Long Reads Are Revolutionizing 20 Years of Insect Genome Sequencing

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

doi:10.1093/gbe/evab138

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Long Reads Are Revolutionizing 20 Years of Insect Genome Sequencing

Journal article

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Long Reads Are Revolutionizing 20 Years of Insect Genome Sequencing

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

Genome biology and evolution, Vol.13(8)

08/03/2021

DOI: https://doi.org/10.1093/gbe/evab138

PMID: 34152413

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Abstract

Animals

Drosophila melanogaster

Genome, Insect

High-Throughput Nucleotide Sequencing

Sequence Analysis, DNA

Genomics

The first insect genome assembly (Drosophila melanogaster) was published two decades ago. Today, nuclear genome assemblies are available for a staggering 601 insect species representing 20 orders. In this study, we analyzed the most-contiguous assembly for each species and provide a "state-of-the-field" perspective, emphasizing taxonomic representation, assembly quality, gene completeness, and sequencing technologies. Relative to species richness, genomic efforts have been biased toward four orders (Diptera, Hymenoptera, Collembola, and Phasmatodea), Coleoptera are underrepresented, and 11 orders still lack a publicly available genome assembly. The average insect genome assembly is 439.2 Mb in length with 87.5% of single-copy benchmarking genes intact. Most notable has been the impact of long-read sequencing; assemblies that incorporate long reads are ∼48× more contiguous than those that do not. We offer four recommendations as we collectively continue building insect genome resources: 1) seek better integration between independent research groups and consortia, 2) balance future sampling between filling taxonomic gaps and generating data for targeted questions, 3) take advantage of long-read sequencing technologies, and 4) expand and improve gene annotations.

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Title: Long Reads Are Revolutionizing 20 Years of Insect Genome Sequencing
Creators: Scott Hotaling - Washington State University, Biological Sciences, School of
John S Sproul - University of Rochester
Jacqueline Heckenhauer - LOEWE Centre for Translational Biodiversity Genomics
Ashlyn Powell - Brigham Young University
Amanda M Larracuente - University of Rochester
Steffen U Pauls - University of Giessen
Joanna L Kelley - Washington State University, Biological Sciences, School of
Paul B Frandsen - LOEWE Centre for Translational Biodiversity Genomics
Publication Details: Genome biology and evolution, Vol.13(8)
Academic Unit: Kelley Lab
Grant note: R35 GM119515 / NIGMS NIH HHS
Identifiers: 99900882931101842
Language: English
Resource Type: Journal article