Biology subjects

Frandsen, P. B.

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

7 recordsLinked to original sources

bioRxiv2021

De novo chromosome level assembly of the mule deer (Odocoileus hemionus) genome

The mule deer (Odocoileus hemionus) is an ungulate species that ranges from western Canada to central Mexico. Mule deer are an essential source of food for many predators, are relatively abundant, and commonly make broad migration movements. A clearer understanding of the mule deer genome can help facilitate knowledge of its population genetics, movements, and demographic history, aiding in conservation efforts. While mule deer are excellent candidates for population genomic studies because of their large population size, continuous distribution, and diversity of habitat, few genomic resources are currently available for this species. Here, we sequence and assemble the mule deer genome into a highly contiguous chromosome-length assembly for use in future research using long-read sequencing and Hi-C. We also provide a genome annotation and compare demographic histories of the mule deer and white-tail deer using PSMC. We expect this assembly to be a valuable resource in the continued study and conservation of mule deer.

genomics↗

bioRxiv2021

Towards a genome sequence for every animal: where are we now?

In less than 25 years, the field of animal genome science has transformed from a discipline seeking its first glimpses into genome sequences across the Tree of Life to a global enterprise with ambitions to sequence genomes for all of Earths eukaryotic diversity (1). As the field rapidly moves forward, it is important to take stock of the progress that has been made to best inform the disciplines future. In this Perspective, we provide a contemporary, quantitative overview of animal genome sequencing. We identified the best available genome assemblies on GenBank, the worlds most extensive genetic database, for 3,278 unique animal species across 24 phyla. We assessed taxonomic representation, assembly quality, and annotation status for major clades. We show that while tremendous taxonomic progress has occurred, stark disparities in genomic representation exist, highlighted by a systemic overrepresentation of vertebrates and underrepresentation of arthropods. In terms of assembly quality, long-read sequencing has dramatically improved contiguity, whereas gene annotations are available for just 34.3% of taxa. Furthermore, we show that animal genome science has diversified in recent years with an ever-expanding pool of researchers participating. However, the field still appears to be dominated by institutions in the Global North, which have been listed as the submitting institution for 77% of all assemblies. We conclude by offering recommendations for how we can collectively improve genomic resource availability and value while also broadening global representation. Significance statementThe field of animal genome science is rapidly developing, and efforts are underway to sequence genomes for all of Earths eukaryotic biodiversity. Here, we provide an overview of animal genome sequencing, with emphases on taxonomic representation, assembly quality, and geographic representation. We show that while a staggering 3,278 unique animal species have had their genomes sequenced, massive disparities exist in terms of the taxonomic groups receiving attention, the quality of the resources being produced, and the institutions driving the field. We highlight areas where improvements can be made, notably by continuing to increase the quality of genome assemblies, including by improving metadata and voucher specimen associations, and actively developing meaningful collaborations between researchers form the Global North and South.

genomics↗

bioRxiv2021

Lessons from 20 years of plant genome sequencing: an unprecedented resource in need of more diverse representation

The field of plant genomics has grown rapidly in the past 20 years, leading to dramatic increases in both the quantity and quality of publicly available genomic resources. With this ever-expanding wealth of genomic data from an increasingly diverse set of taxa, unprecedented potential exists to better understand the genome biology and evolution of plants. Here, we provide a contemporary view of plant genomics, including analyses on the quality of existing plant genome assemblies, the taxonomic distribution of sequenced species, and how national participation has influenced the fields development. We show that genome quality has increased dramatically in recent years, that substantial taxonomic gaps exist, and that the field has been dominated by affluent nations in the Global North and China, despite a wide geographic distribution of sequenced species. We identify multiple disconnects between the native range of focal species and the national affiliation of the researchers studying the plants, which we argue are rooted in colonialism--both past and present. However, falling sequencing costs paired with widening availability of analytical tools and an increasingly connected scientific community provide key opportunities to improve existing assemblies, fill sampling gaps, and, most importantly, empower a more global plant genomics community.

plant biology↗

bioRxiv2021

Genome size evolution in the diverse insect order Trichoptera

BackgroundGenome size is implicated in form, function, and ecological success of a species. Two principally different mechanisms are proposed as major drivers of eukaryotic genome evolution and diversity: Polyploidy (i.e., whole genome duplication: WGD) or smaller duplication events and bursts in the activity of repetitive elements (RE). Here, we generated de novo genome assemblies of 17 caddisflies covering all major lineages of Trichoptera. Using these and previously sequenced genomes, we use caddisflies as a model for understanding genome size evolution in diverse insect lineages. ResultsWe detect a ~14-fold variation in genome size across the order Trichoptera. We find strong evidence that repetitive element (RE) expansions, particularly those of transposable elements (TEs), are important drivers of large caddisfly genome sizes. Using an innovative method to examine TEs associated with universal single copy orthologs (i.e., BUSCO genes), we find that TE expansions have a major impact on protein-coding gene regions, with TE-gene associations showing a linear relationship with increasing genome size. Intriguingly, we find that expanded genomes preferentially evolved in caddisfly clades with a higher ecological diversity (i.e., various feeding modes, diversification in variable, less stable environments). ConclusionOur findings provide a platform to test hypotheses about the potential evolutionary roles of TE activity and TE-gene associations, particularly in groups with high species, ecological, and functional diversities.

evolutionary biology↗

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↗