The high-quality genome of diploid strawberry (Fragaria nilgerrensis) provides new insights into anthocyanin accumulation

Fragaria nilgerrensisis 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 ofF. nilgerrensisusing 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 similar to 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-qualityF. vescareference genome was conducted to obtain the difference among transposable elements, SNPs, Indels, and so on. The genome size ofF. nilgerrensiswas enhanced by around 50 Mb relatively toF. vesca, which is mainly due to expansion of transposable elements. In comparison with theF. vescagenome, 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 inF. nilgerrensis, which may account for its specific phenotypes and considerable environmental adaptability. Interestingly, we found sequence variations in the upstream regulatory region ofFnMYB10, a core transcriptional activator of anthocyanin biosynthesis, resulted in the low expression level of theFnMYB10gene, which is likely responsible for white fruit phenotype ofF. nilgerrensis.The high-qualityF. nilgerrensisgenome will be a valuable resource for biological research and comparative genomics research.