Abstract
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.
Highlights
Supernumerary chromosomes were first discovered in the leaffooted plant bug Metapodius more than a century ago [1]
We sequenced the maize B chromosome introgressed into the B73 inbred line using a combination of chromosome flow sorting, Illumina sequencing, Bionano optical mapping, and high-throughput chromatin conformation capture (Hi-C)
Initial assembly with De-NovoMAGIC software resulted in nearly 67,000 scaffolds representing 2.3 Gb (SI Appendix, Table S2), which exceeded the size of the assembled fraction of the B73 genome [24] by about 200 Mb
Summary
Supernumerary chromosomes were first discovered in the leaffooted plant bug Metapodius more than a century ago [1]. It can be found in numerous landraces and in populations of Mexican teosinte, the maize wild relative [12] Despite being dispensable, it is maintained in populations by two properties: nondisjunction at the second pollen mitosis giving rise to unequal sperm and preferential fertilization of the egg by the B chromosome-containing sperm [4, 13] (Fig. 1). It is maintained in populations by two properties: nondisjunction at the second pollen mitosis giving rise to unequal sperm and preferential fertilization of the egg by the B chromosome-containing sperm [4, 13] (Fig. 1) This acrocentric chromosome is smaller than standard A chromosomes. The gene and transposable element content of the B chromosome and relaxed purifying selection of transposed protein-encoding genes suggest that the chromosome has been present in the evolutionary lineage for millions of years
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