Fig. 1: Gene consolidation and characteristics.
From: European maize genomes highlight intraspecies variation in repeat and gene content
a, Comparison of reciprocal best blast orthologs (bbh), genes with a TPM ≥0.1 (exp) and angiosperm proteins (hom) between the consolidated (B73c and PH207c) and initial B73 and PH207 gene models. b, The number of genes per line that are either singletons (label 1) or syntenic between two and six lines (labels 2–6). c, Expression levels (TPM) of EP1 and F7 genes graded by size of their orthologous clusters. Genes either are singletons (cluster size 1) or have orthologs in one to five maize lines (cluster sizes 2–6). Syntelogs of orthologous clusters comprising 2–4 lines show very low median expression levels (TPM ~0.06). d, Illustration per cluster size of the proportion of orthologous groups with support by bbh and homology (purple), only bbh (red), only homology (hom, blue) and residual clusters (res, tan) matching neither the homology nor the bbh criterion. To record homology, a minimum alignment length of 80% of both maize and angiosperm protein was required in at least three species. The high conservation observed in cluster size 1 reflects, in part, enrichment of tandemly repeated genes duplicated from orthologs of clusters present in five or six lines.
