Genome sequencing provides insights into the evolution of gene families encoding plant cell wall‐degrading enzymes in longhorned beetles

Abstract

With more than 36,000 species, the longhorned beetles (family Cerambycidae) are a mega‐diverse lineage of mostly xylophagous insects, all of which are represented by the sole sequenced genome of the Asian longhorned beetle (Anoplophora glabripennis; Lamiinae). Their successful radiation has been linked to their ability to degrade plant cell wall components using a range of so‐called plant cell wall‐degrading enzymes (PCWDEs). Our previous analysis of larval gut transcriptomes demonstrated that cerambycid beetles horizontally acquired genes encoding PCWDEs from various microbial donors; these genes evolved through multiple duplication events to form gene families. To gain further insights into the evolution of these gene families during the Cerambycidae radiation, we assembled draft genomes for four beetle species belonging to three subfamilies using long‐read nanopore sequencing. All the PCWDE‐encoding genes we annotated from the corresponding larval gut transcriptomes were present in these draft genomes. We confirmed that the newly discovered horizontally acquired glycoside hydrolase family 7 (GH7), subfamily 26 of GH43 (GH43_26), and GH53 (all of which are absent from the A. glabripennis genome) were indeed encoded by these beetles' genome. Most of the PCWDE‐encoding genes of bacterial origin gained introns after their transfer into the beetle genome. Altogether, we show that draft genome assemblies generated from nanopore long‐reads offer meaningful information to the study of the evolution of gene families in insects. We anticipate that our data will support studies aiming to better understand the biology of the Cerambycidae and other beetles in general.

First evidence of a horizontally‐acquired GH‐7 cellobiohydrolase from a longhorned beetle genome

“…Surveying the larval gut transcriptome of the Lamiinae E. adspersus (Shin et al, 2021), we initially identified a transcript with a 1347 bp-long ORF encoding a protein of 448 amino acids sharing up to 69% sequence identity with fungal glycoside hydrolase family 7 (GH7) proteins. We found the corresponding gene located on a 130-kb contig (Genbank accession: JANEYG010000319.1) of a draft genome of the same species (Shin et al, 2023). The only other gene present on this contig encoded another GH7 protein, and both genes were surrounded by insectlike transposable elements.…”

“…The GH7-encoding gene sequence was obtained from two sources: a larval midgut transcriptome of E. adspersus (Shin et al, 2021), and the draft genome of the same species (Shin et al, 2023). The sequences were manually curated and submitted to NCBI (accessions: OQ721898 and OQ721899).…”

“…Secondly, bacterial counterparts of one of the most widely distributed CAZyme families in Phytophaga beetles, GH48, have been characterized as cellobiohydrolases (McKenna et al, 2019;Pauchet et al, 2010;Shin et al, 2021;Sukharnikov et al, 2012). Intriguingly, the genome of E. adspersus lacks genes encoding putative GH48 family members, while other Cerambycidae species have them (McKenna et al, 2019;Shin et al, 2023;Shin et al, 2021). However, the sole functionally characterized GH48 family member of the leaf beetle Gastrophysa atrocyanea seems to be active on chitin (Fujita et al, 2006), which is puzzling since genes encoding the classical chitinase family GH18 are widely distributed in insects in general (Chen et al, 2020).…”

“…Our recent analyses of transcriptomes and genomes of more than two dozen species of Cerambycidae identified the first example in an insect of genes encoding proteins of family 7 of GHs (GH7) in the Lamiinae Exocentrus adspersus (Shin et al, 2023;Shin et al, 2021). GH7 enzymes are involved in the breakdown of complex carbohydrates, specifically cellulose and hemicellulose (Gilkes et al, 1991;Henrissat et al, 1989).…”

Horizontally transferred glycoside hydrolase 26 may aid hemipteran insects in plant tissue digestion

“…There have been many instances of glycoside hydrolase genes being incorporated into the genomes of insects, fungi, and plants via HGT (Acuña et al, 2012; Da Lage et al, 2013; Kfoury et al, 2024; Kirsch et al, 2014; Pauchet and Heckel, 2013; Shelomi et al, 2014; Shen et al, 2003; Shin et al, 2023; Wheeler et al, 2013; Wybouw et al, 2016). In this study, we characterize an HGT event of a gene encoding for a glycoside hydrolase family 26 (GH26) protein, which are enzymes that break down carbohydrates present in plant cell walls, specifically mannans and galactomannans (Braithwaite et al, 1995; Gao et al, 2023; Patel et al, 2016; Zhang et al, 2014).…”