A chromosome-level genome sequence assembly of the red raspberry (Rubus idaeus L.).
Rubus idaeus L. (red raspberry), is a perennial woody plant species of the Rosaceae family that is widely cultivated in the temperate regions of world and is thus an economically important soft fruit species. It is prized for its flavour and aroma, as well as a high content of healthful compounds su...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2022-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0265096 |
| _version_ | 1811252067816177664 |
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| author | Jahn Davik Dag Røen Erik Lysøe Matteo Buti Simeon Rossman Muath Alsheikh Erez Lieberman Aiden Olga Dudchenko Daniel James Sargent |
| author_facet | Jahn Davik Dag Røen Erik Lysøe Matteo Buti Simeon Rossman Muath Alsheikh Erez Lieberman Aiden Olga Dudchenko Daniel James Sargent |
| author_sort | Jahn Davik |
| collection | DOAJ |
| description | Rubus idaeus L. (red raspberry), is a perennial woody plant species of the Rosaceae family that is widely cultivated in the temperate regions of world and is thus an economically important soft fruit species. It is prized for its flavour and aroma, as well as a high content of healthful compounds such as vitamins and antioxidants. Breeding programs exist globally for red raspberry, but variety development is a long and challenging process. Genomic and molecular tools for red raspberry are valuable resources for breeding. Here, a chromosome-length genome sequence assembly and related gene predictions for the red raspberry cultivar 'Anitra' are presented, comprising PacBio long read sequencing scaffolded using Hi-C sequence data. The assembled genome sequence totalled 291.7 Mbp, with 247.5 Mbp (84.8%) incorporated into seven sequencing scaffolds with an average length of 35.4 Mbp. A total of 39,448 protein-coding genes were predicted, 75% of which were functionally annotated. The seven chromosome scaffolds were anchored to a previously published genetic linkage map with a high degree of synteny and comparisons to genomes of closely related species within the Rosoideae revealed chromosome-scale rearrangements that have occurred over relatively short evolutionary periods. A chromosome-level genomic sequence of R. idaeus will be a valuable resource for the knowledge of its genome structure and function in red raspberry and will be a useful and important resource for researchers and plant breeders. |
| first_indexed | 2024-04-12T16:28:21Z |
| format | Article |
| id | doaj.art-75fe8c5499bc48b4b42ec459580cf8a6 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-12T16:28:21Z |
| publishDate | 2022-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-75fe8c5499bc48b4b42ec459580cf8a62022-12-22T03:25:15ZengPublic Library of Science (PLoS)PLoS ONE1932-62032022-01-01173e026509610.1371/journal.pone.0265096A chromosome-level genome sequence assembly of the red raspberry (Rubus idaeus L.).Jahn DavikDag RøenErik LysøeMatteo ButiSimeon RossmanMuath AlsheikhErez Lieberman AidenOlga DudchenkoDaniel James SargentRubus idaeus L. (red raspberry), is a perennial woody plant species of the Rosaceae family that is widely cultivated in the temperate regions of world and is thus an economically important soft fruit species. It is prized for its flavour and aroma, as well as a high content of healthful compounds such as vitamins and antioxidants. Breeding programs exist globally for red raspberry, but variety development is a long and challenging process. Genomic and molecular tools for red raspberry are valuable resources for breeding. Here, a chromosome-length genome sequence assembly and related gene predictions for the red raspberry cultivar 'Anitra' are presented, comprising PacBio long read sequencing scaffolded using Hi-C sequence data. The assembled genome sequence totalled 291.7 Mbp, with 247.5 Mbp (84.8%) incorporated into seven sequencing scaffolds with an average length of 35.4 Mbp. A total of 39,448 protein-coding genes were predicted, 75% of which were functionally annotated. The seven chromosome scaffolds were anchored to a previously published genetic linkage map with a high degree of synteny and comparisons to genomes of closely related species within the Rosoideae revealed chromosome-scale rearrangements that have occurred over relatively short evolutionary periods. A chromosome-level genomic sequence of R. idaeus will be a valuable resource for the knowledge of its genome structure and function in red raspberry and will be a useful and important resource for researchers and plant breeders.https://doi.org/10.1371/journal.pone.0265096 |
| spellingShingle | Jahn Davik Dag Røen Erik Lysøe Matteo Buti Simeon Rossman Muath Alsheikh Erez Lieberman Aiden Olga Dudchenko Daniel James Sargent A chromosome-level genome sequence assembly of the red raspberry (Rubus idaeus L.). PLoS ONE |
| title | A chromosome-level genome sequence assembly of the red raspberry (Rubus idaeus L.). |
| title_full | A chromosome-level genome sequence assembly of the red raspberry (Rubus idaeus L.). |
| title_fullStr | A chromosome-level genome sequence assembly of the red raspberry (Rubus idaeus L.). |
| title_full_unstemmed | A chromosome-level genome sequence assembly of the red raspberry (Rubus idaeus L.). |
| title_short | A chromosome-level genome sequence assembly of the red raspberry (Rubus idaeus L.). |
| title_sort | chromosome level genome sequence assembly of the red raspberry rubus idaeus l |
| url | https://doi.org/10.1371/journal.pone.0265096 |
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