Supporting data for "A chromosome-scale genome assembly of cucumber (<em>Cucumis sativus</em> L.)"

An accurate and complete reference genome assembly is fundamental for biological research. Cucumber is an important vegetable crop and model system for sex determination and vascular biology, and its draft genomes have been assembled using low coverage of Sanger sequences and high coverage of short Illumina sequences, but the incompleteness and low quality of these genomes limit their usage in comparative genomics and genetic research. Therefore, a high-quality and complete cucumber genome assembly is of great necessity. We assembled single-molecule real-time (SMRT) long reads into a significantly improved cucumber reference genome containing 174 contigs with a total length of 226.2 Mb and an N50 of 8.9 Mb, providing an extra of 29.0 Mb sequences. Using 10X genomics, and high-throughput chromosome conformation capture (Hi-C) data, 89 contigs (~211.0 Mb) were directly linked into the seven pseudo-chromosome sequences. The newly assembled regions abundantly show higher GC or AT content, likely inaccessible to Illumina sequencing. The new assembly contains 1,374 full-length long terminal retrotransposons (LTRs) and 1,078 novel genes including 239 tandemly duplicated genes. For example, four tandemly duplicated tyrosylprotein sulfotransferases (TPSTs), which are a single copy gene in the previous assembly and most other plants, were assembled and predicted. <br>This high-quality genome represents novel features of the cucumber genome, and will serve as a valuable resource for genetic research in cucumber as well as plant comparative genomics.

精准且完整的参考基因组组装是生物学研究的核心基础。黄瓜是重要的蔬菜作物，同时也是性别决定与维管生物学研究的模式系统。此前科研人员基于低覆盖度桑格测序（Sanger）序列与高覆盖度短读长Illumina测序（Illumina）序列，完成了黄瓜草图基因组的组装，但此类基因组存在完整性不足、质量欠佳的问题，限制了其在比较基因组学与遗传学研究中的应用。因此，构建高质量且完整的黄瓜参考基因组组装体实属必要。我们通过单分子实时测序（SMRT）长读长序列，组装得到了质量显著提升的黄瓜参考基因组，该组装体包含174个重叠群（contig），总长度为226.2 Mb，N50值（N50）为8.9 Mb，新增了29.0 Mb的序列信息。我们利用10X Genomics技术与高通量染色体构象捕获（Hi-C）数据，将89个重叠群（总长度约211.0 Mb）直接锚定至7条伪染色体（pseudo-chromosome）序列中。新组装的区域普遍具有更高的GC或AT含量，这类区域此前可能难以通过Illumina测序获取有效数据。本次新组装的基因组包含1374个全长长末端重复反转录转座子（LTRs），以及1078个新基因，其中包括239个串联重复基因。例如，我们组装并预测得到4个串联重复的酪氨酸蛋白磺基转移酶（TPSTs），而在此前的组装版本以及多数其他植物中，此类基因均为单拷贝基因。<br>这一高质量黄瓜参考基因组展现了黄瓜基因组的全新特征，将为黄瓜遗传学研究以及植物比较基因组学研究提供极具价值的研究资源。