The final volume/issue numbers and page numbers are available for citation.
Cattle temperament is an interesting trait due to its correlation with production efficiency, labor safety, and animal welfare. To date, however, its genetic basis is not clearly understood. Here, we performed a genome-wide association study for a series of temperament traits in cattle, assessed with via open field and novel object tests, using autosomal single nucleotide polymorphisms (SNPs) derived from the whole-genome sequence. We identified 37 and 29 genome-wide significant loci in the open field and novel object tests, respectively. Gene set analysis revealed the most significant pathway was the neuroactive ligand-receptor interaction pathway, which may be essential for emotional control in cattle. Analysis of the expression levels of 18 tissue-specific genes based on transcriptomic data showed enrichment in the brain, with some candidate genes involved in psychiatric and neurodegenerative diseases in humans. Based on principal component analysis, the first principal component explained the largest variance in the open field and novel object test data, and the most significant loci were assigned to SORCS3 and SESTD1, respectively. Our findings should help facilitate cattle breeding for sound temperament by pyramiding favorable alleles to further improve cattle production.
Multidimensional amphibian diversity and community structure along a 2 600 m elevational gradient on the eastern margin of the Qinghai-Tibetan Plateau
2022, 43(1): 40-51. doi: 10.24272/j.issn.2095-8137.2021.166
, Available online , doi: 10.24272/j.issn.2095-8137.2021.166
Mountain systems harbor an evolutionarily unique and exceptionally rich biodiversity, especially for amphibians. However, the associated elevational gradients and underlying mechanisms of amphibian diversity in most mountain systems remain poorly understood. Here, we explored amphibian phylogenetic and functional diversity along a 2 600 m elevational gradient on Mount Emei on the eastern margin of the Qinghai-Tibetan Plateau in southwestern China. We also assessed the relative importance of spatial (area) and environmental factors (temperature, precipitation, solar radiation, normalized difference vegetation index, and potential evapotranspiration) in shaping amphibian distribution and community structure. Results showed that the phylogenetic and functional diversities were unimodal with elevation, while the standardized effect size of phylogenetic and functional diversity increased linearly with elevation. Phylogenetic net relatedness, nearest taxon index, and functional net relatedness index all showed a positive to negative trend with elevation, indicating a shift from clustering to overdispersion and suggesting a potential change in key processes from environmental filtering to competitive exclusion. Overall, our results illustrate the importance of deterministic processes in structuring amphibian communities in subtropical mountains, with the dominant role potentially switching with elevation. This study provides insights into the underlying assembly mechanisms of mountain amphibians, integrating multidimensional diversity.
Unexpected expression of heat-activated transient receptor potential (TRP) channels in winter torpid bats and cold-activated TRP channels in summer active bats
2022, 43(1): 52-63. doi: 10.24272/j.issn.2095-8137.2021.209
, Available online , doi: 10.24272/j.issn.2095-8137.2021.209
The ability to sense temperature changes is crucial for mammalian survival. Mammalian thermal sensing is primarily carried out by thermosensitive transient receptor potential channels (Thermo-TRPs). Some mammals hibernate to survive cold winter conditions, during which time their body temperature fluctuates dramatically. However, the underlying mechanisms by which these mammals regulate thermal responses remain unclear. Using quantitative real-time polymerase chain reaction (qRT-PCR) and the Western blotting, we found that Myotis ricketti bats had high levels of heat-activated TRPs (e.g., TRPV1 and TRPV4) during torpor in winter and cold-activated TRPs (e.g., TRPM8 and TRPC5) during active states in summer. We also found that laboratory mice had high mRNA levels of cold-activated TRPs (e.g., Trpm8 and Trpc5) under relatively hot conditions (i.e., 40 °C). These data suggest that small mammals up-regulate the expression of cold-activated TRPs even under warm or hot conditions. Binding site analysis showed that some homeobox (HOX) transcription factors (TFs) regulate the expression of hot- and cold-activated TRP genes and that some TFs of the Pit-Oct-Unc (POU) family regulate warm-sensitive and cold-activated TRP genes. The dual-luciferase reporter assay results demonstrated that TFs HOXA9, POU3F1, and POU5F1 regulate TRPC5 expression, suggesting that Thermo-TRP genes are regulated by multiple TFs of the HOX and POU families at different levels. This study provides insights into the adaptive mechanisms underlying thermal sensing used by bats to survive hibernation.
Retinal angiogenesis is a critical process for normal retinal function. However, uncontrolled angiogenesis can lead to pathological neovascularization (NV), which is closely related to most irreversible blindness-causing retinal diseases. Understanding the molecular basis behind pathological NV is important for the treatment of related diseases. Twist-related protein 1 (TWIST1) is a well-known transcription factor and principal inducer of epithelial-mesenchymal transition (EMT) in many human cancers. Our previous study showed that Twist1 expression is elevated in pathological retinal NV. To date, however, the role of TWIST1
in retinal pathological angiogenesis remains to be elucidated. To study the role of TWIST1 in pathological retinal NV and identify specific molecular targets for antagonizing pathological NV, we generated an inducible vascular endothelial cell (EC)-specific Twist1 transgenic mouse model (Tg-Twist1iEC+). Whole-mount retinas from Tg-Twist1iEC+ mice showed retarded vascular progression and increased vascular density in the front end of the growing retinal vasculature, as well as aneurysm-like pathological retinal NV. Furthermore, overexpression of Twist1 in the ECs promoted cell proliferation but disturbed cell polarity, thus leading to uncontrolled retinal angiogenesis. TWIST1 promoted pathological NV by activating the Wnt/β-catenin signaling pathway and inducing the expression of NV formation-related genes, thereby acting as a ‘valve’ in the regulation of pathological angiogenesis. This study identified the critical role of TWIST1 in retinal pathological NV, thus providing a potential therapeutic target for pathological NV.
Endothermy is the ability to generate and conserve metabolic heat to maintain body temperature above that of the surrounding environment. Endothermy enhances the physiological and ecological advantages of mammals, birds, and certain fish species. The opah, Lampris megalopsis (Lampridiformes), is the only known fish to exhibit whole-body endothermy. Currently, however, the underlying molecular mechanism for this remains unclear. Hence, the opah offers an excellent opportunity to study the evolutionary mechanism of whole-body endothermy in aquatic animals. In this study, we assembled a L. megalopsis genome (1.09 Gb in size) and performed comparative genomic analysis with ectothermic fish to reveal the genetic basis of endothermy. Based on analysis of positive selection, rapid evolution, and gene family expansion, we discovered several genes that likely contributed to thermogenesis and heat preservation. As the first reported L. megalopsis genome, our results not only clarify the possible molecular and genetic mechanisms involved in endothermic adaptation but also increase our understanding of endothermic fish biology.
Chedrinae fish, which belong to Danionidae, have important ornamental, economic, and scientific value. At present, however, their mitogenomic features are unclear and their phylogenetic relationships remain controversial. In this study, we presented five new Chedrinae mitochondrial genomes (mitogenomes) and analyzed the conserved and variable mitogenomic characteristics of 17 Chedrinae fish. The gene composition and arrangement and secondary structure of transfer RNAs (tRNAs) were highly conserved among the Chedrinae mitogenomes. However, the length of the control region and base composition were variable. Interestingly, the mitogenome of Barilius barila was unusual, with lower A+T content in the first codon of protein-coding genes (PCGs) (47.32% versus average of 54.47%) and distinct pattern of codons per thousand codons (CDspT). Three Chedrinae fish had a long tandem repeat (>291 bp) in the 5'-end of the control region, which may increase their adaptability. In addition, tRNALys had notably larger DHU and TΨC loops than other tRNAs. The phylogenetic trees of the Chedrinae fish suggested that the Barilius genus was not a monophyletic group but could be divided into two main groups based on significant differences in A+T content. This study provides insights into the mitogenomic features and phylogenetic implications of Chedrinae fish, which should benefit their systematics and conservation.
A new species of the gudgeon genus Huigobio Fang, 1938 (Cypriniformes: Cyprinidae) from the Yangtze River Basin, southern China
2022, 43(1): 33-39. doi: 10.24272/j.issn.2095-8137.2021.168
, Available online , doi: 10.24272/j.issn.2095-8137.2021.168
During revision of the genus Microphysogobio Mori, 1934, we discovered a new species of Huigobio from the Yangtze River Basin in China. The new species, named Huigobio heterocheilus sp. nov. , can be distinguished from its congeners by a combination of the following characters: medial pad on lower lip not visible; ventral region scaleless before pelvic-fin insertion; lateral-line scales 39–40; caudal peduncle depth 49.2%–59.1% of length; barbel length 6.6%–10.7% of head length; black blotch between anterior margin of eye and upper lip. Using the K2P model and cytochrome b (cyt b) sequences, interspecific genetic distances between the new species and Huigobio exilicauda Jiang & Zhang, 2013 and Huigobio chenhsienensis Fang, 1938 were 13.2% and 15.1%, respectively. The new species is known from the upper reaches of the Xiangjiang River in the middle Yangtze River Basin. A diagnostic key for species of Huigobio Fang, 1938 is provided.
Cancer cell genomes originate from single-cell mutation with sequential clonal and subclonal expansion of somatic mutation acquisition during pathogenesis, thus exhibiting a Darwinian evolutionary process (Gerstung et al., 2020; Nik-Zainal et al., 2012). Through next-generation sequencing of tumor tissue, this evolutionary process can be characterized by statistical modelling, which can identify the clonal state, somatic mutation order, and evolutionary process (Gerstung et al., 2020; Mcgranahan & Swanton, 2017). Inference of clonal and subclonal structure from bulk or single-cell tumor genomic sequencing data has a huge impact on studying cancer evolution. Clonal state and mutation order can provide detailed insight into tumor origin and future development. In the past decade, various methods for subclonal reconstruction using bulk tumor sequencing data have been developed. However, these methods had different programming languages and data input formats, which limited their use and comparison. Therefore, we established a web server for Clonal and Subclonal Structure Inference and Evolution (COSINE) of cancer genomic data, which incorporated twelve popular subclonal reconstruction methods. We deconstructed each method to provide a detailed workflow of single processing steps with a user-friendly interface. To the best of our knowledge, this is the first web server providing online subclonal inference based on the integration of most popular subclonal reconstruction methods. COSINE is freely accessible at www.clab-cosine.net.
Cenozoic tectonic evolution in the Tethyan region has greatly changed the landforms and environment of Eurasia, driving the evolution of animals and greatly affecting the diversity patterns of Eurasian animals. By combining the latest Tethyan paleogeographic models and some recently published Eurasian zoological studies, we systematically summarize how tectonic evolution in the Tethyan region has influenced the evolution and diversity patterns of Eurasian animals. The convergence of continental plates, closure of Tethys Sea, and Tethyan sea-level changes have directly affected the composition and spatial distribution of Eurasian animal diversity. The topographic and environmental changes caused by Tethyan tectonics have determined regional animal diversity in Eurasia by influencing animal origin, dispersal, preservation, diversification, and extinction. The ecological transformations resulted in the emergence of new habitats and niches, which promoted animal adaptive evolution, specialization, speciation, and expansion. We highlight that the Cenozoic tectonic evolution of the Tethyan region has been responsible for much of the alteration in Eurasian animal distribution and has been an essential force in shaping organic evolution. Furthermore, we generalize a general pattern that Tethyan geological events are linked with Eurasian animal evolution and diversity dynamics.