Haplotype-resolved genome assembly enables gene discovery in the red palm weevil<i>Rhynchophorus ferrugineus</i>

Dias, Guilherme B.; Altammami, Musaad A.; El-Shafie, Hamadttu A. F.; Alhoshani, Fahad M.; Al-Fageeh, Mohamed B.; Bergman, Casey M.; Manee, Manee M.

doi:10.1101/2020.08.30.273383

Cited by 3 publications

(5 citation statements)

References 52 publications

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“…2B; Table S1). We speculated that the high degree of BUSCO duplication in the Canu S2R+ assembly could be caused by haplotype-induced duplication artifacts in a partially-phased assembly that contained contigs from multiple haplotypes of the same locus (Kelley and Salzberg 2010; Dias et al . 2021).…”

Section: Resultsmentioning

confidence: 99%

Local assembly of long reads enables phylogenomics of transposable elements in a polyploid cell line

Han

Dias

Basting

et al. 2022

Preprint

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Animal cell lines cultured for extended periods often undergo extreme genome restructuring events, including polyploidy and segmental aneuploidy that can impede de novo whole-genome assembly (WGA). In Drosophila, many established cell lines also exhibit massive proliferation of transposable elements (TEs) relative to wild-type flies. To better understand the role of transposition during long-term animal somatic cell culture, we sequenced the genome of the tetraploid Drosophila S2R+ cell line using long-read and linked-read technologies. Relative to comparable data from inbred whole flies, WGAs for S2R+ were highly fragmented and generated variable estimates of TE content across sequencing and assembly technologies. We therefore developed a novel WGA-independent bioinformatics method called "TELR" that identifies, locally assembles, and estimates allele frequency of TEs from long-read sequence data (https://github.com/bergmanlab/telr). Application of TELR to a ~130x PacBio dataset for S2R+ revealed many haplotype-specific TE insertions that arose by somatic transposition in cell culture after initial cell line establishment and subsequent tetraploidization. Local assemblies from TELR also allowed phylogenetic analysis of paralogous TE copies within the S2R+ genome, which revealed that proliferation of different TE families during cell line evolution in vitro can be driven by single or multiple source lineages. Our work provides a model for the analysis of TEs in complex heterozygous or polyploid genomes that are not amenable to WGA and yields new insights into the mechanisms of genome evolution in animal cell culture.

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Section: Resultsmentioning

confidence: 99%

Local assembly of long reads enables phylogenomics of transposable elements in a polyploid cell line

Han

Dias

Basting

et al. 2022

Preprint

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“…The obtained genome indicates a great completeness and quality with a recovering of 82.6% of complete BUSCO genes. The 1.3 GB size for the genome assembly is large compared with other weevil (Coleoptera: Curculionidae) species such as the red palm weevil, Rhynchophorus ferrugineus (589 MB) (Dias et al, 2021), and the rice weevil, Sitophilus oryzae (770 MB) (Parisot et al, 2021), but similar to a sister species, the Argentine stem weevil, Listronotus bonariensis (1.1 GB) (Harrop et al, 2020). As for L .…”

Section: Discussionmentioning

confidence: 99%

Population genetic structure of the carrot weevil (Listronotus oregonensis) in North America

Bessette

Ste‐Croix

Brodeur

et al. 2022

Evolutionary Applications

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Population genetic studies of insect pests enhance our ability to anticipate problems in agroecosystems, such as pest outbreaks, insecticide resistance, or expansions of the host range. This study focuses on geographic distance and host plant selection as potential determinants of genetic differentiation of the carrot weevil Listronotus oregonensis, a major pest of several apiaceous crops in North America. To undertake genetic studies on this species, we assembled the first complete genome sequence for L. oregonensis. Then, we used both haplotype discrimination with mitochondrial DNA (mtDNA) and a genotyping‐by‐sequencing (GBS) approach to characterize the genetic population structure. A total of 220 individuals were sampled from 17 localities in the provinces of Québec, Ontario, Nova Scotia (Canada), and the state of Ohio (USA). Our results showed significant genetic differences between distant populations across North America, indicating that geographic distance represents an important factor of differentiation for the carrot weevil. Furthermore, the GBS analysis revealed more different clusters than COI analysis between Québec and Nova Scotia populations, suggesting a recent differentiation in the latter province. In contrast, we found no clear evidence of population structure associated with the four cultivated apiaceous plants tested (carrot, parsley, celery, and celeriac) using populations from Québec. This first characterization of the genetic structure of the carrot weevil contributes to a better understanding of the gene flow of the species and helps to adapt local pest management measures to better control this agricultural pest.

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“…Following the manufacturer’s protocols, paired-end cDNA libraries were prepared using the TruSeq Stranded mRNA preparation Kit (Illumina Inc.). The cleaned RNA-seq reads were mapped to the R. ferrugineus genome 20 (GenBank assembly accession: GCA_014462685.1) using the ‘RNA-seq analysis procedure’ implemented in CLC Workbench /Server suite (Qiagen). Gene expression levels were quantified and reported as reads per kilobase of transcript per million mapped reads (RPKM) and transcripts per kilobase of exon model per million mapped reads (TPM).…”

Section: Methodsmentioning

confidence: 99%

“…The RferOR sequences were correctly annotated and mapped to the R. ferrugineus genome 20 (GenBank accession numbers GCA_014462685.1 and GCA_014490705.1) using a BLASTN search against the R. ferrugineus genome created on Geneious v 7.1.9 (Biomatters) and correctly annotated. To identify the antenna-specific RferORs 7 , we generated expression profiles in the male and female antennae (from the laboratory and field).…”

Section: Methodsmentioning

confidence: 99%

“…The R. ferrugineus snout raw reads were deposited in the NCBI Sequence Read Archive. The assembled and cleaned RferOR2 reads in the antennae and snout transcriptomes were visualized with the CLC Genomics Server, using marked gene positions in the R. ferrugineus genome (GenBank: GCA_014462685) 20 (see details in Supplementary Methods).…”

Section: Phylogenetic Analysis Gene Structure and Conserved Motif Ana...mentioning

confidence: 99%

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Reverse chemical ecology approach for sustainable palm tree protection against invasive palm weevils

Antony

Montagné

Comte

et al. 2023

Preprint

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The reverse chemical ecology approach facilitates sustainable plant protection by identifying odorant receptors (ORs) tuned to odorants, especially the volatile molecules emitted from host plants that insects use for detection. A few studies have explored such an approach to develop sustainable pest management programs, especially in host-specialized insect species. We revealed the molecular mechanism of host plant detection of a destructive, invasive insect pest of palm trees (Arecaceae), the Asian palm weevil (Rhynchophorus ferrugineus), by deorphanizing an OR (RferOR2) tuned to several palm-emitted odors. We found that RferOR2 responded explicitly to several ecologically relevant palm-emitted odors and significantly to palm esters when transgenically expressed in Drosophila olfactory neurons. We mapped RferOR2 expression in the R. ferrugineus genome and found that odor specificity is likely to develop equally in both sexes. We inferred that the semiochemicals that attract palm weevils to a palm tree might aid in weevil control efforts by improving attraction, enticing many palm weevils to the traps. We demonstrate that including synthetic palm volatiles in pheromone-based mass trapping has a synergistic effect on pheromones, resulting in significantly increased weevil catches. We proved that insect OR deorphanization could aid in the identification of novel behaviorally active volatiles for inclusion in pest management. These results suggest that targeting RferOR2 may help design receptor antagonists that can interfere with weevil host-searching behavior in sustainable pest management applications.

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

Cited by 3 publications

References 52 publications

Local assembly of long reads enables phylogenomics of transposable elements in a polyploid cell line

Local assembly of long reads enables phylogenomics of transposable elements in a polyploid cell line

Population genetic structure of the carrot weevil (Listronotus oregonensis) in North America

Reverse chemical ecology approach for sustainable palm tree protection against invasive palm weevils

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