Biology subjects

Frandsen, P. B.

Publications and source records attributed to Frandsen, P. B..

3 recordsLinked to original sources

bioRxiv2021

Long-reads are revolutionizing 20 years of insect genome sequencing

The first insect genome (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 towards 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 megabases 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 ~48x 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. Significance statementSince the first insect genome was sequenced ~20 years ago, sequencing technologies and the availability of insect genome assemblies have both advanced dramatically. In this study, we curated, analyzed, and summarized the field of insect genomics in terms of taxonomic representation, assembly quality, gene completeness, and sequencing technology. We show that 601 insect species have genome assemblies available, with some groups heavily overrepresented (e.g., Diptera) relative to others (e.g., Coleoptera). The major takeaway of our study is that genome assemblies produced with long reads are ~48x more contiguous than short read assemblies.

genomics↗

bioRxiv2020

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

Trichoptera (caddisflies) play an essential role in freshwater ecosystems; for instance, larvae process organic material from the water and are food for a variety of predators. Knowledge on the genomic diversity of caddisflies can facilitate comparative and phylogenetic studies thereby allowing scientists to better understand the evolutionary history of caddisflies. While Trichoptera are the most diverse aquatic insect order, they remain poorly represented in terms of genomic resources. To date, all long-read based genomes have been sequenced from individuals in the retreat-making suborder, Annulipalpia, leaving [~]275 Ma of evolution without high-quality genomic resources. Here, we report the first long-read based de novo genome assemblies of two tube case-making Trichoptera from the suborder Integripalpia, Agrypnia vestita Walker and Hesperophylax magnus Banks. We find that these tube case-making caddisflies have genome sizes that are at least three-fold larger than those of currently sequenced annulipalpian genomes and that this pattern is at least partly driven by major expansion of repetitive elements. In H. magnus, long interspersed nuclear elements (LINEs) alone exceed the entire genome size of some annulipalpian counterparts suggesting that caddisflies have high potential as a model for understanding genome size evolution in diverse insect lineages. SignificanceThere is a lack of genomic resources for aquatic insects. So far, only three high-quality genomes have been assembled, all from individuals in the retreat-making suborder Annulipalpia. In this article, we report the first high-quality genomes of two case-making species from the suborder Integripalpia, which are essential for studying genomic diversity across this ecologically diverse insect order. Our research reveals larger genome sizes in the tube case-makers (suborder Integripalpia, infraorder Phryganides), accompanied by a disproportionate increase of repetitive DNA. This suggests that genome size is at least partly driven by a major expansion of repetitive elements. Our work shows that caddisflies have high potential as a model for understanding how genomic diversity might be linked to functional diversification and forms the basis for detailed studies on genome size evolution in caddisflies. Data depositionThis project has been deposited at NCBI under the Bioproject ID: PRJNA668166

genomics↗

bioRxiv2020

Aquatic insects are dramatically underrepresented in genomic research

Aquatic insects comprise 10% of all insect diversity, can be found on every continent except Antarctica, and are key components of freshwater ecosystems. Yet 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. Simple SummaryAquatic insects comprise 10% of all insect diversity, can be found on every continent except Antarctica, and are key components of freshwater ecosystems. Yet 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. We argue that the limited availability of aquatic insect genomes is not due to practical limitations--e.g., small body sizes or overly complex genomes--but instead reflects a lack of research interest. We call for targeted efforts to expand the availability of aquatic insect genomic resources to gain key molecular insight into insect diversification and empower future research.

genomics↗