title: Unbiased K-mer Analysis Reveals Changes in Copy Number of Highly Repetitive Sequences During Maize Domestication and Improvement.
abstract: The major component of complex genomes is repetitive elements, which remain recalcitrant to characterization. Using maize as a model system, we analyzed whole genome shotgun (WGS) sequences for the two maize inbred lines B73 and Mo17 using k-mer analysis to quantify the differences between the two genomes. Significant differences were identified in highly repetitive sequences, including centromere, 45S ribosomal DNA (rDNA), knob, and telomere repeats. Genotype specific 45S rDNA sequences were discovered. The B73 and Mo17 polymorphic k-mers were used to examine allele-specific expression of 45S rDNA in the hybrids. Although Mo17 contains higher copy number than B73, equivalent levels of overall 45S rDNA expression indicates that transcriptional or post-transcriptional regulation mechanisms operate for the 45S rDNA in the hybrids. Using WGS sequences of B73xMo17 doubled haploids, genomic locations showing differential repetitive contents were genetically mapped, which displayed different organization of highly repetitive sequences in the two genomes. In an analysis of WGS sequences of HapMap2 lines, including maize wild progenitor, landraces, and improved lines, decreases and increases in abundance of additional sets of k-mers associated with centromere, 45S rDNA, knob, and retrotransposons were found among groups, revealing global evolutionary trends of genomic repeats during maize domestication and improvement.
authors.affiliation: Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
authors.forename: Sanzhen
authors.initials: S
authors.lastname: Liu
authors.affiliation: Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China.
authors.forename: Jun
authors.initials: J
authors.lastname: Zheng
authors.affiliation: Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
authors.forename: Pierre
authors.initials: P
authors.lastname: Migeon
authors.affiliation: Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
authors.forename: Jie
authors.initials: J
authors.lastname: Ren
authors.affiliation: Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
authors.forename: Ying
authors.initials: Y
authors.lastname: Hu
authors.affiliation: Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China.
authors.forename: Cheng
authors.initials: C
authors.lastname: He
authors.affiliation: State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Taian 271018, P.R. China.|College of Life Sciences, Shandong Agricultural University, Taian 271018, P.R. China.
authors.forename: Hongjun
authors.initials: H
authors.lastname: Liu
authors.affiliation: Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China.
authors.forename: Junjie
authors.initials: J
authors.lastname: Fu
authors.affiliation: Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA.
authors.forename: Frank F
authors.initials: FF
authors.lastname: White
authors.affiliation: Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
authors.forename: Christopher
authors.initials: C
authors.lastname: Toomajian
authors.affiliation: Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China.
authors.forename: Guoying
authors.initials: G
authors.lastname: Wang
mesh_terms: D000483:Alleles; D002874:Chromosome Mapping; D000071278:Domestication; D019143:Evolution, Molecular; D018628:Gene Dosage; D018745:Genome, Plant; D023281:Genomics / Q000379:methods; D007178:Inbreeding; D040641:Quantitative Trait Loci; D012335:RNA, Ribosomal / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid; D003313:Zea mays / Q000235:genetics*
chemical_list: D012335:RNA, Ribosomal