Unveiling the expansion of keratin genes in lungfishes: a possible link to terrestrial adaptation

Keratins are intermediate filament proteins that are important for epidermal strength and protection from desiccation. Keratin genes are highly duplicated and have diversified by forming two major clusters in the genomes of terrestrial vertebrates. The keratin genes of lungfishes, the closest fish to tetrapods, have not been studied at the genomic level, despite the importance of lungfishes in terrestrial adaptation. Here, we identified keratin genes in the genomes of two lungfish species and performed syntenic and phylogenetic analyses. Additionally, we identified keratin genes from two gobies and two mudskippers, inhabiting underwater and terrestrial environments. We found that in lungfishes, keratin genes were duplicated and diversified within two major clusters, similar to but independent of terrestrial vertebrates. By contrast, keratin genes were not notably duplicated in mudskippers. The results indicate that keratin gene duplication occurred repeatedly in lineages close to tetrapods, but not in teleost fish, even in species adapted to terrestrial environments.

Plastic loss of motile cilia in the gills of Polypterus in response to high CO2 or terrestrial environments

The evolutionary transition of vertebrates from water to land during the Devonian period was accompanied by major changes in animal respiratory systems in terms of physiology and morphology. Indeed, the fossil record of the early tetrapods has revealed the existence of internal gills, which are vestigial fish-like traits used underwater. However, the fossil record provides only limited data on the process of the evolutionary transition of gills from fish to early tetrapods. This study investigated the gills of Polypterus senegalus, a basal ray-finned/amphibious fish which shows many ancestral features of stem Osteichthyes. Based on scanning electron microscopy observations and transcriptome analysis, the existence of motile cilia in the gills was revealed which may create a flow on the gill surface leading to efficient ventilation or remove particles from the surface. Interestingly, these cilia were observed to disappear after rearing in terrestrial or high CO₂ environments, which mimics the environmental changes in the Devonian period. The cilia re-appeared after being returned to the original aquatic environment. The ability of plastic changes of gills in Polypterus revealed in this study may allow them to survive in fluctuating environments, such as shallow swamps. The ancestor of Osteichthyes is expected to have possessed such plasticity in the gills, which may be one of the driving forces behind the transition of vertebrates from water to land.

Tracing the genetic footprints of vertebrate landing in non-teleost ray-finned fishes

Rich fossil evidence suggests that many traits and functions related to terrestrial evolution were present long before the ancestor of lobe- and ray-finned fishes. Here, we present genome sequences of the bichir, paddlefish, bowfin, and alligator gar, covering all major early divergent lineages of ray-finned fishes. Our analyses show that these species exhibit many mosaic genomic features of lobe- and ray-finned fishes. In particular, many regulatory elements for limb development are present in these fishes, supporting the hypothesis that the relevant ancestral regulation networks emerged before the origin of tetrapods. Transcriptome analyses confirm the homology between the lung and swim bladder and reveal the presence of functional lung-related genes in early ray-finned fishes. Furthermore, we functionally validate the essential role of a jawed vertebrate highly conserved element for cardiovascular development. Our results imply the ancestors of jawed vertebrates already had the potential gene networks for cardio-respiratory systems supporting air breathing.

Comparative osteology of the hynobiid complex Liua-Protohynobius-Pseudohynobius (Amphibia, Urodela): Ⅰ. Cranial anatomy of Pseudohynobius

Hynobiidae are a clade of salamanders that diverged early within the crown radiation and that retain a considerable number of features plesiomorphic for the group. Their evolutionary history is informed by a fossil record that extends to the Middle Jurassic Bathonian time. Our understanding of the evolution within the total group of Hynobiidae has benefited considerably from recent discoveries of stem hynobiids but is constrained by inadequate anatomical knowledge of some extant forms. Pseudohynobius is a derived hynobiid clade consisting of five to seven extant species living endemic to southwestern China. Although this clade has been recognized for over 37 years, osteological details of these extant hynobiids remain elusive, which undoubtedly has contributed to taxonomic controversies over the hynobiid complex Liua-Protohynobius-Pseudohynobius. Here we provide a bone-by-bone study of the cranium in the five extant species of Pseudohynobius (Ps. flavomaculatus, Ps. guizhouensis, Ps. jinfo, Ps. kuankuoshuiensis and Ps. shuichengensis) based on x-ray computer tomography data for 18 specimens. Our results indicate that the cranium in each of these species has a combination of differences in morphology, proportions and articulation patterns in both dermal and endochondral bones. Our study establishes a range of intraspecific differences that will serve as organizing hypotheses for future studies as more extensive collections of these species become available. Morphological features in the cranium for terrestrial ecological adaptation in Hynobiidae are summarized. Based on the results, we also discuss the evolution and development of several potential synapomorphies of Hynobiidae, including features of the orbitosphenoid and articular.

Comparative Transcriptome Analysis During the Seven Developmental Stages of Channel Catfish (Ictalurus punctatus) and Tra Catfish (Pangasianodon hypophthalmus) Provides Novel Insights for Terrestrial Adaptation

Tra catfish (Pangasianodon hypophthalmus), also known as striped catfish, is a facultative air-breather that uses its swim bladder as an air-breathing organ (ABO). A related species in the same order (Siluriformes), channel catfish (Ictalurus punctatus), does not possess an ABO and thus cannot breathe in the air. Tra and channel catfish serve as great comparative models for investigating possible genetic underpinnings of aquatic to land transitions, as well as for understanding genes that are crucial for the development of the swim bladder and the function of air-breathing in tra catfish. In this study, hypoxia challenge and microtomy experiments collectively revealed critical time points for the development of the air-breathing function and swim bladder in tra catfish. Seven developmental stages in tra catfish were selected for RNA-seq analysis based on their transition to a stage that could live at 0 ppm oxygen. More than 587 million sequencing clean reads were generated, and a total of 21,448 unique genes were detected. A comparative genomic analysis between channel catfish and tra catfish revealed 76 genes that were present in tra catfish, but absent from channel catfish. In order to further narrow down the list of these candidate genes, gene expression analysis was performed for these tra catfish-specific genes. Fourteen genes were inferred to be important for air-breathing. Of these, HRG, GRP, and CX3CL1 were identified to be the most likely genes related to air-breathing ability in tra catfish. This study provides a foundational data resource for functional genomic studies in air-breathing function in tra catfish and sheds light on the adaptation of aquatic organisms to the terrestrial environment.

A new millipede-parasitizing horsehair worm, Gordius chiashanus sp. nov., at medium altitudes in Taiwan (Nematomorpha, Gordiida)

Gordiuschiashanussp. nov., a newly described horsehair worm that parasitizes the Spirobolus millipede, is one of the three described horsehair worm species in Taiwan. It is morphologically similar to G.helveticus Schmidt-Rhaesa, 2010 because of the progressively broadening distribution of bristles concentrated on the male tail lobes, but it is distinguishable from G.helveticus because of the stout bristles on the mid-body. In addition, a vertical white stripe on the anterior ventral side and areoles on the inside wall of the cloacal opening are rarely mentioned in other Gordius species. Free-living adults emerged and mated on wet soil under the forest canopy in the winter (late November to early February) at medium altitudes (1100–1700 m). Mucus-like structure covering on the body surface, which creates a rainbow-like reflection, might endow the worm with high tolerance to dehydration. Although Gordiuschiashanussp. nov. seems to be more adaptive to the terrestrial environment than other horsehair worm species, cysts putatively identified as belonging to this hairworm species found in the aquatic paratenic host, Ephemeraorientalis McLachlan, 1875, suggest the life cycle of Gordiuschiashanussp. nov. could involve water and land. The free-living adults emerged from the definitive hosts might reproduce in the terrestrial environment or enter an aquatic habitat by moving or being washed away by heavy rain instead of manipulating the behavior of their terrestrial definitive hosts.

A Comparative Metagenomics Study on Gastrointestinal Microbiota in Amphibious Mudskippers and Other Vertebrate Animals

Simple Summary

Mudskippers are important ecological components of intertidal ecosystems. It was proposed that their guts may play significant roles for terrestrial adaptations of these amphibious fishes. However, their gastrointestinal components and differences in microbiota with other vertebrates were never reported. Here, we performed a comparative metagenome analysis among various vertebrate groups, classified by living habitats and feeding habits, and also acquired microbial gene catalogs of five common fish species. Our findings confirmed the dominant microbial genera in each vertebrate group, as well as bacteriocin-related genes in the five common fish species, for discussion of their relationships with fish pathogenic diseases. Our big data will support in-depth investigations into potential roles of gastrointestinal microbiota to hosts and related applications in aquaculture practices.

Abstract

Gut microbiomes in various fish species were widely investigated with the rapid development of next-generation sequencing technologies. However, little is known about gastrointestinal (GI) microbial communities in mudskippers, a representative group of marine amphibious fishes, and their comparisons with other vertebrate animals from different habitats. Here, we performed a comprehensive analysis on microbial composition in five representative vertebrate groups (including amphibious mudskippers, marine and freshwater aquatic fishes, amphibians, and terrestrial animals) via operational taxonomic unit (OTU) survey and obtained a microbial gene catalog of five common fish species by metagenome sequencing. We observed that Cyanobacteria, Proteobacteria, Firmicutes, Bacteroidetes, and Fusobacteria were the most substantial bacteria in mudskippers. Differential variances in composition patterns of GI microbiota among the vertebrate groups were determined, although Proteobacteria and Firmicutes were the shared phyla with high abundance. In addition, Cetobacterium and Photobacterium were the most abundant genera in core OTUs of these examined omnivores, carnivores, and herbivores. Our metagenomic analysis also showed significant differences between the representative blue-spotted mudskipper and grass carp (both are herbivorous fishes) in microbes at the phylum and class levels and functional gene terms. Moreover, several bacteriocin-related genes were identified in the five common fishes, suggesting their potential contributions to pathogen resistance. In summary, our present work not only sheds new light on the correlation of GI microbiota composition with living habitats and feeding habits of the hosts, but also provides valuable bacterial genetic resources for healthy growth of aquaculture fishes.

Mudskippers and Their Genetic Adaptations to an Amphibious Lifestyle

Mudskippers are the largest group of amphibious teleost fish that are uniquely adapted to live on mudflats. During their successful transition from aqueous life to terrestrial living, these fish have evolved morphological and physiological modifications of aerial vision and olfaction, higher ammonia tolerance, aerial respiration, improved immunological defense against terrestrial pathogens, and terrestrial locomotion using protruded pectoral fins. Comparative genomic and transcriptomic data have been accumulated and analyzed for understanding molecular mechanisms of the terrestrial adaptations. Our current review provides a general introduction to mudskippers and recent research advances of their genetic adaptations to the amphibious lifestyle, which will be helpful for understanding the evolutionary transition of vertebrates from water to land. Our insights into the genomes and transcriptomes will also support molecular breeding, functional identification, and natural compound screening.