Project description:Basidioascus undulatus is a soil basidiomycete belonging to the order Geminibasidiales. The taxonomic status of the order was unclear as originally it was only tentatively classified in the class Wallemiomycetes. The fungi in Geminibasidiales have an ambiguously defined sexual cycle. In this study, we sequenced the genome of B. undulatus to gain insights into its sexuality and evolutionary origins. The assembled genome draft was approximately 32 Mb in size, had a median nucleotide coverage of 24X, and contained 6123 predicted genes. Previous morphological descriptions of B. undulatus relied on interpretation of putative sexual structures. In this study, nuclear staining and confocal microscopy showed meiosis occurring in basidia and genome analysis confirmed the existence of genes involved in meiosis and mating. Using 35 protein-coding genes extracted from genomic information, phylogenomic and molecular dating analyses confirmed that B. undulatus indeed belongs to a lineage distantly related to Wallemia while retaining a basal position in Agaricomycotina. These results, combined with differences in septal pore morphology, led us to move the order Geminibasidiales out of the Wallemiomycetes and into the new class Geminibasidiomycetes cl. nov. Finally, the concept of Agaricomycotina is emended to include both Wallemiomycetes and Geminibasidiomycetes.
Project description:The siphonostomatoid copepod Caligus undulatus Shen & Li, 1959 has been widely reported from plankton samples obtained from neritic and oceanic waters off coasts of the Indo-West Pacific and Atlantic Oceans. Until now, its fish host has remained unknown. This copepod belongs to an intriguing group of congeners that, despite being part of a chiefly parasitic group, are consistently found as zooplankters. Quite unexpectedly, in October 2019, a fish host of C. undulatus was discovered in the Seto Inland Sea, Japan-namely, the Japanese sardinella Sardinella zunasi (Bleeker, 1854). Both juvenile (chalimus) and adult individuals of this caligid were observed as parasites of the fish host. The discovery suggests that the species has an alternative life cycle as previously proposed for other purportedly 'planktonic' congeners and might frequently switch hosts during the adult stage. Thus, the C. undulatus group is newly proposed as a species group in the genus, in which five species are known as planktonic. Some hypotheses on the modified life cycle of caligids also briefly discussed.
Project description:The budgerigar (Melopsittacus undulatus) is one of the most widely studied parrot species, serving as an excellent animal model for behavior and neuroscience research. Until recently, it was unknown how sexual differences in the behavior, physiology, and development of organisms are regulated by differential gene expression. MicroRNAs (miRNAs) are endogenous short non-coding RNA molecules that can post-transcriptionally regulate gene expression and play a critical role in gonadal differentiation as well as early development of animals. However, very little is known about the role gonadal miRNAs play in the early development of birds. Research on the sex-biased expression of miRNAs in avian gonads are limited, and little is known about M. undulatus. In the current study, we sequenced two small non-coding RNA libraries made from the gonads of adult male and female budgerigars using Illumina paired-end sequencing technology. We obtained 254 known and 141 novel miRNAs, and randomly validated five miRNAs. Of these, three miRNAs were differentially expressed miRNAs and 18 miRNAs involved in sexual differentiation as determined by functional analysis with GO annotation and KEGG pathway analysis. In conclusion, this work is the first report of sex-biased miRNAs expression in the budgerigar, and provides additional sequences to the avian miRNAome database which will foster further functional genomic research.
Project description:Impacts of Quaternary environmental changes on mammal faunas of central Asia remain poorly understood due to a lack of geographically comprehensive phylogeographic sampling for most species. To help address this knowledge gap, we conducted the most extensive molecular analysis to date of the long-tailed ground squirrel (Urocitellus undulatus Pallas 1778) in Mongolia, a country that comprises the southern core of this species' range. Drawing on material from recent collaborative field expeditions, we genotyped 128 individuals at 2 mitochondrial genes (cytochrome b and cytochrome oxidase I; 1 797 bp total). Phylogenetic inference supports the existence of two deeply divergent infraspecific lineages (corresponding to subspecies U. u. undulatus and U. u. eversmanni), a result in agreement with previous molecular investigations but discordant with patterns of range-wide craniometric and external phenotypic variation. In the widespread westerneversmanni lineage, we recovered geographically-associated clades from the: (a) Khangai, (b) Mongolian Altai, and (c) Govi Altai mountain ranges. Phylogeographic structure in U. u. eversmanni is consistent with an isolation-by-distance model; however, genetic distances are significantly lower than among subspecies, and intra-clade relationships are largely unresolved. The latter patterns, as well as the relatively higher nucleotide polymorphism of populations from the Great Lakes Depression of northwestern Mongolia, suggest a history of range shifts into these lowland areas in response to Pleistocene glaciation and environmental change, followed by upslope movements and mitochondrial lineage sorting with Holocene aridification. Our study illuminates possible historical mechanisms responsible for U. undulatus genetic structure and contributes to a framework for ongoing exploration of mammalian response to past and present climate change in central Asia.
Project description:The objective of this study was to determine how transcriptomic responses in the spleen and liver are altered in juvenile Micropogonias undulatus exposed to oil, a known fish pathogen (Vibrio anguillarum), or both. Overall design: M. undulatus juveniles were exposed to oil, a pathogen (Vibrio anguillarum) or both. Oil exposure was for 8 days and pathogen exposure was for 1 hour, 24 hours before takedown. Oil solutions used in exposures were derived from high energy water accommodated fractions (HEWAF) prepared using Macondo well oil from the Deepwater Horizon oil spill following established procedures. At the end of the experiments, livers and spleen were taken from organisms, RNA was extracted and sequenced.
Project description:The complete genome sequence of a virulent Newcastle disease virus (vNDV) strain isolated from an exotic parakeet (Melopsittacus undulatus) is described here. The virulent strain parakeet/Pak/R-Pindi/SFR-16/2016 was isolated from a bird reared as a pet in the province of Punjab in the northern region of Pakistan in 2016. Phylogenetic analysis classified the isolate as a member of NDV class II, subgenotype VIIi, in genotype VII.
Project description:BACKGROUND: While considerable scientific effort has been devoted to studying how birds navigate over long distances, relatively little is known about how targets are detected, obstacles are avoided and smooth landings are orchestrated. Here we examine how visual features in the environment, such as contrasting edges, determine where a bird will land. METHODOLOGY/PRINCIPAL FINDINGS: Landing in budgerigars (Melopsittacus undulatus) was investigated by training them to fly from a perch to a feeder, and video-filming their landings. The feeder was placed on a grey disc that produced a contrasting edge against a uniformly blue background. We found that the birds tended to land primarily at the edge of the disc and walk to the feeder, even though the feeder was in the middle of the disc. This suggests that the birds were using the visual contrast at the boundary of the disc to target their landings. When the grey level of the disc was varied systematically, whilst keeping the blue background constant, there was one intermediate grey level at which the budgerigar's preference for the disc boundary disappeared. The budgerigars then landed randomly all over the test surface. Even though this disc is (for humans) clearly distinguishable from the blue background, it offers very little contrast against the background, in the red and green regions of the spectrum. CONCLUSIONS: We conclude that budgerigars use visual edges to target and guide landings. Calculations of photoreceptor excitation reveal that edge detection in landing budgerigars is performed by a color-blind luminance channel that sums the signals from the red and green photoreceptors, or, alternatively, receives input from the red double-cones. This finding has close parallels to vision in honeybees and primates, where edge detection and motion perception are also largely color-blind.