Three genomes of Osteoglossidae shed light on ancient teleost evolution

Osteoglossiformes is a basal clade of teleost, originating from the late Jurassic period, which has experienced the process of continental drift. The genomic differences between Osteoglossiformes species should reflect the unique evolutionary history of that time.

Here, we present the chromosome-level genome of Heterotis niloticus which is the only omnivore species of Osteoglossidae spreading in Africa. Analysis of this species and another two Osteoglossidae species genomes, Arapaima gigas and Scleropages formosus, which spread in South America and Australia, respectively, revealed great evolutionary differences in gene families and transposable elements.

Phylogenetic analysis showed that the ancestor of H. niloticus and A. gigas diverged with S. formosus at ~106.1 Mya, consistent with the time of the Afro-South American drift, and A. gigas speciated from the ancestor of H. niloticus and A. gigas at ~59.2 Mya, consistent with the separation of Eurasia and the North American continents.

We propose the evolutionary history of Osteoglossidae species based on comparative genomics analysis as well as their living geographical habitats.

We identified the rapid loss of LINEs and LTRs in evolution, in parallel with a fast pseudogenization rate in H. niloticus and A. gigas compared to S. formosus during the evolutionary process.

We also found notable olfactory receptor (OR) gene contraction in H. niloticus, which might be related to the dietary transition.

Taken together, we have reconstructed the evolutionary process of Osteoglossidae using three representative genomes, providing insight into the biogeographical changes and evolution of the ancient teleost clade.