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ABSTRACT Single-cell RNA sequencing (scRNAseq) is useful to explore cell heterogeneity. However, for livestocks, much less is known on the SSCs self-renewal regulation, especially in dairy goats. Here, we described a high-resolution single-cell RNA sequencing atlas derived from dairy goats. We identified 6 somatic cells and 5 spermatogenic cell subtypes. During the spermatogenesis of dairy goats, genes whose expression levels change significantly are mainly enriched in the Notch signaling pathway, the TGF-β signaling pathway, the Hippo signaling pathway, and the signaling pathway that regulates the pluripotency of stem cells. And we detected and screened out specific candidate marker genes (TKTL1 and AES) for spermatogonia and it has been verified. In general, our study provides new insights into goat spermatogenesis and the development of testicular somatic cells.
Abstract:
Exploring the spatio-temporal patterns of biological diversity is important to understand the species coexistence mechanisms and community assembly rules. This is especially true for functional diversity, which was considered to be more integrative to better understand biodiversity across space and time. In the present study, Tianping Mountain was selected as the study area to investigate the spatio-temporal patterns (i.e., elevational and seasonal) of anuran functional diversity, as well as its environmental determinants. Specifically, ten transects were selected from low to high elevations, and anuran communities were sampled in spring, early summer, midsummer, and Autumn, 2017, respectively. Four functional diversity indices were computed for each transect in each season using eco-morphological functional traits. First, we found that there was an inverse bell shape relationship between functional richness and elevations. Functional evenness exhibited a hump-shape response to the increasing of elevations. In addition, functional divergence and functional specialization increased significantly along an elevational gradient. In terms of the temporal patterns, these indices were not significantly different between seasons. Finally, we found that each index was determined by distinct environmental variables, such as leaf litter cover, water temperature, tree number, and water conductivity. Overall, our results demonstrated the unique patterns of anuran functional diversity in temperate montane forests, providing valuable results to understand the general patterns of anuran diversity on mountains. Importantly, these findings highlighted the importance of microhabitat features in maintaining anuran diversity. Future work should assess how these unique patterns can affect food webs and ecosystem functioning in temperate montane forests.
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The Chinese Longsnout catfish (Leiocassis longirostris Günther) is one of the most economically important freshwater catfish in China. It is a valuable model for studies on sexual dimorphism, comparative and conservation biology since its wild resources have declined sharply. However, there is a lack of high-quality chromosome-level genome information for comparative genomic analysis and evolutionary studies. Therefore, we constructed the first high-quality chromosome-level reference genome for L. longirostris, which contained a total length of 703.19 Mb with 389 contigs, and a contig N50 of 4.29 Mb. Using the Hi-C data, we successfully generated 82 chromosome-level scaffolds anchored onto 26 chromosomes with a total length of 685.53 Mb (97.44% of the total genome sequences), ranging in size from 17.36 Mb to 43.97 Mb. A total of 23,708 protein-coding genes were identified in the L. longirostris genome. In addition, the phylogenetic analysis indicated that L. longirostris and its closest related species P. fulvidraco diverged approximately 26.6 million years ago. This first high-quality reference genome of L. longirostris will pave the way for genome comparisons and evolution investigations.
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Changes in abiotic and biotic factors may potentially affect animals’ efficiency of biological systems, and force them to adjust their behaviors in response to these daily and seasonal variations. From September 2016 to August 2017, we collected data on ranging behavior of four groups of White-headed langurs (Trachypithecus leucocephalus), living in the Guangxi Chongzuo White-Headed Langur National Nature Reserve, Guangxi, southwest China. The objective was to simultaneous analyze how multiple ecological factors affect langurs’ ranging behavior, which would facilitate to understand the potential mechanisms of their adaptation to the limestone habitat. The results showed that the ranging behavior of langurs was significantly affected by diet composition, food availability and climatic factors. Specifically, the moving time and daily path lengths increased with increase in dietary diversity. Furthermore, langurs’ moving time and daily path lengths were positively associated with availability of fruits, relative humidity of forest, and moderated associated with temperature and relative humidity of bare rock. Our study demonstrates that langurs maintain stable moving and feeding times, and a short daily travel distance, likely adopting an energy-conserving behavioral strategy in response to food shortages and high temperature in the fragmented karst forest, and highlights the importance of food availability and temperature to shape the ranging behavior of these karst-dwelling langurs.
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Review
Parabiosis is a surgical method of animal modeling with a long history. It has been widely used in medical research, particularly in the fields of aging, stem cells, neuroscience, and immunity in the past two decades. The protocols for parabiosis have been improved many times and are now widely accepted. However, researchers need to consider many details, from surgical operation to perioperative management, to reduce mortality and maintain the parabiosis union. Although parabiosis has certain inevitable limitations, it still has broad application prospects as an irreplaceable animal model in the medical research field.
Letters to the editor
The Dianchi golden-line barbel, Sinocyclocheilus grahami (Regan, 1904), is one of the “Four Famous Fishes” of Yunnan Province, China. Given its economic value, this species has been artificially bred successfully since 2007, with a nationally selected breed (“S. grahami, Bayou No. 1”) certified in 2018. For the future utilization of this species, its growth rate, disease resistance, and wild adaptability need to be improved, which could be achieved with the help of molecular marker-assisted selection (MAS). In the current study, we constructed the first chromosome-level genome of S. grahami, assembled 48 pseudo-chromosomes, and obtained a genome assembly of 1.49 Gb. We also performed QTL-seq analysis of S. grahami using the highest and lowest bulks (i.e., largest and smallest size) in both a sibling and random population. We screened two quantitative trait loci (QTLs) (Chr3, 14.9–39.1 Mb and Chr17, 4.1–27.4 Mb) as the major growth-related locations. Several candidate genes (e.g., map2k5, stat1, phf21a, sox6, and smad6) were also identified, with functions related to growth, such as cell differentiation, neuronal development, skeletal muscle development, chondrogenesis, and immunity. These results built a solid foundation for in-depth MAS studies on the growth traits of S. grahami.
Despite 250 years of taxonomic classification and over 1.2 million species already catalogued, known species diversity is only a small part of true species diversity on Earth, and thus, the known species are only the tip of iceberg. Here, we investigated the genus Pholcus Walckenaer, 1805 of the family Pholcidae C. L. Koch, 1850 in the Changbai Mountains, Northeast China, which provides an excellent case of high species diversity. Previously, only 14 endemic Pholcus spiders, all belonging to the P. phungiformes species group, and two introduced species P. manueli Gertsch, 1937 and P. zichyi Kulczyński, 1901 from the P. crypticolens species group, have been recorded from this area. Our study confirmed 11 new species of the P. phungiformes species group based on morphology and three methods of molecular species delimitation: P. gaizhou Yao & Li, sp. nov. , P. guanshui Yao & Li, sp. nov. , P. jiguanshan Yao & Li, sp. nov. , P. longxigu Yao & Li, sp. nov. , P. luoquanbei Yao & Li, sp. nov. , P. shenshi Yao & Li, sp. nov. , P. tianmenshan Yao & Li, sp. nov. , P. wangjiang Yao & Li, sp. nov. , P. xingqi Yao & Li, sp. nov. , P. yaoshan Yao & Li, sp. nov. , and P. yuhuangshan Yao & Li, sp. nov. This study brings the fauna of the P. phungiformes species group from the Changbai Mountains to 25 species, approximately two times more than previously known, which could indicate that species diversity in the area is underestimated for all arthropod fauna.
A new species of the genus Atelopus, Atelopus fronterizo sp. nov. , from eastern Panama is described herein based on molecular, morphological, and bioacoustic evidence. The new species can be distinguished from its congeners occurring in the region by a combination of the following characters: (1) phalangeal reduction in thumb; (2) SVL (females only) (35.1–50.1; n=13), HW/SVL (0.23–0.34; n=59), EYND/HW (0.27–0.39; n=60), TIBL/SVL (0.41–0.56; n=58), and HAL/SVL (0.22–0.28; n=49); (3) dorsal color pattern with green or yellow background and extensive dark olive blotches forming transversal bands or mottling; (4) advertisement call duration 176–235 ms with 19–34 pulses, average pulse rate 131.69 pulses/s, and dominant frequency 2 422.50–2 606.50 Hz. The new species is nested within the Central American clade of Atelopus. The minimum Kimura‐2‐parameter (K2P) genetic divergence between Atelopus fronterizo sp. nov. and its most phylogenetically similar congeners (A. certus and A. glyphus) is >2.6% for 16S and >4.9% for COI (Table 1). The phylogenetic relationship is strongly supported by ultrafast bootstrap values for the maximum-likelihood trees of both genetic markers (16S, 96; COI, 100, Figure 1A). Bayesian analysis of the concatenated sequences resulted in a tree with similar topology and high posterior probability support (0.99; Supplementary Figure S1). In addition, haplotype networks inferred from COI and 16S (Supplementary Figure S2) showed a well-separated clade containing the new species (two for COI, four for 16S). The number of mutational steps between haplotypes for the new species samples is very low (1–4 in 16S; one in COI), and the minimum number of mutational steps from the nearest species is nine for 16S (distance to A. certus) and 28 for COI (distance to A. glyphus).
DNA studies of endangered or extinct species often rely on ancient or degraded remains. The majority of ancient DNA (aDNA) extraction protocols focus on skeletal elements, with skin and hair samples rarely explored. Similar to that found in bones and teeth, DNA extracted from historical or ancient skin and fur samples is also extremely fragmented with low endogenous content due to natural degradation processes. Thus, the development of effective DNA extraction methods is required for these materials. Here, we compared the performance of two DNA extraction protocols (commercial and custom laboratory aDNA methods) on hair and skin samples from decades-old museum specimens to Iron Age archaeological material. We found that apart from the impact sample-specific taphonomic and handling history has on the quantity and quality of DNA preservation, skin yielded more endogenous DNA than hair of the samples and protocols tested. While both methods recovered DNA from ancient soft tissue, the laboratory method performed better overall in terms of DNA yield and quality, which was primarily due to the poorer performance of the commercial binding buffer in recovering aDNA.
The Eremias multiocellata-przewalskii species complex is a viviparous group in the genus Eremias, and a well-known representative of taxonomically complicated taxa. Within this complex, a new species – E. dzungarica (Orlova et al., 2017) – has been described recently from western Mongolia and eastern Kazakhstan, with an apparent distribution gap in northwestern China. In this study, we used an integrative taxonomic framework to address whether E. dzungarica indeed occurs in China. Thirty specimens previously classified as E. multiocellata were collected in eastern Kazakhstan and the adjacent Altay region in China. The cytochrome c oxidase I (COI) barcodes were sequenced and compiled with those from Orlova et al. (2017) and analyzed with the standard and diverse barcoding techniques. We detected an absence of a barcoding gap in this complex, which indicates potential cryptic species in Eremias sp. 3 with high intraspecific diversity and multiple recently evolved species in Clade A. Both BIN and GMYC suggested an unrealistically large number of species (23 and 26, respectively), while ABGD, mPTP and BPP indicated a more conservative number of species (10, 12, and 15, respectively), largely concordant with the previously defined species-level lineages according to phylogenetic trees. Based on molecular phylogeny and morphological examination, all 30 individuals collected in this study were reliably identified as E. dzungarica – a distinct species – confirming the occurrence of this species in the Altay region, Xinjiang, China. Potentially owing to the larger sample size in this study, our morphological analyses revealed many inconsistencies with the original descriptions of E. dzungarica, which were primarily associated with sexual dimorphism and a broader range of values for various traits.
During a terrestrial vertebrate survey of the Dabie Mountains in Anhui Province, eastern China, we collected four Asian shrew mole specimens (hereafter, shrew moles). Based on published literature and comparison with previously collected materials, the four specimens were similar to shrew moles from the mountains of Southwest China; however, no species in this group has been previously recorded from the Dabie Mountains. The genetic and morphological characteristics of the specimens were analyzed, based upon which a new species of shrew mole is described, named Uropsilus dabieshanensis sp. nov.
Article
As small heat shock proteins, α-crystallins function as molecular chaperones and inhibit the misfolding and aggregation of β/γ-crystallins. Genetic mutations of CRYAA are associated with protein aggregation and cataract occurrence. One possible process underlying cataract formation is that endoplasmic reticulum stress (ERS) induces the unfolded protein response (UPR), leading to apoptosis. However, the pathogenic mechanism related to this remains unexplored. Here, we successfully constructed a cataract-causing CRYAA (Y118D) mutant mouse model, in which the lenses of the CRYAA-Y118D mutant mice showed severe posterior rupture, abnormal morphological changes, and aberrant arrangement of crystallin fibers. Histological analysis was consistent with the clinical pathological characteristics. We also explored the pathogenic factors involved in cataract development through transcriptome analysis. In addition, based on key pathway analysis, up-regulated genes in CRYAA-Y118D mutant mice were implicated in the ERS-UPR pathway. This study showed that prolonged activation of the UPR pathway and severe stress response can cause proteotoxic and ERS-induced cell death in CRYAA-Y118D mutant mice.
The loach tribe Yunnanilini from China is reviewed here using morphological characters and complete mitochondrial genomes of select species. Molecular data suggest that the tribe Yunnanilini is not monophyletic and can be divided into three clades. Species of the Yunnanilus nigromaculatus group form an independent genus and are placed in Eonemachilus. In the phylogenetic tree, Y. jinxiensis clusters with Paranemachilus genilepis, and Y. pulcherrimus clusters with Micronemacheilus cruciatus, indicating that Y. jinxiensis and Y. pulcherrimus belong to Paranemachilus and Micronemacheilus, respectively. Based on morphological data, Y. bailianensis and Y. longibarbatus are placed in Heminoemacheilus, while Y. jinxiensis and Y. pulcherrimus, are placed in Paranemachilus and Micronemacheilus, respectively. Yunnanilus niulanensis and Y. qujinensis are treated as junior synonyms of Eonemachilus caohaiensis. Eonemachilus, Micronemacheilus, and Yunnanilus are show short separation between anterior and posterior nostrils. The genera can be distinguished from each other by mouth structure, lateral line and cephalic lateral-line canals, and papillae on median part of both lips. The anterior and posterior nostrils of Heminoemacheilus and Paranemachilus are closely set. Paranemachilus and Micronemacheilus are distinguished by cheeks covered with scales and lips with papillae, respectively. Our phylogenetic tree and morphological characters support Traccatichthys as a valid genus, which can be distinguished from Micronemacheilus by anterior and posterior nostrils closely set (vs. clearly separated). Four species are placed in Traccatichthys.
Letters to the editor
The global outbreak of coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as of 8 May 2021, has surpassed 150 700 000 infections and 3 279 000 deaths worldwide. Evidence indicates that SARS-CoV-2 RNA can be detected on particulate matter (PM), and COVID-19 cases are correlated with levels of air pollutants. However, the mechanisms of PM involvement in the spread of SARS-CoV-2 remain poorly understood. Here, we found that PM exposure increased the expression level of angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2) in several epithelial cells and increased the adsorption of the SARS-CoV-2 spike protein. Instillation of PM in a hACE2 mouse model significantly increased the expression of ACE2 and Tmprss2 and viral replication in the lungs. Furthermore, PM exacerbated the pulmonary lesions caused by SARS-CoV-2 infection in the hACE2 mice. In conclusion, our study demonstrated that PM is an epidemiological factor of COVID-19, emphasizing the necessity of wearing anti-PM masks to cope with this global pandemic.
Article
Chronic pollution in aquatic ecosystems can lead to many adverse effects, including a greater susceptibility to pathogens among resident biota. Trifloxystrobin (TFS) is a strobilurin fungicide widely used in Asia to control soybean rust. However, it has the potential to enter aquatic ecosystems, where it may impair fish resistance to viral infections. To explore the potential environmental risks of TFS, we characterized the antiviral capacities of fish chronically exposed to TFS and subsequently infected with spring viraemia of carp virus (SVCV). Although TFS exhibited no significant cytotoxicity at the tested environmental concentrations during viral challenge, SVCV replication increased significantly in a time-dependent manner within epithelioma papulosum cyprini (EPC) cells and zebrafish exposed to 25 μg/L TFS. Results showed that the highest viral load was more than 100-fold that of the controls. Intracellular biochemical assays indicated that autophagy was induced by TFS, and associated changes included an increase in autophagosomes, conversion of LC3-II, accumulation of Beclin-1, and degradation of P62 in EPC cells and zebrafish. In addition, TFS markedly decreased the expression and phosphorylation of mTOR, indicating that activation of TFS may be associated with the mTOR-mediated autophagy pathway. This study provides new insights into the mechanism of the immunosuppressive effects of TFS on non-target aquatic hosts and suggests that the existence of TFS in aquatic environments may contribute to outbreaks of viral diseases.
Letters to the editor
Coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus (SARS-CoV-2), has become an unprecedented global health emergency. At present, SARS-CoV-2-infected nonhuman primates are considered the gold standard animal model for COVID-19 research. Here, we showed that northern pig-tailed macaques (Macaca leonina, NPMs) supported SARS-CoV-2 replication. Furthermore, compared with rhesus macaques, NPMs showed rapid viral clearance in lung tissues, nose swabs, throat swabs, and rectal swabs, which may be due to higher expression of interferon (IFN)-α in lung tissue. However, the rapid viral clearance was not associated with good outcome. In the second week post infection, NPMs developed persistent or even more severe inflammation and body injury compared with rhesus macaques. These results suggest that viral clearance may have no relationship with COVID-19 progression and SARS-CoV-2-infected NPMs could be considered as a critically ill animal model in COVID-19 research.
Article
Scientific research provides essential information for conservation of threatened species. Data deficiency due to insufficient research impedes the design of conservation plans, and research bias may mistakenly direct limited resources to low biodiversity regions or less threatened species. Here, we conducted a systematic review of published papers, grants, and graduate student training on carnivorans in China to identify species bias and research gaps. Furthermore, we collected intrinsic and extrinsic features of carnivorans, and identified features that impact research intensity using generalized linear models. We found that the amount of research on carnivorans increased markedly after 2000, but species bias existed. Bears and big cats received the greatest research attention, while most small- and medium-sized carnivorans received little attention, thus showing the 80-20 phenomenon. Species with a higher level of endemism and protection under Chinese law received more consideration. As an animal conservation icon in China, the giant panda (Ailuropoda melanoleuca) attracted more than 50% of overall carnivoran research resources. However, the giant panda also showed spillover effects, i.e., post-doctoral graduates who studied the giant panda shifted their research focus to other species after graduation, which may help improve research on other species. Thus, to improve and strengthen Carnivora research and conservation, we suggest investing greater effort in species of less concern, training of more graduate students, and reinforcing academic exchange. If such actions are not taken, many carnivoran species will continue being data deficient and threatened.
Review
Intermuscular bones (IBs) are slender linear bones embedded in muscle, which ossify from tendons through a process of intramembranous ossification, and only exist in basal teleosts. IBs are essential for fish swimming, but they present a choking risk during human consumption, especially in children, which can lead to commercial risks that have a negative impact on the aquaculture of these fish. In this review, we discuss the morphogenesis and functions of IBs, including their underlying molecular mechanisms, as well as the advantages and disadvantages of different methods for IB studies and techniques for breeding and generating IB-free fish lines. This review reveals that the many key genes involved in tendon development, osteoblast differentiation, and bone formation, e.g., scxa, msxC, sost, twist, bmps, and osterix, also play roles in IB development. Thus, this paper provides useful information for the breeding of new fish strains without IBs via genome editing and artificial selection.
Article
LIN28A, an RNA-binding protein, plays an important role in porcine induced pluripotent stem cells (piPSCs). However, the molecular mechanism underlying the function of LIN28A in the maintenance of pluripotency in piPSCs remains unclear. Here, we explored the function of LIN28A in piPSCs based on its overexpression and knockdown. We performed total RNA sequencing (RNA-seq) of piPSCs and detected the expression levels of relevant genes by quantitative real-time polymerase chain reaction (qRT-PCR), western blot analysis, and immunofluorescence staining. Results indicated that piPSC proliferation ability decreased following LIN28A knockdown. Furthermore, when LIN28A expression in the shLIN28A2 group was lower (by 20%) than that in the negative control knockdown group (shNC), the pluripotency of piPSCs disappeared and they differentiated into neuroectoderm cells. Results also showed that LIN28A overexpression inhibited the expression of DUSP (dual-specificity phosphatases) family phosphatases and activated the mitogen-activated protein kinase (MAPK) signaling pathway. Thus, LIN28A appears to activate the MAPK signaling pathway to maintain the pluripotency and proliferation ability of piPSCs. Our study provides a new resource for exploring the functions of LIN28A in piPSCs.

Vol 42, No 3 (18 May 2021)

Indexed by SCI-E

2019 Impact Factor 2.638

12/168 Zoology (Q1)

2020 Journal Citation Reports®

Bimonthly, Since 1980

Editor-in-Chief: Yong-Gang Yao

ISSN 2095-8137

CN 53-1229/Q

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