The evolution of antimicrobial peptides in Chiroptera

Abstract

High viral tolerance coupled with an extraordinary regulation of the immune response makes bats a great model to study host-pathogen evolution. Although many immune-related gene gains and losses have been previously reported in bats, important gene families such as antimicrobial peptides (AMPs) remain understudied. We built an exhaustive bioinformatic pipeline targeting the major gene families of defensins and cathelicidins to explore AMP diversity and analyze their evolution and distribution across six bat families. A combination of manual and automated procedures identified 29 AMP families across queried species, with α-, β-defensins, and cathelicidins representing around 10% of AMP diversity. Gene duplications were inferred in both α-defensins, which were absent in five species, and three β-defensin gene subfamilies, but cathelicidins did not show significant shifts in gene family size and were absent in Anoura caudifer and the pteropodids. Based on lineage-specific gains and losses, we propose diet and diet-related microbiome evolution may determine the evolution of α- and β-defensins gene families and subfamilies. These results highlight the importance of building species-specific libraries for genome annotation in non-model organisms and shed light on possible drivers responsible for the rapid evolution of AMPs. By focusing on these understudied defenses, we provide a robust framework for explaining bat responses to pathogens.

Keywords: bioinformatics pipelines; defensins; gene annotation; innate immunity; non-model organisms; transposable elements.

Figure 1

Histogram (A) and stacked density (B) plots display predicted AMPs present in at least five Chiropteran species with counts greater than seven. The total counts of the targeted defensins and cathelicidins families can be seen in Table S4 . The x-axis in B is expressed as a logarithmic scale.

Figure 2

Distribution of putative defensin and cathelicidins subfamilies in Chiroptera. The size and color of the circles represent the number of genes per subfamily. The circles with a black stroke are subfamilies previously reported as absent in Chiroptera.

Figure 3

Boxplots depicting the distribution of gene lengths in different AMPs (A). Stacked barplot shows the number and types of TEs accumulated in the introns of AMPs (B), and linear regression showing the relationship between gene and TE lengths (C).

Figure 4

Gene family size changes in the evolutionary history of six Chiropteran families. The color-coded circles in nodes and branches of the ultrametric tree display the number of significant expansions and contractions of gene subfamilies. β-defensin expansions are shown as a total and detailed in Table S8 . The proportion of each subfamily per species is shown in a stacked bar plot.

Figure 5

Rooted reconciled amino acid gene trees and multiple sequence alignment of three HOGs: (A) α-defensin; (B) cathelicidin; (C) β-defensin DEFB30 subfamily. Outgroups are not shown. Amino acids are colored according to their side-chain chemistry. Significant duplication events inferred by OrthoFinder are colored red on the labels of terminal branches. The degree of conservation of the sequences is shown above each alignment as bar plots and identical positions are marked with an asterisk, highly similar with a colon, and with a moderate identity with a period. The conserved cysteine residues are enclosed in a rectangle.