The genome sequence of the small white, Pieris rapae (Linnaeus, 1758)

Lohse, Konrad; Ebdon, Sam; Vila, Roger

doi:10.12688/wellcomeopenres.17288.1

Cited by 4 publications

(8 citation statements)

References 18 publications

(9 reference statements)

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“…2B), suggesting divergence through genome contraction/expansion between the sister species. For consistency, the P. mannii chromosomes in the v2 genomes are numbered according to their homologues in P. rapae (Lohse et al 2021). Both v2 assemblies were subjected to ab initio gene prediction, and functional annotation identified 14,010 (UniProt/Swiss-Prot) and 9,769 (UniProt/TrEMBL) protein coding sequences for the male, and 14,183 and 10,369 genes for the female.…”

Section: Resultsmentioning

confidence: 99%

“…Finally, the candidate W contig exhibited an unusually high GC content (fig. 4, right), which appears to be a characteristic feature of lepidopteran W chromosomes (Wan et al 2019; Lewis et al 2021; Lohse et al 2021). Taken together, these analyses made clear that the female v1 assembly contained the W chromosome, which was retained for the female v2 assembly (fig.…”

Section: Resultsmentioning

confidence: 99%

“…The two raw contig-level (‘v1’) assemblies directly returned from the Hifiasm assembler were subjected to homology search using the chromosome-level genome of Pieris rapae (Lohse et al 2021; GenBank accession GCF_905147795.1), the sister species of P. mannii (Wiemers et al 2020). For this, we mapped each of the 26 P. rapae chromosomes (including the W) separately against our male and female v1 assemblies using Minimap2 (v2.20; Li et al 2018).…”

Section: Methodsmentioning

confidence: 99%

“…Aligning the v1 assemblies to a high-quality genome (Lohse et al 2021) of the closely related sister species Pieris rapae (divergence time around 3.3 million years; Wiemers et al 2020) revealed that the vast majority of the 25 P. mannii chromosomes, as determined cytogenetically (Lorkovic 1985; this excludes the W chromosome), were already represented in full length by contigs of the v1 assemblies (fig. S1; table S1).…”

Section: Chromosome-level Genome Assemblies For Pieris Manniimentioning

confidence: 99%

Section: Chromosome-level Genome Assemblies For Pieris Manniimentioning

confidence: 99%

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Chromosome-level assemblies of thePieris manniibutterfly genome suggest Z-origin and rapid evolution of the W chromosome

Blattner

Ruffener

Berner

2023

Preprint

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The insect order Lepidoptera (butterflies and moth) represents the largest group of organisms with ZW/ZZ sex determination. While the origin of the Z chromosome predates the evolution of the Lepidoptera, the W chromosome is considered younger, but its origin is debated. To shed light on the origin of the lepidopteran W, we here produce chromosome-level genome assemblies for the butterfly Pieris mannii, and compare the sex chromosomes within and between P. mannii and its sister species P. rapae. Our analyses clearly indicate a common origin of the W chromosomes of the two Pieris species, and reveal similarity between the Z and W in chromosome sequence and structure. This supports the view that the W originates from Z-autosome fusion rather than from a redundant B chromosome. We further demonstrate the extremely rapid evolution of the W relative to the other chromosomes and argue that this may preclude reliable conclusions about the origin of the W based on comparisons among distantly related Lepidoptera. Finally, we find that sequence similarity between the Z and W chromosomes is greatest toward the chromosome ends, perhaps reflecting selection for the maintenance of recognition sites essential to chromosome segregation. Our study highlights the utility of long-read sequencing technology for illuminating chromosome evolution.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Chromosome-level Genome Assemblies For Pieris Manniimentioning

confidence: 99%

Section: Chromosome-level Genome Assemblies For Pieris Manniimentioning

confidence: 99%

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Chromosome-level assemblies of thePieris manniibutterfly genome suggest Z-origin and rapid evolution of the W chromosome

Blattner

Ruffener

Berner

2023

Preprint

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Current stewardship practices in invasion biology limit the value and secondary use of genomic data

Vaughan,

Parvizi,

Matheson

et al. 2023

Molecular Ecology Resources

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Invasive species threaten native biota, putting fragile ecosystems at risk and having a large‐scale impact on primary industries. Growing trade networks and the popularity of personal travel make incursions a more frequent risk, one only compounded by global climate change. With increasing publication of whole‐genome sequences lies an opportunity for cross‐species assessment of invasive potential. However, the degree to which published sequences are accompanied by satisfactory spatiotemporal data is unclear. We assessed the metadata associated with 199 whole‐genome assemblies of 89 invasive terrestrial invertebrate species and found that only 38% of these were derived from field‐collected samples. Seventy‐six assemblies (38%) reported an ‘undescribed’ sample origin and, while further examination of associated literature closed this gap to 23.6%, an absence of spatial data remained for 47 of the total assemblies. Of the 76 assemblies that were ultimately determined to be field‐collected, associated metadata relevant for invasion studies was predominantly lacking: only 35% (27 assemblies) provided granular location data, and 33% (n = 25) lacked sufficient collection date information. Our results support recent calls for standardized metadata in genome sequencing data submissions, highlighting the impact of missing metadata on current research in invasion biology (and likely other fields). Notably, large‐scale consortia tended to provide the most complete metadata submissions in our analysis—such cross‐institutional collaborations can foster a culture of increased adherence to improved metadata submission standards and a standard of metadata stewardship that enables reuse of genomes in invasion science.

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A time course analysis through diapause reveals dynamic temporal patterns of microRNAs associated with endocrine regulation in the butterfly Pieris napi

Roberts,

Steward,

Süess

et al. 2024

Molecular Ecology

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Organisms inhabiting highly seasonal environments must cope with a wide range of environmentally induced challenges. Many seasonal challenges require extensive physiological modification to survive. In winter, to survive extreme cold and limited resources, insects commonly enter diapause, which is an endogenously derived dormant state associated with minimized cellular processes and low energetic expenditure. Due to the high degree of complexity involved in diapause, substantial cellular regulation is required, of which our understanding primarily derives from the transcriptome via messenger RNA expression dynamics. Here we aim to advance our understanding of diapause by investigating microRNA (miRNA) expression in diapausing and direct developing pupae of the butterfly Pieris napi. We identified coordinated patterns of miRNA expression throughout diapause in both head and abdomen tissues of pupae, and via miRNA target identification, found several expression patterns to be enriched for relevant diapause‐related physiological processes. We also identified two candidate miRNAs, miR‐14‐5p and miR‐2a‐3p, that are likely involved in diapause progression through their activity in the ecdysone pathway, a critical regulator of diapause termination. miR‐14‐5p targets phantom, a gene in the ecdysone synthesis pathway, and is upregulated early in diapause. miR‐2a‐3p has been found to be expressed in response to ecdysone, and is upregulated during diapause termination. Together, the expression patterns of these two miRNAs match our current understanding of the timing of hormonal regulation of diapause in P. napi and provide interesting candidates to further explore the mechanistic role of microRNAs in diapause regulation.

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The genome sequence of the small white, Pieris rapae (Linnaeus, 1758)

Cited by 4 publications

References 18 publications

Chromosome-level assemblies of thePieris manniibutterfly genome suggest Z-origin and rapid evolution of the W chromosome

Chromosome-level assemblies of thePieris manniibutterfly genome suggest Z-origin and rapid evolution of the W chromosome

Current stewardship practices in invasion biology limit the value and secondary use of genomic data

A time course analysis through diapause reveals dynamic temporal patterns of microRNAs associated with endocrine regulation in the butterfly Pieris napi

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