The Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan.
Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima 411-8540, Japan.
DNA Res. 2021 Jun 25;28(3). doi: 10.1093/dnares/dsab004.
Spinach (Spinacia oleracea) is grown as a nutritious leafy vegetable worldwide. To accelerate spinach breeding efficiency, a high-quality reference genome sequence with great completeness and continuity is needed as a basic infrastructure. Here, we used long-read and linked-read technologies to construct a de novo spinach genome assembly, designated SOL_r1.1, which was comprised of 287 scaffolds (total size: 935.7 Mb; N50 = 11.3 Mb) with a low proportion of undetermined nucleotides (Ns = 0.34%) and with high gene completeness (BUSCO complete 96.9%). A genome-wide survey of resistance gene analogues identified 695 genes encoding nucleotide-binding site domains, receptor-like protein kinases, receptor-like proteins and transmembrane-coiled coil domains. Based on a high-density double-digest restriction-site associated DNA sequencing-based linkage map, the genome assembly was anchored to six pseudomolecules representing ∼73.5% of the whole genome assembly. In addition, we used SOL_r1.1 to identify quantitative trait loci for bolting timing and fruit/seed shape, which harbour biologically plausible candidate genes, such as homologues of the FLOWERING LOCUS T and EPIDERMAL PATTERNING FACTOR-LIKE genes. The new genome assembly, SOL_r1.1, will serve as a useful resource for identifying loci associated with important agronomic traits and for developing molecular markers for spinach breeding/selection programs.
菠菜（Spinacia oleracea）作为一种营养丰富的绿叶蔬菜在全世界范围内种植。为了加速菠菜的育种效率，需要一个具有高完整性和连续性的高质量参考基因组序列作为基础架构。在这里，我们使用长读长和连接读技术构建了一个从头开始的菠菜基因组组装，命名为 SOL_r1.1，它由 287 个支架（总大小：935.7 Mb；N50 = 11.3 Mb）组成，具有低比例的未确定核苷酸（Ns = 0.34%）和高基因完整性（BUSCO 完整 96.9%）。对抗病基因类似物的全基因组调查鉴定出 695 个编码核苷酸结合位点结构域、受体样蛋白激酶、受体样蛋白和跨膜卷曲螺旋结构域的基因。基于高密度双酶切限制位点相关 DNA 测序的连锁图谱，将基因组组装锚定到六个代表约 73.5%整个基因组组装的假染色体上。此外，我们使用 SOL_r1.1 来鉴定抽薹时间和果实/种子形状的数量性状位点，这些位点包含有生物学意义的候选基因，如 FLOWERING LOCUS T 和 EPIDERMAL PATTERNING FACTOR-LIKE 基因的同源物。新的基因组组装 SOL_r1.1 将成为鉴定与重要农艺性状相关的基因座和开发用于菠菜育种/选择计划的分子标记的有用资源。
