De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes
| Autor: | Qiuhan Jiang, David E. Hufnagel, Rebecca D. Piri, Jianming Yu, John L. Portwood, Carson M. Andorf, Shujun Ou, Matthew B. Hufford, Doreen Ware, Margaret R. Woodhouse, Xianran Li, Jonathan I. Gent, William A. Ricci, Erin Baggs, Dong Won Kim, Na Wang, Samantha J. Snodgrass, Silas Tittes, Tingting Guo, Sharon Wei, Andrew Olson, Ethalinda K. S. Cannon, Amanda M. Gilbert, Kevin Fengler, Michael Syring, Arun S. Seetharam, Rafael Della Coletta, Zhenyuan Lu, David Kudrna, Victor Llaca, R. Kelly Dawe, Ksenia V. Krasileva, Jeffrey Ross-Ibarra, Robert J. Schmitz, Nancy Manchanda, Yinjie Qiu, Alexandre P. Marand, Bo Wang, Sarah Pedersen, Kapeel Chougule, Marcela K. Tello-Ruiz, Christine H. O’Connor, Yibing Zeng, Candice N. Hirsch, Asher I. Hudson, Jianing Liu |
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| Rok vydání: | 2021 |
| Předmět: |
2. Zero hunger
0106 biological sciences 0303 health sciences education.field_of_study Population Sequence assembly Computational biology Quantitative trait locus Biology 01 natural sciences Genome Structural variation 03 medical and health sciences DNA methylation Nested association mapping education Gene 030304 developmental biology 010606 plant biology & botany |
| DOI: | 10.1101/2021.01.14.426684 |
| Popis: | 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 data indicate that the number of pan-genes 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 reveal 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 overlap QTL and contribute to changes in gene expression.One sentence summaryA multi-genome analysis of maize reveals previously unknown variation in gene content, genome structure, and methylation. |
| Databáze: | OpenAIRE |
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