Fig. 4

Phylogenetic tree of chemokines and expression levels of their gene copies. a A maximum likelihood phylogenetic tree of chemokine genes that at least one of their copies was a DEG in response to infection. The tree includes carp transcripts (cypCar ID), and their homologs from ZF (dr and gene name) and, as an outgroup, homologs from red-bellied piranha (pn and Ensembl ID). Bootstrap values (%) are given at branching points. Different clades of the tree are different chemokines, colored and named after ZF gene family. Note that ZF gene cxcl18a.2 does not cluster with other cxcl18 homologs and therefore, might be a wrong annotation. Asterisks adjacent to cypCar IDs mark significantly up-regulated genes in response to infection (in either fish type). b Level of gene expression for carp copies of ccl19 and cxcl8/il8 gene families. For each homolog of ZF, expression of carp copies are plotted (normalized read count means and standard error bars) for each of the combinations of fish type (R/S) and day (0/4). Carp genes not sharing the same capital letters on top have significantly different expression levels. Note, the evolutionary relationship among gene copies of carp, the expression levels of which shown in (b) are derived from (a)