Fig. 5

A comparison of snailfish AFP genes with respect to repeats, sequence identities, and codon biases. A) Schematics of an AFP-containing gene locus from dusky snailfish (GenBank accession JBEEID010000351 bases 1861 to 88,664) with the entire region, including the flanking genes ETV6 and PARP12, shown on top. An expansion of the AFP-containing region is shown beneath this in two segments. AFP coding sequences are indicated with blue arrows, repetitive elements with bars, and simple repeats with narrow red bars. Bars of the same color indicate that the repetitive elements are homologous and unique elements are shown in alternating shades of light and dark grey. The matching regions of AFP3 and the inverted AFP4 are indicated by black lines beneath. Segments corresponding to fragments that match the PARP12 gene are colored dark red and labelled. B) Characteristics of the locus encoding Tanaka-1 (GenBank accession JAYMGU010000011.1, 3811k-3878k), showing flanking genes (light brown). The expansion of the AFP-containing region is colored as above, with inverted repeats indicated with arrows and the matching region of the AFP and pseudogene by black lines beneath. C) Detailed schematics of four genes encoding AFPs from above. Repetitive elements identified as transposable elements (TEs) by Dfam [50] are indicated with wider bars and colored by type, other repetitive sequences are indicated by narrower bars with color indicating similarity. Matching segments are indicated with gray shading, with percent identity indicated. D) Ala codon usage in the AFPs from Fig. 6, the Ala-rich segment within intron 3 of PARP12 and a D. rerio Copia transposon