Long Reads Are Revolutionizing 20 Years of Insect Genome Sequencing

Hotaling, Scott; Sproul, John S.; Heckenhauer, Jacqueline; Powell, Ashlyn; Larracuente, Amanda M.; Pauls, Steffen U.; Kelley, Joanna L.; Frandsen, Paul B.

doi:10.1093/gbe/evab138

Cited by 87 publications

(98 citation statements)

References 26 publications

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“…In other words, the assemblies are nearly at the chromosome level. For comparison, of the 76 representative drosophilid genomes that were previously available on NCBI (Hotaling et al, 2021), only have an N50 greater than 1Mb…”

Section: Near Chromosome-scale Assembly With Ultra-long Readsmentioning

confidence: 99%

“…We have built an open resource of 101 nearly chromosome-level drosophilid genome assemblies, adding to the rapidly growing number of high-quality genomes available for this model system (Hotaling et al, 2021;Suvorov et al, 2021). We envision this dataset being used to address a large number of outstanding questions entailing large comparative analyses among species, including the comparison of population genomic data between a large number of species, providing unprecedented resolution to investigate fundamental questions about the evolutionary process.…”

Section: Next Stepsmentioning

confidence: 99%

“…(B) The BUSCO (Simão et al, 2015) completeness (sum of complete single-copy and complete duplicated) of the NCBI assemblies of our assemblies is compared to the BUSCO completeness of our assemblies. The list of drosophilid genomes, contig N50s, and BUSCO completeness statistics were obtained from Hotaling et al (2021). Note, BUSCO v4 was used for both genome assessments, but the OrthoDB v10 (Kriventseva et al, 2019) Diptera gene set was used to evaluate our assemblies while the OrthoDB v10 Insecta set was used to evaluate the NCBI assemblies.…”

Section: Compute Containersmentioning

confidence: 99%

“…As it is a popular model system, an extensive collection of genomic resources exists for drosophilids today. Excluding genomes from this study, there are representative genome assemblies available on NCBI databases (GenBank and RefSeq) for about 75 different drosophilid species (Hotaling et al, 2021). About a third of these genomes are provided as chromosome-level scaffolds.…”

Section: Introductionmentioning

confidence: 99%

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Highly contiguous assemblies of 101 drosophilid genomes

Kim

Wang²,

Miller

et al. 2021

eLife

125

168

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Over 100 years of studies in Drosophila melanogaster and related species in the genus Drosophila have facilitated key discoveries in genetics, genomics, and evolution. While high-quality genome assemblies exist for several species in this group, they only encompass a small fraction of the genus. Recent advances in long-read sequencing allow high-quality genome assemblies for tens or even hundreds of species to be efficiently generated. Here, we utilize Oxford Nanopore sequencing to build an open community resource of genome assemblies for 101 lines of 93 drosophilid species encompassing 14 species groups and 35 sub-groups. The genomes are highly contiguous and complete, with an average contig N50 of 10.5 Mb and greater than 97% BUSCO completeness in 97/101 assemblies. We show that Nanopore-based assemblies are highly accurate in coding regions, particularly with respect to coding insertions and deletions. These assemblies, along with a detailed laboratory protocol and assembly pipelines, are released as a public resource and will serve as a starting point for addressing broad questions of genetics, ecology, and evolution at the scale of hundreds of species.

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Section: Near Chromosome-scale Assembly With Ultra-long Readsmentioning

confidence: 99%

Section: Next Stepsmentioning

confidence: 99%

Section: Compute Containersmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Highly contiguous assemblies of 101 drosophilid genomes

Kim

Wang²,

Miller

et al. 2021

eLife

125

168

View full text Add to dashboard Cite

show abstract

“…Non-model insect clades are largely underrepresented in genomic research, especially aquatic insects [51], [52]. This makes studying broad trends of genome evolution, such as the evolution of genome size and the links between ecological diversification and genome evolution, very difficult.…”

Section: Data Descriptionmentioning

confidence: 99%

Genome size evolution in the diverse insect order Trichoptera

Heckenhauer

Frandsen

et al. 2021

Preprint

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Genome size can vary widely over relatively short evolutionary time scales and is implicated in form, function and ecological success of a species. Here, we generated 17 new de novo whole genome assemblies and present a holistic view on genome size diversity of the highly diversified, non-model insect order, Trichoptera (caddisflies). We detect large variation in genome size and find strong evidence that transposable element (TE) expansions are the primary driver of genome size evolution: TE expansions contribute to larger genomes in clades with higher ecological diversity and have a major impact on protein-coding gene regions. These TE-gene associations show a linear relationship with increasing genome size. Our findings suggest new hypotheses for future testing, especially the effects of TE activity and TE-gene associations on genome stability, gene expression, phenotypes, and their potential adaptive advantages in groups with high species, ecological, and functional diversities.

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New insights into immune genes and other expanded gene families of the house fly, Musca domestica, from an improved whole genome sequence

Meisel,

Freeman,

Asgari

et al. 2023

Arch Insect Biochem Physiol

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The house fly, Musca domestica, is a pest of livestock, transmits pathogens of human diseases, and is a model organism in multiple biological research areas. The first house fly genome assembly was published in 2014 and has been of tremendous use to the community of house fly biologists, but that genome is discontiguous and incomplete by contemporary standards. To improve the house fly reference genome, we sequenced, assembled, and annotated the house fly genome using improved techniques and technologies that were not available at the time of the original genome sequencing project. The new genome assembly is substantially more contiguous and complete than the previous genome. The new genome assembly has a scaffold N50 of 12.46 Mb, which is a 50‐fold improvement over the previous assembly. In addition, the new genome assembly is within 1% of the estimated genome size based on flow cytometry, whereas the previous assembly was missing nearly one‐third of the predicted genome sequence. The improved genome assembly has much more contiguous scaffolds containing large gene families. To provide an example of the benefit of the new genome, we used it to investigate tandemly arrayed immune gene families. The new contiguous assembly of these loci provides a clearer picture of the regulation of the expression of immune genes, and it leads to new insights into the selection pressures that shape their evolution.

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Long Reads Are Revolutionizing 20 Years of Insect Genome Sequencing

Cited by 87 publications

References 26 publications

Highly contiguous assemblies of 101 drosophilid genomes

Highly contiguous assemblies of 101 drosophilid genomes

Genome size evolution in the diverse insect order Trichoptera

New insights into immune genes and other expanded gene families of the house fly, Musca domestica, from an improved whole genome sequence

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