Transcriptome and microbiome of coconut rhinoceros beetle (Oryctes rhinoceros) larvae

Abstract

Background: The coconut rhinoceros beetle, Oryctes rhinoceros, is a major pest of palm crops in tropical Asia and the Pacific Islands. Little molecular data exists for this pest, impeding our ability to develop effective countermeasures and deal with the species' growing resistance to viral biocontrols. We present the first molecular biology analyses of this species, including a metagenomic assay to understand the microbiome of different sections of its digestive tract, and a transcriptomics assay to complement the microbiome data and to shed light on genes of interest like plant cell wall degrading enzymes and immunity and xenobiotic resistance genes.

Results: The gut microbiota of Oryctes rhinoceros larvae is quite similar to that of the termite gut, as both species feed on decaying wood. We found the first evidence for endogenous beta-1,4-endoglucanase in the beetle, plus evidence for microbial cellobiase, suggesting the beetle can degrade cellulose together with its gut microfauna. A number of antimicrobial peptides are expressed, particularly by the fat body but also by the midgut and hindgut.

Conclusions: This transcriptome provides a wealth of data about the species' defense against chemical and biological threats, has uncovered several potentially new species of microbial symbionts, and significantly expands our knowledge about this pest.

Keywords: Antimicrobial peptides; Cellulase; Microbiome; Oryctes; Rhinoceros beetle; Transcriptome.

Fig. 1

The Coconut Rhinoceros Beetle, Oryctes rhinoceros. Adult, pupa, and third (final) instar larva are shown. Scale bar is 1 cm. Photo credit: M. Shelomi

Fig. 2

Phylogenetic Trees of Microbes Identified from the Oryctes rhinoceros Transcriptome. Neighbor-joining trees of the 16S ribosomal RNA sequences were generated by MAFFT v7 and rendered with Phylo.io. The GenBank Oryctes rhinoceros transcripts start with “CG” and the rest are the closest BLASTn hits to the transcripts, given with their GenBank Accession numbers. A) Desulfovibrio tree including transcript CG_43109. B) Elusimicrobium and Endomicrobium tree including transcript CG_28726. C) Treponema tree including transcript CG_34404

Fig. 3

Amino Acid Sequence Similarity of the Oryctes rhinoceros Cellulase to Termite Cellulases. Amino acids are shaded darker with increased sequence similarity. The Oryctes rhinoceros cellulase (transcript CG_7403) is clearly an endogenous insect cellulase, not microbial

Fig. 4

Predicted Structure of the Oryctes rhinoceros Cellulase. Secondary structure modeled by Phyre2 [45] with 93% of residues modeled at > 90% confidence and rendered with EzMol [46]. A) Cartoon-style backbone colored from light to dark blue from N to C terminus with the predicted catalytic site residues 81 (Aspartic Acid), 84 (Aspartic Acid) and 438 (Glutamic Acid) labeled and colored yellow, orange, and pink respectively. B) Predicted surface rendering of the protein from the same angle, with the catalytic residues colored as before