Toward a genome sequence for every animal: Where are we now?

Abstract

In less than 25 y, 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 Earth’s eukaryotic diversity [H. A. Lewin et al., Proc. Natl. Acad. Sci. U.S.A. 115, 4325–4333 (2018)]. As the field rapidly moves forward, it is important to take stock of the progress that has been made to best inform the discipline’s future. In this Perspective, we provide a contemporary, quantitative overview of animal genome sequencing. We identified the best available genome assemblies in GenBank, the world’s 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 improving genomic resource availability and research value while also broadening global representation.

Long-read HiFi sequencing correctly assembles repetitive heavy fibroin silk genes in new moth and caddisfly genomes

“…Eubasilissa regina, on the other hand, is a member of the insect order Trichoptera, whose larvae secrete silk in aquatic environments to produce protective silk cases made of broader leaf pieces from deciduous trees, cut to size [13]. These new resources not only expand our knowledge of a primary silk gene in Lepidoptera and Trichoptera, but also contribute new, high-quality genomic resources for aquatic insects and arthropods, which have thus far been underrepresented in genome biology [14][15][16].…”

Reference genome choice and filtering thresholds jointly influence phylogenomic analyses

“…Another promising possibility to improve such bias is using multiple references to create a “pseudogenome” for the species of interest (Huang et al, 2014), as demonstrated in Sarver et al (2017). Both of these options are increasingly possible due to the acceleration in genome sequencing for non-model taxa (Hotaling et al, 2021; Rhie et al, 2021; Formenti et al, 2022). However, not every clade of interest will have multiple reasonable reference genome options.…”

“…Recent advances in sequencing technologies along with falling sequencing costs have made it increasingly feasible to sequence and assemble reference genomes for non-model species (Feng et al, 2020; Kolora et al, 2021; Hotaling et al, 2021; Formenti et al, 2022; Rhie et al, 2021). Non-model reference genomes can then be used to assemble short reads from reduced-representation or whole genome sequencing into shared loci across individuals, and an increasing number of studies use a reference genome of a focal study taxon for assembly.…”

Long-read HiFi Sequencing Correctly Assembles Repetitive heavy fibroin Silk Genes in New Moth and Caddisfly Genomes

“…We show that PacBio HiFi sequencing allows for accurate generation of repetitive protein-coding regions of the genome (silk fibroins ), and this likely applies to other similarly repetitive regions of the genome. For Trichoptera, there are only four other HiFi genome assemblies available on Genbank, only one of which has been published [38] and insects have generally been neglected (relative to their total species diversity) with respect to genome sequencing efforts [15-16], which is especially true for aquatic insects [14]. These data serve as the first step to study the evolution of adhesive silk in Amphiesmenoptera, which is an innovation that is beneficial for survival in aquatic and terrestrial environments.…”