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.
Highlights
Cytogenetics, genetics, and a few genomics studies have documented variation for many high repetitive sequences among maize lines, which may contribute to maize evolution and domestication[2,18,19,20]
The slightly larger estimated genome size of Mo17 versus B73 but the smaller proportion of single-copy sequences in Mo17 implies that repetitive sequences make distinct contributions to the two genomes, which can be observed on the curves of cumulative k-mer contribution to the genome at high abundance k-mers that represent highly repetitive sequences (Fig. 1b)
Reference-independent quantification of next-generation sequencing (NGS) data allows precise and unbiased comparison of the genomic constitutions, highly repetitive sequences that are generally overlooked from regular analyses
Summary
Cytogenetics, genetics, and a few genomics studies have documented variation for many high repetitive sequences among maize lines, which may contribute to maize evolution and domestication[2,18,19,20]. Highly repetitive sequences are comprised of several major classes, including ribosome DNA (rDNA), knob repeats, centromere satellite C DNAs (CentC), telomere repeats, and various retrotransposon families. Whole genome data of diverse maize lines and wild relatives indicate that genome size variation correlates with knob content[14]. Maize sub-telomeres consist of highly repetitive tandem sequences[32]. Highly repetitive sequences are largely organized into clusters in maize genomes and variation in copy number is frequently observed. Genomic locations influencing variation in copy number at highly repetitive sequences were genetically mapped using WGS sequencing data of 280 intermated B73 and Mo17 doubled haploids[10]. Highly variable k-mers in diverse lines using Zea mays HapMap[2] WGS data[14,15] were identified, revealing significant changes in highly repetitive sequences during maize domestication and improvement
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
