A chromosome-level assembly of the seed beetle <i>Callosobruchus maculatus</i> genome with annotation of its repetitive elements

Arnqvist, Göran; Westerberg, Ivar; Galbraith, James; Sayadi, Ahmed; Scofield, Douglas G; Olsen, Remi-André; Immonen, Elina; Bonath, Franziska; Ewels, Philip; Suh, Alexander

doi:10.1093/g3journal/jkad266

Cited by 4 publications

(2 citation statements)

References 39 publications

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“…Finally, reads shorter than 20 bp were discarded. Resulting read pairs were mapped to the Callosobruchus maculatus genome 106 using HISAT2 2.2.1 107 with default settings for stranded libraries and sensitivity set to “--very-sensitive”. Number of reads per gene was then determined using HTSeq 2.0.2 108 with default settings for stranded libraries.…”

Section: Methodsmentioning

confidence: 99%

Life-history adaptation under climate warming magnifies the agricultural footprint of a cosmopolitan insect pest

Burc,

Girard-Tercieux,

Metz

et al. 2024

Preprint

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Climate change is affecting the distributions and growth rates of cold-blooded pest species, with dire consequences for agriculture and global food security. To address this challenge, it is essential to forecast how pests will respond to changing climates. However, current projection models typically overlook the potential for climate change adaptation. By unifying life-history theory with thermodynamics based on first principles, we here show that pest species' climate adaptation can cause substantial increases in their agricultural impact via changes in temperature-dependent resource acquisition and allocation strategies. We test these predictions by studying thermal adaptation in life-history traits and gene expression in the cosmopolitan insect pest, Callosobruchus maculatus. Five years of adaptation to simulated warming caused an almost two-fold increase in the predicted agricultural footprint of C. maculatus, while adaptation to cold temperature had little effect. Consistent with the theoretical predictions, the magnified impact under warming was driven by synergistic increases in larval resource acquisition and adult reproductive potential, resulting in a predicted double blow on agricultural yields. This suggests that adaptation in insect life-history will significantly worsen agricultural loss under future climate change and emphasizes the need for integrating a mechanistic understanding of life-history evolution into ecological forecasts of pests.

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Section: Methodsmentioning

confidence: 99%

Life-history adaptation under climate warming magnifies the agricultural footprint of a cosmopolitan insect pest

Burc,

Girard-Tercieux,

Metz

et al. 2024

Preprint

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show abstract

“…A documentation of conspecific sperm precedence in seed beetles also implies that reproductive proteins may be involved in incipient speciation ( Rugman-Jones and Eady 2007 ). Here, we sequenced and de novo assembled the genomes of Callosobruchus chinensis and Callosobruchus analis which then enabled the first comparative genomic analyses of SFP and FRP orthologs in four species of seed beetles, given that genome assemblies are already available for two species ( C. maculatus and Acanthoscelides obtectus ) ( Sayadi et al 2019 ; Immonen et al 2023 ; Arnqvist et al 2024 ).…”

Section: Introductionmentioning

confidence: 99%

Comparative Genomic Analysis of the Pattern of Evolution of Male and Female Reproductive Proteins in Seed Beetles

Papachristos,

Sayadi,

Arnqvist

2024

Genome Biology and Evolution

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Male seminal fluid proteins (SFPs) often show signs of positive selection and divergent evolution, believed to reflect male – female coevolution. Yet, our understanding of the predicted concerted evolution of SFPs and female reproductive proteins (FRPs) is limited. We sequenced, assembled and annotated the genome of two species of seed beetles allowing a comparative analysis of four closely related species of these herbivorous insects. We compare the general pattern of evolution in genes encoding SFPs and FRPs with those in digestive protein genes and well-conserved reference genes. We found that FRPs showed an overall dN/dS ratio (ω) similar to that of conserved genes, while SFPs and digestive proteins exhibited higher overall ω values. Further, SFPs and digestive proteins showed a higher proportion of sites putatively under positive selection and explicit tests showed no difference in relaxed selection between protein types. Evolutionary rate covariation analyses showed that evolutionary rates among SFPs were on average more closely correlated with those in FRPs than with either digestive or conserved genes. Gene expression showed the expected negative covariation with ω values, except for male-biased genes where this negative relationship was reversed. In conclusion, SFPs showed relatively rapid evolution and signs of positive selection. In contrast, FRPs evolved at a lower rate under selective constraints, on par with genes known to be well-conserved. Although our findings provide support for concerted evolution of SFPs and FRPs, they also suggest that these two classes of proteins evolve under partly distinct selective regimes.

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A near-complete genome assembly of Monochamus alternatus a major vector beetle of pinewood nematode

Xing,

Liu,

et al. 2024

Sci Data

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The Japanese sawyer beetle, Monochamus alternatus, is not only one of the most important wood boring pest itself, but also a major vector of the invasive pinewood nematode (PWN), which is the causal agent of the devastative pine wilt disease (PWD) and threats the global pine forest. Here, we present a near-complete genome of M. alternatus at the chromosome level. The assembled genome was 792.05 Mb with contig N50 length of 55.99 Mb, which is the largest N50 size among the sequenced Coleoptera insects currently. 99.57% of sequence was anchored onto ten pseudochromosomes (one X-chromosome and nine autosomes), and the final genome harbored only 13 gaps. BUSCO evaluation revealed the presence of 99.0% of complete core genes. Thus, our genome assembly represented the highest-contiguity genome assembly as well as high completeness in insects so far. We identified 20,471 protein-coding genes, of which 20,070 (98.04%) were functionally annotated. The genome assembly of M. alternatus provides a valuable resource for exploring the evolution of the symbiosis between PWN and the vector insects.

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A chromosome-level assembly of the seed beetle Callosobruchus maculatus genome with annotation of its repetitive elements

Cited by 4 publications

References 39 publications

Life-history adaptation under climate warming magnifies the agricultural footprint of a cosmopolitan insect pest

Life-history adaptation under climate warming magnifies the agricultural footprint of a cosmopolitan insect pest

Comparative Genomic Analysis of the Pattern of Evolution of Male and Female Reproductive Proteins in Seed Beetles

A near-complete genome assembly of Monochamus alternatus a major vector beetle of pinewood nematode

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