ArticlePlant biotechnology journal2020
The high-quality genome of diploid strawberry (Fragaria nilgerrensis) provides new insights into anthocyanin accumulation.
Article in Plant biotechnology journal, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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43 citing papers in PubMed, 78 citations in OpenAlex.
- Multifaceted mechanisms underlying species- and cultivar-associated differential anthocyanin accumulation in fruits.Horticulture research · 2026Article
- Genome-wide identification of the FAD gene family in Fragaria nilgerrensis reveals distinct roles of two FnFAD3 genes in peach-like aroma formation.Genes & genomics · 2026Article
- A single nucleotide mutation in FngMYB10 causes white fruit phenotype in Fragaria nilgerrensis.BMC plant biology · 2026Article
- Identification of genome size and heterozygosity in 510 Jujube (Frontiers in plant science · 2026Article
- The shallow domestication bottleneck of strawberry: recovering secondary metabolite-based defenses from wildFrontiers in plant science · 2026Review
- Metabolomic and transcriptomic analyses provide insights into metabolic networks during Fragaria nilgerrensis fruit development and ripening.BMC plant biology · 2025Article
- Recent advances in biosynthesis and regulation of strawberry anthocyanins.Horticulture research · 2025Article
- Article
- Transcriptomic and Physiological Analyses for the Role of Hormones and Sugar in Axillary Bud Development of Wild Strawberry Stolon.Plants (Basel, Switzerland) · 2024Article
- Chromosome-scale genome assembly and annotation of Cotoneaster glaucophyllus.Scientific data · 2024Article
- Chromosome-level genome assembly of Hippophae tibetana provides insights into high-altitude adaptation and flavonoid biosynthesis.BMC biology · 2024Article
- Comparative analysis of the microbiomes of strawberry wild speciesFrontiers in microbiology · 2024Article
- Advances in genomics and genome editing for improving strawberry (Frontiers in genetics · 2024Review
- Combined transcriptome and metabolome analysis revealed the molecular mechanisms of fruit skin coloration in pink strawberry.Frontiers in plant science · 2024Article
- The High-Quality Genome Sequencing and Analysis of Red Raspberry (International journal of genomics · 2024Article
- Characteristics of Amorphophallus konjac as indicated by its genome.Scientific reports · 2023Article
- Comparative Analysis of Transposable Elements in Strawberry Genomes of Different Ploidy Levels.International journal of molecular sciences · 2023Article
- Deciphering the genetic architecture of fruit color in strawberry.Journal of experimental botany · 2023Review
- Haplotype-resolved genomes of wild octoploid progenitors illuminate genomic diversifications from wild relatives to cultivated strawberry.Nature plants · 2023Article
- Transcriptomic analysis reveals the mechanism underlying the anthocyanin changes in Fragaria nilgerrensis Schlecht. and its interspecific hybrids.BMC plant biology · 2023Article
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12 authors at 2 institutions in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
Fragaria nilgerrensis is a wild diploid strawberry species endemic to east and southeast region in Asia and provides a rich source of genetic variations for strawberry improvement. Here, we present a chromosome-scale assembly of F. nilgerrensis using single-molecule real-time (SMRT) Pacific Biosciences sequencing and chromosome conformation capture (Hi-C) genome scaffolding. The genome assembly size was 270.3 Mb, with a contig N50 of ∼8.5 Mb. A total of 28 780 genes and 117.2 Mb of transposable elements were annotated for this genome. Next, detailed comparative genomics with the high-quality F. vesca reference genome was conducted to obtain the difference among transposable elements, SNPs, Indels, and so on. The genome size of F. nilgerrensis was enhanced by around 50 Mb relatively to F. vesca, which is mainly due to expansion of transposable elements. In comparison with the F. vesca genome, we identified 4 561 825 SNPs, 846 301 Indels, 4243 inversions, 35 498 translocations and 10 099 relocations. We also found a marked expansion of genes involved in phenylpropanoid biosynthesis, starch and sucrose metabolism, cyanoamino acid metabolism, plant-pathogen interaction, brassinosteroid biosynthesis and plant hormone signal transduction in F. nilgerrensis, which may account for its specific phenotypes and considerable environmental adaptability. Interestingly, we found sequence variations in the upstream regulatory region of FnMYB10, a core transcriptional activator of anthocyanin biosynthesis, resulted in the low expression level of the FnMYB10 gene, which is likely responsible for white fruit phenotype of F. nilgerrensis. The high-quality F. nilgerrensis genome will be a valuable resource for biological research and comparative genomics research.
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