Comparative genomic analysis revealed the ancient duplication of Factor D genes in horseshoe crabs

Abstract

Horseshoe crabs are famous for their blood lysate that is extensively used for the detection of bacterial endotoxin contamination in injectable drugs and medical equipment. However, their existence is now threatened because of overexploitation for bleeding. Synthetic antimicrobial peptides or proteins created by bioengineering may be effective in solving the present predicament. Factor D (FD) is a bioactive substance that shows significant sensitivity to gram-negative bacteria. However, little is known about the expansion information of FD orthologs. In the present study, a total of nine FD orthologs were detected in horseshoe crabs according to the reference genomes. The composition of the FD orthologs in different species was highly conserved, although the common ancestor of the extant horseshoe crabs dates back to the Silurian period. These data suggested that the composition of FD orthologs in horseshoe crabs was formed before the speciation of these species. Considering that three rounds of whole-genome duplication (WGD) events may expanded the homologs in horseshoe crabs, while only one pair of FD orthologs showed significant collinearity according to the intraspecies comparative analysis. Unexpectedly, tandem duplication events that occurred before speciation also expanded the FD orthologs. In addition, several separately distributed FD orthologs also showed high conservation with each other. These data revealed that transposon-mediated duplication may have expanded the FD orthologs in horseshoe crabs. Intriguingly, the C-terminus of the FD orthologs is extremely conserved, although the expansion occurred more than 400 million years ago. In summary, our research provides evidence for the [abstract limit 250 words]