A chromosome-level genome assembly of longnose gar, Lepisosteus osseus

Abstract

Holosteans (gars and bowfins) represent the sister lineage to teleost fishes, the latter being a clade that comprises over half of all living vertebrates and includes important models for comparative genomics and human health. A major distinction between the evolutionary history of teleosts and holosteans is that all teleosts experienced a genome duplication event in their early evolutionary history. As the teleost genome duplication occurred after teleosts diverged from holosteans, holosteans have been heralded as a means to bridge teleost models to other vertebrate genomes. However, only three species of holosteans have been genome-sequenced to date, and sequencing of more species is needed to fill sequence sampling gaps and provide a broader comparative basis for understanding holostean genome evolution. Here we report the first high quality reference genome assembly and annotation of the longnose gar (Lepisosteus osseus). Our final assembly consists of 22,709 scaffolds with a total length of 945 bp with contig N50 of 116.61 kb. Using BRAKER2, we annotated a total of 30,068 genes. Analysis of the repetitive regions of the genome reveals the genome to contain 29.12% transposable elements, and the longnose gar to be the only other known vertebrate outside of the spotted gar and bowfin to contain CR1, L2, Rex1, and Babar. These results highlight the potential utility of holostean genomes for understanding the evolution of vertebrate repetitive elements, and provide a critical reference for comparative genomic studies utilizing ray-finned fish models.

Investigating the impact of whole genome duplication on transposable element evolution in ray-finned fishes

“…To assemble a dataset of TE content across major ray-finned fish lineages, we integrated the results of the repeat analysis of the P. bichir genome with other publicly available analyses of transposable elements in ray-finned fishes. For non-teleosts, this captured TE content from two additional polypteriform genomes for E. calabaricus (Helfenrath et al 2021) and P. senegalus (Fujito and Nonaka 2012), Acipenser ruthenus (Du et al 2020) as a representative of Chondrostei, as well as Lepisosteus oculatus (Braasch et al 2016), L. osseus (Mallik et al 2023), and Amia calva (Thompson et al 2021) as representative holosteans. These data were integrated with data from 98 teleost genomes previously analyzed for TE content (Reinar et al 2023), that capture the majority of major teleost lineages including Elopomorpha, Osteoglossomorpha, Otocephala, and a large number of acanthomorph and non-acanthomorph euteleosts.…”

“…In contrast, the three remaining extant ray-finned fish lineages – Holostei (gars and bowfin, 8 species), Acipenseriformes (sturgeon and paddlefish, 29 species), and Polypteridae (bichirs and ropefishes, 14 species)– did not undergo the teleost specific genome duplication event. Recent studies of holostean genomes have highlighted differences in the composition of TEs between holosteans and model teleosts such as zebrafish ( Danio rerio ) and medaka ( Oryzias latipes ) (Braasch et al 2016; Thompson et al 2021; Mallik et al 2023), raising the possibility of an evolutionary shift following a genome duplication event in teleosts. Comparative genomic studies are needed to rule out the possibility that the mobilomes of holosteans, and not teleosts, are unusual relative to all other ray-finned fishes.…”