B chromosomes are enigmatic elements in thousands of plant and animal genomes that persist in populations despite being nones- sential. 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 pref- erential 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 demon- strate that transposable elements in the B chromosome are shared with the standard A chromosome set but multiple lines of evi- dence 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.
Nicolas Blaveta,1, Hua Yangb,1, Handong Suc,1, Pavel Solanskýa, Ryan N. Douglasb, Miroslava Karafiátováa, Lucie Sˇimkováa, Jing Zhangc, Yalin Liuc, Jie Houd, Xiaowen Shib, Chen Chend, Mohamed El-Walidb,
Morgan E. McCawb, Patrice S. Albertb, Zhi Gaob, Changzeng Zhaob, Gil Ben-Zvie, Lior Glicke,2, Guy Kole,
Jinghua Shif, Jan Vránaa, Hana Sˇimkováa, Jonathan C. Lambg, Kathleen Newtonb, R. Kelly Daweh,
Jaroslav Dolezela, Tieming Jii,3, Kobi Baruche, Jianlin Chengd, Fangpu Hanc,j,4, James A. Birchlerb,4, and Jan Bartoša,4