期刊
NATURE GENETICS
卷 50, 期 9, 页码 1282-+出版社
NATURE PUBLISHING GROUP
DOI: 10.1038/s41588-018-0158-0
关键词
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资金
- National Science Foundation [NSF-MCB 0920218, NSF-MCB 1025976, NSF-IOS 1031416, NSF-IOS 1237931, NSF-IOS 1116561, NSF-IOS 1238014, NSF-IOS 1314143, NSF IOS-1339237, IOS-1139329, NSF MCB-1412218, NSF IOS-1444514, NSF-IOS 1521100, NSF-IOS 1547787]
- NSF
- University of Florida
- NSF [DGE-0802270]
- United States Department of Agriculture (USDA)
- USDA-ARS [6036-21000-011-00D]
- USDA-NIFA [2016-67013-24747, 2011-67003-30215, 2011-67013-30082]
- USDA-ARS
- NSF-IOS Plant Genome [1238014]
- Enterprise Rent-A-Car Institute for Renewable Fuels at the Donald Danforth Plant Science Center
- Vasil-Monsanto Endowment
- NIFA [2011-67013-30082, 810756, 2016-67013-24747, 2011-67003-30215, 687293, 579704] Funding Source: Federal RePORTER
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.
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