African Arowana Genome Provides Insights on Ancient Teleost Evolution

Abstract

Summary Osteoglossiformes is a basal clade of teleost, evolving since the Jurassic period. The genomes of Osteoglossiformes species would shed light on the evolution and adaptation of teleost. Here, we established a chromosome-level genome of African arowana. Together with the genomes of pirarucu and Asian arowana, we found that they diverged at ∼106.1 million years ago (MYA) and ∼59.2 MYA, respectively, which are coincident with continental separation. Interestingly, we identified a dynamic genome evolution characterized by a fast evolutionary rate and a high pseudogenization rate in African arowana and pirarucu. Additionally, more transposable elements were found in Asian arowana which confer more gene duplications. Moreover, we found the contraction of olfactory receptor and the expansion of UGT in African arowana might be related to its transformation from carnivore to be omnivore. Taken together, we provided valuable genomic resource of Osteoglossidae and revealed the correlation of biogeography and teleost evolution.

The Emerging Phylogenetic Perspective on the Evolution of Actinopterygian Fishes

“…Subsequent analyses of whole mitochondrial (mt)DNA genomes, concatenated data sets from a few nuclear genes, combinations of mtDNA and nuclear genes, and ultraconserved elements (UCEs) have resulted in phylogenies in which either the osteoglossomorphs or elopomorphs are resolved as the sister lineage of all other teleosts, often with weak to moderate node support (Betancur-R et al 2013, Faircloth et al 2013, Inoue et al 2001, Near et al 2012). More recently, several phylogenomic-scale analyses (Chen et al 2015;Hao et al 2020;Hughes et al 2018, figures S2, S3, S4, and S5;Vialle et al 2018;Wcisel et al 2020) of whole genomes or transcriptomes using both DNA sequences and amino acids from protein-coding genes harken to the earliest molecular studies in strongly resolving elopomorphs and osteoglossomorphs as a clade (Figure 3c). In these phylogenomic studies, statistical tree topology tests soundly reject the two alternative hypotheses (Bian et al 2016).…”

“…Although recent work using phylogenetic informativeness profiles suggests that homoplasy is masking the signal of elopomorphs as sister to all other teleosts (Takezaki 2021), consideration of the signal-to-noise ratios supporting this relationship as well as other sources of conflict are needed to increase confidence in this resolution. To motivate such studies, we retain the unconventional and intriguing possibility of an osteoglossomorph and elopomorph sister group relationship as a resolution requiring additional investigation and scrutiny (Figure 3c), because it is one that appears frequently and is surprisingly well supported by available phylogenomic data sets (Bayesian and bootstrap values >95%) (e.g., Bian et al 2016;Hao et al 2020;Hughes et al 2018, figures S2, S3, S4, and S5).…”

Phylogenetic Classification of Living and Fossil Ray-Finned Fishes (Actinopterygii)

“…The earliest molecular phylogenetic studies of teleosts resolved Elopomorpha and Osteoglossomorpha as sister lineages (Lê et al 1993), which is a frequent result in phylogenomic analyses (M.-Y. Chen et al 2015;Bian et al 2016;Lin et al 2016;Hughes et al 2018;Vialle et al 2018;Hao et al 2020;Roth et al 2020;Wcisel et al 2020;Takezaki 2021;Parey et al 2023). Evidence from genomic organization in the form of the conservation of gene adjacency and the proportion of shared chromosomal breakpoints support monophyly of Oseanacephala (Parey et al 2023).…”