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Discrimintion and Mapping of the Primary and Processed Transcripts in Maize Mitochondrion Using a Circular RT-PCR-based Strategy
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Large haplotypes highlight a complex age structure within the maize pan-genome.

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Maize genomes reveal ancient diversity in low-recombination regions. Stable centromere haplotypes (cenhaps) and other long DNA segments show deep evolutionary history, dating back hundreds of thousands of years.

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Area of Science:

  • Plant Genomics
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Eukaryotic genomes, including maize, possess stable haplotypes in low-recombination areas like centromeres and heterochromatic blocks.
  • Analyzing diversity and origins in these complex genomic regions has been historically challenging.
  • Recent advancements in genome assembly provide new opportunities for comparative genomics in non-genic regions.

Purpose of the Study:

  • To develop and apply methods for aligning intergenic sequences in low-recombination regions of the maize genome.
  • To investigate the evolutionary history and diversity of centromere haplotypes (cenhaps) and other stable genomic segments.
  • To understand the impact of gene flow and population size changes on maize genome evolution.

Main Methods:

  • Utilized 26 complete maize genome assemblies for comparative analysis.
  • Developed novel alignment methods to specifically analyze intergenic sequences, excluding genes and regulatory elements.
  • Applied these methods to centromeres, heterochromatic knobs, rDNA arrays, and all intergenic spaces.

Main Results:

  • Identified centromere haplotypes (cenhaps) extending megabases, exhibiting evolutionary strata with divergence times up to 450,000 years ago (kya).
  • Demonstrated ubiquitous deep coalescence times across the maize pan-genome in low-recombination regions.
  • Revealed divergence estimates peaking at approximately 16,000 and 300,000 years ago, indicating complex population dynamics and domestication history.

Conclusions:

  • Centromere haplotypes and other long haplotypes in maize are reservoirs of ancient genetic diversity.
  • These regions provide critical insights into the complex evolutionary history of maize populations, including past gene flow and demographic shifts.
  • The developed methods enable deeper exploration of previously intractable genomic regions.