Yasufumi Kobayashi ¹ Hideki Hirakawa ² Kenta Shirasawa ² Kazusa Nishimura ³ Kenichiro Fujii ¹ Rolando Oros ⁴ Giovanna R. Almanza ⁵ Yukari Nagatoshi ¹ Yasuo Yasui ⁶ Yasunari Fujita ^7*

• ¹ Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Japan
• ² Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
• ³ Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama, Okayama, Japan
• ⁴ Fundación PROINPA, Cochabamba, Bolivia
• ⁵ Instituto de Investigaciones Químicas, Universidad Mayor de San Andres, La Paz, La Paz, Bolivia
• ⁶ Graduate School of Agriculture, Kyoto University, Kyoto, Kyōto, Japan
• ⁷ Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Japan

Quinoa is emerging as a key seed crop for global food security due to its ability to grow in marginal environments and its excellent nutritional properties. Because quinoa is partially allogamous, we have developed quinoa inbred lines necessary for molecular genetic analysis.Our comprehensive genomic analysis showed that the quinoa inbred lines fall into three genetic subpopulations: northern highland, southern highland, and lowland. Lowland and highland quinoa are the same species, but have very different genotypes and phenotypes. Lowland quinoa has relatively small grains and a darker grain color, and is widely tested and grown around the world. In contrast, the white, large-grained highland quinoa is grown in the Andean highlands, including the region where quinoa originated, and is exported worldwide as highquality quinoa. Recently, we have shown that viral vectors can be used to regulate endogenous genes in quinoa, paving the way for functional genomics to reveal the diversity of quinoa.However, although a high-quality assembly has recently been reported for a lowland quinoa line, genomic resources of the quality required for functional genomics are not available for highland quinoa lines. In addition, we demonstrate the importance of verifying and correcting reference-based scaffold assembly with other approaches such as linkage maps. Here we present high-quality chromosome-level genome assemblies for two highland inbred quinoa lines, J075 representing the northern highland line and J100 representing the southern highland line, using PacBio HiFi sequencing and dpMIG-seq. The assembled genome sizes of J075 and J100 are 1.29 and 1.32 Gb, with contigs N50 of 66.3 and 12.6 Mb, and scaffold N50 of 71.2 and 70.6 Mb, respectively, comprising 18 pseudochromosomes. The repetitive sequences of J075 and J100 represent 72.6% and 71.5% of the genome, the majority of which are long terminal repeats, representing 44.0% and 42.7% of the genome, respectively. The de novo assembled genomes of J075 and J100 were predicted to contain 64,945 and 65,303 proteincoding genes, respectively. The high quality genomes of these highland quinoa lines will facilitate quinoa functional genomics research on quinoa and contribute to the identification of key genes involved in environmental adaptation and quinoa domestication.