Genome wide identification of AHL family genes in Cardamina hirsuta plant

AT-hook motif nuclear localization (AHL) proteins play a critical role in plant biological processes, and it is highly conserved in terrestrial plants. In Arabidopsis thaliana this gene family data is available. We used this data to detect and interpret the AHL gene family in the Cardamine hirsuta. In Silico analysis was launched and initially 29 AHL genes were detected. Phylogenetic analysis afterward exhibits that AHL in C. hirsuta has been grouped into two clades, clade B with 3-5 introns, and clade A intron-free similar to A. thaliana. According to the combination of AT-hook motif(s) and PPC domain, AHL proteins are divided into three subclades (sub-clades-I/-II/-III). Subclades-I are related to Clade-A, while subclades-II and subclades-III are related to Clade-B. The motif analysis exhibits that the three genes including AHL1, AHL10, and AHL11, although had the AT-hook motifs, lacked the PCC domain, and therefore the actual number of AHL family genes decreased to 26. Looking at duplication events in the AHL gene family in C. hirsuta, 16 homologous genes were found due to segmental duplication, and no tandem sequences were observed in these genes. In-depth inspection showed that segment genomic duplication events could cause the expansion of these genes. Examining ratios of non-synonymous (Ka) and synonymous (Ks) substitution rates, i.e. Ka/Ks, in 5 pairs of homologous genes showed those with Ka/Ks < 1 were exposed to the adverse selection. These findings reveal a possible evolutionary relationship for the AHL gene family in C. hirsuta, providing helpful information for future analysis to investigate their biological functions.