Fig. 5

Evidence for gene conversion between putative paired receptor ceacam genes. (a) Alignment of exons 1 and 2 encoding the leader and N domain, respectively, and flanking introns of ceacam301 and ceacam303. Note the strong sequence conservation restricted to the N domain exon. The start codons are marked in green, the splice acceptor and splice donor sequences are highlighted in yellow and blue, respectively. (b) The nucleotide sequence of ITIM/ITSM-encoding ceacam301 gene was compared with that of ITAM-like motif-encoding ceacam303 from X. tropicalis. For contiguous stretches of nucleotides conserved between the gene pairs using a sliding window, the degree of identity was calculated and displayed as horizontal lines. The location of ceacam301 exons is indicated by numbered boxes. The genomic region involved in gene conversion is marked with a red box, the affected N exon is shown in red. Different repeat sequences are indicated by differently shaped forms. (c-f) The accumulation of nonsynonymous (green curves) and synonymous substitutions (red curves) along the N exons of putative paired receptor genes were determined after manual removal of gaps in the compared nucleotide sequences. The type of encoded signaling motif is indicated by the color of the gene name: red, ITIM/ITSM; green, ITAM; blue, ITAM-like motif. Stretches of codons with no or minimal accumulation of synonymous substitutions which run parallel to the x-axis suggest recent gene conversion/recombination events. Note the rapid accumulation of nonsynonymous mutations in the CC’C”FG β-strand regions (black broken lines) which indicates selection for diversification. This contrasts with conserved regions indicated by red broken lines. For comparison, N exon sequences of an orthologous gene pair (Xtr ceacam362/Xla ceacam380) were analyzed (g). The location of CC’C”and FG β-strand regions determined by 3D modeling (Additional file 4) are indicated by gray boxes above the graphs. N, N domain exon; TM, transmembrane domain exon; Xla, X. laevis; Xtr, X. tropicalis