Genetic parameters and quantitative trait loci analysis associated with body size and timing at metamorphosis into glass eels in captive-bred Japanese eels (Anguilla japonica)

Genomic Footprints of Hybridisation in North Atlantic Eels (Anguilla anguilla and A. rostrata)

Understanding interspecific introgressive hybridisation and the biological significance of introgressed variation remains an important goal in population genomics. European (Anguilla anguilla) and American eel (A. rostrata) represent a remarkable case of hybridisation. Both are panmictic and spawn in partial sympatry in the Sargasso Sea, occasionally producing viable, fertile hybrids, primarily found in Iceland. We studied introgressive hybridisation from American into European eel using whole-genome sequences of 78 individuals, including European, American and 21 putative hybrid eels. Previous studies using few genetic markers could not resolve whether hybridisation involved simple unidirectional backcrossing or a more complex hybrid swarm scenario. However, local ancestry inference along individual chromosomes revealed that Icelandic hybrids were primarily F1 or first-generation backcrosses towards European eel, with some showing more complex backcrossing. All European eels outside Iceland contained short chromosomal blocks from American eel, indicating a porous genome. We found no evidence for previously hypothesised geographical gradients of introgression in European eel outside Iceland. Several chromosomal regions showed high interspecific divergence, but haplotype blocks introgressed from American eel were identified both within and outside these regions. There was little correspondence between regions of high relative (FST) and absolute divergence (dXY), with the former reflecting selective sweeps within species or reduced recombination rather than barrier loci. A single genomic region showed evidence of repeated introgression from American into European eel under positive selection in both species. The study illustrates that species can maintain genetic integrity despite porous genomes and that standing variation in one species can potentially be available for future adaptive responses in the other species.

Transcriptome analysis of the Japanese eel (Anguilla japonica) during larval metamorphosis

BACKGROUND

Anguillid eels spend their larval period as leptocephalus larvae that have a unique and specialized body form with leaf-like and transparent features, and they undergo drastic metamorphosis to juvenile glass eels. Less is known about the transition of leptocephali to the glass eel stage, because it is difficult to catch the metamorphosing larvae in the open ocean. However, recent advances in rearing techniques for the Japanese eel have made it possible to study the larval metamorphosis of anguillid eels. In the present study, we investigated the dynamics of gene expression during the metamorphosis of Japanese eel leptocephali using RNA sequencing.

RESULTS

During metamorphosis, Japanese eels were classified into 7 developmental stages according to their morphological characteristics, and RNA sequencing was used to collect gene expression data from each stage. A total of 354.8 million clean reads were generated from the body and 365.5 million from the head, after the processing of raw reads. For filtering of genes that characterize developmental stages, a classification model created by a Random Forest algorithm was built. Using the importance of explanatory variables feature obtained from the created model, we identified 46 genes selected in the body and 169 genes selected in the head that were defined as the "most characteristic genes" during eel metamorphosis. Next, network analysis and subsequently gene clustering were conducted using the most characteristic genes and their correlated genes, and then 6 clusters in the body and 5 clusters in the head were constructed. Then, the characteristics of the clusters were revealed by Gene Ontology (GO) enrichment analysis. The expression patterns and GO terms of each stage were consistent with previous observations and experiments during the larval metamorphosis of the Japanese eel.

CONCLUSION

Genome and transcriptome resources have been generated for metamorphosing Japanese eels. Genes that characterized metamorphosis of the Japanese eel were identified through statistical modeling by a Random Forest algorithm. The functions of these genes were consistent with previous observations and experiments during the metamorphosis of anguillid eels.

Developmental features of Japanese eels, Anguilla japonica, from the late leptocephalus to the yellow eel stages: an early metamorphosis to the eel-like form and a prolonged transition to the juvenile

Organogenesis of Japanese eels (Anguilla japonica) was investigated histologically from the late leptocephalus to the yellow eel stages. Early organogenesis, such as the formation of inner ears and the appearance of round blood cells that might be larval erythrocytes, had already begun at the late leptocephalus stage. During the first developmental phase (M1-M3 stages) of metamorphosing into early glass eels (G1 stage), the formation of gills and lateral muscles progressed conspicuously with a drastic body shape change from leaf-like to eel-like. In contrast, obvious regression in oesophageal muscle and pancreas occurred during metamorphosis. Formation of lateral line canals advanced continuously until the yellow eel stage. When the second developmental phase was initiated at the G1 stage, cone photoreceptor cells appeared, and the formation of oesophageal, stomach and intestinal muscles was initiated. Differentiation of gastric glands began at 1 week after metamorphosis. Erythrocytes increased continuously in density in glass eels and elvers (G1-E2 stages), and the morphological features of cone cells and olfactory epidermal cells became clearer with stage progression. In early elvers (E1 stage), the swimbladder initiated inflation, the stomach fully expanded and the rectal longitudinal fold changed to a circle. Swimbladder gas glands appeared in late elvers (E2 stage). In the yellow eels (juvenile stage), almost all organ structures were formed. These observations indicate that the organogenesis of A. japonica is ongoing after metamorphosis into glass eels, and the M1-E2 stages are considered to be a homologous phase to first metamorphosis, which is a transformation from the larval to the juvenile stages in other teleosts. In comparison to conger eels, the completion of the body shape change to eel-like occurs at the G1 stage, when organogenesis is still in progress, being followed by a prolonged duration of the G1-E2 stages before reaching the yellow eel juvenile stage, which may be a unique characteristic that is related to the early migratory life history of A. japonica.

Phylogeny of teleost connexins reveals highly inconsistent intra- and interspecies use of nomenclature and misassemblies in recent teleost chromosome assemblies

BACKGROUND

Based on an initial collecting of database sequences from the gap junction protein gene family (also called connexin genes) in a few teleosts, the naming of these sequences appeared variable. The reasons could be (i) that the structure in this family is variable across teleosts, or (ii) unfortunate naming. Rather clear rules for the naming of genes in fish and mammals have been outlined by nomenclature committees, including the naming of orthologous and ohnologous genes. We therefore analyzed the connexin gene family in teleosts in more detail. We covered the range of divergence times in teleosts (eel, Atlantic herring, zebrafish, Atlantic cod, three-spined stickleback, Japanese pufferfish and spotted pufferfish; listed from early divergence to late divergence).

RESULTS

The gene family pattern of connexin genes is similar across the analyzed teleosts. However, (i) several nomenclature systems are used, (ii) specific orthologous groups contain genes that are named differently in different species, (iii) several distinct genes have the same name in a species, and (iv) some genes have incorrect names. The latter includes a human connexin pseudogene, claimed as GJA4P, but which in reality is Cx39.2P (a delta subfamily gene often called GJD2like). We point out the ohnologous pairs of genes in teleosts, and we suggest a more consistent nomenclature following the outlined rules from the nomenclature committees. We further show that connexin sequences can indicate some errors in two high-quality chromosome assemblies that became available very recently.

CONCLUSIONS

Minimal consistency exists in the present practice of naming teleost connexin genes. A consistent and unified nomenclature would be an advantage for future automatic annotations and would make various types of subsequent genetic analyses easier. Additionally, roughly 5% of the connexin sequences point out misassemblies in the new high-quality chromosome assemblies from herring and cod.

Genome Sequencing of the Japanese Eel (Anguilla japonica) for Comparative Genomic Studies on tbx4 and a tbx4 Gene Cluster in Teleost Fishes

Limbs originated from paired fish fins are an important innovation in Gnathostomata. Many studies have focused on limb development-related genes, of which the T-box transcription factor 4 gene (tbx4) has been considered as one of the most essential factors in the regulation of the hindlimb development. We previously confirmed pelvic fin loss in tbx4-knockout zebrafish. Here, we report a high-quality genome assembly of the Japanese eel (Anguilla japonica), which is an economically important fish without pelvic fins. The assembled genome is 1.13 Gb in size, with a scaffold N50 of 1.03 Mb. In addition, we collected 24 tbx4 sequences from 22 teleost fishes to explore the correlation between tbx4 and pelvic fin evolution. However, we observed complete exon structures of tbx4 in several pelvic-fin-loss species such as Ocean sunfish (Mola mola) and ricefield eel (Monopterus albus). More interestingly, an inversion of a special tbx4 gene cluster (brip1-tbx4-tbx2b- bcas3) occurred twice independently, which coincides with the presence of fin spines. A nonsynonymous mutation (M82L) was identified in the nuclear localization sequence (NLS) of the Japanese eel tbx4. We also examined variation and loss of hindlimb enhancer B (HLEB), which may account for pelvic fin loss in Tetraodontidae and Diodontidae. In summary, we generated a genome assembly of the Japanese eel, which provides a valuable genomic resource to study the evolution of fish tbx4 and helps elucidate the mechanism of pelvic fin loss in teleost fishes. Our comparative genomic studies, revealed for the first time a potential correlation between the tbx4 gene cluster and the evolutionary development of toxic fin spines. Because fin spines in teleosts are usually venoms, this tbx4 gene cluster may facilitate the genetic engineering of toxin-related marine drugs.

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

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.