ArticleScientific reports2017
Unbiased K-mer Analysis Reveals Changes in Copy Number of Highly Repetitive Sequences During Maize Domestication and Improvement.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Article
- An alignment-free strategy for circulating tumor DNA detection and tumor fraction estimation from whole-genome sequencing data.PLoS computational biology · 2026Article
- Understanding Callus Types in Maize by Genetic Mapping and Transcriptional Profiling.Plants (Basel, Switzerland) · 2025Article
- Empowering plant epigenetics to breed resilience of crops: From nucleolar dominance to transgenerational epigenetic inheritance.The plant genome · 2025Review
- K-mer-based Approaches to Bridging Pangenomics and Population Genetics.Molecular biology and evolution · 2025Review
- Review
- A survey of k-mer methods and applications in bioinformatics.Computational and structural biotechnology journal · 2024Review
- Early Detection of BothInternational journal of molecular sciences · 2024Article
- SPRISS: approximating frequent k-mers by sampling reads, and applications.Bioinformatics (Oxford, England) · 2022Article
- Repetitive Sequence Barcode Probe for Karyotype Analysis inInternational journal of molecular sciences · 2022Article
- Chromosome-level genome assembly of a regenerable maize inbred line A188.Genome biology · 2021Article
- Factorial estimating assembly base errors usingNAR genomics and bioinformatics · 2020Article
- On the Close Relatedness of Two Rice-Parasitic Root-Knot Nematode Species and the Recent Expansion ofGenes · 2019Article
- Analysis of Extreme Phenotype Bulk Copy Number Variation (XP-CNV) Identified the Association ofFrontiers in plant science · 2018Article
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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