PMC

(A) Number of distinct DNA transposon-related small RNAs under different genetic backgrounds. (B) The total number of DNA transposon-related small RNAs under different genetic backgrounds. (C) Small RNAs discrepancies between B73 and K55-wt backgrounds.

Protein coding length ratio (length of maize/length of sorghum or rice) between highest scoring homologs is used as a measure of truncation. Non-syntenic loci contrast with syntenic loci in showing a bimodal distribution.

The distribution was constructed based on nucleotide length of the related TE in 100-kb sliding windows. The numbers at the left vertical axis represent the nucleotide length of related TE classifications. The numbers in the right axis are the gene number counts.

(A) Ks. (B) Ka. Genes were categorized by CDS length ratio using a threshold of 0.8 (maize CDS length / sorghum CDS length). Sample sizes: nSYN(<0.8) n = 68; nSYN(≥0.8) n = 32; SYN(<0.8) n = 54; SYN(≥0.8) n = 340.

Abbreviations: Osj2 = rice (japonica) chromosome 2; Sb4 = sorghum chromosome 4; Zm4 = maize chromosome 4 (AR182); Zm5 = maize chromosome 5 (homeologous region). All mappings are drawn relative to rice as a common reference. Genes are shown as tick marks in the outer radius of correspondence lines. Inversions are indicated with yellow highlighting. For Zm4 the density of repetitive sequence is shown in gray. Zm5 mappings are to individual BACs (boxes) projected onto the FPC map. (A) Mappings of protein-coding genes based on reciprocal best hit. (B) Mappings of miRNA genes based on family membership.

Genetic (center), Optical (left), and physical and synteny maps (right) of AR182 are shown. (A) Magnified view of the AR182 pseudomolecule in silico restriction map (blue track) and Optical Map (gold track) alignment after finishing (each box = 1 restriction fragment); turquoise box demarcates zoomed region on (B) showing the entire alignment ∼22 Mb (∼1,000 ordered restriction fragments); (C) A simplified maize Chr4 genetic map; (D) The maize Chr4 physical map; (E) Overall syntenic relationships among maize, sorghum and rice with respect to AR182. This three-way synteny map was built by SyMap from pseudomolecule to pseudomolecule comparisons.