De novo European eel transcriptome provides insights into the evolutionary history of duplicated genes in teleost lineages

Abstract

Paralogues pairs are more frequently observed in eels (Anguilla sp.) than in other teleosts. The paralogues often show low phylogenetic distances; however, they have been assigned to the third round of whole genome duplication (WGD), shared by all teleosts (3R), due to their conserved synteny. The apparent contradiction of low phylogenetic difference and 3R conserved synteny led us to study the duplicated gene complement of the freshwater eels. With this aim, we assembled de novo transcriptomes of two highly relevant freshwater eel species: The European (Anguilla anguilla) and the Japanese eel (Anguilla japonica). The duplicated gene complement was analysed in these transcriptomes, and in the genomes and transcriptomes of other Actinopterygii species. The study included an assessment of neutral genetic divergence (4dTv), synteny, and the phylogenetic origins and relationships of the duplicated gene complements. The analyses indicated a high accumulation of duplications (1217 paralogue pairs) among freshwater eel genes, which may have originated in a WGD event after the Elopomorpha lineage diverged from the remaining teleosts, and thus not at the 3R. However, very similar results were observed in the basal Osteoglossomorpha and Clupeocephala branches, indicating that the specific genomic regions of these paralogues may still have been under tetrasomic inheritance at the split of the teleost lineages. Therefore, two potential hypotheses may explain the results: i) The freshwater eel lineage experienced an additional WGD to 3R, and ii) Some duplicated genomic regions experienced lineage specific rediploidization after 3R in the ancestor to freshwater eels. The supporting/opposing evidence for both hypotheses is discussed.

Fig 1. Methodology.

Pipeline of the bioinformatics methodology. Folders describe the software used, light grey boxes describe the action taken, light brown bubbles describes the rationale for selected actions, and light blue boxes describe the specific goal of each section. Finally, green boxes represent external data input.

Fig 2. Synteny illustration.

Visualization of the assigned synteny types: “some synteny” ($●$), paralogues of genes found close to one duplicate are also found close to the other duplicate; “no synteny” ($●$), less than two paralogues for other genes are found close to both paralogue duplicates; “close” ($●$), duplicated genes are close in the genome; “no information” ($●$), the duplicated genes are located in small scaffolds with too few gene families close by; “conflicting syntenies” ($●$), different synteny classification found in the genomes of the different species affected by the duplication. Sand coloured boxes represent genes which have not been assigned to a gene family, pink boxes represent the gene from which synteny is being assessed; all other colour boxes represent other genes which have been assigned to a gene family.

Fig 3. BUSCO analysis.

BUSCO (Benchmarking set of Universal Single-Copy Orthologues) result for included genomes and transcriptomes. The sequence of a BUSCO gene can be found complete or fragmented in each genome and it can be found once (single copy), more than once (duplicated) or not found (missing). Included genomes are: European eel (Anguilla anguilla), Japanese eel (Anguilla japonica), Asian arowana (Scleropages formosus), zebrafish (Danio rerio), northern pike (Esox lucius), spotted gar (Lepisosteus oculatus), fugu (Takifugu rubripes), platyfish (Xiphophorus maculatus) and Atlantic salmon (Salmo salar). Included transcriptomes: European eel, Japanese eel, northern pike, elephantnose fish (Gnathonemus petersii) and silver arowana (Osteoglossum bicirrhosum).

Fig 4. 4dTv and synteny distributions of duplications per branch of the PHYLDOG species tree.

Quantity, 4dTv and synteny distributions of duplications assigned to each branch of the PHYLDOG species tree. Each panel represents the branch with the corresponding number in the cladogram in the bottom right-hand corner. Species included in this study are: European eel (Anguilla anguilla), Japanese eel (Anguilla japonica), zebrafish (Danio rerio), northern pike (Esox lucius), spotted gar (Lepisosteus oculatus), fugu (Takifugu rubripes), platyfish (Xiphophorus maculatus), Atlantic salmon (Salmo salar), elephantnose fish (Gnathonemus petersii), Asian arowana (Scleropages formosus) and silver arowana (Osteoglossum bicirrhosum). The synteny types are the following: close ($●$), duplicated genes are close in the genome; some synteny ($●$), paralogues of genes found close to one duplicate are also found close to the other duplicate; no synteny ($●$), less than two paralogeus for other genes are found close to both paralogue duplicates; no information ($●$), the duplicated genes are located in small scaffolds with too few genes close by; conflicting syntenies ($●$), different synteny classifications found in the genomes of the different species affected by the duplication.

Fig 5. 4dTv distribution between European eel, elephantnose fish, and the arowanas homologs.

4dTv distribution of European eel (Anguilla anguilla) and Japanese eel homologs ($▬$), European eel and elephantnose fish (Gnathonemus petersii) homologs ($▬$), and European eel, silver arowana (Osteoglossum bicirrhosum) homologs ($▬$), and European eel and Asian arowana (Scleropages formosus) homologs ($▬$).

Fig 6. Density distribution of all 4dTv distances between teleost paralogues.

Histograms of all 4dTv distances between paralogues of the included teleosts, presented with yellow and blue bars. Furthermore, a probability density estimate curve is plotted on top of the histograms in red. Density values (y-axis) do not correspond to the density estimate. The included species are: European eel (Anguilla anguilla), Japanese eel (Anguilla japonica), zebrafish (Danio rerio), northern pike (Esox lucius), spotted gar (Lepisosteus oculatus), fugu (Takifugu rubripes), platyfish (Xiphophorus maculatus), Atlantic salmon (Salmo salar), elephantnose fish (Gnathonemus petersii), Asian arowana (Scleropages formosus) and silver arowana (Osteoglossum bicirrhosum).