Figure 2.

Extensive recent recombination within the SAR11 Subclade Ic and comparison with E. coli–E. fergusonii genomes. (A) Pairwise RBM genes were identified for 10 SAR11 Subclade Ic SAGs against the same reference, SAG AM-660-D08; (B) similarly, for 10 E. coli–E. coli (top 6 rows) and E. coli–E. fergusonii (bottom 4 rows) genomes (reference genome is E. coli ASM1374039 from [38]). Each query genome is represented in a different row, and the query genomes are sorted based on decreasing ANI relatedness to the reference (rightmost values). Each rectangular marker represents a gene, colored differently for highly conserved/universal, core, and accessory genes (see figure key). The marker represents the nucleotide sequence identity between the reference and the query genome when the gene is RBM-conserved between the two genomes (y-axis) plotted against the position of the gene in the reference genome (x-axis). Blue arrows highlight genes that have most likely undergone recent recombination between the reference and the corresponding query genomes as reflected by their high nucleotide identity (>99.8%) compared to the ANI value of the genomes and/or the (lower) identity of the same genes between the reference and another query genome(s), i.e. more related to the reference based on ANI. The green arrows denote a genomic island specific to the reference genome, i.e. not shared by most query genomes and was likely brought into the reference genome by a non-homologous recombination mechanism. The red boxes highlight the highly conserved narG and related genes discussed in the text; first box from the left contained narG OP-3 type, second box (middle) the narG gamma type. See also Supplementary Tables S4 and S5 for details on the genes contained within the boxes.