A high-quality genome assembly highlights rye genomic characteristics and agronomically important genes

Rye is a valuable food and forage crop, an important genetic resource for wheat and triticale improvement, and an indispensable material for efficient comparative genomic studies in grasses. Here, we sequenced the genome of Weining rye, an elite Chinese rye variety. The assembled contigs (7.74 Gb) accounted for 98.47% of the estimated genome size (7.86 Gb), with 93.67% of the contigs (7.25 Gb) assigned to seven chromosomes. Repetitive elements constituted 90.31% of the assembled genome. Compared to previously sequenced Triticeae genomes, Daniela, Sumaya and Sumana retrotransposons showed strong expansion in rye. Further analyses of the Weining assembly shed new light on genome-wide gene duplications and their impact on starch biosynthesis genes, physical organization of complex prolamin loci, gene expression features underlying early heading trait and putative domestication-associated chromosomal regions and loci in rye. This genome sequence promises to accelerate genomic and breeding studies in rye and related cereal crops.

Guangwei Li, Lijian Wang, Jianping Yang, Hang He, Huaibing Jin, Xuming Li, Tianheng Ren, Zhenglong Ren, Feng Li, Xue Han, Xiaoge Zhao, Lingli Dong, Yiwen Li, Zhongping Song, Zehong Yan, Nannan Zheng, Cuilan Shi, Zhaohui Wang, Shuling Yang, Zijun Xiong, Menglan Zhang, Guanghua Sun, Xu Zheng, Mingyue Gou, Changmian Ji, Junkai Du, Hongkun Zheng, Jaroslav Doležel, Xing Wang Deng, Nils Stein, Qinghua Yang, Kunpu Zhang, Daowen Wang