A Genome for Edith’s Checkerspot Butterfly: An Insect with Complex Host-Adaptive Suites and Rapid Evolutionary Responses to Environmental Changes

Tunström, Kalle; Wheat, Christopher W.; Parmesan, Camille; Singer, Michael C.; Mikheyev, Alexander S.

doi:10.1093/gbe/evac113

Cited by 5 publications

(4 citation statements)

References 53 publications

(53 reference statements)

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“…Overall, for most Morpho species, we annotated between 18,159 and 21,017 protein coding genes in their genomes (see table S2). These values are close to what has been found using similar procedures in other Nymphalidae species, as Euphydryas editha [67] or Lacanobia w − latinum [5]. In M.helenor however, we found an excess of annotated genes, as we recovered 29,734 complete genes.This elevated number of annotated genes is unlikely to stem from artefactual gene duplications since the BUSCO score in this species did not revealed any increase in gene duplication as compared to the other species.…”

Section: Resultssupporting

confidence: 89%

“…Euphydryas editha [67] or Lacanobia w − latinum [5]. In M.helenor however, we found an excess of annotated genes, as we recovered 29,734 complete genes.This elevated number of annotated genes is unlikely to stem from artefactual gene duplications since the BUSCO score in this species did not revealed any increase in gene duplication as compared to the other species.…”

Section: Genome Annotationmentioning

confidence: 64%

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Increased evolutionary rate in the Z-chromosome ofMorphobutterflies and implications for speciation

Villavicencio,

Ledamoisel,

Lopez-Roques

et al. 2024

Preprint

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The evolution of reproductive isolation between populations shapes divergence in genome structure and content: comparing the genomes of closely-related species can thus enlighten the speciation process. Comparisons of genomes of allopatric vs. sympatric species sharing similar vs. dissimilar ecological niches allows to specifically investigate the effect of reinforcement and ecological specialization on genome evolution. In the butterfly genus Morpho, several species can be found in sympatry presenting specialisation in different microhabitats and temporal niches. Here, we sequenced, assembled and annotated the genomes of 8 Morpho species and used previously published genomes of three other Morpho species to study genomic rearrangements and signatures of positive selection. We found extensive chromosomal rearrangements in the Z chromosome compared to the autosomes, particularly among closely related sympatric species occupying similar niches, pointing at the putative role of inversions in preventing gene flow at a postzygotic level. We also detected a higher proportion of genes under positive selection on the Z-chromosome compared to the autosomes, suggesting a potential role of the Z-chromosome in driving adaptive evolution in Morpho. Finally, because of the divergence in daily activities between species, we studied the evolution of eight genes involved in the circadian clock and detected a signature of positive selection on the gene Period, located in the Z chromosome. By studying the evolution of genome structure and coding sequences, our study indicates fast evolution of the Z-chromosome, partly driven by selection, throughout this genus, highlighting the putative implication of this sexual chromosome on pre and post-zygotic isolation.

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Section: Resultssupporting

confidence: 89%

Section: Genome Annotationmentioning

confidence: 64%

Increased evolutionary rate in the Z-chromosome ofMorphobutterflies and implications for speciation

Villavicencio,

Ledamoisel,

Lopez-Roques

et al. 2024

Preprint

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“…We used nucmer from mummer4 ( Marçais et al 2018 ) to align our M. mineus genome to 28 chromosomes of B. anynana genome and visualized the synteny in R using scripts from Tunstrom et al (2022) .…”

Section: Methodsmentioning

confidence: 99%

Genome Assembly and Annotation of the Dark-Branded Bushbrown Butterfly Mycalesis mineus (Nymphalidae: Satyrinae)

Murugesan,

Tian,

Monteiro

2024

Genome Biology and Evolution

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We report a high-quality genome draft assembly of the Dark-branded Bushbrown, Mycalesis mineus, a member of the Satyrinae subfamily of nymphalid butterflies. This species is emerging as a promising model organism for investigating the evolution and development of phenotypic plasticity. Using 45.99 Gb of long-read data (N50=11.11 Kb), we assembled a genome size of 497.4 Mb for M. mineus. The assembly is highly contiguous and nearly complete (96.8% of BUSCO lepidopteran genes were complete and single-copy). The genome comprises 38.71% of repetitive elements and includes 20,967 predicted protein coding genes. The assembled genome was super-scaffolded into 28 pseudo-chromosomes using a closely related species, Bicyclus anynana, with a chromosomal-level genome as a template. This valuable genomic tool will advance both ongoing and future research focused on this model organism.

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“…[ 8 , 9 , 10 , 11 , 12 ]. As a result of developments in sequencing technology, samples can now be directly collected from the wild for sequencing and subsequent analysis, bypassing some of the time-consuming processes in laboratory rearing and inbreeding [ 13 , 14 , 15 , 16 , 17 ]. This provides great possibilities to learn more about butterflies, particularly for some uncommon and rare species.…”

Section: Introductionmentioning

confidence: 99%

Chromosome-Level Genome Assembly of Papilio elwesi Leech, 1889 (Lepidoptera: Papilionidae)

Pan

Ding²,

Zhang³

et al. 2023

Insects

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A rarely seen butterfly species, the large swallowtail butterfly Papilio elwesi Leech, 1889 (Lepidoptera: Papilionidae), endemic to the Chinese mainland, has been declared a state-protected animal in China since 2000, but its genome is not yet available. To obtain high-quality genome assembly and annotation, we sequenced the genome and transcriptome of P. elwesi using the PacBio and PromethION platforms, respectively. The final assembled genome was 358.51 Mb, of which 97.59% was anchored to chromosomes (30 autosomes and 1 Z sex chromosome), with a contig/scaffold N50 length of 6.79/12.32 Mb and 99.0% (n = 1367) BUSCO completeness. The genome annotation pointed to 36.82% (131.99 Mb) repetitive elements and 1296 non-coding RNAs in the genome, along with 13,681 protein-coding genes that cover 98.6% (1348) of the BUSCO genes. Among the 11,499 identified gene families, 104 underwent significantly rapid expansions or contractions, and these rapidly expanding families play roles in detoxification and metabolism. Additionally, strong synteny exists between the chromosomes of P. elwesi and P. machaon. The chromosome-level genome of P. elwesi could serve as an important genomic resource for furthering our understanding of butterfly evolution and for more in-depth genomic analyses.

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A Genome for Edith’s Checkerspot Butterfly: An Insect with Complex Host-Adaptive Suites and Rapid Evolutionary Responses to Environmental Changes

Cited by 5 publications

References 53 publications

Increased evolutionary rate in the Z-chromosome ofMorphobutterflies and implications for speciation

Increased evolutionary rate in the Z-chromosome ofMorphobutterflies and implications for speciation

Genome Assembly and Annotation of the Dark-Branded Bushbrown Butterfly Mycalesis mineus (Nymphalidae: Satyrinae)

Chromosome-Level Genome Assembly of Papilio elwesi Leech, 1889 (Lepidoptera: Papilionidae)

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