B chromosomes are enigmatic elements in thousands of plant and animal genomes that persist in populations despite being nonessential. They circumvent the laws of Mendelian inheritance but the molecular mechanisms underlying this behavior remain unknown. Here we present the sequence, annotation, and analysis of the maize B chromosome providing insight into its drive mechanism. The sequence assembly reveals detailed locations of the elements involved with the cis and trans functions of its drive mechanism, consisting of nondisjunction at the second pollen mitosis and preferential fertilization of the egg by the B-containing sperm. We identified 758 protein-coding genes in 125.9 Mb of B chromosome sequence, of which at least 88 are expressed. Our results demonstrate that transposable elements in the B chromosome are shared with the standard A chromosome set but multiple lines of evidence fail to detect a syntenic genic region in the A chromosomes, suggesting a distant origin. The current gene content is a result of continuous transfer from the A chromosomal complement over an extended evolutionary time with subsequent degradation but with selection for maintenance of this nonvital chromosome.

Bayer Crop Science Chesterfield MO 63017

Bionano Genomics San Diego CA 92121

Centre of the Region Haná for Biotechnological and Agricultural Research Institute of Experimental Botany of the Czech Academy of Sciences Olomouc 77900 Czech Republic

Centre of the Region Haná for Biotechnological and Agricultural Research Institute of Experimental Botany of the Czech Academy of Sciences Olomouc 77900 Czech Republic;

College of Advanced Agricultural Science University of Chinese Academy of Sciences 100049 Beijing China

Department of Electrical Engineering and Computer Science University of Missouri Columbia MO 65211

Department of Plant Biology University of Georgia Athens GA 30602

Department of Statistics University of Missouri Columbia MO 65211

Division of Biological Sciences University of Missouri Columbia MO 65211

Division of Biological Sciences University of Missouri Columbia MO 65211;

NRGene Ness Ziona 7403649 Israel

State Key Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental Biology Innovation Academy for Seed Design Chinese Academy of Sciences 100101 Beijing China

State Key Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental Biology Innovation Academy for Seed Design Chinese Academy of Sciences 100101 Beijing China;

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