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Maize Centromere Structure and Evolution: Sequence Analysis of Centromeres 2 and 5 Reveals Dynamic Loci Shaped Primarily by Retrotransposons

Figure 2

Fine-scale physical maps of centromere 2.

(A,B) Chromosomal views. (A) Moving average of 9 windows of the number of sequence reads mapped per 100 kb window using MUMmer (red line) or BLAST (purple line) [2]. Colored boxes denote single CRM elements whose insertion was dated using the method of San Miguel et al. [1]. Only elements that have inserted outside of the functional centromere are shown. Filled squares = full-length elements, empty squares = fragmented elements. κ = estimated number of nucleotide substitutions per site. (B) centromeric repeats CRM1, CRM2, CRM3, CRM4 and CentC mapped onto the reference chromosomes using competitive BLAST and graphed as number of nucleotides per 100 kb window. (C–E) Close-up of centromere region. The functional centromere plus approximately 2.3 Mb of pericentromeric region are shown. (C) CENH3 data same as (A). Retroelements include CRMs not pictured in (A) and non-CRM elements (triangles - details in Table S6); filled symbols = full-length elements, empty symbols = fragmented elements. Only two bak1 elements have κ>0.1 and are located at 91,278,432 (κ = 0.24) and 92,902,773 (κ = 0.16) and for space reasons are drawn at κ = 0.1. (D) Genetic and molecular markers used to anchor this region to chromosome 2 – see Table S7 for details. Large vertical bar denotes contig gap in reference chromosome. (E) Centromeric repeats as in (B).

Figure 2

doi: https://doi.org/10.1371/journal.pgen.1000743.g002