The genome sequence of the ringlet, Aphantopus hyperantus Linnaeus 1758

Mead, Daniel; Saccheri, Ilik J.; Yung, Carl J.; Lohse, Konrad; Lohse, Carla; Ashmole, Philip; Smith, Michelle; Corton, Craig; Oliver, Karen; Skelton, Jason; Betteridge, Emma; Quail, Michael A.; Dolucan, Jale; McCarthy, Shane; Howe, Kerstin; Wood, Jonathan; Torrance, James; Tracey, Alan S.; Whiteford, Sam; Challis, Richard; Durbin, Richard; Blaxter, Mark

doi:10.12688/wellcomeopenres.16983.1

Cited by 6 publications

(4 citation statements)

References 11 publications

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“…In short, Maker is usually run several times successively and uses the gene models generated in one round to train ab initio gene-predictors and improve the initial gene models in the next round (see below). We used the above-mentioned hardmasked genomes and carried out their annotation using the proteomes of three closely-related species, namely Pararge aegeria [29], Maniola hyperantus [30] and Bicyclus anynana [31]. For each species, the output files were merged into a gff3 file that was then used to generate the necessary files to train SNAP (version 2006-07-28), an ab initio gene finding program [32].…”

Section: Methodsmentioning

confidence: 99%

Genome assembly of three AmazonianMorphobutterfly species reveals Z-chromosome rearrangements between closely-related species living in sympatry

Bastide¹,

López‐Villavicencio

Ogereau³

et al. 2022

Preprint

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The genomic processes enabling speciation and the coexistence of species in sympatry are still largely unknown. Here we describe the whole genome sequence of three closely-related species from the butterfly genus Morpho : Morpho achilles (Linnaeus, 1758), M. helenor (Cramer, 1776) and M. deidamia (H ̈ubner, 1819). These large blue butterflies are emblematic species of the Amazonian rainforest. They live in sympatry in a wide range of their geographical distribution and display parallel diversification of dorsal wing colour pattern, suggesting local mimicry. By sequencing, assembling and annotating their genomes, we aim at uncovering pre-zygotic barriers preventing gene flow between these sympatric species. We found a genome size of 480 Mb for the three species and a chromosomal number ranging from 2n = 54 for M. deidamia to 2n = 56 for M. achilles and M. helenor. We also detected inversions on the sex chromosome Z that were differentially fixed between species, suggesting that chromosomal rearrangements may contribute to their reproductive isolation. The annotation of their genomes allowed us to recover in each species at least 12,000 protein-coding genes and to discover duplications of genes potentially involved in pre-zygotic isolation like genes controlling colour discrimination (L-opsin). Altogether, the assembly and the annotation of these three new reference genomes open new research avenues into the genomic architecture of speciation and reinforcement in sympatry, establishing Morpho butterflies as a new eco-evolutionary model.

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Section: Methodsmentioning

confidence: 99%

Genome assembly of three AmazonianMorphobutterfly species reveals Z-chromosome rearrangements between closely-related species living in sympatry

Bastide¹,

López‐Villavicencio

Ogereau³

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…In short, MAKER is usually run several times successively and uses the gene models generated in 1 round to train ab initio gene predictors and improve the initial gene models in the next round (see below). We used the abovementioned hardmasked genomes and carried out their annotation using the proteomes of 3 closely related species, namely, P. aegeria [ 29 ], Maniola hyperantus [ 30 ], and Bicyclus anynana [ 31 ]. For each species, the output files were merged into a gff3 file that was then used to generate the necessary files to train SNAP (version 2006-07-28), an ab initio gene-finding program [ 32 ].…”

Section: Methodsmentioning

confidence: 99%

Genome assembly of 3 Amazonian Morpho butterfly species reveals Z-chromosome rearrangements between closely related species living in sympatry

Bastide¹,

López‐Villavicencio

Ogereau³

et al. 2022

GigaScience

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The genomic processes enabling speciation and species coexistence in sympatry are still largely unknown. Here we describe the whole-genome sequencing and assembly of 3 closely related species from the butterfly genus Morpho: Morpho achilles (Linnaeus, 1758), Morpho helenor (Cramer, 1776), and Morpho deidamia (Höbner, 1819). These large blue butterflies are emblematic species of the Amazonian rainforest. They live in sympatry in a wide range of their geographical distribution and display parallel diversification of dorsal wing color pattern, suggesting local mimicry. By sequencing, assembling, and annotating their genomes, we aim at uncovering prezygotic barriers preventing gene flow between these sympatric species. We found a genome size of 480 Mb for the 3 species and a chromosomal number ranging from 2n = 54 for M. deidamia to 2n = 56 for M. achilles and M. helenor. We also detected inversions on the sex chromosome Z that were differentially fixed between species, suggesting that chromosomal rearrangements may contribute to their reproductive isolation. The annotation of their genomes allowed us to recover in each species at least 12,000 protein-coding genes and to discover duplications of genes potentially involved in prezygotic isolation like genes controlling color discrimination (L-opsin). Altogether, the assembly and the annotation of these 3 new reference genomes open new research avenues into the genomic architecture of speciation and reinforcement in sympatry, establishing Morpho butterflies as a new eco-evolutionary model.

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“…Outgroup data were taken from chromosome-resolved assemblies of other Nymphalid butterflies that were publicly available at the time of analysis: the Satyrini Pararge aegeria ( 80 ), Aphantopus hyperantus ( 81 ), and more distant outgroups Aglais urticae ( 82 ), Vanessa atalanta ( 83 ), and Vanessa cardui ( 84 ). To obtain single copy orthologs (SCOs) among all assemblies, each assembly including E. ligea was annotated with WebAugustus ( 85 , 86 ) in two steps: First, gene prediction was run using the standard Augustus species parameters for Heliconius melpomene.…”

Section: Methodsmentioning

confidence: 99%

A macroevolutionary role for chromosomal fusion and fission in Erebia butterflies

Augustijnen,

Bätscher,

Cesanek

et al. 2024

Sci. Adv.

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The impact of large-scale chromosomal rearrangements, such as fusions and fissions, on speciation is a long-standing conundrum. We assessed whether bursts of change in chromosome numbers resulting from chromosomal fusion or fission are related to increased speciation rates in Erebia , one of the most species-rich and karyotypically variable butterfly groups. We established a genome-based phylogeny and used state-dependent birth-death models to infer trajectories of karyotype evolution. We demonstrated that rates of anagenetic chromosomal changes (i.e., along phylogenetic branches) exceed cladogenetic changes (i.e., at speciation events), but, when cladogenetic changes occur, they are mostly associated with chromosomal fissions rather than fusions. We found that the relative importance of fusion and fission differs among Erebia clades of different ages and that especially in younger, more karyotypically diverse clades, speciation is more frequently associated with cladogenetic chromosomal changes. Overall, our results imply that chromosomal fusions and fissions have contrasting macroevolutionary roles and that large-scale chromosomal rearrangements are associated with bursts of species diversification.

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The genome sequence of the ringlet, Aphantopus hyperantus Linnaeus 1758

Cited by 6 publications

References 11 publications

Genome assembly of three AmazonianMorphobutterfly species reveals Z-chromosome rearrangements between closely-related species living in sympatry

Genome assembly of three AmazonianMorphobutterfly species reveals Z-chromosome rearrangements between closely-related species living in sympatry

Genome assembly of 3 Amazonian Morpho butterfly species reveals Z-chromosome rearrangements between closely related species living in sympatry

A macroevolutionary role for chromosomal fusion and fission in Erebia butterflies

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