Considerations regarding centromere assembly in plant whole-genome sequencing.

The assembly of centromeric regions has become one of the most intractable tasks in whole-genome sequencing due to the enrichment of highly repetitive DNA sequences in most eukaryotic centromeres. Here, we describe a method used to identify centromeric DNAs through chromatin immunoprecipitation and sequencing (ChIP-seq). By mapping ChIP-seq reads, centromeric regions can be indicated in genome assemblies. We demonstrated that the assembly quality of centromeres obtained using ChIP-seq mapping can reflect and indicate the quality of a whole-genome assembly. We discuss an expected 'high-quality' centromere assembly obtained via centromere ChIP-seq mapping.

Super-Resolution Microscopy Reveals Diversity of Plant Centromere Architecture.

Centromeres are essential for proper chromosome segregation to the daughter cells during mitosis and meiosis. Chromosomes of most eukaryotes studied so far have regional centromeres that form primary constrictions on metaphase chromosomes. These monocentric chromosomes vary from point centromeres to so-called "meta-polycentromeres", with multiple centromere domains in an extended primary constriction, as identified in Pisum and Lathyrus species. However, in various animal and plant lineages centromeres are distributed along almost the entire chromosome length. Therefore, they are called holocentromeres. In holocentric plants, centromere-specific proteins, at which spindle fibers usually attach, are arranged contiguously (line-like), in clusters along the chromosomes or in bands. Here, we summarize findings of ultrastructural investigations using immunolabeling with centromere-specific antibodies and super-resolution microscopy to demonstrate the structural diversity of plant centromeres. A classification of the different centromere types has been suggested based on the distribution of spindle attachment sites. Based on these findings we discuss the possible evolution and advantages of holocentricity, and potential strategies to segregate holocentric chromosomes correctly.