气候变化领域集成服务门户(CCPortal): De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes

CCPortal

DOI	10.1126/science.abg5289
	De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes
	Hufford M.B.; Seetharam A.S.; Woodhouse M.R.; Chougule K.M.; Ou S.; Liu J.; Ricci W.A.; Guo T.; Olson A.; Qiu Y.; Coletta R.D.; Tittes S.; Hudson A.I.; Marand A.P.; Wei S.; Lu Z.; Wang B.; Tello-Ruiz M.K.; Piri R.D.; Wang N.; Kim D.W.; Zeng Y.; O'Connor C.H.; Li X.; Gilbert A.M.; Baggs E.; Krasileva K.V.; Portwood J.L.; Cannon E.K.S.; Andorf C.M.; Manchanda N.; Snodgrass S.J.; Hufnagel D.E.; Jiang Q.; Pedersen S.; Syring M.L.; Kudrna D.A.; Llaca V.; Fengler K.; Schmitz R.J.; Ross-Ibarra J.; Yu J.; Gent J.I.; Hirsch C.N.; Ware D.; Dawe R.K.
发表日期	2021
ISSN	0036-8075
起始页码	655
结束页码	662
卷号	373 期号:6555
英文摘要	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. © 2021 American Association for the Advancement of Science. All rights reserved.
英文关键词	DNA; genome; isotopic fractionation; maize; mapping; methylation; transcriptome; centromere; chromosomal mapping; disease resistance; DNA methylation; DNA sequence; genetic variation; genetics; genotype; high throughput sequencing; maize; molecular genetics; multifactorial inheritance; phenotype; plant chromosome; plant disease; plant gene; plant genome; regulatory sequence; single nucleotide polymorphism; tetraploidy; whole genome sequencing; Centromere; Chromosome Mapping; Chromosomes, Plant; Disease Resistance; DNA Methylation; Genes, Plant; Genetic Variation; Genome, Plant; Genotype; High-Throughput Nucleotide Sequencing; Molecular Sequence Annotation; Multifactorial Inheritance; Phenotype; Plant Diseases; Polymorphism, Single Nucleotide; Regulatory Sequences, Nucleic Acid; Sequence Analysis, DNA; Tetraploidy; Transcriptome; Whole Genome Sequencing; Zea mays
语种	英语
来源期刊	Science
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/244097
作者单位	Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, United States; Genome Informatics Facility, Iowa State University, Ames, IA 50011, United States; USDA-ARS, Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011, United States; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, United States; Department of Genetics, University of Georgia, Athens, GA 30602, United States; Department of Plant Biology, University of Georgia, Athens, GA 30602, United States; Department of Agronomy, Iowa State University, Ames, IA 50011, United States; Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, United States; Center for Population Biology, University of California, Davis, CA 95616, United States; Department of Evolution and Ecology, University of California, Davis, CA 95616, United States; Institute of Bioinformatics, University of Georgia, Athens, GA 30602, United States; Department of...
推荐引用方式 GB/T 7714	Hufford M.B.,Seetharam A.S.,Woodhouse M.R.,et al. De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes[J],2021,373(6555).
APA	Hufford M.B..,Seetharam A.S..,Woodhouse M.R..,Chougule K.M..,Ou S..,...&Dawe R.K..(2021).De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes.Science,373(6555).
MLA	Hufford M.B.,et al."De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes".Science 373.6555(2021).