<i>De novo</i> genome assemblies of butterflies

Ellis, Emily A.; Storer, Caroline; Kawahara, Akito Y.

doi:10.1093/gigascience/giab041

Cited by 26 publications

(21 citation statements)

References 41 publications

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“…Here we present our assembly for E. editha , an established model system for studying geographic mosaics of ecological adaptation and rapid evolutionary responses to anthropogenically driven environmental change. Our assembly placed 98% of the 608 Mb genome into a chromosomal framework and exhibited exceptionally high and accurate gene content as measured using BUSCO, placing this species among the best assembled Lepidopteran genomes to date ( Ellis et al 2021 ). We were able to annotate 23,870 high-quality genes and provide functional information for 20,771 of these.…”

Section: Discussionmentioning

confidence: 98%

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

Tunström

Wheat

Parmesan

et al. 2022

Genome Biology and Evolution

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Insects have been key players in assessments of biodiversity impacts of anthropogenically-driven environmental change, including the evolutionary and ecological impacts of climate change. Populations of Edith's Checkerspot Butterfly (Euphydryas editha) adapt rapidly to diverse environmental conditions, with numerous high-impact studies documenting these dynamics over several decades. However, studies of the underlying genetic bases of these responses have been hampered by missing genomic resources, limiting the ability to connect genomic responses to environmental change. Using a combination of Oxford Nanopore long reads, haplotype merging, HiC scaffolding followed by Illumina polishing, we generated a highly contiguous and complete assembly (contigs n = 142, N50 = 21.2 Mbp, total length= 607.8 Mbp; BUSCOs n = 5286, single copy complete = 97.8%, duplicated = 0.9%, fragmented = 0.3%, missing = 1.0%). A total of 98% of the assembled genome was placed into 31 chromosomes, which displayed large-scale synteny with other well characterized lepidopteran genomes. The E. editha genome, annotation and functional descriptions now fill a missing gap for one of the leading field-based ecological model systems in North America.

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Section: Discussionmentioning

confidence: 98%

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

Tunström

Wheat

Parmesan

et al. 2022

Genome Biology and Evolution

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“…Excluding Lepidoptera, which are skewed by a large number of poor-quality assemblies [ 39 ], median N50 lengths per order represented by ≥5 assemblies (shown in Fig. 2C ) range from 11.6 kb for Sarcoptiformes (mites, 15 assemblies for 12 species) to 96.3 Mb for Xiphosura (horseshoe crabs, 8 assemblies for 4 species).…”

Section: Resultsmentioning

confidence: 99%

Assessing species coverage and assembly quality of rapidly accumulating sequenced genomes

Féron

Waterhouse

2022

GigaScience

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Background Ambitious initiatives to coordinate genome sequencing of Earth's biodiversity mean that the accumulation of genomic data is growing rapidly. In addition to cataloguing biodiversity, these data provide the basis for understanding biological function and evolution. Accurate and complete genome assemblies offer a comprehensive and reliable foundation upon which to advance our understanding of organismal biology at genetic, species, and ecosystem levels. However, ever-changing sequencing technologies and analysis methods mean that available data are often heterogeneous in quality. To guide forthcoming genome generation efforts and promote efficient prioritization of resources, it is thus essential to define and monitor taxonomic coverage and quality of the data. Findings Here we present an automated analysis workflow that surveys genome assemblies from the United States NCBI, assesses their completeness using the relevant BUSCO datasets, and collates the results into an interactively browsable resource. We apply our workflow to produce a community resource of available assemblies from the phylum Arthropoda, the Arthropoda Assembly Assessment Catalogue. Using this resource, we survey current taxonomic coverage and assembly quality at the NCBI, examine how key assembly metrics relate to gene content completeness, and compare results from using different BUSCO lineage datasets. Conclusions These results demonstrate how the workflow can be used to build a community resource that enables large-scale assessments to survey species coverage and data quality of available genome assemblies, and to guide prioritizations for ongoing and future sampling, sequencing, and genome generation initiatives.

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“…Excluding Lepidoptera that are skewed by a large number of poor-quality assemblies (Ellis et al 2021), median N50 lengths per order represented by at least five assemblies (shown in Figure 2C) range from 11.6 Kbp for Sarcoptiformes (mites, 15 assemblies for 12 species) to 96.3 Mbp for Xiphosura (horseshoe crabs, 8 assemblies for 4 species).…”

Section: A Survey Of Arthropod Genome Assembly Resourcesmentioning

confidence: 99%

Assessing species coverage and assembly quality of rapidly accumulating sequenced genomes

Féron

Waterhouse

2021

Preprint

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Ambitious initiatives to coordinate genome sequencing of Earth's biodiversity mean that the accumulation of genomic data is growing rapidly. In addition to cataloguing biodiversity, these data provide the basis for understanding biological function and evolution. Accurate and complete genome assemblies offer a comprehensive and reliable foundation upon which to advance our understanding of organismal biology at genetic, species, and ecosystem levels. However, ever-changing sequencing technologies and analysis methods mean that available data are often heterogeneous in quality. In order to guide forthcoming genome generation efforts and promote efficient prioritisation of resources, it is thus essential to define and monitor taxonomic coverage and quality of the data. Here we present an automated analysis workflow that surveys genome assemblies from the United States National Center for Biotechnology Information (NCBI), assesses their completeness using the relevant Benchmarking Universal Single-Copy Orthologue (BUSCO) datasets, and collates the results into an interactively browsable resource. We apply our workflow to produce a community resource of available assemblies from the phylum Arthropoda, the Arthropoda Assembly Assessment Catalogue. Using this resource, we survey current taxonomic coverage and assembly quality at the NCBI, we examine how key assembly metrics relate to gene content completeness, and we compare results from using different BUSCO lineage datasets. These results demonstrate how the workflow can be used to build a community resource that enables large-scale assessments to survey species coverage and data quality of available genome assemblies, and to guide prioritisations for ongoing and future sampling, sequencing, and genome generation initiatives.

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De novo genome assemblies of butterflies

Cited by 26 publications

References 41 publications

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

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

Assessing species coverage and assembly quality of rapidly accumulating sequenced genomes

Assessing species coverage and assembly quality of rapidly accumulating sequenced genomes

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