Reviewing the Long Sequencing Road in Twenty Years (1): Insect Genomics

Insect genomics has come a long way since the Drosophila melanogaster genome was published in 2000

As of November 2020, the nuclear genomes of 601 different insect species were assembled in the GenBank database

Taxonomic representation of genome assemblies of 601 insect species in GenBank

Today, a new insect species genome is deposited into GenBank every two to three days

As Washington State University postdoc Scott Hotaling noted in his review of 20 years of insect genome sequencing, "We have entered a new era of insect genome biology

"Most noteworthy is the impact of long-read sequencing; assemblies that included long reads were about 48-fold more contiguous than assemblies that did not include long reads," he added

According to PacBio, the new low-input and ultra-low-input workflows on the Sequel II Sequencing System benefit entomologists as it advances the sequencing of the smallest insect species

Scott Hotaling and Paul Frandsen of Brigham Young University and others published a review titled "Long Reads Are Revolutionizing 20 Years of Insect Genome Sequencing" in the journal Genome Biology and Evolution

The researchers noted that while more than 600 taxa seem impressive, there are still many taxonomic gaps

"Aquatic insects are underrepresented as a group relative to terrestrial insects

specific number:

▪Genome sequencing and assembly efforts are currently focused on four orders: Diptera, Hymenoptera, Collembola, and Stick Insects

▪The order Coleoptera (the first order of insects), which contains 387,100 species of insects, is significantly underrepresented

▪Six orders have only one representative genome assembly, while 11 orders have no published assemblies

The authors call for greater integration between independent groups and research consortia, such as the i5K project, which prepares to sequence the genomes of 5,000 different arthropod species

As of 2019, only 40% of insect genome assemblies have corresponding gene annotations in GenBank; the authors believe that expanding and refining gene annotations in insects will drive a corresponding increase in the size of taxonomic comparisons that will be feasible for many analyses

HiFi sequencing enables the rapid assembly of complex organisms and helps scientists build more diverse clade datasets
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"With genome assemblies in public repositories representing more than 600 taxa and about 480 million years of evolutionary history, the power and promise of insect genome research has never been greater," concluded Hotaling
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"We agree with the Vertebrate Genome Project's findings—that long-read assemblies are more sequential than short-read methods—and recommend these techniques to insect genome scientists
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