Divergent selection causes whole genome differentiation without physical linkage among the targets in <i>Spodoptera frugiperda</i> (Noctuidae)

Nam, Kiwoong; Nhim, Sandra; Robin, Stéphanie; Bretaudeau, Anthony; Nègre, Nicolas; d’Alençon, Emmanuelle

doi:10.1101/452870

Cited by 9 publications

(17 citation statements)

References 81 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Then, Dovetail™ Hi-C library was constructed from this strain, followed by Illumina Hiseq-X sequencing. Then, we used Hi-Rise™ software 24 to perform scaffolding from a PacBio genome assembly 22 , which was generated from individuals from the same insectarium. Then, the gene annotation was also transferred from this PacBio genome assembly to newly scaffoled-assembly.…”

Section: Methods Datamentioning

confidence: 99%

“…The resequencing data from the MS was obtained from NCBI SRA (PRJNA494340), which was generated for the fall armyworm genome project 10 and speciation study 22 . For PR, we collected larvae samples at Santa Isabella (see 38 for more detail).…”

Section: Methods Datamentioning

confidence: 99%

“…We improved the reference genome assemblies from sfC and sfR used in our previous study 22 because the existing reference genome assembly from Pac-Bio reads is moderately fragmented (1,000 scaffolds, N50 = 900kb for sfC). We performed super-scaffolding from the genome assembly from sfC using Hi-C 23 data and HiRise software 24 .…”

Section: Reference Genome and Resequencing Datamentioning

confidence: 99%

See 2 more Smart Citations

Adaptation by copy number variation increases insecticide resistance in fall armyworms

Nam

Gimenez

Hilliou³

et al. 2019

Preprint

Self Cite

View full text Add to dashboard Cite

Insecticide resistance is a major main challenge in pest control, and understanding its genetic basis is a key topic in agricultural ecology. Detoxification genes are well-known genetic elements that play a key role in adaptation to xenobiotics. The adaptive evolution of detoxification genes by copy number variations has been interpreted as a cause of insecticide resistance. However, the same pattern can be generated by the adaptation to host-plant defense toxins as well. In this study, we tested in fall armyworms (Lepidoptera Spodoptera frugiperda) if adaptation by copy number variation is the cause of the increased level of insecticide resistance from two geographic populations with different levels of resistance and two strains with different host plants. Following the generation of an assembly with chromosome-sized scaffolds (N50 = 13.2Mb), we observed that these two populations show a significant allelic differentiation of copy number variations, which is not observed between strains. In particular, a locus with almost complete allelic differentiation (Fst > 0.8) includes a cluster of P450 genes, which are well-known key players in detoxification. Detoxification genes are overrepresented in the genes with copy number variations, and the observed copy number variation appears to have beneficial effects in general. From this result, we concluded that copy number variation of detoxification genes in fall armyworms plays a key role in the insecticide resistance but not in the adaptation to host-plants, suggesting that the evolution of insecticide resistance may occur independently from host-plant adaptation.

show abstract

Section: Methods Datamentioning

confidence: 99%

Section: Methods Datamentioning

confidence: 99%

Section: Reference Genome and Resequencing Datamentioning

confidence: 99%

See 1 more Smart Citation

Adaptation by copy number variation increases insecticide resistance in fall armyworms

Nam

Gimenez

Hilliou³

et al. 2019

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…Further quality control and confirmation that adapter and non-relevant (contaminants, primer artifacts) sequences were removed from filtered reads were performed using FastQC [35]. Given the prevalence of C-strain among our samples and similar number of variants called when using both S. frugiperda corn and rice genomes [36], we mapped the remaining reads to the S. frugiperda corn reference genome (v3.1) downloaded from https://bipaa.genouest.org/sp/spodoptera_frugiperda_pub/ (assembled length of 312 Mb across 29,949 scaffolds [17]) using a Burrows-Wheeler aligner algorithm (bwa-mem) [37]. Variants were then called using the SAMtools mpileup utility [38], resulting in detection of 126,977,977 single nucleotide polymorphisms (SNPs) and indels.…”

Section: Filtering and Mappingmentioning

confidence: 99%

Whole genome comparisons reveal panmixia among fall armyworm (Spodoptera frugiperda) from diverse locations

Schlum

Lamour

Bortoli

et al. 2020

Preprint

View full text Add to dashboard Cite

The fall armyworm (Spodoptera frugiperda (J.E. Smith)) is a highly polyphagous agricultural pest with long-distance migratory behavior threatening food security worldwide. This pest has a host range of >80 plant species, but two host strains are recognized based on their association with corn (C-strain) or rice and smaller grasses (R-strain). In this study, the population structure and genetic diversity in 55 S. frugiperda samples from Argentina, Brazil, Kenya, Puerto Rico and the United States (USA) were surveyed to further our understanding of whole genome nuclear diversity. Comparisons at the genomic level suggest panmixia in this population, other than a minor reduction in gene flow between the two overwintering populations in the continental USA that also corresponded to genetically distinct host strains. Two maternal lines were detected from analysis of mitochondrial genomes. We found members from the Eastern Hemisphere interspersed within both continental USA overwintering subpopulations, suggesting multiple individuals were likely introduced to Africa. Comparisons between laboratory-reared and field collected S. frugiperda support similar genomic diversity, validating the experimental use of laboratory strains. Our research is the largest diverse collection of United States S. frugiperda whole genome sequences characterized to date, covering eight continental states and a USA territory (Puerto Rico). The genomic resources presented provide foundational information to understand gene flow at the whole genome level among S. frugiperda populations.

show abstract

“…with ~20X coverage was used to perform whole genome resequencing with 150bp paired-end and 300bp insert length. Then, we combined the resequencing data from Puerto Rico and Mississippi, which were generated for our previous studies (Hiseq 2500, Hiseq 4000, and Novaseq 6000) 31,32 , as well as the resequencing data of Brazil, Malawi, and Uganda from CSIRO (Novaseq 6000, 150bp paired-end sequencing) 28 . Lastly, resequencing data from China 33 was also combined with the dataset.…”

Section: Genome Assemblymentioning

confidence: 99%

Genomic balancing selection is key to the invasive success of the fall armyworm

Yainna

Tay

Fiteni

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

A successful biological invasion involves survival in a newly occupied environment. If a population bottleneck occurs during an invasion, the resulting depletion of genetic variants could cause increased inbreeding depression and decreased adaptive potential, which may result in a fitness reduction. How invasive populations survive in the newly occupied environment despite reduced heterozygosity and how, in many cases, they maintain moderate levels of heterozygosity are still contentious issues 1 . The Fall armyworm (FAW; Lepidoptera: Spodoptera frugiperda), a polyphagous pest, is native to the Western hemisphere. Its invasion in the Old World was first reported from West Africa in early 2016, and in less than four years, it swept sub-Saharan Africa and Asia, finally reaching Australia. We used population genomics approaches to investigate the factors that may explain the invasive success of the FAW. Here we show that genomic balancing selection played a key role in invasive success by restoring heterozygosity before the global invasion. We observe a drastic loss of mitochondrial polymorphism in invasive populations, whereas nuclear heterozygosity exhibits a mild reduction. The population from Benin in West Africa has the lowest length of linkage disequilibrium amongst all invasive and native populations despite its reduced population size. This result indicates that balancing selection increased heterozygosity by facilitating the admixture of invasive populations from distinct origins and that, once heterozygosity was sufficiently high, FAW started spreading globally in the Old World. As comparable heterozygosity levels between invasive and native populations are commonly observed 1 , we postulate that the restoration of heterozygosity through balancing selection could be widespread among successful cases of biological invasions.

show abstract

Divergent selection causes whole genome differentiation without physical linkage among the targets in Spodoptera frugiperda (Noctuidae)

Cited by 9 publications

References 81 publications

Adaptation by copy number variation increases insecticide resistance in fall armyworms

Adaptation by copy number variation increases insecticide resistance in fall armyworms

Whole genome comparisons reveal panmixia among fall armyworm (Spodoptera frugiperda) from diverse locations

Genomic balancing selection is key to the invasive success of the fall armyworm

Contact Info

Product

Resources

About