The genome of pest Rhynchophorus ferrugineus reveals gene families important at the plant-beetle interface

Abstract

The red palm weevil, Rhynchophorus ferrugineus, infests palm plantations, leading to large financial losses and soil erosion. Pest-host interactions are poorly understood in R. ferrugineus, but the analysis of genetic diversity and pest origins will help advance efforts to eradicate this pest. We sequenced the genome of R. ferrugineus using a combination of paired-end Illumina sequencing (150 bp), Oxford Nanopore long reads, 10X Genomics and synteny analysis to produce an assembly with a scaffold N50 of~60 Mb. Structural variations showed duplication of detoxifying and insecticide resistance genes (e.g., glutathione S-transferase, P450, Rdl). Furthermore, the evolution of gene families identified those under positive selection including one glycosyl hydrolase (GH16) gene family, which appears to result from horizontal gene transfer. This genome will be a valuable resource to understand insect evolution and behavior and to allow the genetic modification of key genes that will help control this pest.

Mitochondrial genomes of twelve species of hyperdiverse Trigonopterus weevils

“…Interestingly, the Rhynchophorus mitogenome of Zhang et al (2017) shows strange duplications of tRNA-Ile, tRNA-Met and tRNA-Thr, while the Eucryptorhynchus mitogenomes of Zhang et al, 2017 are missing the tRNA-Ile. A more recent mitogenome assembly of Rhynchophorus ferrugineus was published within a whole genome project ( Hazzouri et al, 2020 ). Its published sequence is in reverse-complement and contains numerous indels.…”

Haplotype-resolved genome assembly enables gene discovery in the red palm weevilRhynchophorus ferrugineus

“…Both pseudo-haplotypes were deposited in GenBank (see Data availability section for accession numbers). To better understand differences between our pseudo-haplotype assemblies and the hybrid assemblies of Hazzouri et al 13 , we also exported our RPW Supernova assembly in ‘megabubbles’ style 17 which includes maternal and paternal phase blocks together with unphased blocks in a single file (Supplementary Figure S1).…”

“…General metrics for unmasked versions of both pseudo-haplotypes of our phased genome assembly, the megabubbles version of our phased genome assembly, assemblies from Hazzouri et al 13 (David Nelson, personal communication; GCA_012979105.1) and the Tribolium castaneum reference genome (GCF_000002335.3) 31 were collected with the ‘stats.sh’ utility script from BBMap v38.76 32 . Completeness of unmasked genome assemblies was assessed with BUSCO v4.0.6 (-m genome -l arthropoda_-odb10 --augustus_species tribolium2012) 14 using the Arthropoda gene set from OrthoDB v10 33 .…”

“…PacBio or Oxford Nanopore) reads 12 . Recently, a hybrid assembly using a combination of Illumina, 10x Genomics and Oxford Nanopore sequencing was reported for the RPW that was used for gene discovery and analysis of gene family evolution 13 . This hybrid assembly reported an unusually high rate of gene family expansion in the RPW genome relative to other beetle species, and also reported a very high number of duplicated genes in the BUSCO gene set, which are expected to be present in a single copy in most organisms 14 .…”

“…This hybrid assembly reported an unusually high rate of gene family expansion in the RPW genome relative to other beetle species, and also reported a very high number of duplicated genes in the BUSCO gene set, which are expected to be present in a single copy in most organisms 14 . To overcome limitations of previous transcriptome-based gene discovery efforts in the RPW 6–11 and to evaluate the correctness of the previously-reported RPW genome assembly 13 , here we report a haplotype-resolved (“phased”) diploid genome assembly from an independent RPW sample generated using 10x Genomics linked-read sequencing. We provide evidence that the previously-reported RPW genome hybrid assembly contains a large proportion of artifactually duplicated sequences that have arisen from multiple haplotypes being scaffolded into a single haploid representation of the genome 15 .…”