The transposable element-rich genome of the cereal pest Sitophilus oryzae

Abstract

Background The rice weevil Sitophilus oryzae is one of the most important agricultural pests, causing extensive damage to cereal in fields and to stored grains. S. oryzae has an intracellular symbiotic relationship (endosymbiosis) with the Gram-negative bacterium Sodalis pierantonius and is a valuable model to decipher host-symbiont molecular interactions. Results We sequenced the Sitophilus oryzae genome using a combination of short and long reads to produce the best assembly for a Curculionidae species to date. We show that S. oryzae has undergone successive bursts of transposable element (TE) amplification, representing 72% of the genome. In addition, we show that many TE families are transcriptionally active, and changes in their expression are associated with insect endosymbiotic state. S. oryzae has undergone a high gene expansion rate, when compared to other beetles. Reconstruction of host-symbiont metabolic networks revealed that, despite its recent association with cereal weevils (30 kyear), S. pierantonius relies on the host for several amino acids and nucleotides to survive and to produce vitamins and essential amino acids required for insect development and cuticle biosynthesis. Conclusions Here we present the genome of an agricultural pest beetle, which may act as a foundation for pest control. In addition, S. oryzae may be a useful model for endosymbiosis, and studying TE evolution and regulation, along with the impact of TEs on eukaryotic genomes.

Transposons and non-coding regions drive the intrafamily differences of genome size in insects

“…For example, locust ( Locusta migratoria , Orthoptera) carries the largest insect genome published to date, ∼6.5 Gb, ∼60% of which is comprised of TEs ( Wang et al., 2014 ). In other large genomes, such as that of the grasshopper Vandiemenella viatica (∼4.5 Gb) ( Palacios-Gimenez et al., 2020 ) or the rice weevil Sitophilus oryzae (770 Mbp) ( Parisot et al., 2021 ), TEs account for an even greater proportion of the genome, exceeding 70%. By contrast, TE represent less than 1% of the genomes of the Antarctic midge ( Belgica antarctica , Diptera, 83.9 Mb) ( Kelley et al., 2014 ) and the body louse ( Pediculus humanus humanus , Phthiraptera, 108 Mb) ( Kirkness et al., 2010 ).…”

The genome of the forest insect pest Pissodes strobi reveals genome expansion and evidence of a Wolbachia endosymbiont

“…2021 ), the Eurasian spruce bark beetle ( Ips typographus ) ( Powell et al . 2021 ), and the rice weevil ( Sitophilus oryzae ) ( Parisot et al . 2021 ).…”

Efficient compartmentalization in insect bacteriomes protects symbiotic bacteria from host immune system

“…RT-qPCR experiments confirmed the TCT-dependent induction of all 11 up-regulated genes (Figure 2, Additional Figure 1). Eight of these genes encode AMPs and all possess a predicted signal peptide: colA (Coleoptericin A), Coleoptericin B ( colB ), Sarcotoxin ( srx ), Luxoriosin ( lux ), a Gly-rich AMP ( gly-rich AMP ), and three Diptericins ( dpt-2, 3 and 4 , Figure 2) [35]. This AMP induction is in agreement with previous reports, where AMPs induced in larvae by immune challenge included colA [17,20,21,24], colB , srx [20,21,24], dpt , cecropin and defensins [20,24].…”