ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2014
Dissection of the octoploid strawberry genome by deep sequencing of the genomes of Fragaria species.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 112 papers, 1 of them a synthesis that pooled it.
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Who cites it
112 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Pooled it
- Sustainable strawberry DNA-based biomimetic interphase with synergistic buffering and directional transport for dendrite-free lithium metal batteries.RSC advances · 2026Article
- Recent progress in DNA marker-assisted selection for vegetable breeding in Japan.Breeding science · 2026Article
- A haplotype-phased genome characterizes the genomic architecture and causal variants for RXf1 conferring resistance to Xanthomonas fragariae in strawberry (F. × ananassa).BMC genomics · 2025Article
- A near-complete genome assembly of Fragaria iinumae.BMC genomics · 2025Article
- Inferring complex evolutionary history of the closely related East Asian wild roses in Rosa sect. Synstylae (Rosaceae) based on genomic evidence from conserved orthologues.Annals of botany · 2025Article
- Development of genome-wide SSR markers throughFrontiers in plant science · 2025Article
- Light-dependent chloroplast relocation in wild strawberry (Plant signaling & behavior · 2024Article
- Article
- findGSEP: estimating genome size of polyploid species using k-mer frequencies.Bioinformatics (Oxford, England) · 2024Article
- Members of WRKY Group III Transcription Factors Are Important in Mite Infestation in Strawberry (Plants (Basel, Switzerland) · 2024Article
- Study of Endogenous Viruses in the Strawberry Plants.Viruses · 2024Article
- Advances in genomics and genome editing for improving strawberry (Frontiers in genetics · 2024Review
- The High-Quality Genome Sequencing and Analysis of Red Raspberry (International journal of genomics · 2024Article
- Comparative Analysis of Transposable Elements in Strawberry Genomes of Different Ploidy Levels.International journal of molecular sciences · 2023Article
- Subgenome phasing for complex allopolyploidy: case-based benchmarking and recommendations.Briefings in bioinformatics · 2023Article
- Haplotype-resolved genomes of wild octoploid progenitors illuminate genomic diversifications from wild relatives to cultivated strawberry.Nature plants · 2023Article
- ploidyfrost: Reference-free estimation of ploidy level from whole genome sequencing data based on de Bruijn graphs.Molecular ecology resources · 2023Article
- High-quality haplotype-resolved genome assembly of cultivated octoploid strawberry.Horticulture research · 2023Article
- Article
52 more citing papers are in PubMed but not listed here.
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24 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cultivated strawberry (Fragaria x ananassa) is octoploid and shows allogamous behaviour. The present study aims at dissecting this octoploid genome through comparison with its wild relatives, F. iinumae, F. nipponica, F. nubicola, and F. orientalis by de novo whole-genome sequencing on an Illumina and Roche 454 platforms. The total length of the assembled Illumina genome sequences obtained was 698 Mb for F. x ananassa, and ∼200 Mb each for the four wild species. Subsequently, a virtual reference genome termed FANhybrid_r1.2 was constructed by integrating the sequences of the four homoeologous subgenomes of F. x ananassa, from which heterozygous regions in the Roche 454 and Illumina genome sequences were eliminated. The total length of FANhybrid_r1.2 thus created was 173.2 Mb with the N50 length of 5137 bp. The Illumina-assembled genome sequences of F. x ananassa and the four wild species were then mapped onto the reference genome, along with the previously published F. vesca genome sequence to establish the subgenomic structure of F. x ananassa. The strategy adopted in this study has turned out to be successful in dissecting the genome of octoploid F. x ananassa and appears promising when applied to the analysis of other polyploid plant species.
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