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2022, Volume 43,  Issue 1

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2022, 43(1): 1-1.
Editorial
Review
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.
Article
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.
Letter to the editor
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.
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.
Article
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.
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.
Letter to the editor
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.
Understanding the genetic basis of phenotypes is of importance in evolutionary biology and for genetic improvement of economically valuable animals. The giant phenotype of the fighting fish, Betta splendens, provides a unique opportunity to explore the genetic architecture of overgrowth in body size. As such, we re-sequenced and analyzed the genomes of 54 fighting fish. Genome-wide FST and selective sweep analyses using 3 582 429 DNA variants revealed three genomic regions at chr1, chr9, and chr11 that were associated with the giant phenotype. With a total length of ~3.5 Mb, these regions showed high divergence between the giant and non-giant bettas. In contrast, no signature of selection was detected in the wild-type fish. Transcriptome analysis of brain and muscle samples from giant and normal bettas identified 14 candidate genes that were likely responsible for the giant phenotype. Overall, our data provide novel insights into the genetic basis of body size variation. The genome sequences, transcriptome sequences, DNA sequence variants, and candidate genes for body size provide valuable resources for further biological and evolutionary studies, as well as for rapid improvement in growth-related traits.
The molecular mechanisms underpinning temperature-dependent sex determination (TSD) in reptiles have attracted great biological interest for many years. However, which genetic factors are essential for TSD remain elusive, especially regarding female sex determination. Cytochrome P450 family 19 subfamily A member 1 (Cyp19a1) encodes the endoplasmic reticulum enzyme aromatase, which participates in the catalytic conversion of androgens to estrogens, and is implicated in sexual differentiation in many species. However, whether Cyp19a1 plays a critical role in determining gonadal sexual fate in TSD species remains to be elucidated. In the current study, Cyp19a1 exhibited a temperature-dependent and sexually dimorphic expression pattern, preceding gonadal sex differentiation in a TSD turtle species (Mauremys reevesii). Sexual phenotype of the turtles was successfully reversed by aromatase inhibitor treatment at the female-producing temperature (FPT). Furthermore, exogenous estradiol (E2) treatment led to complete male-to-female sex reversal at the male-producing temperature (MPT), accompanied by rapid up-regulation of Cyp19a1. Thus, Cyp19a1 appears to be essential for female sex determination in M. reevesii, suggesting a vital role in the female TSD pathway.
A new species of the genus Occidozyga is reported from Southern Guangxi, China, based on morphological characters and molecular analyses. Morphological data revealed that the new species, Occidozyga shiwandashanensis sp. nov. , differs from its congeners by a combination of the following characters: (1) medium body size (SVL 25.2−33.8 mm in males, 34.9−38.9 mm in females); (2) pale brown dorsum with irregular pale dark spots, especially on head; (3) creamy white ventral surface with brown spots on lateral margin and throat; (4) tongue fleshy, rounded, without notch, (5) tympanum hidden; (6) finger webbing absent and toe webbing full, but fourth toe not webbed to discs; (7) tips of fingers pointed, tips of toes rounded, slightly expanded into disc. The new species occurs on Mt. Shiwandashan and inhabits montane evergreen forests at 500−600 m above sea level.
Combining morphological and molecular data, we describe a new amphibian species of the genus Kurixalus Ye, Fei, & Dubois, 1999 from the Qionglai Mountain within the western margin of the Sichuan Basin in China. Kurixalus qionglaiensis sp. nov. can be diagnosed based on a combination of the following morphological characters: medium-sized within genus (snout-vent length (SVL) in males 28.9−33.3 mm); tympanum distinct, subequal to half of eye diameter; snout pointed, prominence on tip; iris golden with brown spots; slight nuptial pad on first finger in males; background coloration of dorsal surface brown, lateral body and femoral yellow; white, dark brown edged triangular markings on cheek; chin shaded dark brown; pair of large symmetrical dark patches on chest; belly clouded brown and scattered black spots; toes moderately webbed, formula Ⅰ 2–2 Ⅱ 1.5–2.5 Ⅲ 1.5–2.5 Ⅳ 2.5–1.5 Ⅴ; tibia length slightly shorter than half of SVL, tibiotarsal articulation reaching posterior border of eye; single external vocal sac present. Based on the 16S rRNA gene, the genetic distance between the new species and its sister taxon K. idiootocus (Kuramoto & Wang, 1987) was 4%. At present, the new species is known only from a single location at an elevation of ~600 m in Pingle Town, Qionglai City, Sichuan, southwestern China. This location can represent a new northernmost geographical limit of the genus Kurixalus.
News
The Sichuan hot-spring snake (Thermophis zhaoermii) is a rare and endemic species found at high elevations in the Hengduan Mountains of China. Recent species-specific investigations showed that the Sichuan hot-spring snake is still restricted to geothermal zones at elevations higher than 3 000 m a.s.l. The species also remains at risk of extinction, with the effective population size showing continual decline over the past one million years based on coalescent inference from genome-level single nucleotide polymorphism (SNP) data. We propose several approaches for protecting Sichuan hot-spring snake populations and their habitat.
Article
As a highly important fish virus, nervous necrosis virus (NNV) has caused severe economic losses to the aquaculture industry worldwide. Autophagy, an evolutionarily conserved intracellular degradation process, is involved in the pathogenesis of several viruses. Although NNV can induce autophagy to facilitate infection in grouper fish spleen cells, how it initiates and mediates autophagy pathways during the initial stage of infection is still unclear. Here, we found that red-spotted grouper NNV (RGNNV) induced autophagosome formation in two fish cell lines at 1.5 and 3 h post infection, indicating that autophagy is activated upon entry of RGNNV. Moreover, autophagic detection showed that RGNNV entry induced incomplete autophagy by impairing the fusion of autophagosomes with lysosomes. Further investigation revealed that binding of the RGNNV capsid protein (CP) to the Lateolabrax japonicus heat shock protein HSP90ab1 (LjHSP90ab1), a cell surface receptor of RGNNV, contributed to RGNNV invasion-induced autophagy. Finally, we found that CP blocked the interaction of L. japonicus protein kinase B (AKT) with LjHSP90ab1 by competitively binding the NM domain of LjHSP90ab1 to inhibit the AKT-mechanistic target of the rapamycin (MTOR) pathway. This study provides novel insight into the relationship between NNV receptors and autophagy, which may help clarify the pathogenesis of NNV.
In most eukaryotes, oxidative phosphorylation (OXPHOS) is the main energy production process and it involves both mitochondrial and nuclear genomes. The close interaction between the two genomes is critical for the coordinated function of the OXPHOS process. Some bivalves show doubly uniparental inheritance (DUI) of mitochondria, where two highly divergent mitochondrial genomes, one inherited through eggs (F-type) and the other through sperm (M-type), coexist in the same individual. However, it remains a puzzle how nuclear OXPHOS genes coordinate with two divergent mitochondrial genomes in DUI species. In this study, we compared transcription, polymorphism, and synonymous codon usage in the mitochondrial and nuclear OXPHOS genes of the DUI species Ruditapes philippinarum using sex- and tissue-specific transcriptomes. Mitochondrial and nuclear OXPHOS genes showed different transcription profiles. Strong co-transcription signal was observed within mitochondrial (separate for F- and M-type) and within nuclear OXPHOS genes but the signal was weak or absent between mitochondrial and nuclear OXPHOS genes, suggesting that the coordination between mitochondrial and nuclear OXPHOS subunits is not achieved transcriptionally. McDonald-Kreitman and frequency-spectrum based tests indicated that M-type OXPHOS genes deviated significantly from neutrality, and that F-type and M-type OXPHOS genes undergo different selection patterns. Codon usage analysis revealed that mutation bias and translational selection were the major factors affecting the codon usage bias in different OXPHOS genes, nevertheless, translational selection in mitochondrial OXPHOS genes appears to be less efficient than nuclear OXPHOS genes. Therefore, we speculate that the coordination between OXPHOS genes may involve post-transcriptional/translational regulation.
The Hengduan Mountains Region (HMR) is the largest “evolutionary frontier” of the northern temperate zone, and the origin and maintenance of species in this area is a research hotspot. Exploring species-specific responses to historical and contemporary environmental changes will improve our understanding of the role of this region in maintaining biodiversity. In this study, mitochondrial and microsatellite diversities were used to assess the contributions of paleogeological events, Pleistocene climatic oscillations, and contemporary landscape characteristics to the rapid intraspecific diversification of Liangshantriton taliangensis, a vulnerable amphibian species endemic to several sky-island mountains in the southeastern HMR. Divergence date estimations suggested that the East Asian monsoon, local uplifting events (Xigeda Formation strata), and Early-Middle Pleistocene transition (EMPT) promoted rapid divergence of L. taliangensis during the Pleistocene, yielding eight mitochondrial lineages and six nuclear genetic lineages. Moreover, population genetic structures were mainly fixed through isolation by resistance. Multiple in situ refugia were identified by ecological niche models and high genetic diversity, which played crucial roles in the persistence and divergence of L. taliangensis during glacial-interglacial cycles. Dramatic climatic fluctuations further promoted recurrent isolation and admixing of populations in scattered glacial refugia. The apparent mitonuclear discordance was likely the result of introgression by secondary contact and/or female-biased dispersal. Postglacial expansion generated two major secondary contact zones (Ganluo (GL) and Chuhongjue (CHJ)). Identification of conservation management units and dispersal corridors offers important recommendations for the conservation of this species.