Analysis of the spotted gar genome suggests absence of causative link between ancestral genome duplication and transposable element diversification in teleost fish

Abstract

Teleost fish have been shown to contain many superfamilies of transposable elements (TEs) that are absent from most tetrapod genomes. Since theories predict an increase in TE activity following polyploidization, such diversity might be linked to the 3R whole-genome duplication that occurred approximately 300 million years ago before the teleost radiation. To test this hypothesis, we have analyzed the genome of the spotted gar Lepisosteus oculatus, which diverged from the teleost lineage before the 3R duplication. Our results indicate that TE diversity and copy numbers are similar in gar and teleost genomes, suggesting that TE diversity was ancestral and not linked to the 3R whole-genome duplication. We propose that about 25 distinct superfamilies of TEs were present in the last ancestor of gars and teleost fish about 300 million years ago in the ray-finned fish lineage.

Rex Retroelements and Teleost Genomes: An Overview

“…TEs exhibiting a great variety in structure, size and mechanisms of transposition can represent powerful drivers of species diversity [ 31 , 32 ]. Most teleost genomes are predominantly composed of DNA transposons, exception made for tetraodon and stickleback, in which no prevalence of particular type of TEs has been evidenced and for fugu which is rich in LINEs and SINEs.…”

Identification and characterization of homeobox (Hox) genes and conservation of the single Hox cluster (324.6 kb) in the water flea Daphnia magna

“…The Hox genes from the planulozoa lineage of cnidarians including the sea anemone Nematostella vectensis retained a duplicated primordial homeobox gene, forming a protohox cluster, while plant, fungi, and many unicellular animals also have homeobox-containing genes (Lappin, Grier, Thompson, & Halliday, 2006;Holland, 2013). In vertebrates, the structure of Hox gene clusters is more compact compared to their genome size, different from invertebrates (Pace et al, 2016 (Okada, Shedlock, & Nikaido, 2004;Chalopin & Volff, 2017), which is important in phylogenetic analysis. Thus, the presence of LINE/R2-NeSL in D. magna Hox genes (Figure 1) is likely due to a sporadic event caused by the retrotransposition of LINE transposons in the genome.…”

“…In invertebrate and vertebrate genomes, the expansion of genome size by incorporation of various LINEs with tandem duplication is quite common (Okada, Shedlock, & Nikaido, ; Chalopin & Volff, ), which is important in phylogenetic analysis. Thus, the presence of LINE/R2‐NeSL in D. magna Hox genes (Figure ) is likely due to a sporadic event caused by the retrotransposition of LINE transposons in the genome.…”

The Spotted Gar: Genomic Journeys into a Lost World

“…Chalopin and Volff () analyzed the TE content of the spotted gar genome, concluding that because of the similarity of TE diversity in gar and teleosts, the TGD did not lead to TE diversification.…”

“…Majtanova, Symonova, Arias-Rodriguez, Sallan, and Rab (2017) characterized the karyotype of bowfin (Amia calva), the only living representative of the Amiiformes, compared it with gar and other ray-finned species, and discussed it in the context of the notoriously controversial gar-bowfin-teleost interrelationships. Chalopin and Volff (2017) analyzed the TE content of the spotted gar genome, concluding that because of the similarity of TE diversity in gar and teleosts, the TGD did not lead to TE diversification. Martin and Holland (2017) used the spotted gar hox gene cluster complement as a pre-TGD reference point to follow the dynamic evolution of hox genes within the genomically underexplored teleost lineage of osteoglossomorphs.…”