Retrotransposed gene copies persist under relaxed selection in wild Spodoptera frugiperda
Abstract
Copy number variations (CNVs) are major sources of genetic variation, affecting large portions of genomes. Typical CNVs are known to have short evolutionary half-lives due to deleterious effects, with documented events of adaptive evolution. However, it is not known whether the same trends apply to CNVs preserving intact open reading frames (iORF-CNVs), which can encode functional proteins. Here, we investigate the mechanistic origins and evolutionary dynamics of iORF-CNVs in Spodoptera frugiperda, a globally distributed pest species where CNV-mediated adaptive evolution has been reported. Using PacBio HiFi reads, we generated high-quality, individually assembled genomes for 36 field-collected individuals and identified 349 genes with polymorphic iORF-CNVs. These elements are short, intronless, and display molecular signatures of LINE-mediated retrotransposition, including cis- and trans-acting effects. A majority of iORF-CNVs (68.0%–77.28%) exhibited at least one molecular signature of retrotransposition. iORF-CNVs showed lower divergence at the first and second codon positions than at the third codon positions, but they had higher nonsynonymous-to-synonymous polymorphism ratios than non-iORF-CNV genes, implying purifying selection with relaxed constraint. Orthology analyses indicated that these CNVs originate from genes under weak evolutionary constraint, while transcriptomic and promoter motif analyses revealed that many are transcribed and retain regulatory features. We conclude that observed iORF-CNVs are generated through retrotransposition from weakly constrained genes and that the duplicates are selectively maintained for coding potential, albeit under reduced purifying selection compared with non-iORF-CNV genes. These results imply that pseudogenization is not an inevitable evolutionary fate of retrotransposed gene copies when the open reading frame is preserved.
Related
- Low Risk of Resistance Evolution of Spodoptera frugiperda to Lufenuron and Chlorfenapyr in China
- Host-Plant-Mediated Effects on the Demography, Parasitism Rates and Functional Response of Bracon hebetor on Spodoptera frugiperda
- Insecticidal Activity of Essential Oils from Syzygium aromaticum and Foeniculum vulgare Var. dulce and Their Major Compounds Against Spodoptera frugiperda and Physiological Selectivity for Trichogramma pretiosum
- Low levels of Fall Armyworm (Spodoptera frugiperda J.E. Smith) damage in Bangladesh are linked to farmers’ integrated pest management practices and weather conditions
- Insecticidal and antifeedant activity of cadalene isolated from Cyperus rotundus against fall armyworm (Spodoptera frugiperda)
BibTeX
@article{nam2026retrotransposed,
title = {{Retrotransposed gene copies persist under relaxed selection in wild Spodoptera frugiperda}},
author = {Kiwoong Nam and Sylvie Gimenez and Hyerin An and Karine Durand and Mélanie Gasser and Sudeeptha Yainna and Fabrice Legeai and Julien M Beuzelin and David G Heckel and Sabine Hänniger and Emmanuelle d'Alençon},
journal = {Molecular Biology and Evolution},
year = {2026},
month = oct,
doi = {10.1093/molbev/msag124},
url = {https://hal.science/hal-05651863v1},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Retrotransposed gene copies persist under relaxed selection in wild Spodoptera frugiperda
AU - Kiwoong Nam
AU - Sylvie Gimenez
AU - Hyerin An
AU - Karine Durand
AU - Mélanie Gasser
AU - Sudeeptha Yainna
AU - Fabrice Legeai
AU - Julien M Beuzelin
AU - David G Heckel
AU - Sabine Hänniger
AU - Emmanuelle d'Alençon
PY - 2026
DA - 2026/10/23
JO - Molecular Biology and Evolution
DO - 10.1093/molbev/msag124
UR - https://hal.science/hal-05651863v1
AB - Copy number variations (CNVs) are major sources of genetic variation, affecting large portions of genomes. Typical CNVs are known to have short evolutionary half-lives due to deleterious effects, with documented events of adaptive evolution. However, it is not known whether the same trends apply to CNVs preserving intact open reading frames (iORF-CNVs), which can encode functional proteins. Here, we investigate the mechanistic origins and evolutionary dynamics of iORF-CNVs in Spodoptera frugiperda, a globally distributed pest species where CNV-mediated adaptive evolution has been reported. Using PacBio HiFi reads, we generated high-quality, individually assembled genomes for 36 field-collected individuals and identified 349 genes with polymorphic iORF-CNVs. These elements are short, intronless, and display molecular signatures of LINE-mediated retrotransposition, including cis- and trans-acting effects. A majority of iORF-CNVs (68.0%–77.28%) exhibited at least one molecular signature of retrotransposition. iORF-CNVs showed lower divergence at the first and second codon positions than at the third codon positions, but they had higher nonsynonymous-to-synonymous polymorphism ratios than non-iORF-CNV genes, implying purifying selection with relaxed constraint. Orthology analyses indicated that these CNVs originate from genes under weak evolutionary constraint, while transcriptomic and promoter motif analyses revealed that many are transcribed and retain regulatory features. We conclude that observed iORF-CNVs are generated through retrotransposition from weakly constrained genes and that the duplicates are selectively maintained for coding potential, albeit under reduced purifying selection compared with non-iORF-CNV genes. These results imply that pseudogenization is not an inevitable evolutionary fate of retrotransposed gene copies when the open reading frame is preserved.
SN - 0737-4038
SN - 1537-1719
ER -