L.) genome based on chromatin interaction data |
| title_sort | chromosome scale scaffolding of the black raspberry rubus occidentalis l genome based on chromatin interaction data |
| url | https://doi.org/10.1038/s41438-017-0013-y |
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