Roles of air stored in burrows of the mudskipper Boleophthalmus pectinirostris for adult respiration and embryonic development

Klumpy: A tool to evaluate the integrity of long-read genome assemblies and illusive sequence motifs

The improvement and decreasing costs of third-generation sequencing technologies has widened the scope of biological questions researchers can address with de novo genome assemblies. With the increasing number of reference genomes, validating their integrity with minimal overhead is vital for establishing confident results in their applications. Here, we present Klumpy, a tool for detecting and visualizing both misassembled regions in a genome assembly and genetic elements (e.g. genes) of interest in a set of sequences. By leveraging the initial raw reads in combination with their respective genome assembly, we illustrate Klumpy's utility by investigating antifreeze glycoprotein (afgp) loci across two icefishes, by searching for a reported absent gene in the northern snakehead fish, and by scanning the reference genomes of a mudskipper and bumblebee for misassembled regions. In the two former cases, we were able to provide support for the noncanonical placement of an afgp locus in the icefishes and locate the missing snakehead gene. Furthermore, our genome scans were able identify an unmappable locus in the mudskipper reference genome and identify a putative repetitive element shared among several species of bees.

Morphology of the respiratory vasculature of the mudskipper Boleophthalmus pectinirostris (Gobiidae: Oxudercinae)

The gross morphology of the circulatory system in the amphibious mudskipper, Boleophthalmus pectinirostris, conforms with the typical teleost configuration, in which gills and systemic vascular beds are connected in series. However, at the microscopic level, the vasculatures of the respiratory organs, the inner epithelium of the bucco-opercular cavity, gills and skin, all show specializations for aerial gas exchange. The epithelium of the bucco-opercular cavity is heavily vascularized by respiratory capillaries that are derived from systemic arteries of the head, mainly branches of the hyomandibular artery and the dorsal opercular artery. The respiratory circuit of the secondary lamellae of the gills consists of 15-17 channels running in parallel, unlike the lacuna-like blood space of aquatic fishes. The most notable specialization is found in the microcirculation of the respiratory papillae in the skin. Each respiratory papilla is supplied by an arteriole that is derived from a systemic artery, mainly the cranial artery in the head and the segmental artery in the trunk. The arteriole divides several times along its course to the apical region of a papilla, where the branches split into approximately 65 capillaries that radiate to the periphery of the papilla. The capillaries twist 5-10 times before they unite to form the venules that encircle maximally half the circumference of a papilla. A variable number of venules merge into a vein, which progressively coalesces with veins from other papillae. There is no morphological specialization that separates oxygen-rich effluent blood of the epithelia of the bucco-opercular cavity and the respiratory papillae of the skin from the oxygen-poor systemic venous blood. The ecophysiological implications of these findings are discussed in relation to the environmental conditions that B. pectinirostris experience during tidal cycles in the warm months and during overwintering.

Patterns of Fish Reproduction at the Interface between Air and Water

Although fishes by nature are aquatic, many species reproduce in such a way that their embryos are exposed to air either occasionally or constantly during incubation. We examine the ecological context and review specific examples of reproduction by fishes at the air-water interface, including fishes that do and do not breathe air. Four modes of reproduction at the air-water interface are described across 18 teleost orders, from fresh water, estuaries, and sea water. Mode 1, the most common type of reproduction by fishes at the air-water interface, includes 21 families of mostly marine teleosts that spawn in water onto a substrate surface, on vegetation, or into hollow objects such as shells that will later be continuously or occasionally exposed to air. Although the eggs are emerged into air, many of these species do not emerge into air as adults, and only about half of them breathe air. Mode 2 involves six families of freshwater fishes setting up and guarding a nest and guarding on the water surface, either with bubbles or in vegetation. Most of these species breathe air. In Mode 3, annual killifishes in at least two families in seasonally dry habitats bury eggs in mud in temporary pools, then die before the next generation emerges. These species neither guard nests nor breathe air. Mudskippers (Gobiidae) breathe air and use Mode 4, excavating burrows in a soft substrate and then storing air in a subterranean chamber. In a variation of Mode 4, eggs are placed on bubbles within a nesting burrow by swamp eels (Synbranchidae). No fishes from basal taxa are known to place their embryos where they will be exposed to air, although most of these species breathe air as adults. The widespread but still rare, diverse forms of fish reproduction at the air-water interface across a broad taxonomic spectrum suggest repeated independent evolutionary events and strong selection pressure for adult fishes to protect their embryos from hypoxic waters, aquatic predators, pathogens, and UV radiation. Air-breathing by adult fishes appears to be de-coupled from air exposure of developing embryos or aerial emersion of adults during spawning.