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| Status |
Public on Feb 01, 2021 |
| Title |
De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes |
| Organism |
Zea mays |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 maize inbreds that serve as the founders for the maize nested association mapping population. The data indicate that the number of pan-genes in maize exceeds 103,000 and 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 further revealed the locations and internal structures of major cytological landmarks. We show that combining structural variation with SNPs can improve the power of quantitative mapping studies. Finally, we document variation at the level of DNA methylation, and demonstrate that unmethylated regions are enriched for cis-regulatory elements that correlate with known QTLs and changes in gene expression.
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| Overall design |
Genotype pooling of NAM founder leaf tissues across three biological replicates and two technical replicates of single-cell ATAC-seq libraries. Individual cells were genotyped and reads from cells from the same founder were aggregated.
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| Contributor(s) |
Marand A, Schmitz B |
| Citation missing |
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| Submission date |
Jan 29, 2021 |
| Last update date |
Apr 27, 2021 |
| Contact name |
Robert J Schmitz |
| E-mail(s) |
schmitz@uga.edu
|
| Organization name |
University of Georgia
|
| Department |
Genetics
|
| Street address |
B416 Davison Life Sciences
|
| City |
Athens |
| State/province |
GA |
| ZIP/Postal code |
30602 |
| Country |
USA |
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| Platforms (1) |
| GPL25410 |
Illumina NovaSeq 6000 (Zea mays) |
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| Samples (104)
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| Relations |
| BioProject |
PRJNA697943 |
| SRA |
SRP303852 |
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