Draft genome and reference transcriptomic resources for the urticating pine defoliator <i>Thaumetopoea pityocampa</i> (Lepidoptera: Notodontidae)

Gschloessl, Bernhard; Dorkeld, Franck; Bergès, Hélène; Beydon, Genséric; Bouchez, Olivier; Branco, Manuela; Bretaudeau, Anthony; Burban, Christian; Dubois, Emeric; Gauthier, Philippe; Lhuillier, Émeline; Nichols, Jenna; Nidelet, Sabine; Rocha, Susana; Sauné, Laure; Streiff, Réjane; Gautier, Mathieu; Kerdelhué, Carole

doi:10.1111/1755-0998.12756

Cited by 24 publications

(24 citation statements)

References 86 publications

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“…To that end, a BAC library of 13,824 BACs (141+/−41 kb insert size after sizing of 48 BACs) with ca. five genome equivalent coverage was constructed in the vector pIndigoBAC-5 using high molecular weight DNA extracted from 300 B4sIL larvae (of developmental stage L1), as described in [51]. The BAC library, deposited at the CNRGV (INRA, Toulouse, France; https://cnrgv.toulouse.inra.fr/Library/Asian-ladybird), was organized in 2-dimension pools for PCR screening.…”

Section: Methodsmentioning

confidence: 99%

“…This allowed defining a Minimum Tiling Path of 14 BACs covering 1.9 Mb for local correction of scaffold mis-assembly. Shotgun sequencing was carried out using the Pacific Biosciences RS II system and Illumina MiSeq sequencer for 3 and 10 BACs, respectively [51]. Finally, we manually edited the HaxB4 assembly using the BAC sequences to derive a high quality 2.87 Mb sequence (% N = 0.96) including the candidate region of the Black-4Spots allele of the color pattern locus as well as adjacent regions.…”

Section: Methodsmentioning

confidence: 99%

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The Genomic Basis of Color Pattern Polymorphism in the Harlequin Ladybird

et al. 2018

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SummaryMany animal species comprise discrete phenotypic forms. A common example in natural populations of insects is the occurrence of different color patterns, which has motivated a rich body of ecological and genetic research [1, 2, 3, 4, 5, 6]. The occurrence of dark, i.e., melanic, forms displaying discrete color patterns is found across multiple taxa, but the underlying genomic basis remains poorly characterized. In numerous ladybird species (Coccinellidae), the spatial arrangement of black and red patches on adult elytra varies wildly within species, forming strikingly different complex color patterns [7, 8]. In the harlequin ladybird, Harmonia axyridis, more than 200 distinct color forms have been described, which classic genetic studies suggest result from allelic variation at a single, unknown, locus [9, 10]. Here, we combined whole-genome sequencing, population-based genome-wide association studies, gene expression, and functional analyses to establish that the transcription factor Pannier controls melanic pattern polymorphism in H. axyridis. We show that pannier is necessary for the formation of melanic elements on the elytra. Allelic variation in pannier leads to protein expression in distinct domains on the elytra and thus determines the distinct color patterns in H. axyridis. Recombination between pannier alleles may be reduced by a highly divergent sequence of ∼170 kb in the cis-regulatory regions of pannier, with a 50 kb inversion between color forms. This most likely helps maintain the distinct alleles found in natural populations. Thus, we propose that highly variable discrete color forms can arise in natural populations through cis-regulatory allelic variation of a single gene.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

The Genomic Basis of Color Pattern Polymorphism in the Harlequin Ladybird

et al. 2018

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“…Hybrid zones were defined as natural laboratories of evolutionary studies by Hewitt (), or “windows on evolutionary process” by Harrison (). In the case study presented here, hybrid characterization will offer the possibility to explore the mosaic of introgression along the genome concerning selected adaptive genes and to detect genes involved in reproductive isolation, owing to the recent development of genomics resources in the PPM (Gschloessl et al, ; Leblois et al, ). Monitoring the hybrid zone using systematic sampling will help us understand whether this pattern is stable over time and whether F 1 can ever be identified in nature.…”

Section: Discussionmentioning

confidence: 99%

From refugia to contact: Pine processionary moth hybrid zone in a complex biogeographic setting

İpekdal

Burban

Sauné

et al. 2020

Ecology and Evolution

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Contact zones occur at the crossroad between specific dispersal routes and are facilitated by biogeographic discontinuities. Here, we focused on two Lepidoptera sister species that come in contact near the Turkish Straits System (TSS). We aimed to infer their phylogeographic histories in the Eastern Mediterranean and finely analyze their co‐occurrence and hybridization patterns in this biogeographic context. We used molecular mitochondrial and nuclear markers to study 224 individuals from 42 localities. We used discordances between markers and complementary assignment methods to identify and map hybrids and parental individuals. We confirmed the parapatric distribution of Thaumetopoea pityocampa (Lepidoptera: Notodontidae) in the west and Thaumetopoea wilkinsoni in the east and identified a narrow contact zone. We identified several glacial refugia of T. wilkinsoni in southern Turkey with a strong east–west differentiation in this species. Unexpectedly, T. pityocampa crossed the TSS and occur in northern Aegean Turkey and some eastern Greek islands. We found robust evidence of introgression between the two species in a restricted zone in northwestern Turkey, but we did not identify any F1 individuals. The identified hybrid zone was mostly bimodal. The distributions and genetic patterns of the studied species were strongly influenced both by the Quaternary climatic oscillations and the complex geological history of the Aegean region. T. pityocampa and T. wilkinsoni survived the last glacial maximum in disjoint refugia and met in western Turkey at the edge of the recolonization routes. Expanding population of T. wilkinsoni constrained T. pityocampa to the western Turkish shore. Additionally, we found evidence of recurrent introgression by T. wilkinsoni males in several T. pityocampa populations. Our results suggest that some prezygotic isolation mechanisms, such as differences in timing of the adult emergences, might be a driver of the isolation between the sister species.

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“…2). Shotgun sequencing was carried out using the Pacific Biosciences RS II system and Illumina MiSeq sequencer for 3 and 10 BACs, respectively 21 .…”

Section: Genome-wide Scan For Association With the Proportion Of Red-mentioning

confidence: 99%

“…Possibilities include ancient mutational events or even across species introgression events 10,21 . .…”

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confidence: 99%

The genomic basis of colour pattern polymorphism in the harlequin ladybird

Gautier

Yamaguchi

Foucaud

et al. 2018

Preprint

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2Many animal species are comprised of discrete phenotypic forms. Understanding the genetic mechanisms generating and maintaining such phenotypic variation within species is essential to comprehending morphological diversity. A common and conspicuous example of discrete phenotypic variation in natural populations of insects is the occurrence of different colour patterns, which has motivated a rich body of ecological and genetic research [1][2][3][4][5][6] . The occurrence of dark, i.e. melanic, forms, displaying discrete colour patterns, is found across multiple taxa, but the underlying genomic basis remains poorly characterized. In numerous ladybird species (Coccinellidae), the spatial arrangement of black and orange patches on adult elytra varies wildly within species, forming strikingly different complex colour patterns 7,8 (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint . http://dx.doi.org/10.1101/345942 doi: bioRxiv preprint first posted online Jun. 13, 2018; 3 wild has been attributed to a combination of allelic diversity, interactions between allelic forms, and plastic response to environmental factors 12,13 . Genetic crosses have demonstrated that the majority of H. axyridis melanic forms result from variation of multiple alleles segregating at a single, uncharacterised, autosomal locus 9,10 , hereafter referred to as the colour pattern locus.To identify this colour pattern locus, and the mechanisms underlying discrete colour pattern variation, we used a population genomics approach, taking advantage of the cooccurrence of multiple colour pattern forms in natural populations. To that end, we first performed a de novo genome assembly of the H. axyridis Red-nSpots form (HaxR) using long reads produced by a MinION sequencer (Oxford Nanopore) (see Extended Data Table 1).Then, to fine map the colour pattern locus on this assembly, DNA from 14 pools of individuals (from n=40 to n=100 individuals per pool) representative of the world-wide genetic diversity and the four main colour pattern forms of H. axyridis was sequenced on a HiSeq 2500 (Illumina, Inc.) (Extended Data Table 2). Our aim was to characterize genetic variation associated with phenotypic differences across pool samples, using the proportion of individuals of a given colour form in each pool as a covariate. To do so, we called 18,425,210autosomal SNPs, and we performed a population-based genome-wide association study accounting for the covariance of allele frequencies across pools 14 . Given the dominance hierarchy of colour morph alleles with Black-2Spots > Black-4Spots > Black-nSpots > RednSpots 9,12,13 , we first performed the association study using the proportion of Red-nSpots individuals, carrying two copies of the most recessive allele, in each DNA pool as a covariate.We found 710 SNPs strongly associated with the proportion of the Red-nSpots form (Bayes factor > 30 db), the vast majority (86%) of which are located within a s...

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Draft genome and reference transcriptomic resources for the urticating pine defoliator Thaumetopoea pityocampa (Lepidoptera: Notodontidae)

Cited by 24 publications

References 86 publications

The Genomic Basis of Color Pattern Polymorphism in the Harlequin Ladybird

The Genomic Basis of Color Pattern Polymorphism in the Harlequin Ladybird

From refugia to contact: Pine processionary moth hybrid zone in a complex biogeographic setting

The genomic basis of colour pattern polymorphism in the harlequin ladybird

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