The genomic basis of herbivory in beetles: Gene duplications and pseudogenes related to host specialization

Gene duplication plays a critical role in genome evolution by increasing the number of gene copies, increasing the frequency of mutations affecting protein function, and facilitating subfunctionalization and neofunctionalization. An increased mutation rate in genes affecting protein function may facilitate adaptation to challenging environments. Recent studies have shown that Phytophaga acquired plant cell wall degrading enzymes (PCWDEs) via horizontal gene transfer (HGT) from various microbial donors. Post-HGT, many PCWDE-encoding genes underwent duplication events, resulting in increased gene expression levels and expanded substrate specificity. Closely related species of Phytophaga typically encode the same gene families despite differing host preferences; however, these genes frequently display copy number variations (CNVs). Recently, we discovered that some beetles possess a large number of non-processed pseudogenes in gene families putatively encoding PCWDEs. We also found that some beetles, particularly those with broad host ranges, have significantly more CNVs among genes encoding putative PCWDEs than their near relatives. This raises the question of whether host preferences might drive pseudogenization and CNV. To investigate this observation further, we manually annotated genes encoding putative PCWDEs in phytophagous beetle genomes and inferred gene trees. We also compared chromosome-scale genome and long-read sequences to analyze patterns of conserved synteny among Phytophaga. These comparative genomic analyses revealed a role for host preferences in pseudogene proliferation and gene expansions supporting new metabolic functions. Our results help illuminate the role of gene duplications and CNVs in the evolution of host specialization in Phytophaga, suggesting the ongoing potential for co-evolution between phytophagous beetles and plants.