The genome sequence of the lesser marbled fritillary, <i>Brenthis ino</i>, and evidence for a segregating neo-Z chromosome

Mackintosh, Alexander; Laetsch, Dominik R.; Baril, Tobias; Foster, Robert G.; Dincă, Vlad; Vila, Roger; Hayward, Alexander; Lohse, Konrad

doi:10.1093/g3journal/jkac069

Cited by 10 publications

(10 citation statements)

References 52 publications

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“…As the Hi-C signal of chromosome fusions in the H. congener female represents a mix of signals from the fused and unfused haplotypes (Fig 7C-D), we phased the Hi-C data across the chromosomes of interest (Chr4, Chr14, W, Z) and used chomper (46) to split the Hi-C data into two subsets of read pairs representing the two haplotypes (47.5% and 52.2% of the read pairs in each subset). The excess of Hi-C contacts between Chr4 and Chr14 was completely absent on one haplotype (Fig 7E) and very strong on the other haplotype (Fig 7F).…”

Section: Resultsmentioning

confidence: 99%

“…Because any possible Sex-A fusion would produce heterozygous females and homozygous males, we identified sites with this pattern (see hypotheses in Fig 2). We first calculated the number of heterozygous and homozygous individuals per species and site using the --hardy option in vcftools version 0.1.14 (46). Then, we used custom scripts to find sites where each species in the sapho subclade met the following criteria: (i) no males were heterozygous, (ii) at least one female was heterozygous, and (iii) not more than one female was homozygous (allowing for one female with one allele not called).…”

Section: Methodsmentioning

confidence: 99%

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Genomic evidence reveals three sequential W-autosome fusions in Heliconius butterflies

Rueda-M

Jiggins

Pardo‐Díaz

et al. 2023

Preprint

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Sex chromosomes are evolutionarily labile in many animals, and fusion with an autosome is one of the mechanisms by which they can evolve. Sex chromosome-autosome (SA) fusions can reduce sexual conflict and promote adaptation and reproductive isolation among species. Recently, advances in genomics have fuelled the discovery of SA fusions in multiple vertebrates and in some invertebrates such as Lepidoptera. Here, we discovered multiple SA fusions in the sara/sapho clade of the classical adaptive radiation of Heliconius butterflies. While the vast majority of Heliconius species have 21 chromosomes, species of this particularly rapidly diversifying clade have up to 60 chromosomes. We found a sex chromosome fusion with chromosome 4 at the base of the sapho clade and two additional sex chromosome fusions, each shared by two species. These sequential fusions between autosomes and sex chromosomes make the Heliconius sapho clade an ideal system to study the role of neo-sex chromosomes in adaptive radiations and the degeneration of sex chromosomes over time. Our study adds to a growing number of examples in butterflies that, in the future, may help to unravel the importance of such rearrangements in the evolution of Lepidoptera and animals in general.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Genomic evidence reveals three sequential W-autosome fusions in Heliconius butterflies

Rueda-M

Jiggins

Pardo‐Díaz

et al. 2023

Preprint

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“…Two male individuals (MO_IP_500 and MO_IP_504) were collected with a hand net at Le Moulin de Bertrand, Saint-Martin-de-Londres, Montpellier, France, and flash frozen in liquid nitrogen. High-molecular-weight (HMW) DNA was extracted from the thorax of one of these individuals (MO_IP_504) using a salting out extraction protocol as described in Mackintosh et al (2022) .…”

Section: Methodsmentioning

confidence: 99%

“…TEs were annotated using the Earl Grey TE annotation pipeline ( Jurka et al 2005 ; Xu and Wang 2007 ; Rubino and Creevey 2014 ; Smit et al 2015 ; Hubley et al 2016 ; Platt et al 2016 ; Ou and Jiang 2019 ; Wong and Simakov 2019 ; Flynn et al 2020 ; Baril et al 2022 ) as in Mackintosh et al (2022) .…”

Section: Methodsmentioning

confidence: 99%

The genome sequence of the scarce swallowtail, Iphiclides podalirius

Mackintosh

Laetsch

Baril

et al. 2022

G3 Genes|Genomes|Genetics

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The scarce swallowtail, Iphiclides podalirius (Linnaeus, 1758), is a species of butterfly in the family Papilionidae. Here we present a chromosome-level genome assembly for I. podalirius as well as gene and transposable element annotations. We investigate how the density of genomic features differ between the 30 I. podalirius chromosomes. We find that shorter chromosomes have higher heterozygosity at fourfold-degenerate sites and a greater density of transposable elements. While the first result is an expected consequence of differences in recombination rate, the second suggests a counter-intuitive relationship between recombination and transposable element evolution. This high quality genome assembly, the first for any species in the tribe Leptocircini, will be a valuable resource for population genomics in the genus Iphiclides and comparative genomics more generally.

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“…While many of the neo-sex chromosomes known in Lepidoptera are old (i.e. shared by multiple genera), young neo-sex chromosomes have been described in a handful of taxa (Smith et al 2016, Mongue et al 2017, Mackintosh et al 2022, Rueda-M et al 2023, Höök et al 2023. Some of these neo-sex chromosomes are nonetheless highly diverged, meaning that little can be inferred about the early stages of neo-W degeneration (Mongue et al 2017).…”

Section: Introductionmentioning

confidence: 99%

Rewinding the ratchet: rare recombination locally rescues neo-W degeneration and generates plateaus of sex-chromosome divergence

Decroly,

Vila,

Lohse

et al. 2024

Preprint

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Natural selection is less efficient in the absence of recombination. As a result, non-recombining sequences, such as sex chromosomes, tend to degenerate over time. Although the outcomes of recombination arrest are typically observed after many millions of generations, recent neo-sex chromosomes can give insight into the early stages of this process. Here we investigate the evolution of neo-sex chromosomes in the Spanish marbled white butterfly, Melanargia ines, where a Z-autosome fusion has turned the homologous autosome into a non-recombining neo-W chromosome. We show that these neo-sex chromosomes are likely limited to the Iberian population of M. ines, and that they arose around the time when populations in Iberia and North-Africa split, around 1.5 million years ago. Recombination arrest of the neo-W chromosome has led to an excess of premature stop codons and frameshift mutations, while levels of gene expression have remained similar for the neo-W and neo-Z chromosomes, even for genes with loss-of-function mutations. Surprisingly, we identified two regions of ~1 Mb at one end of the neo-W that are both less diverged from the neo-Z and less degraded than the rest of the chromosome, suggesting a history of rare but repeated genetic exchange between the two neo-sex chromosomes. These plateaus of neo-sex chromosome divergence suggest that neo-W degradation can be locally reversed by rare recombination between neo-W and neo-Z chromosomes.

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The genome sequence of the lesser marbled fritillary, Brenthis ino, and evidence for a segregating neo-Z chromosome

Cited by 10 publications

References 52 publications

Genomic evidence reveals three sequential W-autosome fusions in Heliconius butterflies

Genomic evidence reveals three sequential W-autosome fusions in Heliconius butterflies

The genome sequence of the scarce swallowtail, Iphiclides podalirius

Rewinding the ratchet: rare recombination locally rescues neo-W degeneration and generates plateaus of sex-chromosome divergence

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