Cargando…
High-quality haplotype-resolved genome assembly of cultivated octoploid strawberry
Cultivated strawberry (Fragaria × ananassa), a perennial herb belonging to the family Rosaceae, is a complex octoploid with high heterozygosity at most loci. However, there is no research on the haplotype of the octoploid strawberry genome. Here we aimed to obtain a high-quality genome of the cultiv...
Autores principales: | , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2023
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10108017/ https://www.ncbi.nlm.nih.gov/pubmed/37077373 http://dx.doi.org/10.1093/hr/uhad002 |
_version_ | 1785026748947103744 |
---|---|
author | Mao, Jianxin Wang, Yan Wang, Baotian Li, Jiqi Zhang, Chao Zhang, Wenshuo Li, Xue Li, Jie Zhang, Junxiang Li, He Zhang, Zhihong |
author_facet | Mao, Jianxin Wang, Yan Wang, Baotian Li, Jiqi Zhang, Chao Zhang, Wenshuo Li, Xue Li, Jie Zhang, Junxiang Li, He Zhang, Zhihong |
author_sort | Mao, Jianxin |
collection | PubMed |
description | Cultivated strawberry (Fragaria × ananassa), a perennial herb belonging to the family Rosaceae, is a complex octoploid with high heterozygosity at most loci. However, there is no research on the haplotype of the octoploid strawberry genome. Here we aimed to obtain a high-quality genome of the cultivated strawberry cultivar, “Yanli”, using single molecule real-time sequencing and high-throughput chromosome conformation capture technology. The “Yanli” genome was 823 Mb in size, with a long terminal repeat assembly index of 14.99. The genome was phased into two haplotypes, Hap1 (825 Mb with contig N50 of 26.70 Mb) and Hap2 (808 Mb with contig N50 of 27.51 Mb). Using the combination of Hap1 and Hap2, we obtained for the first time a haplotype-resolved genome with 56 chromosomes for the cultivated octoploid strawberry. We identified a ~ 10 Mb inversion and translocation on chromosome 2-1. 104 957 and 102 356 protein-coding genes were annotated in Hap1 and Hap2, respectively. Analysis of the genes related to the anthocyanin biosynthesis pathway revealed the structural diversity and complexity in the expression of the alleles in the octoploid F. × ananassa genome. In summary, we obtained a high-quality haplotype-resolved genome assembly of F. × ananassa, which will provide the foundation for investigating gene function and evolution of the genome of cultivated octoploid strawberry. |
format | Online Article Text |
id | pubmed-10108017 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-101080172023-04-18 High-quality haplotype-resolved genome assembly of cultivated octoploid strawberry Mao, Jianxin Wang, Yan Wang, Baotian Li, Jiqi Zhang, Chao Zhang, Wenshuo Li, Xue Li, Jie Zhang, Junxiang Li, He Zhang, Zhihong Hortic Res Article Cultivated strawberry (Fragaria × ananassa), a perennial herb belonging to the family Rosaceae, is a complex octoploid with high heterozygosity at most loci. However, there is no research on the haplotype of the octoploid strawberry genome. Here we aimed to obtain a high-quality genome of the cultivated strawberry cultivar, “Yanli”, using single molecule real-time sequencing and high-throughput chromosome conformation capture technology. The “Yanli” genome was 823 Mb in size, with a long terminal repeat assembly index of 14.99. The genome was phased into two haplotypes, Hap1 (825 Mb with contig N50 of 26.70 Mb) and Hap2 (808 Mb with contig N50 of 27.51 Mb). Using the combination of Hap1 and Hap2, we obtained for the first time a haplotype-resolved genome with 56 chromosomes for the cultivated octoploid strawberry. We identified a ~ 10 Mb inversion and translocation on chromosome 2-1. 104 957 and 102 356 protein-coding genes were annotated in Hap1 and Hap2, respectively. Analysis of the genes related to the anthocyanin biosynthesis pathway revealed the structural diversity and complexity in the expression of the alleles in the octoploid F. × ananassa genome. In summary, we obtained a high-quality haplotype-resolved genome assembly of F. × ananassa, which will provide the foundation for investigating gene function and evolution of the genome of cultivated octoploid strawberry. Oxford University Press 2023-01-04 /pmc/articles/PMC10108017/ /pubmed/37077373 http://dx.doi.org/10.1093/hr/uhad002 Text en © The Author(s) 2023. Published by Oxford University Press on behalf of Nanjing Agricultural University. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Article Mao, Jianxin Wang, Yan Wang, Baotian Li, Jiqi Zhang, Chao Zhang, Wenshuo Li, Xue Li, Jie Zhang, Junxiang Li, He Zhang, Zhihong High-quality haplotype-resolved genome assembly of cultivated octoploid strawberry |
title | High-quality haplotype-resolved genome assembly of cultivated octoploid strawberry |
title_full | High-quality haplotype-resolved genome assembly of cultivated octoploid strawberry |
title_fullStr | High-quality haplotype-resolved genome assembly of cultivated octoploid strawberry |
title_full_unstemmed | High-quality haplotype-resolved genome assembly of cultivated octoploid strawberry |
title_short | High-quality haplotype-resolved genome assembly of cultivated octoploid strawberry |
title_sort | high-quality haplotype-resolved genome assembly of cultivated octoploid strawberry |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10108017/ https://www.ncbi.nlm.nih.gov/pubmed/37077373 http://dx.doi.org/10.1093/hr/uhad002 |
work_keys_str_mv | AT maojianxin highqualityhaplotyperesolvedgenomeassemblyofcultivatedoctoploidstrawberry AT wangyan highqualityhaplotyperesolvedgenomeassemblyofcultivatedoctoploidstrawberry AT wangbaotian highqualityhaplotyperesolvedgenomeassemblyofcultivatedoctoploidstrawberry AT lijiqi highqualityhaplotyperesolvedgenomeassemblyofcultivatedoctoploidstrawberry AT zhangchao highqualityhaplotyperesolvedgenomeassemblyofcultivatedoctoploidstrawberry AT zhangwenshuo highqualityhaplotyperesolvedgenomeassemblyofcultivatedoctoploidstrawberry AT lixue highqualityhaplotyperesolvedgenomeassemblyofcultivatedoctoploidstrawberry AT lijie highqualityhaplotyperesolvedgenomeassemblyofcultivatedoctoploidstrawberry AT zhangjunxiang highqualityhaplotyperesolvedgenomeassemblyofcultivatedoctoploidstrawberry AT lihe highqualityhaplotyperesolvedgenomeassemblyofcultivatedoctoploidstrawberry AT zhangzhihong highqualityhaplotyperesolvedgenomeassemblyofcultivatedoctoploidstrawberry |