Genome assembly of the maize B chromosome provides insight into its epigenetic characteristics and effects on the host genome

B chromosomes contribute to the genetic variation in numerous eukaryotes. Yet their genetic and epigenetic characteristics, as well as their effects on the host genome remain poorly understood. Here, we present a comprehensive genome assembly of diploid maize B73 with two copies of B chromosomes using long-read sequencing. We annotate a total of 1124 high-confidence protein-coding genes and 119,579,190 bp repeat elements representing 88.55% of the B chromosome assembly. Using CENH3 ChIP-seq data, we accurately determined the position of the B chromosome centromere, which features a unique monomer-composed satellite array distinct from that found on the chromosome arms. Our research provides detailed genetic and epigenetic maps of the B chromosome, shedding light on its molecular landscape, including DNA sequence composition, DNA methylation patterns, histone modifications, and R-loop distributions across various chromatin regions. Consistent with the cytological morphology of the B chromosome, the less condensed euchromatin regions displayed high levels of H3K4me3, H3K9ac, gene expression, and dense R-loop distributions. DNA methylation on the B chromosome was primarily observed at CG sites. The centromeric region is notably enriched with H3K4me3 and H3K9ac histone modifications and has lower CHG methylation compared to the pericentromeric regions. Moreover, our findings reveal that B chromosome accumulation affects R-loop formation on A chromosomes, and exerts tissue-specific influences on A chromosome gene expression. The accurate assembly and detailed epigenetic maps of the maize B chromosome will help understand the drive mechanism, reveal its conflict with the host genome, and accelerate the construction of artificial chromosomes.