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.

Agronomy College Sichuan Agricultural University Chengdu China

Biomarker Technologies Corporation Beijing China

Center for Integrated Breeding Research Department of Crop Sciences Georg August University Göttingen Germany

College of Agronomy Longzi Lake Campus Henan Agricultural University Zhengzhou China

Institute of Experimental Botany of the Czech Academy of Sciences Centre of the Region Hana for Biotechnological and Agricultural Research Olomouc Czech Republic

Leibniz Institute of Plant Genetics and Crop Plant Research Seeland Germany

Peking University Institute of Advanced Agricultural Sciences Weifang China

School of Advanced Agriculture Sciences and School of Life Sciences State Key Laboratory of Protein and Plant Gene Research Peking University Beijing China

The State Key Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental Biology Chinese Academy of Sciences Beijing China

The State Key Laboratory of Wheat and Maize Crop Science Center for Crop Genome Engineering Henan Agricultural University Zhengzhou China

Triticeae Research Institute Sichuan Agricultural University Chengdu China

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