Aquatic Insects Are Dramatically Underrepresented in Genomic Research

Abstract

Aquatic insects comprise 10% of all insect diversity, can be found on every continent except Antarctica, and are key components of freshwater ecosystems. However, aquatic insect genome biology lags dramatically behind that of terrestrial insects. If genomic effort was spread evenly, one aquatic insect genome would be sequenced for every ~9 terrestrial insect genomes. Instead, ~24 terrestrial insect genomes have been sequenced for every aquatic insect genome. This discrepancy is even more dramatic if the quality of genomic resources is considered; for instance, while no aquatic insect genome has been assembled to the chromosome level, 29 terrestrial insect genomes spanning four orders have. We argue that a lack of aquatic insect genomes is not due to any underlying difficulty (e.g., small body sizes or unusually large genomes), yet it is severely hampering aquatic insect research at both fundamental and applied scales. By expanding the availability of aquatic insect genomes, we will gain key insight into insect diversification and empower future research for a globally important taxonomic group.

Draft Genome Assemblies and Annotations of Agrypnia vestita Walker, and Hesperophylax magnus Banks Reveal Substantial Repetitive Element Expansion in Tube Case-Making Caddisflies (Insecta: Trichoptera)

“…Relative to their diversity, most insect groups remain poorly represented in existing genomic resources—a trend which is particularly pronounced in aquatic insects ( Hotaling et al. 2020 ).…”

Genome size evolution in the diverse insect order Trichoptera

“…These new assemblies increase available assemblies in the order from nine to 26, nearly tripling the number of publicly available caddisfly reference genomes. The new genomes are of comparable or better quality than other Trichoptera genomes previously reported in terms of BUSCO completeness and contiguity (Table 1, Data S1) and expand the availability of genomic resources of aquatic insects which are underrepresented in genomic research (51).…”

Long-reads are revolutionizing 20 years of insect genome sequencing

“…We focused on taxonomic breadth rather than within-group efforts (e.g., The Anopheles gambiae 1000 Genomes Consortium 16 ) to gain more holistic insight on the field. Following similar studies 4,15,17 , we defined insects to include all groups within the subphylum Hexapoda. We then downloaded metadata for all nuclear Insecta genomes on GenBank 2 (accessed 2 November 2020).…”

“…Genome sequencing efforts in insects, however, have not been spread evenly. Aquatic insects, as a group, are underrepresented relative to their terrestrial counterparts (Hotaling, et al 2020). And, some orders (e.g., Diptera) are represented by far more genome assemblies than their species diversity alone would warrant-likely reflecting the model organisms within them-while many orders still have no genomic representation.…”