A chromosome-level genome assembly and intestinal transcriptome of Trypoxylus dichotomus (Coleoptera: Scarabaeidae) to understand its lignocellulose digestion ability

Abstract

Lignocellulose, as the key structural component of plant biomass, is a recalcitrant structure, difficult to degrade. The traditional management of plant waste, including landfill and incineration, usually causes serious environmental pollution and health problems. Interestingly, the xylophagous beetle, Trypoxylus dichotomus, can decompose lignocellulosic biomass. However, the genomics around the digestion mechanism of this beetle remain to be elucidated. Here, we assembled the genome of T. dichotomus, showing that the draft genome size of T. dichotomus is 636.27 Mb, with 95.37% scaffolds anchored onto 10 chromosomes. Phylogenetic results indicated that a divergent evolution between the ancestors of T. dichotomus and the closely related scarabaeid species Onthophagus taurus occurred in the early Cretaceous (120 million years ago). Through gene family evolution analysis, we found 67 rapidly evolving gene families, within which there were 2 digestive gene families (encoding Trypsin and Enoyl-(Acyl carrier protein) reductase) that have experienced significant expansion, indicating that they may contribute to the high degradation efficiency of lignocellulose in T. dichotomus. Additionally, events of chromosome breakage and rearrangement were observed by synteny analysis during the evolution of T. dichotomus due to chromosomes 6 and 8 of T. dichotomus being intersected with chromosomes 2 and 10 of Tribolium castaneum, respectively. Furthermore, the comparative transcriptome analyses of larval guts showed that the digestion-related genes were more commonly expressed in the midgut or mushroom residue group than the hindgut or sawdust group. This study reports the well-assembled and annotated genome of T. dichotomus, providing genomic and transcriptomic bases for further understanding the functional and evolutionary mechanisms of lignocellulose digestion in T. dichotomus.

The draft genome sequence of the Japanese rhinoceros beetle Trypoxylus dichotomus septentrionalis towards an understanding of horn formation

“…Recently, a chromosome-level genome assembly of the Chinese population of T. dichotomus was generated through a combination of ONT long read and Hi-C sequencing, as reported by Wang et al 46 . We compared our T. dichotomus assembly of the Japanese population with that of the Chinese population.…”

“…We compared our T. dichotomus assembly with another published assembly derived from the Chinese population, as reported by Wang et al 46 . The assembly of T. dichotomus isolate ZJPA, in FASTA format, was downloaded from the publication’s supporting data website on GigaScience ( http://gigadb.org/dataset/102226 ).…”

“…Despite the excellent properties of this beetle as a research model, limited genetic information has been available for T. dichotomus until recently, despite a growing number of NGS studies including genomic and transcriptomic analyses being reported 15 , 18 , 45 , 46 . In the present study, we present the draft genome of T. dichotomus septentrionalis, along with functional annotation and gene expression data.…”

Evolution of horn length and lifting strength in the Japanese rhinoceros beetleTrypoxylus dichotomus

“…Japanese rhinoceros beetles ('Yamato kabutomushi') are large, abundant, and often observed scarabs native to Eastern Asia, including mainland China, Taiwan, Korea and Japan (Laurent 2000;New 2005;Brock 2006;Kawahara 2007;Takada 2013;Wang et al, 2022). Males have a short, curved horn extending from the dorsal prothorax and a much longer, four-tined "pitchfork" shaped horn extending from the top of the head (Figure 2).…”

Trypoxylus dichotomus Gut Bacteria Provides an Effective System for Bamboo Lignocellulose Degradation

“…The rhinoceros beetle Trypoxylus dichotomus feeds on both wood and bamboo fibers and serves as an important decomposer. Like the stag beetle (Lucanidae) ( 12 ), T. dichotomus possesses a powerful gut microflora, which has been observed to ferment and decompose lignocellulose ( 18 ). It remains unclear whether T. dichotomus exhibits enrichment in bamboo-degrading gut bacteria, and whether there is a microbiome difference between individuals feeding on wood fiber or bamboo fiber.…”