Tanaka Tsuyoshi, Nishijima Ryo, Teramoto Shota, Kitomi Yuka, Hayashi Takeshi, Uga Yusaku, Kawakatsu Taiji
Division of Basic Research, Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8518, Japan.
Division of Biotechnology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8604, Japan.
G3 (Bethesda). 2020 May 4;10(5):1495-1501. doi: 10.1534/g3.119.400871.
IR64 is a rice variety with high-yield that has been widely cultivated around the world. IR64 has been replaced by modern varieties in most growing areas. Given that modern varieties are mostly progenies or relatives of IR64, genetic analysis of IR64 is valuable for rice functional genomics. However, chromosome-level genome sequences of IR64 have not been available previously. Here, we sequenced the IR64 genome using synthetic long reads obtained by linked-read sequencing and ultra-long reads obtained by nanopore sequencing. We integrated these data and generated the assembly of the IR64 genome of 367 Mb, equivalent to 99% of the estimated size. Continuity of the IR64 genome assembly was improved compared with that of a publicly available IR64 genome assembly generated by short reads only. We annotated 41,458 protein-coding genes, including 657 IR64-specific genes, that are missing in other high-quality rice genome assemblies IRGSP-1.0 of cultivar Nipponbare or R498 of cultivar Shuhui498. The IR64 genome assembly will serve as a genome resource for rice functional genomics as well as genomics-driven and/or molecular breeding.
IR64是一个高产水稻品种，已在世界各地广泛种植。在大多数种植地区，IR64已被现代品种所取代。鉴于现代品种大多是IR64的后代或亲缘品种，对IR64进行遗传分析对水稻功能基因组学具有重要价值。然而，此前尚未获得IR64的染色体水平基因组序列。在此，我们使用通过连接 reads 测序获得的合成长 reads 和通过纳米孔测序获得的超长 reads 对IR64基因组进行了测序。我们整合了这些数据，并生成了367 Mb的IR64基因组组装序列，相当于估计大小的99%。与仅通过短 reads 生成的公开可用的IR64基因组组装序列相比，IR64基因组组装的连续性得到了改善。我们注释了41,458个蛋白质编码基因，其中包括657个IR64特有的基因，这些基因在日本晴品种的IRGSP-1.0或蜀恢498品种的R498等其他高质量水稻基因组组装序列中缺失。IR64基因组组装序列将作为水稻功能基因组学以及基因组驱动和/或分子育种的基因组资源。
