Maize abnormal chromosome 10 (Ab10) encodes a classic example of true meiotic drive that converts heterochromatic regions called knobs into motile neocentromeres that are preferentially transmitted to egg cells. Here, we identify a cluster of eight genes on Ab10, called the Kinesin driver (Kindr) complex, that are required for both neocentromere motility and preferential transmission. Two meiotic drive mutants that lack neocentromere activity proved to be kindr epimutants with increased DNA methylation across the entire gene cluster. RNAi of Kindr induced a third epimutant and corresponding loss of meiotic drive. Kinesin gliding assays and immunolocalization revealed that KINDR is a functional minus-end-directed kinesin that localizes specifically to knobs containing 180 bp repeats. Sequence comparisons suggest that Kindr diverged from a Kinesin-14A ancestor ∼12 mya and has driven the accumulation of > 500 Mb of knob repeats and affected the segregation of thousands of genes linked to knobs on all 10 chromosomes.

Creating gapless telomere-to-telomere assemblies of complex genomes is one of the ultimate challenges in genomics. We use two independent assemblies and an optical map-based merging pipeline to produce a maize genome (B73-Ab10) composed of 63 contigs and a contig N50 of 162 Mb. This genome includes gapless assemblies of chromosome 3 (236 Mb) and chromosome 9 (162 Mb), and 53 Mb of the Ab10 meiotic drive haplotype. The data also reveal the internal structure of seven centromeres and five heterochromatic knobs, showing that the major tandem repeat arrays (CentC, knob180, and TR-1) are discontinuous and frequently interspersed with retroelements.

Creating gapless telomere-to-telomere assemblies of complex genomes is one of the ultimate challenges in genomics. We used long read technologies and an optical map based approach to produce a maize genome assembly composed of only 63 contigs. The B73-Ab10 genome includes gapless assemblies of chromosome 3 (236 Mb) and chromosome 9 (162 Mb), multiple highly repetitive centromeres and heterochromatic knobs, and 53 Mb of the Ab10 meiotic drive haplotype.Maize is a classic genetic model, known for its excellent chromosome cytology and rich history of transposon research 1 . Transposons make up the majority of the maize genome 2 , and their accumulation over millions of years has driven genes far apart from each other and separated genes from their regulatory sequences 3 . There are also large inversions and other structural variations that contribute to fitness 4,5 and significant variation in genome size caused by tandem repeat arrays 6 . Understanding this remarkable structural diversity is important for the continued improvement of maize, but the high repeat content has impeded progress 2,5 . Here we describe an automated assembly merging approach that yields gapless maize chromosomes and dramatically improves contiguity throughout the genome, including centromere and knob regions.The most challenging genomic regions to assemble are tandem repeat arrays that exceed the read length of the current sequencing technologies. In most eukaryotes, these arrays are enriched in centromeres and ribosomal DNA (rDNA). Maize contains a centromeric repeat of 156 bp 7 , an 45S rDNA repeat of 9349 bp, and a 5S rDNA repeat of 341 bp. In addition, maize contains two abundant classes of knob repeats that are found on chromosome arms, the major knob180 repeat (180 bp) 8 and the minor TR-1 repeat (360 bp) 9 . Knob repeats occur in arrays that extend into the tens of megabases and present a significant barrier to full genome assembly. In most maize lines, knobs appear as inert heterochromatic bulges 8 , but in lines with a meiotic drive system on Abnormal chromosome 10 (Ab10) they have centromere-like properties and are preferentially segregated to progeny 10 . Ab10 is considerably longer than chromosome 10 and contains two inversions 11 , three knobs, and long spans of uncharacterized DNA that include a cluster of Kinesin driver (Kindr) genes required for meiotic drive 9 . Meiotic drive systems have been documented in many organisms and often lie within large inversions that contain novel repeat arrays 12 , yet no meiotic drive haplotype has been fully sequenced and assembled.

In most eukaryotes, cytoplasmic dynein serves as the primary cytoskeletal motor for minus-end-directed processes along microtubules. However, land plants lack dynein, having instead a large number of kinesin-14s, which suggests that kinesin-14s may have evolved to fill the cellular niche left by dynein. In addition, land plants do not have centrosomes, but contain specialized microtubule-based structures called phragmoplasts that facilitate the formation of new cell walls following cell division. This Review aims to compile the evidence for functional diversification of kinesin-14s in land plants. Known functions include spindle morphogenesis, microtubule-based trafficking, nuclear migration, chloroplast distribution, and phragmoplast expansion. Plant kinesin-14s have also evolved direct roles in chromosome segregation in maize and novel biochemical features such as actin transport and processive motility in the homodimeric state.

A maize chromosome variant called abnormal chromosome 10 (Ab10) converts knobs on chromosome arms into neocentromeres, causing their preferential segregation to egg cells in a process known as meiotic drive. We previously demonstrated that the gene Kinesin driver (Kindr) on Ab10 encodes a kinesin-14 required to mobilize neocentromeres made up of the major tandem repeat knob180. Here we describe a second kinesin-14 gene, TR-1 kinesin (Trkin), that is required to mobilize neocentromeres made up of the minor tandem repeat TR-1. Trkin lies in a 4-Mb region of Ab10 that is not syntenic with any other region of the maize genome and shows extraordinary sequence divergence from Kindr and other kinesins in plants. Despite its unusual structure, Trkin encodes a functional minus end-directed kinesin that specifically colocalizes with TR-1 in meiosis, forming long drawn out neocentromeres. TRKIN contains a nuclear localization signal and localizes to knobs earlier in prophase than KINDR. The fact that TR-1 repeats often co-occur with knob180 repeats suggests that the current role of the TRKIN/TR-1 system is to facilitate the meiotic drive of the KINDR/knob180 system.

Demethylation of transposons can activate the expression of nearby genes and cause imprinted gene expression in the endosperm; this demethylation is hypothesized to lead to expression of transposon small interfering RNAs (siRNAs) that reinforce silencing in the next generation through transfer either into egg or embryo. Here we describe maize (Zea mays) maternal derepression of r1 (mdr1), which encodes a DNA glycosylase with homology to Arabidopsis thaliana DEMETER and which is partially responsible for demethylation of thousands of regions in endosperm. Instead of promoting siRNA expression in endosperm, MDR1 activity inhibits it. Methylation of most repetitive DNA elements in endosperm is not significantly affected by MDR1, with an exception of Helitrons. While maternally-expressed imprinted genes preferentially overlap with MDR1 demethylated regions, the majority of genes that overlap demethylated regions are not imprinted. Double mutant megagametophytes lacking both MDR1 and its close homolog DNG102 result in early seed failure, and double mutant microgametophytes fail pre-fertilization. These data establish DNA demethylation by glycosylases as essential in maize endosperm and pollen and suggest that neither transposon repression nor genomic imprinting are its main function in endosperm.

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Centromeres are long, often repetitive regions of genomes that bind kinetochore proteins and ensure normal chromosome segregation. Engineering centromeres that function in vivo has proven to be difficult. Here we describe a LexA-CENH3 tethering approach that activates functional centromeres at maize synthetic repeat arrays containing LexO binding sites. The synthetic centromeres are sufficient to cause chromosome breakage and release of chromosome fragments that are passed through meiosis and into progeny. Several independent chromosomes were identified, each with newly created centromeres localized over the repeat arrays where they were directed. The new centromeres were self-sustaining and stably transmitted chromosomes to progeny in the absence of the LexA-CENH3 activator. Our results demonstrate the feasibility of using synthetic centromeres for karyotype engineering applications.