De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes

Science. 2021 Aug 6;373(6555):655-662. doi: 10.1126/science.abg5289.


We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 inbreds that serve as the founders for the maize nested association mapping population. The number of pan-genes in these diverse genomes exceeds 103,000, with approximately a third found across all genotypes. The results demonstrate that the ancient tetraploid character of maize continues to degrade by fractionation to the present day. Excellent contiguity over repeat arrays and complete annotation of centromeres revealed additional variation in major cytological landmarks. We show that combining structural variation with single-nucleotide polymorphisms can improve the power of quantitative mapping studies. We also document variation at the level of DNA methylation and demonstrate that unmethylated regions are enriched for cis-regulatory elements that contribute to phenotypic variation.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Centromere / genetics
  • Chromosome Mapping
  • Chromosomes, Plant
  • DNA Methylation
  • Disease Resistance / genetics
  • Genes, Plant
  • Genetic Variation
  • Genome, Plant*
  • Genotype
  • High-Throughput Nucleotide Sequencing
  • Molecular Sequence Annotation*
  • Multifactorial Inheritance / genetics
  • Phenotype
  • Plant Diseases
  • Polymorphism, Single Nucleotide
  • Regulatory Sequences, Nucleic Acid
  • Sequence Analysis, DNA
  • Tetraploidy
  • Transcriptome
  • Whole Genome Sequencing
  • Zea mays / genetics*