Whole-Genome Sequencing of 84 Japanese Eels Reveals Evidence against Panmixia and Support for Sympatric Speciation

Genetic architecture of long-distance migration and population genomics of the endangered Japanese eel

The Japanese eel (Anguilla japonica), a flagship anguillid species for conservation, is known for its long-distance-oriented migration. However, our understanding of the genetic architecture underlying long-distance migration and population genomic characteristics of A. japonica is still limited. Here, we generated a high-quality chromosome-level genome assembly and conducted whole-genome resequencing of 218 individuals to explore these aspects. Strong signals of selection were found on genes involved in long-distance aerobic exercise and navigation, which might be associated with evolutionary adaptation to long-distance migrations. Low genetic diversity was detected, which might result from genetic drift associated with demographic declines. Both mitochondrial and nuclear genomic datasets supported the existence of a single panmictic population for Japanese eel, despite signals of single-generation selection. Candidate genes for local selection involved in functions like development and circadian rhythm. The findings can provide insights to adaptative evolution to long-distance migration and inform conservation efforts for A. japonica.

Genomic signatures for latitudinal selection in the tropical eel Anguilla marmorata

Selection acting across environmental gradients, such as latitudes, can cause spatial structuring of genomic variants even within panmictic populations. In this study, we focused on the within-generation latitudinal selection between northernmost and southernmost individuals of the North Pacific population of a tropical eel Anguilla marmorata, which shares its northernmost distribution with a temperate eel Anguilla japonica. Whole-genome sequencing data indicated that the northernmost and southernmost individuals of A. marmorata belong to a single panmictic population, as suggested by previous studies. On the contrary, parts of genomic regions across multiple chromosomes exhibited significant genetic differentiation between the northernmost and southernmost individuals, and in these genomic regions, the genotypes of the northernmost individuals were similar to those of A. japonica. These findings suggested within-generation latitudinal selection of A. marmorata, which might have led to genetic closeness between northernmost A. marmorata and A. japonica.

Histological Evidence of Multiple Spawning in Wild Female Japanese Eel Anguilla japonica

The post ovulatory follicle (POF) is an important and reliable tissue structure used to investigate the spawning history in teleost fish. Fresh POFs shortly after spawning are comprised of cellular (follicular cells) and acellular (basement membrane and fibrils such as elastic fibers) components. The cellular components are quickly disintegrated by means of apoptosis, while the acellular components persist for a longer period. Since cellular components are well visualized by conventional hematoxylin-eosin (HE) staining but acellular components are not stained well, old POFs that have lost cellular components are difficult to identify. In this study, periodic acid-Schiff and Victoria blue staining, which can distinctly visualize acellular POF components, were applied to the ovarian tissues of Japanese eel (Anguilla japonica) (n = 9) captured from June to August of 2008, 2009, and 2013 at the southern West Mariana Ridge, a spawning area for Japanese eels. Only new POFs were observed in seven females caught in June, and these females had ovaries with early-to mid-vitellogenic stage oocytes. Both fresh and old POFs were observed in a female caught in July, and only mid-vitellogenic stage oocytes were observed. Only old POFs and no vitellogenic stage oocyte were observed in a female caught in August. A progressive decrease in muscle lipid content, gonad somatic index, and condition factors was observed from June to August. Thus, the female Japanese eel can spawn at least twice or three times at most during spawning season, depending on energy reserve.

Investigating Diadromy in Fishes and Its Loss in an -Omics Era

Diadromy, the predictable movements of individuals between marine and freshwater environments, is biogeographically and phylogenetically widespread across fishes. Thus, despite the high energetic and potential fitness costs involved in moving between distinct environments, diadromy appears to be an effective life history strategy. Yet, the origin and molecular mechanisms that underpin this migratory behavior are not fully understood. In this review, we aim first to summarize what is known about diadromy in fishes; this includes the phylogenetic relationship among diadromous species, a description of the main hypotheses regarding its origin, and a discussion of the presence of non-migratory populations within diadromous species. Second, we discuss how recent research based on -omics approaches (chiefly genomics, transcriptomics, and epigenomics) is beginning to provide answers to questions on the genetic bases and origin(s) of diadromy. Finally, we suggest future directions for -omics research that can help tackle questions on the evolution of diadromy.

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.

Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives

The sea represents a major source of biodiversity. It exhibits many different ecosystems in a huge variety of environmental conditions where marine organisms have evolved with extensive diversification of structures and functions, making the marine environment a treasure trove of molecules with potential for biotechnological applications and innovation in many different areas. Rapid progress of the omics sciences has revealed novel opportunities to advance the knowledge of biological systems, paving the way for an unprecedented revolution in the field and expanding marine research from model organisms to an increasing number of marine species. Multi-level approaches based on molecular investigations at genomic, metagenomic, transcriptomic, metatranscriptomic, proteomic, and metabolomic levels are essential to discover marine resources and further explore key molecular processes involved in their production and action. As a consequence, omics approaches, accompanied by the associated bioinformatic resources and computational tools for molecular analyses and modeling, are boosting the rapid advancement of biotechnologies. In this review, we provide an overview of the most relevant bioinformatic resources and major approaches, highlighting perspectives and bottlenecks for an appropriate exploitation of these opportunities for biotechnology applications from marine resources.