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.

中文翻译：

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二倍体草莓（Fragaria nilgerrensis）的高质量基因组为花青素积累提供了新的见解。


Fragaria nilgerrensis是亚洲东部和东南部地区特有的野生二倍体草莓品种，为草莓改良提供了丰富的遗传变异来源。在这里，我们使用单分子实时（SMRT）太平洋生物科学测序和染色体构象捕获（Hi-C）基因组支架展示了F. nilgerrensis的染色体规模组装。基因组组装大小为 270.3 Mb，重叠群 N50 约为 8.5 Mb。该基因组总共注释了 28 780 个基因和 117.2 Mb 的转座元件。接下来，与高质量的F. vesca参考基因组进行详细的比较基因组学，以获得转座元件、SNP、Indels等之间的差异。 F. nilgerrensis的基因组大小相对于F. vesca增加了约 50 Mb，这主要是由于转座元件的扩展。与F相比。在vesca基因组中，我们鉴定了 4 561 825 个 SNP、846 301 个插入缺失、4 243 个倒位、35 498 个易位和 10 099 个重定位。我们还发现F. nilgerrensis中涉及苯丙素生物合成、淀粉和蔗糖代谢、氰基氨基酸代谢、植物与病原体相互作用、油菜素类固醇生物合成和植物激素信号转导的基因显着扩展，这可能解释了其特定的表型和相当大的环境适应性。 有趣的是，我们发现FnMYB10 （花青素生物合成的核心转录激活因子）上游调控区的序列变异导致FnMYB10基因的低表达水平，这可能是FnMYB10 白色果实表型的原因。高质量的尼尔格尔基因组将成为生物学研究和比较基因组学研究的宝贵资源。