The maize W22 inbred has served as a platform for maize genetics since the mid twentieth century. To streamline maize genome analyses, we have sequenced and de novo assembled a W22 reference genome using short-read sequencing technologies. We show that significant structural heterogeneity exists in comparison to the B73 reference genome at multiple scales, from transposon composition and copy number variation to single-nucleotide polymorphisms. The generation of this reference genome enables accurate placement of thousands of Mutator (Mu) and Dissociation (Ds) transposable element insertions for reverse and forward genetics studies. Annotation of the genome has been achieved using RNA-seq analysis, differential nuclease sensitivity profiling and bisulfite sequencing to map open reading frames, open chromatin sites and DNA methylation profiles, respectively. Collectively, the resources developed here integrate W22 as a community reference genome for functional genomics and provide a foundation for the maize pan-genome.

Endosperm and embryo development are coordinated via epigenetic regulation and signaling between these tissues. In maize (Zea mays), the endosperm-embryo signals are not known, but endosperm cellularization is a key event for embryos to form shoots and roots. We screened seed mutants for nonautonomous functions in endosperm and embryo development with genetically nonconcordant seeds and identified the recessive mutant rough endosperm3 (rgh3). The wild-type Rgh3 allele is required in the endosperm for embryos to develop and has an autonomous role in embryo and seedling development. Endosperm cell differentiation is defective in rgh3. Results from endosperm cell culture indicate that rgh3 mutants remain in a proliferative state through mid-seed development. Rgh3 encodes the maize U2AF 35 Related Protein (URP), an RNA splicing factor involved in both U2 and U12 splicing. The Rgh3 allele produces at least 19 alternative splice variants with only one isoform encoding a full-length ortholog to URP. The full-length RGH3a isoform localizes to the nucleolus and displays a speckled pattern within the nucleoplasm, and RGH3a colocalizes with U2AF 65 . A survey of alternatively spliced transcripts found that, in the rgh3 mutant, a fraction of noncanonical splicing events are altered. Our findings suggest that differentiation of maize endosperm cell types is necessary for embryos to develop. The molecular cloning of Rgh3 suggests that alternative RNA splicing is needed for cell differentiation, development, and plant viability.

SignificanceThe last eukaryotic common ancestor had two spliceosomes. The major spliceosome acts on nearly all introns, whereas the minor spliceosome removes rare, U12-type introns. Based on in vitro RNA-splicing assays, the RGH3/ZRSR2 RNA-splicing factor has functions in both spliceosomes. Here, we show that the maize rgh3 mutant allele primarily disrupts U12 splicing, similar to human ZRSR2 mutants, indicating a conserved in vivo function in the minor spliceosome. These mutant alleles block cell differentiation leading to overaccumulation of stem cells in endosperm and blood, respectively. We found extensive conservation between maize and human U12-type intron-containing genes, demonstrating that a common genetic architecture controls at least a subset of cell differentiation pathways in both plants and animals.

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Core Ideas Maize genes with protein evidence have higher expression and GC content Tripsacum homologs of maize genes exhibit the same trends as in maize Maize proteome genes have more highly correlated gene expression with Tripsacum Expression dominance for homeologs occurs similarly between maize and Tripsacum homologs A similar set of genes may be decaying into pseudogenes in maize and Tripsacum Plant genomes reduce in size following a whole‐genome duplication event, and one gene in a duplicate gene pair can lose function in absence of selective pressure to maintain duplicate gene copies. Maize (Zea mays L.) and its sister genus, Tripsacum, share a genome duplication event that occurred 5 to 26 million years ago. Because few genomic resources for Tripsacum exist, it is unknown whether Tripsacum grasses and maize have maintained a similar set of genes that have resisted decay into pseudogenes. Here we present high‐quality de novo transcriptome assemblies for two species: Tripsacum dactyloides (L.) L. and T. floridanum Porter ex Vasey. Genes with experimental protein evidence in maize were good candidates for genes resistant to pseudogenization in both genera because pseudogenes by definition do not produce protein. We tested whether 15,160 maize genes with protein evidence are resisting gene loss and whether their Tripsacum homologs are also resisting gene loss. Protein‐encoding maize transcripts and their Tripsacum homologs have higher guanine–cytosine (GC) content, higher gene expression levels, and more conserved expression levels than putatively untranslated maize transcripts and their Tripsacum homologs. These results suggest that similar genes may be decaying into pseudogenes in both genera after a shared ancient polyploidy event. The Tripsacum transcriptome assemblies provide a high‐quality genomic resource that can provide insight into the evolution of maize, a highly valuable crop worldwide.