Spinach (Spinacia oleracea L.) is a member of the Caryophyllales family, a basal eudicot asterid that consists of sugar beet (Beta vulgaris L. subsp. vulgaris), quinoa (Chenopodium quinoa Willd.), and amaranth (Amaranthus hypochondriacus L.). With the introduction of baby leaf types, spinach has become a staple food in many homes. Production issues focus on yield, nitrogen-use efficiency and resistance to downy mildew (Peronospora effusa). Although genomes are available for the above species, a chromosome-level assembly exists only for quinoa, allowing for proper annotation and structural analyses to enhance crop improvement. We independently assembled and annotated genomes of the cultivar Viroflay using short-read strategy (Illumina) and long-read strategies (Pacific Biosciences) to develop a chromosome-level, genetically anchored assembly for spinach. Scaffold N50 for the Illumina assembly was 389 kb, whereas that for Pacific BioSciences was 4.43 Mb, representing 911 Mb (93% of the genome) in 221 scaffolds, 80% of which are anchored and oriented on a sequence-based genetic map, also described within this work. The two assemblies were 99.5% collinear. Independent annotation of the two assemblies with the same comprehensive transcriptome dataset show that the quality of the assembly directly affects the annotation with significantly more genes predicted (26,862 vs. 34,877) in the long-read assembly. Analysis of resistance genes confirms a bias in resistant gene motifs more typical of monocots. Evolutionary analysis indicates that Spinacia is a paleohexaploid with a whole-genome triplication followed by extensive gene rearrangements identified in this work. Diversity analysis of 75 lines indicate that variation in genes is ample for hypothesis-driven, genomic-assisted breeding enabled by this work.

中文翻译：

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菠菜的锚定染色体规模基因组组装改进了注释并揭示了真阿斯特类中的广泛基因重排

菠菜 ( Spinacia oleracea L.) 是石竹目家族的一员，是一种由甜菜 ( Beta vulgaris L. subsp. vulgaris )、藜麦 ( Chenopodium quinoa Willd. ) 和苋菜 ( Amaranthus hypochondriacus L. )组成的基础真双子叶植物。 . 随着婴儿叶类型的引入，菠菜已成为许多家庭的主食。生产问题集中在产量、氮利用效率和对霜霉病的抵抗力（Peronospora effusa）。尽管上述物种的基因组可用，但染色体水平的组装仅存在于藜麦，允许进行适当的注释和结构分析以增强作物改良。我们使用短读策略 (Illumina) 和长读策略 (Pacific Biosciences) 独立组装和注释了栽培品种 Viroflay 的基因组，以开发菠菜的染色体水平、遗传锚定组装。Illumina 组装的支架 N50 为 389 kb，而 Pacific BioSciences 的支架 N50 为 4.43 Mb，代表 221 个支架中的 911 Mb（基因组的 93%），其中 80% 锚定和定向在基于序列的遗传图谱上，也在这部作品中进行了描述。两个组件 99.5% 共线。具有相同综合转录组数据集的两个程序集的独立注释表明，程序集的质量直接影响注释，在长读取程序集中预测的基因显着更多（26,862 对 34,877）。抗性基因的分析证实了更典型的单子叶植物抗性基因基序的偏倚。进化分析表明Spinacia是一种古六倍体，具有全基因组三倍重复，随后在这项工作中发现了广泛的基因重排。75 个品系的多样性分析表明，基因的变异对于这项工作所支持的假设驱动、基因组辅助育种来说是充足的。