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

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:10.1038/s41598-021-89091-w

Cited by 26 publications

(28 citation statements)

References 56 publications

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“…A high proportion of BUSCO core genes are expected to be present, complete, and single-copy in any genome, and deviations from this expectation are indicative of issues with assembly quality. In fact, Dias et al [ 70 ] have shown that this hybrid assembly [ 68 ] includes a high degree of artifactually duplicated sequences resulting from uncollapsed haplotypes, likely stemming from the use of a heterozygous sample containing multiple individuals. This implies that the unusually high rate of gene family expansion reported by Hazzouri et al [ 68 ] should be taken with caution and/or reassessed.…”

Section: Omics Technologies and Their Impact On Pest Sciencementioning

confidence: 99%

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Omics in the Red Palm Weevil Rhynchophorus ferrugineus (Olivier) (Coleoptera: Curculionidae): A Bridge to the Pest

Manee

Alqahtani

Al-Shomrani

et al. 2023

Insects

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The red palm weevil (RPW), Rhynchophorus ferrugineus (Coleoptera: Curculionidae), is the most devastating pest of palm trees worldwide. Mitigation of the economic and biodiversity impact it causes is an international priority that could be greatly aided by a better understanding of its biology and genetics. Despite its relevance, the biology of the RPW remains poorly understood, and research on management strategies often focuses on outdated empirical methods that produce sub-optimal results. With the development of omics approaches in genetic research, new avenues for pest control are becoming increasingly feasible. For example, genetic engineering approaches become available once a species’s target genes are well characterized in terms of their sequence, but also population variability, epistatic interactions, and more. In the last few years alone, there have been major advances in omics studies of the RPW. Multiple draft genomes are currently available, along with short and long-read transcriptomes, and metagenomes, which have facilitated the identification of genes of interest to the RPW scientific community. This review describes omics approaches previously applied to RPW research, highlights findings that could be impactful for pest management, and emphasizes future opportunities and challenges in this area of research.

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Section: Omics Technologies and Their Impact On Pest Sciencementioning

confidence: 99%

“…In September 2021, a second draft genome was published for the RPW [ 70 ]. This assembly was produced from a single RPW larva using 10× Genomics linked reads.…”

Section: Omics Technologies and Their Impact On Pest Sciencementioning

confidence: 99%

Omics in the Red Palm Weevil Rhynchophorus ferrugineus (Olivier) (Coleoptera: Curculionidae): A Bridge to the Pest

Manee

Alqahtani

Al-Shomrani

et al. 2023

Insects

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“…Canu assembly of the S2R+ PacBio data displayed the highest level of BUSCO duplication (Figure 2B ) and the longest total assembly length ( Supplementary 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 ( 69 , 70 ). To test this, we took advantage of the fact that FALCON-Unzip leverages structural variants to phase heterozygous regions into a primary assembly (‘FALCON-Unzip_p’) and alternative haplotigs ( 43 ).…”

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

Nucleic Acids Research

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Animal cell lines often undergo extreme genome restructuring events, including polyploidy and segmental aneuploidy that can impede de novo whole-genome assembly (WGA). In some species like Drosophila, cell lines also exhibit massive proliferation of transposable elements (TEs). To better understand the role of transposition during animal cell culture, we sequenced the genome of the tetraploid Drosophila S2R+ cell line using long-read and linked-read technologies. 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 transposition after initial cell line establishment and subsequent tetraploidization. Local assemblies from TELR also allowed phylogenetic analysis of paralogous TEs, which revealed that proliferation of TE families 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 recalcitrant to WGA and yields new insights into the mechanisms of genome evolution in animal cell culture.

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“…To observe the synteny between the two beetle genomes, we combined the associations inferred from the MUMmer plot with the localization of the orthologous genes and constructed a Circos plot 39 (Circos, RRID:SCR_011798). Finally, 9,760 reciprocal best matches out of the total best hits (10,495) corresponded to orthologous genes between the 16 T. molitor scaffolds and the 10 T. castaneum chromosomes.…”

Section: Comparative Genomicsmentioning

confidence: 99%

“…Previous efforts to produce T. molitor transcriptomes and more recently the draft genome using 10X genomics technology have been published 8 . While this latter technology was promising on diploid and heterozygous insects [9][10][11][12] , its application to T. molitor produced a fragmented assembly with a 90% of BUSCO completeness and no genome annotation. This particular effort motivated the development of a new genome assembly that would allow deeper genomic analyses such as quantitative trait locus mapping or genomic estimated breeding values analysis.…”

Section: Introductionmentioning

confidence: 99%

Chromosome-scale assembly of the yellow mealworm genome

Eleftheriou¹,

Aury²,

Vacherie³

et al. 2022

Open Res Europe

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Background: The yellow mealworm beetle, Tenebrio molitor, is a promising alternative protein source for animal and human nutrition and its farming involves relatively low environmental costs. For these reasons, its industrial scale production started this century. However, to optimize and breed sustainable new T. molitor lines, the access to its genome remains essential. Methods: By combining Oxford Nanopore and Illumina Hi-C data, we constructed a high-quality chromosome-scale assembly of T. molitor. Then, we combined RNA-seq data and available coleoptera proteomes for gene prediction with GMOVE. Results: We produced a high-quality genome with a N50 = 21.9Mb with a completeness of 99.5% and predicted 21,435 genes with a median size of 1,780 bp. Gene orthology between T. molitor and Tribolium castaneum showed a highly conserved synteny between the two coleoptera and paralogs search revealed an expansion of histones in the T. molitor genome. Conclusions: The present genome will greatly help fundamental and applied research such as genetic breeding and will contribute to the sustainable production of the yellow mealworm.

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

Cited by 26 publications

References 56 publications

Omics in the Red Palm Weevil Rhynchophorus ferrugineus (Olivier) (Coleoptera: Curculionidae): A Bridge to the Pest

Omics in the Red Palm Weevil Rhynchophorus ferrugineus (Olivier) (Coleoptera: Curculionidae): A Bridge to the Pest

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

Chromosome-scale assembly of the yellow mealworm genome

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