Genomic Diversity and Demographic History of the Endangered Sichuan hill-partridge (Arborophila rufipectus)

Species conservation can be improved by knowledge of genetic diversity and demographic history. The Sichuan hill-partridge (Arborophila rufipectus, SP) is an endangered species endemic to the mountains in southwestern China. However, little is known about this species' genomic variation and demographic history. Here, we present a comprehensive whole-genome analysis of six SP individuals from the Laojunshan National Nature Reserve in Sichuan Province, China. We observe a relatively high genetic diversity and low level of recent inbreeding in the studied SP individuals. This suggests that the current population carries genetic variability that may benefit the long-term survival of this species, and that the present population may be larger than currently recognized. Analyses of demographic history showed that fluctuations in the effective population size of SP are inconsistent with changes of the historical climate. Strikingly, evidence from demographic modeling suggests SPs population decreased dramatically 15,100 years ago after the Last Glacial Maximum (LGM), possibly due to refugial isolation and later human interference. These results provide the first detailed and comprehensive genomic insights into genetic diversity, genomic inbreeding levels, and demographic history of the Sichuan hill-partridge, which are crucial for the conservation and management of this endangered species.

Genomic Evidence for the Complex Evolutionary History of Macaques (Genus Macaca)

The genus Macaca is widely distributed, occupies a variety of habitats, shows diverse phenotypic characteristics, and is one of the best-studied genera of nonhuman primates. Here, we reported five re-sequencing Macaca genomes, including one M. cyclopis, one M. fuscata, one M. thibetana, one M. silenus, and one M. sylvanus. Together with published genomes of other macaque species, we combined 20 genome sequences of 10 macaque species to investigate the gene introgression and genetic differences among the species. The network analysis of the SNV-fragment trees indicates a reticular phylogeny of macaque species. Combining the results from various analytical methods, we identified extensive ancient introgression events among macaque species. The multiple introgression signals between different species groups were also observed, such as between fascicularis group species and silenus group species. However, gene flow signals between fascicularis and sinica group were not as strong as those between fascicularis group and silenus group. On the other hand, the unidirect gene flow in M. arctoides probably occurred between the progenitor of M. arctoides and the common ancestor of fascicularis group. Our study also shows that the genetic backgrounds and genetic diversity of different macaques vary dramatically among species, even among populations of the same species. In conclusion, using whole genome sequences and multiple methods, we have studied the evolutionary history of the genus Macaca and provided evidence for extensive introgression among the species.

Interpretation of vaginal metagenomic characteristics in different types of vaginitis

Although vaginitis is closely related to vaginal microecology in females, the precise composition and functional potential of different types of vaginitis remain unclear. Here, metagenomic sequencing was applied to analyze the vaginal flora in patients with various forms of vaginitis, including cases with a clue cell proportion ranging from 1% to 20% (Clue1_20), bacterial vaginitis (BV), vulvovaginal candidiasis (VVC), and BV combined with VVC (VVC_BV). Our results identified Prevotella as an important biomarker between BV and Clue1_20. Moreover, a gradual decrease was observed in the relative abundance of shikimic acid metabolism associated with bacteria producing indole as well as a decline in the abundance of Gardnerella vaginalis in patients with BV, Clue1_20, and healthy women. Interestingly, the vaginal flora of patients in the VVC_BV group exhibited structural similarities to that of the VVC group, and its potentially functional characteristics resembled those of the BV and VVC groups. Finally, Lactobacillus crispatus was found in high abundance in healthy samples, greatly contributing to the stability of the vaginal environment. For the further study of L. crispatus, we isolated five strains of L. crispatus from healthy samples and evaluated their capacity to inhibit G. vaginalis biofilms and produce lactic acid in vitro to select the potential probiotic candidate for improving vaginitis in future clinical studies. Overall, we successfully identified bacterial biomarkers of different vaginitis and characterized the dynamic shifts in vaginal flora between patients with BV and healthy females. This research advances our understanding and holds great promise in enhancing clinical approaches for the treatment of vaginitis.

IMPORTANCE

Vaginitis is one of the most common gynecological diseases, mostly caused by infections of pathogens such as Candida albicans and Gardnerella vaginalis. In recent years, it has been found that the stability of the vaginal flora plays an important role in vaginitis. Furthermore, the abundant Lactobacillus-producing rich lactic acid in the vagina provides a healthy acidic environment such as Lactobacillus crispatus. The metabolites of Lactobacillus can inhibit the colonization of pathogens. Here, we collected the vaginal samples of patients with bacterial vaginitis (BV), vulvovaginal candidiasis (VVC), and BV combined with VVC to discover the differences and relationships among the different kinds of vaginitis by metagenomic sequencing. Furthermore, because of the importance of L. crispatus in promoting vaginal health, we isolated multiple strains from vaginal samples of healthy females and chose the most promising strain with potential probiotic benefits to provide clinical implications for treatment strategies.

Red pandas with different diets and environments exhibit different gut microbial functional composition and capacity

The red panda (Ailurus fulgens) is a distinctive mammal known for its reliance on a diet primarily consisting of bamboo. The gut microbiota and overall health of animals are strongly influenced by diets and environments. Therefore, conducting research to explore the taxonomical and functional variances within the gut microbiota of red pandas exposed to various dietary and environmental conditions could shed light on the dynamic complexities of their microbial communities. In this study, normal fecal samples were obtained from red pandas residing in captive and semi-free environments under different dietary regimes and used for metabolomic, 16S rRNA, and metagenomic sequencing analysis, with the pandas classified into four distinct cohorts according to diet and environment. In addition, metagenomic sequencing was conducted on mucus fecal samples to elucidate potential etiological agents of disease. Results revealed an increased risk of gastrointestinal diseases in red pandas consuming bamboo shoots due to the heightened presence of pathogenic bacteria, although an increased presence of microbiota-derived tryptophan metabolites appeared to facilitate intestinal balance. The red pandas fed bamboo leaves also exhibited a decrease in gut microbial diversity, which may be attributed to the antibacterial flavonoids and lower protein levels in leaves. Notably, red pandas residing in semi-free environments demonstrated an enriched gut microbial diversity. Moreover, the occurrence of mucus secretion may be due to an increased presence of species associated with diarrhea and a reduced level of microbiota-derived tryptophan metabolites. In summary, our findings substantiate the influential role of diet and environment in modulating the gut microbiota of red pandas, offering potential implications for improved captive breeding practices.

Unraveling the antimicrobial potential of Lactiplantibacillus plantarum strains TE0907 and TE1809 sourced from Bufo gargarizans: advancing the frontier of probiotic-based therapeutics

Introduction

In an era increasingly defined by the challenge of antibiotic resistance, this study offers groundbreaking insights into the antibacterial properties of two distinct Lactiplantibacillus plantarum strains, TE0907 and TE1809, hailing from the unique ecosystem of Bufo gargarizans. It uniquely focuses on elucidating the intricate components and mechanisms that empower these strains with their notable antibacterial capabilities.

Methods

The research employs a multi-omics approach, including agar diffusion tests to assess antibacterial efficacy and adhesion assays with HT-29 cells to understand the preliminary mechanisms. Additionally, gas chromatography-mass spectrometry (GC-MS) is employed to analyze the production of organic acids, notably acetic acid, and whole-genome sequencing is utilized to identify genes linked to the biosynthesis of antibiotics and bacteriocin-coding domains.

Results

The comparative analysis highlighted the exceptional antibacterial efficacy of strains TE0907 and TE1809, with mean inhibitory zones measured at 14.97 and 15.98 mm, respectively. A pivotal discovery was the significant synthesis of acetic acid in both strains, demonstrated by a robust correlation coefficient (cor ≥ 0.943), linking its abundance to their antimicrobial efficiency. Genomic exploration uncovered a diverse range of elements involved in the biosynthesis of antibiotics similar to tetracycline and vancomycin and potential regions encoding bacteriocins, including Enterolysin and Plantaricin.

Conclusion

This research illuminates the remarkable antibacterial efficacy and mechanisms intrinsic to L. plantarum strains TE0907 and TE1809, sourced from B. gargarizans. The findings underscore the strains' extensive biochemical and enzymatic armamentarium, offering valuable insights into their role in antagonizing enteric pathogens. These results lay down a comprehensive analytical foundation for the potential clinical deployment of these strains in safeguarding animal gut health, thereby enriching our understanding of the role of probiotic bacteria in the realm of antimicrobial interventions.

Demonstrating Agreement between Radio and Fluorescence Measurements of the Depth of Maximum of Extensive Air Showers at the Pierre Auger Observatory

We show, for the first time, radio measurements of the depth of shower maximum (X_{max}) of air showers induced by cosmic rays that are compared to measurements of the established fluorescence method at the same location. Using measurements at the Pierre Auger Observatory we show full compatibility between our radio and the previously published fluorescence dataset, and between a subset of air showers observed simultaneously with both radio and fluorescence techniques, a measurement setup unique to the Pierre Auger Observatory. Furthermore, we show radio X_{max} resolution as a function of energy and demonstrate the ability to make competitive high-resolution X_{max} measurements with even a sparse radio array. With this, we show that the radio technique is capable of cosmic-ray mass composition studies, both at Auger and at other experiments.

Chromosome-level genome assembly of the kiang (Equus kiang) illuminates genomic basis for its high-altitude adaptation

The kiang (Equus kiang) can only be observed in the Qinghai-Tibet Plateau (QTP). The kiang displayed excellent athletic performance in the high-altitude environment, which attracted wide interest in the investigation of the potential adaptive mechanisms to the extreme environment. Here, we assembled a chromosome-level genome of the kiang based on Hi-C sequencing technology. A total of 324.14 Gb clean data were generated, and the chromosome-level genome with 26 chromosomes (25 + X) and scaffold N50 of 101.77 Mb was obtained for the kiang. The genomic synteny analysis revealed large-scale chromosomal rearrangement during the evolution process of Equus species. Phylogenetic and divergence analyses revealed that the kiang was the sister branch to the ass and diverged from a common ancestor at approximately 13.5 Mya. The expanded gene families were mainly related to the hypoxia response, metabolism, and immunity. The kiang suffered a significant loss of olfaction-related genes, which might indicate decreased olfactory sensibility. Positively selected genes (PSGs) detected in the kiang were mainly associated with hypoxia response. Especially, there were two species-specific missense amino acid mutations in the PSG STAT3 annotated in the hypoxia-inducible factor 1 signal pathway, which may play an important role in the high-altitude adaptation of the kiang. Moreover, structure variations in the kiang genome were also identified, which possibly contributed to the high-altitude adaptation of the kiang. Comparative analysis revealed a lot of species-specific insertions and deletions in the kiang genome, such as PIK3CB and AKT with 3258 and 189 bp insertions in the intron region, respectively, possibly affecting the expression and regulation of hypoxia-related downstream pathways. This study provided valuable genomic resources, and our findings help a better understanding of the underlying adaptive strategies to the high-altitude environment in the kiang.

Temporal and spatial differences in the vaginal microbiome of Chinese healthy women

Background

Up the reproductive tract, there are large differences in the composition of vaginal microbes. Throughout the menstrual cycle, the structure of the vaginal microbiome shifts. Few studies have examined both in combination. Our study was designed to explore trends in the microbiome of different parts of the vagina in healthy women over the menstrual cycle.

Methods

We performed metagenomic sequencing to characterize the microbiome differences between the cervical orifice and mid-vagina throughout the menstrual cycle.

Results

Our results showed the vaginal microbiome of healthy women in the cervical orifice and the mid-vagina was similar during the periovulatory and luteal phases, with Lactobacillus being the dominant bacteria. In the follicular phase, Acinetobacter was detected in the cervical orifice. From the follicular phase to the luteal phase, the community state types (all five community status types were defined as CSTs) in samples No. 10 and No. 11 changed from CST III to CST I. In addition, the composition of the vaginal microbiome in healthy women from different regions of China was significantly different. We also detected viruses including Human alphaherpesvirus 1 (HSV-1) during periovulatory phase.

Conclusion

This study is valuable for understanding whether the microbial composition of the vagina is consistent in different parts of the menstrual cycle.

The first chromosome-level genome assembly and transcriptome sequencing provide insights into cantharidin production of the blister beetles

Blister beetles (Coleoptera: Meloidae) produce a natural defensive toxin cantharidin (CTD), which has been used for various cancer treatments and other diseases. Currently, the lack of chromosome-level reference genomes in Meloidae limits further understanding of the mechanism of CTD biosynthesis and environmental adaptation. In this study, the chromosome-level genome assembly of Mylabris phalerata was generated based on PacBio and Hi-C sequencing. This reference genome was about 136.68 Mb in size with contig N50 of 9.17 Mb and composed of 12 chromosomes. In comparison to six other Coleoptera insects, M. phalerata exhibited multiple expanded gene families enriched in juvenile hormone (JH) biosynthetic process pathway, farnesol dehydrogenase activity, and cytochrome P450, which may be related to CTD biosynthesis. Consistently, the transcriptomic analysis suggested the "terpenoid backbone biosynthesis" pathway and "the juvenile hormone" as putative core pathways of CTD biosynthesis and presented eight up-regulated differential expression genes in male adults as candidate genes. It is possible that the restricted feeding niche and lifestyle of M. phalerata were the cause of the gene family's contraction of odorant binding proteins. The ABC transporters (ABCs) related to exporting bound toxins out of the cell and the resistance to the self-secreted toxins (e.g. CTD) were also contracted, possibly due to other self-protection strategies in M. phalerata. A foundation of understanding CTD biosynthesis and environmental adaptation of blister beetles will be established by our reference genome and discoveries.

Transposable Elements Shape the Genome Diversity and the Evolution of Noctuidae Species

Noctuidae is known to have high species diversity, although the genomic diversity of Noctuidae species has yet to be studied extensively. Investigation of transposable elements (TEs) in this family can improve our understanding of the genomic diversity of Noctuidae. In this study, we annotated and characterized genome-wide TEs in ten noctuid species belonging to seven genera. With multiple annotation pipelines, we constructed a consensus sequence library containing 1038-2826 TE consensus. The genome content of TEs showed high variation in the ten Noctuidae genomes, ranging from 11.3% to 45.0%. The relatedness analysis indicated that the TE content, especially the content of LINEs and DNA transposons, is positively correlated with the genome size (r = 0.86, p-value = 0.001). We identified SINE/B2 as a lineage-specific subfamily in Trichoplusia ni, a species-specific expansion of the LTR/Gypsy subfamily in Spodoptera exigua, and a recent expansion of SINE/5S subfamily in Busseola fusca. We further revealed that of the four TE classes, only LINEs showed phylogenetic signals with high confidence. We also examined how the expansion of TEs contributed to the evolution of noctuid genomes. Moreover, we identified 56 horizontal transfer TE (HTT) events among the ten noctuid species and at least three HTT events between the nine Noctuidae species and 11 non-noctuid arthropods. One of the HTT events of a Gypsy transposon might have caused the recent expansion of the Gypsy subfamily in the S. exigua genome. By determining the TE content, dynamics, and HTT events in the Noctuidae genomes, our study emphasized that TE activities and HTT events substantially impacted the Noctuidae genome evolution.

Multi-omics analysis reveals changes in tryptophan and cholesterol metabolism before and after sexual maturation in captive macaques

Rhesus macaques (Macaca mulatta, RMs) are widely used in sexual maturation studies due to their high genetic and physiological similarity to humans. However, judging sexual maturity in captive RMs based on blood physiological indicators, female menstruation, and male ejaculation behavior can be inaccurate. Here, we explored changes in RMs before and after sexual maturation based on multi-omics analysis and identified markers for determining sexual maturity. We found that differentially expressed microbiota, metabolites, and genes before and after sexual maturation showed many potential correlations. Specifically, genes involved in spermatogenesis (TSSK2, HSP90AA1, SOX5, SPAG16, and SPATC1) were up-regulated in male macaques, and significant changes in gene (CD36), metabolites (cholesterol, 7-ketolithocholic acid, and 12-ketolithocholic acid), and microbiota (Lactobacillus) related to cholesterol metabolism were also found, suggesting the sexually mature males have stronger sperm fertility and cholesterol metabolism compared to sexually immature males. In female macaques, most differences before and after sexual maturity were related to tryptophan metabolism, including changes in IDO1, IDO2, IFNGR2, IL1Β, IL10, L-tryptophan, kynurenic acid (KA), indole-3-acetic acid (IAA), indoleacetaldehyde, and Bifidobacteria, indicating that sexually mature females exhibit stronger neuromodulation and intestinal immunity than sexually immature females. Cholesterol metabolism-related changes (CD36, 7-ketolithocholic acid, 12-ketolithocholic acid) were also observed in female and male macaques. Exploring differences before and after sexual maturation through multi-omics, we identified potential biomarkers of sexual maturity in RMs, including Lactobacillus (for males) and Bifidobacterium (for females) valuable for RM breeding and sexual maturation research.

[Pathological features of early gastric cancer and its background mucosa after eradication of Helicobacter pylori and their implications for biopsy diagnosis]

Objective: To investigate the clinicopathological changes of early gastric cancer, especially its background mucosa, after the eradication of Helicobacter pylori (H. pylori), and to investigate the causes of underdiagnosis in preoperative biopsy pathology. Methods: Ninety cases of early gastric cancer after H. pylori eradication and 120 cases of endoscopic submucosal dissection (ESD) specimens without H. pylori eradication and their corresponding biopsy specimens were collected from Beijing Friendship Hospital Affiliated to Capital Medical University during 2016-2021. The clinicopathological data of the patients were analyzed, and the histopathological characteristics and immunophenotypic results compared. Results: Compared with the early gastric cancer without H. pylori eradication history, the histopathological type of early gastric cancer after H. pylori eradication was differentiated adenocarcinoma, with staggered distribution of cancerous and non-cancerous epithelium in the tumor area. The morphologic characteristics of gastric mucosa in the background of early gastric cancer after H. pylori eradication, were distinctive, including widening of the opening of enterosylated glandular ducts, serrated change of luminal margin, eosinophilic and microvesicular cytoplasm of enterosylated epithelium. Low-grade atypia existed in gastric cancer epithelial cells after sterilization, which might lead to underdiagnosis or missed diagnosis in biopsy pathology. Conclusions: Early gastric cancer and its background mucosa after H. pylori eradication have unique morphological characteristics, which can be used as a clue for pathological diagnosis, improve the accuracy of biopsy pathology and reduce the underdiagnosis.

A snapshot of climate drivers and temporal variation of Ixodes ovatus abundance from a giant panda living in the wild

Ticks and tick-borne diseases have negative impacts on the health of wild animals including endangered and vulnerable species. The giant panda (Ailuropoda melanoleuca), a vulnerable and iconic flagship species, is threatened by tick infestation as well. Not only can ticks cause anemia and immunosuppression in the giant panda, but also bacterial and viral diseases. However, previous studies regarding tick infestation on giant pandas were limited in scope as case reports from sick or dead animals. In this study, an investigation focusing on the tick infestation of a reintroduced giant panda at the Daxiangling Reintroduction Base in Sichuan, China was conducted. Ticks were routinely collected and identified from the ears of the giant panda from March to September in 2021. A linear model was used to test the correlation between tick abundance and climate factors. All ticks were identified as Ixodes ovatus. Tick abundance was significantly different among months. Results from the linear model showed temperature positively correlated to tick abundance, while air pressure had a negative correlation with tick abundance. To the best of our knowledge, this study is the first reported investigation of tick species and abundance on a healthy giant panda living in the natural environment, and provides important information for the conservation of giant pandas and other species sharing the same habitat.

Revalidation and expanded description of Mustela aistoodonnivalis (Mustelidae: Carnivora) based on a multigene phylogeny and morphology

The lacked-teeth pygmy weasel, Mustela aistoodonnivalis Wu & Kao, 1991, was originally described as being from Taibai Mountain and Zhashui county, Shaanxi, China. Subsequently, it was considered a subspecies or synonym of Mustela nivalis. In a faunal survey of northwestern Sichuan, eight specimens of M. aistoodonnivalis were collected. A molecular phylogenetic analysis of one mitochondrial and six nuclear genes clustered the specimens as a distinct clade and not with M. nivalis. Morphologically, the lack of the second lower molar differentiated them from M. nivalis, and genetic distances were typical of discrete species. These analyses confirmed that M. aistoodonnivalis is an independent species in the genus Mustela.

Comparative Analysis of Olfactory Receptor Repertoires Sheds Light on the Diet Adaptation of the Bamboo-Eating Giant Panda Based on the Chromosome-Level Genome

The giant panda (Ailuropoda melanoleuca) is the epitome of a flagship species for wildlife conservation and also an ideal model of adaptive evolution. As an obligate bamboo feeder, the giant panda relies on the olfaction for food recognition. The number of olfactory receptor (OR) genes and the rate of pseudogenes are the main factors affecting the olfactory ability of animals. In this study, we used the chromosome-level genome of the giant panda to identify OR genes and compared the genome sequences of OR genes with five other Ursidae species (spectacled bear (Tremarctos ornatus), American black bear (Ursus americanus), brown bear (Ursus arctos), polar bear (Ursus maritimus) and Asian black bear (Ursus thibetanus)). The giant panda had 639 OR genes, including 408 functional genes, 94 partial OR genes and 137 pseudogenes. Among them, 222 OR genes were detected and distributed on 18 chromosomes, and chromosome 8 had the most OR genes. A total of 448, 617, 582, 521 and 792 OR genes were identified in the spectacled bear, American black bear, brown bear, polar bear and Asian black bear, respectively. Clustering analysis based on the OR protein sequences of the six species showed that the OR genes distributed in 69 families and 438 subfamilies based on sequence similarity, and the six mammals shared 72 OR gene subfamilies, while the giant panda had 31 unique OR gene subfamilies (containing 35 genes). Among the 35 genes, there are 10 genes clustered into 8 clusters with 10 known human OR genes (OR8J3, OR51I1, OR10AC1, OR1S2, OR1S1, OR51S1, OR4M1, OR4M2, OR51T1 and OR5W2). However, the kind of odor molecules can be recognized by the 10 known human OR genes separately, which needs further research. The phylogenetic tree showed that 345 (about 84.56%) functional OR genes were clustered as Class-II, while only 63 (about 15.44%) functional OR genes were clustered as Class-I, which required further and more in-depth research. The potential odor specificity of some giant panda OR genes was identified through the similarity to human protein sequences. Sequences similar to OR2B1, OR10G3, OR11H6 and OR11H7P were giant panda-specific lacking, which may be related to the transformation and specialization from carnivore to herbivore of the giant panda. Since our reference to flavoring agents comes from human research, the possible flavoring agents from giant panda-specific OR genes need further investigation. Moreover, the conserved motifs of OR genes were highly conserved in Ursidae species. This systematic study of OR genes in the giant panda will provide a solid foundation for further research on the olfactory function and variation of the giant panda.

Large‐scale genetic surveys for main extant population of wild giant panda ( Ailuropoda melanoleuca ) reveals an urgent need of human management

There are only six isolated living giant panda populations, and a comprehensive understanding of their genetic health status is crucial for the conservation of this vulnerable species. Liangshan Mountains is one of the main distribution areas of living giant pandas and is outside the newly established Giant panda national park. In this study, 971 giant panda fecal samples were collected in the heartland of Liangshan Mountains (Mabian Dafengding Nature Reserve: MB; Meigu Dafengding Nature Reserve: MG; and Heizhugou Nature Reserve: HZG). Microsatellite markers and mitochondrial D-loop sequences were used to estimate population size and genetic diversity. We identified 92 individuals (MB: 27, MG: 22, HZG: 43) from the three reserves. Our results showed that: (1) genetic diversity of three giant panda populations was moderate; (2) several loci deviated significantly from the Hardy-Weinberg equilibrium and almost all these deviated loci showed significant heterozygote deficiencies and inbreeding; (3) three giant panda populations have substantial genetic differentiation with the most differentiation between MB and the two other populations; and (4) a large amount of giant panda feces outside the three reserves were found, implying the existence of protection gap. These results indicated that under stochastic events, the giant panda populations in Liangshan Mountains are at risk of genetic decline or extinction and urgent need of human management. This study revealed that high attention should be paid to the protection of these giant panda populations outside the Giant panda national park, to ensure their survival in their distribution areas.

Comparative Analyses Reveal the Genetic Mechanism of Ambergris Production in the Sperm Whale Based on the Chromosome-Level Genome

Sperm whales are a marine mammal famous for the aromatic substance, the ambergris, produced from its colon. Little is known about the biological processes of ambergris production, and this study aims to investigate the genetic mechanism of ambergris production in the sperm whale based on its chromosome-level genome. Comparative genomics analyses found 1207 expanded gene families and 321 positive selected genes (PSGs) in the sperm whale, and functional enrichment analyses suggested revelatory pathways and terms related to the metabolism of steroids, terpenoids, and aldosterone, as well as microbiota interaction and immune network in the intestine. Furthermore, two sperm-whale-specific missense mutations (Tyr393His and Leu567Val) were detected in the PSG LIPE, which has been reported to play vital roles in lipid and cholesterol metabolism. In total, 46 CYP genes and 22 HSD genes were annotated, and then mapped to sperm whale chromosomes. Furthermore, phylogenetic analysis of CYP genes in six mammals found that CYP2E1, CYP51A and CYP8 subfamilies exhibited relative expansion in the sperm whale. Our results could help understand the genetic mechanism of ambergris production, and further reveal the convergent evolution pattern among animals that produce similar odorants.

Involvement of the E3 ubiquitin ligase Cblb in host defense and evaluation of transcriptome during Trueperella pyogenes infection

Trueperella pyogenes (T. pyogenes) is a versatile and ingenious bacterium that causes severe suppurative injuries in lots of economically important ruminants. The underlying pathogenesis of T. pyogenes infection remains poorly understood. In the current study, we performed transcriptome sequencing of mouse blood tissue infected with T. pyogenes. A total of 36.73 G clean data were collected, and 136 differentially expressed genes were obtained in the infection group compared to the control group. In addition, we found that the E3 ubiquitin ligase Cblb exhibited significant upregulation in the infection groups compared to the control group. Mechanistically, T. pyogenes infection markedly enhanced the expression of Cblb and regulated the host defense response. Inhibiting Cblb expression with Cblb siRNA impaired the inflammatory response and reduced the effect of phagocytosis in RAW264.7 murine macrophages. Intriguingly, overexpression of Cblb induced a strong inflammatory response and enhanced phagocytosis against T. pyogenes infection in macrophages. More importantly, the overexpression of Cblb significantly reduced the bacterial load and protected mice from the T. pyogenes infections. Therefore, our findings reveal that Cblb is a novel and potential regulator in response to T. pyogenes infection and shed new light on the development of promising treatments against T. pyogenes-related diseases.

Gene expressions between obligate bamboo-eating pandas and non-herbivorous mammals reveal converged specialized bamboo diet adaptation

BACKGROUND

It is inevitable to change the function or expression of genes during the environmental adaption of species. Both the giant panda (Ailuropoda melanoleuca) and red panda (Ailurus fulgens) belong to Carnivora and have developed similar adaptations to the same dietary switch to bamboos at the morphological and genomic levels. However, the genetic adaptation at the gene expression level is unclear. Therefore, we aimed to examine the gene expression patterns of giant and red panda convergent specialized bamboo-diets. We examined differences in liver and pancreas transcriptomes between the two panda species and other non-herbivorous species.

RESULTS

The clustering and PCA plots suggested that the specialized bamboo diet may drive similar expression shifts in these two species of pandas. Therefore, we focused on shared liver and pancreas DEGs (differentially expressed genes) in the giant and red panda relative to other non-herbivorous species. Genetic convergence occurred at multiple levels spanning carbohydrate metabolism, lipid metabolism, and lysine degradation. The shared adaptive convergence DEGs in both organs probably be an evolutionary response to the high carbohydrate, low lipid and lysine bamboo diet. Convergent expression of those nutrient metabolism-related genes in both pandas was an intricate process and subjected to multi-level regulation, including DNA methylation and transcription factor. A large number of lysine degradation and lipid metabolism related genes were hypermethylated in promoter regions in the red panda. Most genes related to carbohydrate metabolism had reduced DNA methylation with increased mRNA expression in giant pandas. Unlike the red panda, the core gene of the lysine degradation pathway (AASS) doesn't exhibit hypermethylation modification in the giant panda, and dual-luciferase reporter assay showed that transcription factor, NR3C1, functions as a transcriptional activator in AASS transcription through the binding to AASS promoter region.

CONCLUSIONS

Our results revealed the adaptive expressions and regulations of the metabolism-related genes responding to the unique nutrients in bamboo food and provided data accumulation and research hints for the future revelation of complex mechanism of two pandas underlying convergent adaptation to a specialized bamboo diet.

Assembly of novel microbial genomes from gut metagenomes of rhesus macaque (Macaca mulatta)

Rhesus macaque (RM, Macaca mulatta), as an important model animal, commonly suffers from chronic diarrheal disease, challenging the breeding of RMs. Gut microbiomes play key roles in maintaining intestinal health of RMs. However, it is still unclear about more features of gut microbiome as responsible for intestinal health of RMs. In this study, we performed de novo assembly of metagenome-assembled genomes (MAGs) based on fecal metagenomes from chronic diarrheal RMs and asymptomatic individuals. In total of 731 non-redundant MAGs with at least 80% completeness were reconstructed in this study. More than 97% MAGs were novel genomes compared with more than 250,000 reference genomes. MAGs of Campylobacter and Helicobacteraceae from RM guts mainly carried flagella-associated virulence genes and chemotaxis-associated virulence genes, which might mediate motility and adhesion of bacteria. Comparing to MAGs of Campylobacter from humans, distributions and functions of these MAGs of Campylobacter from RMs exhibited significant differences. Most members of Bacteroidota, Spirochaetota, Helicobacteraceae, Lactobacillaceae and Anaerovibrio significantly decreased in guts of chronic diarrhea RMs. More than 92% MAGs in this study were not contained in 2,985 MAGs previously reported from other 22 non-human primates (NHPs), expanding the microbial diversity in guts of NHPs. The distributions and functions of gut microbiome were prominently influenced by host phylogeny of NHPs. Our results could help to more clearly understand about the diversity and function of RMs gut microbiome.

The draft genome of the Tibetan partridge (Perdix hodgsoniae) provides insights into its phylogenetic position and high-altitude adaptation

The Tibetan partridge (Perdix hodgsoniae) is a widely distributed endemic species in high-altitude areas across the Tibetan Plateau where the hypoxia, lower temperature and high ultraviolet (UV) radiation are pivotal factors influencing survival. However, the underlying genetic adaptation of the Tibetan partridge to extreme environments remains uncertain due to limited genomic resources. Similarly, the phylogenetic position of Perdix within Phasianidae remains controversial due to lacking information. Consequently, we de novo assembled and annotated the whole genome of the Tibetan partridge. The genome size was 1.15 Gb with contig N50 of 3.70 Mb. A total of 202.30 Mb (17.61%) repetitive elements and 445,876 perfect microsatellites were identified. A total of 16,845 functionally annotated protein-coding genes were identified in the Tibetan partridge. Genomic phylogenetic analysis across 30 Galliformes species indicated a close relationship between Perdix and typical pheasants composed of Chrysolophus, Symaticus, Phasianus, Crossopilon, Lophura. However, the phylogenetic relationship of (Perdix + (Chrysolophus + (Syrmaticus + other pheasants))) was different from those of (Perdix + (Syrmaticus + (Chrysolophus + other pheasants))) in previous studies. Comparative genomic results identified NFKB1 and CREBBP positively selected genes (PSGs) related to hypoxia with three and two Tibetan partridge-specific missense mutations, respectively. Expanded gene families were mainly associated with energy metabolism and steroid hydroxylase activity, meanwhile, contracted gene families were mainly related to immunity and olfactory perception. Our genomic data considerably contributes to the phylogeny of Perdix and the underlying adaptation strategies of the Tibetan partridge to a high-altitude environment.

Comparative transcriptomes of nine tissues for the Heilongjiang brown frog (Rana amurensis)

The Heilongjiang brown frog (Rana amurensis) is widely used in traditional Chinese medicine. In particular, the oviduct and skin have been developed into various health products. However, limited numbers of complete genomes of amphibian species have been reported, excluding the Heilongjiang brown frog. Here, the transcriptomes of 45 samples from the liver, spleen, heart, ovaries, thigh muscles, skin, oviduct, stomach and intestine of five Heilongjiang brown frog were reassembled and analyzed. A total of 1,085,532 unigenes with an average length of 676.6 bp and N50 of 722 bp were obtained. Comparative transcriptomics of different tissues detected tissue-specific expression. There were 3248 differentially expressed genes (DEGs) in the ovary, and the number of unique DEGs between the ovary and spleen was the largest. The results of DEGs enrichment showed there were many pathways and items related to protein synthesis and metabolism in the oviduct. The DEGs of the skin were enriched with many bacterial defense items, indicating that there were a large number of antimicrobial peptides in the skin. Thus, these were suitable as biological sources for the development and extraction of antimicrobial peptides. Through the assembly of transcriptome sequencing data and functional annotation of the Heilongjiang brown frog genome, this study provides reference materials for further exploring and utilizing functional gene resources of frogs and lays a foundation for medical research and the development of new products.

Improved genome assembly provides new insights into the environmental adaptation of the American cockroach, Periplaneta americana

The synanthropic pest and a model organism for entomological research, American cockroach, Periplaneta americana (Linnaeus), can survive in unfavorable environments for humans. To investigate the genetic mechanisms of success in environmental adaptation of P. americana, we de novo reassembled its whole genome based on next-generation sequencing and PacBio sequencing. The final genome reassembly consisted of approximately 3.34 Gb with scaffold N50 of 465.51 Kb. The completeness (95.4%) of the complete genome was evaluated with single-copy orthologous genes using BUSCO. We identified 18,618 protein-coding genes, 16,443 (88.32%) of which were well supported by public protein databases. We identified 482.04 Mb (approximately 14.45%) repeat elements, 1,385,093 perfect microsatellites simple sequence repeats in P. americana genome, which was higher than other four Blattaria insects. Comparative genomics analysis revealed obvious expansion in the gene families associated with chemoreception (olfactory receptors, gustatory receptors, ionotropic glutamate receptors, chemosensory protein, and sensory neuron membrane protein), which provided the necessary information for functional characterization of the chemosensory receptors of P. americana, with potential for new or refined applications of semiochemicals-based control of this pest insect. Similarly, gene families (cytochrome P450s, carboxyl/choline esterases, and UDP-glycosyl-transferases) encoding receptors for bitter or toxic substances and detoxification enzymes were obviously expanded in P. americana, enabling its ability to detect and detoxify many toxins. Enrichment analysis of positively selected genes in P. americana revealed items associated with metabolic process and catalytic activity, which possibly contributed to the pesticide resistance of P. americana. We also analyzed the homologs to antimicrobial peptide genes reported in the Drosophila genome, and identified two attacins and seven defensins in P. americana. Our data and findings will substantially facilitate molecular studies in P. americana, including elucidation of detoxification mechanisms of xenobiotic, as well as development of new pest management strategies for the control of pests like P. americana.

Characterization of Seventeen Complete Mitochondrial Genomes: Structural Features and Phylogenetic Implications of the Lepidopteran Insects

Lepidoptera (moths and butterflies) are widely distributed in the world, but high-level phylogeny in Lepidoptera remains uncertain. More mitochondrial genome (mitogenome) data can help to conduct comprehensive analysis and construct a robust phylogenetic tree. Here, we sequenced and annotated 17 complete moth mitogenomes and made comparative analysis with other moths. The gene order of trnM-trnI-trnQ in 17 moths was different from trnI-trnQ-trnM of ancestral insects. The number, type, and order of genes were consistent with reported moths. The length of newly sequenced complete mitogenomes ranged from 14,231 bp of Rhagastis albomarginatus to 15,756 bp of Numenes albofascia. These moth mitogenomes were typically with high A+T contents varied from 76.0% to 81.7% and exhibited negative GC skews. Among 13 protein coding genes (PCGs), some unusual initiations and terminations were found in part of newly sequenced moth mitogenomes. Three conserved gene-overlapping regions and one conserved intergenic region were detected among 17 mitogenomes. The phylogenetic relationship of major superfamilies in Macroheterocera was as follows: (Bombycoidea + Lasiocampoidea) + ((Drepanoidea + Geometroidea) + Noctuoidea)), which was different from previous studies. Moreover, the topology of Noctuoidea as (Notodontidae + (Erebidae + Noctuidae)) was supported by high Bayesian posterior probabilities (BPP = 1.0) and bootstrapping values (BSV = 100). This study greatly enriched the mitogenome database of moth and strengthened the high-level phylogenetic relationships of Lepidoptera.

Whole genome bisulfite sequencing reveals DNA methylation roles in the adaptive response of wildness training giant pandas to wild environment

DNA methylation modification can regulate gene expression without changing the genome sequence, which helps organisms to rapidly adapt to new environments. However, few studies have been reported in non-model mammals. Giant panda (Ailuropoda melanoleuca) is a flagship species for global biodiversity conservation. Wildness and reintroduction of giant pandas are the important content of giant pandas’ protection. However, it is unclear how wildness training affects the epigenetics of giant pandas, and we lack the means to assess the adaptive capacity of wildness training giant pandas. We comparatively analyzed genome-level methylation differences in captive giant pandas with and without wildness training to determine whether methylation modification played a role in the adaptive response of wildness training pandas. The whole genome DNA methylation sequencing results showed that genomic cytosine methylation ratio of all samples was 5.35%–5.49%, and the methylation ratio of the CpG site was the highest. Differential methylation analysis identified 544 differentially methylated genes (DMGs). The results of KEGG pathway enrichment of DMGs showed that VAV3, PLCG2, TEC and PTPRC participated in multiple immune-related pathways, and may participate in the immune response of wildness training giant pandas by regulating adaptive immune cells. A large number of DMGs enriched in GO terms may also be related to the regulation of immune activation during wildness training of giant pandas. Promoter differentially methylation analysis identified 1,199 genes with differential methylation at promoter regions. Genes with low methylation level at promoter regions and high expression such as, CCL5, P2Y13, GZMA, ANP32A, VWF, MYOZ1, NME7, MRPS31 and TPM1 were important in environmental adaptation for wildness training giant pandas. The methylation and expression patterns of these genes indicated that wildness training giant pandas have strong immunity, blood coagulation, athletic abilities and disease resistance. The adaptive response of giant pandas undergoing wildness training may be regulated by their negatively related promoter methylation. We are the first to describe the DNA methylation profile of giant panda blood tissue and our results indicated methylation modification is involved in the adaptation of captive giant pandas when undergoing wildness training. Our study also provided potential monitoring indicators for the successful reintroduction of valuable and threatened animals to the wild.

Multi-omics analysis reveals the host–microbe interactions in aged rhesus macaques

Aging is a complex multifactorial process that greatly affects animal health. Multi-omics analysis is widely applied in evolutionary biology and biomedical research. However, whether multi-omics can provide sufficient information to reveal comprehensive changes in aged non-human primates remains unclear. Here, we explored changes in host–microbe interactions with aging in Chinese rhesus macaques (Macaca mulatta lasiota, CRs) using multi-omics analysis. Results showed marked changes in the oral and gut microbiomes between young and aged CRs, including significantly reduced probiotic abundance and increased pathogenic bacterial abundance in aged CRs. Notably, the abundance of Lactobacillus, which can metabolize tryptophan to produce aryl hydrocarbon receptor (AhR) ligands, was decreased in aged CRs. Consistently, metabolomics detected a decrease in the plasma levels of AhR ligands. In addition, free fatty acid, acyl carnitine, heparin, 2-(4-hydroxyphenyl) propionic acid, and docosahexaenoic acid ethyl ester levels were increased in aged CRs, which may contribute to abnormal fatty acid metabolism and cardiovascular disease. Transcriptome analysis identified changes in the expression of genes associated with tryptophan metabolism and inflammation. In conclusion, many potential links among different omics were found, suggesting that aged CRs face multiple metabolic problems, immunological disorders, and oral and gut diseases. We determined that tryptophan metabolism is critical for the physiological health of aged CRs. Our findings demonstrate the value of multi-omics analyses in revealing host–microbe interactions in non-human primates and suggest that similar approaches could be applied in evolutionary and ecological research of other species.

Enhanced Resolution of Evolution and Phylogeny of the Moths Inferred from Nineteen Mitochondrial Genomes

The vast majority (approximately 90%) of Lepidoptera species belong to moths whose phylogeny has been widely discussed and highly controversial. For the further understanding of phylogenetic relationships of moths, nineteen nearly complete mitochondrial genomes (mitogenomes) of moths involved in six major lineages were sequenced and characterized. These mitogenomes ranged from 15,177 bp (Cyclidia fractifasciata) to 15,749 bp (Ophthalmitis albosignaria) in length, comprising of the core 37 mitochondrial genes (13 protein-coding genes (PCGs) + 22 tRNAs + two rRNAs) and an incomplete control region. The order and orientation of genes showed the same pattern and the gene order of trnM-trnI-trnQ showed a typical rearrangement of Lepidoptera compared with the ancestral order of trnI-trnQ-trnM. Among these 13 PCGs, ATP8 exhibited the fastest evolutionary rate, and Drepanidae showed the highest average evolutionary rate among six families involved in 66 species. The phylogenetic analyses based on the dataset of 13 PCGs suggested the relationship of (Notodontidae + (Noctuidae + Erebidae)) + (Geometridae + (Sphingidae + Drepanidae)), which suggested a slightly different pattern from previous studies. Most groups were well defined in the subfamily level except Erebidae, which was not fully consistent across bayesian and maximum likelihood methods. Several formerly unassigned tribes of Geometridae were suggested based on mitogenome sequences despite a not very strong support in partial nodes. The study of mitogenomes of these moths can provide fundamental information of mitogenome architecture, and the phylogenetic position of moths, and contributes to further phylogeographical studies and the biological control of pests.

Chromosome-level Genome Assembly of the High-altitude Leopard (Panthera pardus) Sheds Light on Its Environmental Adaptation

The leopard (Panthera pardus) has the largest natural distribution from low- to high-altitude areas of any wild felid species, but recent studies have revealed that leopards have disappeared from large areas, probably owing to poaching, a decline of prey species, and habitat degradation. Here, we reported the chromosome-scale genome assembly of the high-altitude leopard (HL) based on nanopore sequencing and high-throughput chromatin conformation capture (Hi-C) technology. Panthera genomes revealed similar repeat composition, and there was an appreciably conserved synteny between HL and the other two Panthera genomes. Divergence time analysis based on the whole genomes revealed that the HL and the low-altitude leopard differentiate from a common ancestor ∼2.2 Ma. Through comparative genomics analyses, we found molecular genetic signatures that may reflect high-altitude adaptation of the HL. Three HL-specific missense mutations were detected in two positively selected genes, that is, ITGA7 (Ala112Gly, Asp113Val, and Gln115Pro) and NOTCH2 (Ala2398Ser), which are likely to be associated with hypoxia adaptation. The chromosome-level genome of the HL provides valuable resources for the investigation of high-altitude adaptation and protection management of the vulnerable leopard.

Blood transcriptome analysis revealing aging gene expression profiles in red panda

The red panda is an endangered forest species distributed on the edge of the Qinghai Tibet Plateau. The species has been conserved in ex-situ in many countries and its survival is threatened by many diseases. Its immune system is vulnerable to age-associated alterations, which accumulate and result in a progressive deterioration that leads to an increased incidence of diseases. We identified 2,219 differentially expressed genes (DEGs) between geriatric (11-16 years) and adult individuals (4-8 years), and 1690 DEGs between adults and juveniles (1 year). The gene expression and functional annotation results showed that the innate immunity of red pandas increases significantly in geriatric individuals, whereas its change remains unclear when comparing adults and juveniles. We found that the adaptive immunity of red pandas first increased and then decreased with age. We identified CXCR3, BLNK, and CCR4 as the hub genes in the age-related protein-protein interaction network, which showed their central role in age-related immune changes. Many DNA repair genes were down-regulated in geriatric red pandas, suggesting that the DNA repair ability of the blood tissue in geriatric red pandas is significantly reduced. The significantly up-regulated TLR5 in geriatric individuals also suggests the possibility of enhancing the vaccination immune response by incorporating flagellin, which could be used to address decreased vaccine responses caused by age-related declines in immune system function. This work provides an insight into gene expression changes associated with aging and paves the way for effective disease prevention and treatment strategies for red pandas in the future.

Complete mitochondrial genome of Episymploce splendens (Blattodea: Ectobiidae): A large intergenic spacer and lacking of two tRNA genes

The complete mitochondrial genome of Episymploce splendens, 15,802 bp in length, was determined and annotated in this study. The mito-genome included 13 PCGs, 20 tRNAs and 2 rRNAs. Unlike most typical mito-genomes with conservative gene arrangement and exceptional economic organization, E. splendens mito-genome has two tRNAs (tRNA-Gln and tRNA-Met) absence and a long intergenic spacer sequence (93 bp) between tRNA-Val and srRNA, showing the diversified features of insect mito-genomes. This is the first report of the tRNAs deletion in blattarian mito-genomes and we supported the duplication/random loss model as the origin mechanism of the long intergenic spacer. Two Numts, Numt-1 (557 bp) and Numt-2 (975 bp) transferred to the nucleus at about 14.15 Ma to 22.34 Ma, and 19.19 Ma to 24.06 Ma respectively, were found in E. splendens. They can be used as molecular fossils in insect phylogenetic relationship inference. Our study provided useful data for further studies on the evolution of insect mito-genome.

Heterologous Prime-Boost Immunization with DNA Vaccine and Modified Recombinant Proteins Enhances Immune Response against Trueperella pyogenes in Mice

Trueperella pyogenes (T. pyogenes) is a crucial opportunistic pathogen normally causing mastitis, abscesses and pneumonia in economically important ruminants. Although only one commercial vaccine of T. pyogenes is currently obtainable, its immunoprotective effect is limited. Pyolysin (PLO) is the most predominant virulence factor highly expressed in T. pyogenes and is an excellent target for the development of novel vaccines against T. pyogenes. In this study, we designed a heterologous prime-boost vaccination scheme combining a DNA vaccine pVAX1-PLO and a subunit vaccine His-PLO to maximize host responses in mice. Humoral and cellular immune responses and protective effects were evaluated in mice to compare the immunogenicity induced by different immunization schemes. Compared to the PBS-control group, in vivo immunization results showed that better immune responses of mice immunized with the pVAX1-PLO plasmids and His-PLO proteins were induced. The residual bacterial burdens from the liver and peritoneal fluid were remarkably decreased in the immunized mice compared with the PBS group. Notably, the heterologous prime-boost vaccination groups significantly enhanced host humoral and cellular immune responses and protected mice from different virulent T. pyogenes strains infection. Conclusively, this study provides a favorable strategy for the further development of next-generation vaccines against T. pyogenes infections.

Transcriptomics and metagenomics of common cutworm (Spodoptera litura) and fall armyworm (Spodoptera frugiperda) demonstrate differences in detoxification and development

BACKGROUND

Spodoptera litura is an important polyphagous pest that causes significant damage to the agricultural sector. We performed RNA-seq of 15 S. litura individuals from larval (fifth and sixth instar larvae), chrysalis, and adult developmental stages. We also compared the S. litura transcriptome data with Spodoptera frugiperda across the same developmental stages, which was sequenced in our previous study.

RESULTS

A total of 101,885 differentially expressed transcripts (DETs) were identified in S. litura. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that S. litura may undergo active xenobiotic and detoxifying metabolism during its larval and adult stages, which may explain difficulties with current population control measures. We also found that DETs of single-copy orthologous genes between S. litura and S. frugiperda were involved in basic metabolism and development. However, energy and metabolic processes genes had a higher expression in S. litura, whereas nervous and olfactory function genes had a higher expression in S. frugiperda. Metagenomics analysis in larval S. litura and S. frugiperda revealed that microbiota participate in the detoxification and metabolism processes, but the relative abundance of detoxification-related microbiota was more abundant in S. frugiperda. Transcriptome results also confirmed the detoxification-related pathway of S. frugiperda was more abundant than in S. litura.

CONCLUSIONS

Significant changes at transcriptional level were identified during the different development stages of S. litura. Importantly, we also identified detoxification associated genes and gut microbiota between S. litura and S. frugiperda at different developmental stages, which will be valuable in revealing possible mechanisms of detoxification and development in these two lepidopterans.

Epigenomic profiling indicates a role for DNA methylation in the postnatal liver and pancreas development of giant pandas

Giant pandas are unique within Carnivora with a strict bamboo diet. Here, the epigenomic profiles of giant panda liver and pancreas tissues collected from three important feeding stages were investigated using BS-seq. Few differences in DNA methylation profiles were exhibited between no feeding and suckling groups in both tissues. However, we observed a tendency toward a global loss of DNA methylation in the gene-body and promoter region of metabolism-related genes from newborn to adult. Correlation analysis revealed a significant negative correlation between the changes in methylation levels within gene promoters and gene expression. The majority of genes related to nutrition metabolism had lost DNA methylation with increased mRNA expression in adult giant pandas. The few galactose metabolism and unsaturated fatty acid metabolism related genes that were hypomethylated and highly-expressed at early stages of giant panda development may meet the nutritional requirement of this species' highly altricial neonates.

Whole blood transcriptome profiling identifies candidate genes associated with alopecia in male giant pandas (Ailuropoda melanoleuca)

Background

The giant panda (Ailuropoda melanoleuca) is a threatened species endemic to China. Alopecia, characterized by thinning and broken hair, mostly occurs in breeding males. Alopecia significantly affects the health and public image of the giant panda and the cause of alopecia is unclear.

Results

Here, we researched gene expression profiles of four alopecia giant pandas and seven healthy giant pandas. All pandas were approximately ten years old and their blood samples collected during the breeding season. A total of 458 up-regulated DEGs and 211 down-regulated DEGs were identified. KEGG pathway enrichment identified that upregulated genes were enriched in the Notch signaling pathway and downregulated genes were enriched in ribosome, oxidative phosphorylation, and thermogenesis pathways. We obtained 28 hair growth-related DEGs, and identified three hub genes NOTCH1, SMAD3, and TGFB1 in PPI analysis. Five hair growth-related signaling pathways were identified with abnormal expression, these were Notch, Wnt, TGF-β, Mapk, and PI3K-Akt. The overexpression of NOTCH1 delays inner root sheath differentiation and results in hair shaft abnormalities. The delayed hair regression was associated with a significant decrease in the expression levels of TGFB1.

Conclusions

Our data confirmed the abnormal expression of several hair-related genes and pathways and identified alopecia candidate genes in the giant panda. Results of this study provide theoretical basis for the establishment of prevention and treatment strategies for giant pandas with alopecia.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08501-z.

Intraspecific variation in microhabitat selection in reintroduced Chinese giant salamanders

Reintroduction of captive-bred Chinese giant salamanders is a primary approach for restoring wild populations. Despite previous studies have investigated the habitat preferences of reintroduced Chinese giant salamanders, the intraspecific variation in their habitat selection has been neglected. In the present study, 30 captive-bred Chinese giant salamanders belonging to three groups (i.e., 10 males, 10 females, and 10 juveniles) were released into a montane stream to explore whether intraspecific variation in habitat selection occurred in this species using radiotelemetry. Our results indicated that linear home range and daily movement of males were significantly higher than those of females and juveniles. Male sedentariness was significantly lower than that of females and juveniles. No significant differences were detected between females and juveniles these measures. Importantly, we found that males preferred microhabitats with low water conductivity and deep water depth. Females preferred microhabitats with high water conductivity, low dissolved oxygen and ammonium-nitrogen, and slow current velocity, while juveniles occupied microhabitat with low ammonium-nitrogen. In addition, males and juveniles exhibited higher niche breadth than females. Niche overlap was high between adults and juveniles but low between males and females. Our study revealed the presence of spatial segregation in reintroduced Chinese giant salamanders. Males, females, and juveniles exhibited variation in microhabitat selection. These results provide important information for use when planning strategies for conservation of Chinese giant salamanders.

Characterization of olfactory receptor repertoires provides insights into the high-altitude adaptation of the yak based on the chromosome-level genome

Olfaction in vertebrates plays pivotal parts in many aspects, such as localizing prey or food, mating behavior, avoiding predators, and social communication. Yak (Bos grunniens) is the only Bos species that can thrive in high-altitude areas. In view of the critical role of olfactory receptors (ORs) in the specific recognition of diverse stimuli, investigating the evolutionary dynamics of ORs in the yak means a lot. In this study, we used the chromosome-level genome of the yak to identify the ORs genes and discussed the effects of high altitude on the yak's olfaction by comparing the yak with other low-altitude living Bos species (Bos frontalis (gayal), Bos gaurus (gaur), Bos indicus (zebu) and Bos taurus (cattle)). The yak had 400 OR genes, including 264 functional genes, 16 partial genes and 120 OR pseudo genes. There were 387 OR genes mapped to yak 31 chromosomes, and chromosomes 13 and 8 had the most OR genes and functional OR genes. Among these five Bos species, yak had the least number of OR gene subfamilies, OR genes and functional OR genes, while the total number of OR genes in gayal (n = 784) was almost twice as many as that of yak, indicating that the olfaction of yak may be less developed. In addition, the phylogenetic relationships of the functional Bos OR genes were illustrated, which comprised 79 families and 466 subfamilies distributed in two classes (Class I and Class II). There were 76 OR gene subfamilies shared by these five Bos species and 17 OR gene subfamilies were unique to the yak. The potential odor specificity of 44 yak OR genes was identified through the similarity to human OR protein sequences. Remarkably, yak lacks β-ionone and Isovaleric acid(IVA)-related ORs, which may be related to the decline of high-altitude herbaceous plant diversity and underdeveloped yak sweat glands. The conserved motifs of OR genes were highly conserved in Bos species. These results provided a solid foundation for further studies on the molecular mechanisms of the yak's adaptation to the high-altitude environment in olfaction.

Antibacterial and anti-virulence effects of furazolidone on Trueperella pyogenes and Pseudomonas aeruginosa

Background

Trueperella pyogenes and Pseudomonas aeruginosa are two important bacterial pathogens closely relating to the occurrence and development of forest musk deer respiratory purulent disease. Although T. pyogenes is the causative agent of the disease, the subsequently invaded P. aeruginosa will predominate the infection by producing a substantial amount of quorum-sensing (QS)-controlled virulence factors, and co-infection of them usually creates serious difficulties for veterinary treatment. In order to find a potential compound that targets both T. pyogenes and P. aeruginosa, the antibacterial and anti-virulence capacities of 55 compounds, which have similar core structure to the signal molecules of P. aeruginosa QS system, were tested in this study by performing a series of in vitro screening experiments.

Results

We identified that furazolidone could significantly reduce the cell densities of T. pyogenes in mono-culture or in the co-culture with P. aeruginosa. Although the growth of P. aeruginosa could also be moderately inhibited by furazolidone, the results of phenotypic identification and transcriptomic analysis further revealed that sub-inhibitory furazolidone had remarkable inhibitory effect on the biofilm production, motility, and QS system of P. aeruginosa. Moreover, furazolidone could efficiently protect Caenorhabditis elegans models from P. aeruginosa infection under both fast-killing and slow-killing conditions.

Conclusions

This study reports the antibacterial and anti-virulence abilities of furazolidone on T. pyogenes and P. aeruginosa, and provides a promising strategy and molecular basis for the development of novel anti-infectious drugs to dealing with forest musk deer purulent disease, or other diseases caused by T. pyogenes and P. aeruginosa co-infection.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12917-022-03216-5.

Comparative transcriptomes of three different skin sites for the Asiatic toad (Bufo gargarizans)

Toads release toxic dry secretions from glands in their skin. Toxin possesses a wide range of biological effects, but little is known about its specific gene expression pattern and regulatory mechanisms. The Asiatic toad (Bufo gargarizans) is widely used to produce toxin. Here, we explored the gene expression of 30 tissue samples from three different skin sites (parotoid gland, dorsal skin, and abdomen skin) of B. gargarizans. After de novo assembly, 783,130 unigenes with an average length of 489 bp (N50 = 556 bp) were obtained. A total of 9,248 significant differentially expressed genes (DEGs) were detected. There were 8,819 DEGs between the parotoid gland and abdomen skin and 1,299 DEGs between the dorsal skin and abdomen skin, while only 1,283 DEGs were obtained between the parotoid gland and dorsal skin. Through enrichment analysis, it was found that the detected differential gene expressions corresponded to the different functions of different skin sites. Our key findings were the genetic expression of toxin secretion, the protection function of skin, and the related genes such as HSD3B, Cyp2c, and CAT, LGALS9. In conclusion, we provide useful transcript resources to study the gene expression and gene function of B. gargarizans and other amphibians. The detected DEGs between different sites of the skin provided better insights into the genetic mechanisms of toxin secretion and the protection function of skin for amphibians.

The gut microbiome and antibiotic resistome of chronic diarrhea rhesus macaques (Macaca mulatta) and its similarity to the human gut microbiome

BACKGROUND

Chronic diarrhea is a common disease causing morbidity and mortality of captive rhesus macaques (RMs, Macaca mulatta). Chronic diarrhea in RMs is typically characterized by long-term diarrhea and a weak response to antibiotic treatment. Diarrhea is also a common disease in humans and can cause death. However, the etiology of about half of diarrheal cases of humans is still unclear. Therefore, we performed shotgun metagenomic sequencing to characterize the differences in the gut microbiome and resistome of chronic diarrhea RMs and asymptomatic individuals.

RESULTS

Our results showed Lactobacillus spp. (mainly L. johnsonii, L. reuteri and L. amylovorus) were significantly depleted in chronic diarrhea RM guts compared to asymptomatic individuals (5.2 vs 42.4%). Functional annotation of genes suggested these Lactobacillus spp. carried genes involved in the adhesion of intestinal epithelial cells and production of bacteriocin. Chronic diarrhea RM guts also had a significantly greater abundance of many other gut bacteria, including mucin-degrading bacteria and opportunistic pathogens. The metabolic pathways of chronic diarrhea RM gut microbiome were enriched in aerobactin biosynthesis, while the metabolic pathways of asymptomatic RM gut microbiome were enriched in the production of short-chain fatty acids (SCFAs). Chronic diarrhea RM guts had a significantly greater abundance of antibiotic resistance genes (ARGs), such as ermF, aph(3')-IIIa, ermB, and floR. The strains isolated from feces and tissue fluid of chronic diarrhea RMs had higher resistance rates to the majority of tested antibiotics, but not cephamycin and carbapenem antibiotics. Gut microbial composition comparisons showed that several captive nonhuman primate (NHP) guts were more similar to the guts of humans with a non-westernized diet than humans with a westernized diet. Chronic diarrhea RM gut microbiome was strikingly similar to rural-living humans with diarrhea and humans with a non-westernized diet than asymptomatic RMs.

CONCLUSIONS

Our results suggested chronic diarrhea significantly altered the composition and metabolic pathways of the RM gut microbiome. The frequent use of antibiotics caused antibiotic resistance in chronic diarrhea RM gut microbiome with serious consequences for individual treatment and survival. The findings of this study will help us to improve the effective prevention and treatment of diarrhea in RMs. Video Abstract.

Blood transcriptome analysis revealed the immune changes and immunological adaptation of wildness training giant pandas

The giant panda (Ailuropoda melanoleuca) is a global flagship species for biodiversity conservation. As the time for captive giant pandas to be released into the wild matures, wildness training is provided to allow adaptation to their natural environment. It is assumed that changes in the immune system would be integral in this adaptation from captive to wild, where many more pathogens would be encountered in their natural habitats. Therefore, this study aims to determine the expression changes of immune-related genes and their potential as immunoassay markers for adaptation monitoring in wildness training giant pandas, and then to understand the adaptation strategy of wildness training giant pandas to the wild environment, thereby improving the success rate of panda reintroduction. We obtained 300 differentially expressed genes (DEGs) by RNA-seq, with 239 up-regulated and 61 down-regulated DEGs in wildness training giant pandas compared to captive pandas. Functional enrichment analysis indicated that up-regulated DEGs were enriched in several immune-related terms and pathways. There were 21 immune-related DEGs, in which most of them were up-regulated in wildness training giant pandas, including several critical innate and cellular immune genes. IL1R2 was the most significantly up-regulated gene and is a signature of homeostasis within the immune system. In the protein-protein interaction (PPI) analysis, CXCL8, CXCL10, and CCL5 were identified as the hub immune genes. Our results suggested that wildness training giant pandas have stronger innate and cellular immunity than captive giant pandas, and we proposed that a gene set of CXCL8, CXCL10, CCL5, CD3D, NFKBIA, TBX21, IL12RB2, and IL1R2 may serve as potential immunoassay markers to monitor and assess the immune status of wildness training giant pandas. Our study offers the first insight into immune alterations of wildness training giant pandas, paving the way for monitoring and evaluating the immune status of giant pandas when reintroducing them into the wild.

Comparative metagenomics analysis reveals how the diet shapes the gut microbiota in several small mammals

The gut microbiomes of the host are large and complex communities, which helps to maintain homeostasis, improves digestive efficiency, and promotes the development of the immune system. The small mammals distributed in Sichuan Province are the most popular species for biodiversity research in Southwest China. However, the effects of different diets on the structure and function of the gut microbial community of these small mammals are poorly understood. In this study, whole-metagenome shotgun sequencing has been used to analyze the composition and functional structures of the gut microbiota of seven small mammals in Laojunshan National Nature Reserve, Sichuan Province, China. Taxonomic classification revealed that the most abundant phyla in the gut of seven small mammals were Bacteroides, Proteobacteria, and Firmicutes. Moreover, Hafnia, Lactobacillus, and Yersinia were the most abundant genus in the gut microbiomes of these seven species. At the functional level, we annotated a series of KEGG functional pathways, six Cazy categories, and 46,163 AROs in the gut microbiomes of the seven species. Comparative analysis found that the difference in the gut microbiomes between the Soricidea and Muridae concentrated on the increase in the F/B (Firmicutes/Bacteroides) ratio in the Soricidea group, probably driven by the high-fat and -calorie digestive requirements due to their insectivorous diet. The comparative functional profiling revealed that functions related to metabolism and carbohydrates were significantly more abundant in Muridae group, which may be attributed to their high carbohydrate digestion requirements caused by their herbivorous diet. These data suggested that different diets in the host may play an important role in shaping the gut microbiota, and lay the foundation for teasing apart the influences of heritable and environmental factors on the evolution of gut microbial communities.

Transcriptomic landscape of persistent diarrhoea in rhesus macaques and comparison with humans and mouse models with inflammatory bowel disease

Diarrhoea is a widespread disease in captive rhesus macaques (Macaca mulatta) and a small proportion of individuals may experience persistent diarrhoea. Persistent diarrhoea can lead to a compromised immune system, intestinal inflammation and malnutrition. We analyzed the blood transcriptomes of 10 persistent diarrhoeal and 12 healthy rhesus macaques to investigate the gene expression differences between the two groups. We identified 330 DEGs between persistent diarrhoeal and healthy rhesus macaques. The 211 up-regulated DEGs in the diarrhoeal group were mainly enriched in immune-related and interleukin-related categories. Among them, three interleukin (IL) 18 related DEGs (IL18, IL18R1, and IL18BP) played important roles in actively regulating pro-inflammatory responses. Interestingly, the up- and down-regulated DEGs were both enriched in the same immune-related categories. Thus, we applied a new method to examine the distribution of DEGs in all child categories. We found that interleukin and T cell related categories were mainly occupied by up-regulated DEGs, while immunoglobulin production and B cell related categories were enriched by down-regulated DEGs. We also compared rhesus macaque DEGs with the DEGs of inflammatory bowel disease (IBD) humans and IBD mouse models and found that 30-40% of macaque DEGs were shared with IBD humans and mouse models. In conclusion, our results showed that there were significant immune differences between persistent diarrhoeal rhesus macaques and healthy macaques, which was similar to the expression differences in IBD patients and mouse models.

De Novo Sequencing and High-Contiguity Genome Assembly of Moniezia expansa Reveals Its Specific Fatty Acid Metabolism and Reproductive Stem Cell Regulatory Network

Moniezia expansa (M. expansa) parasitizes the small intestine of sheep and causes inhibited growth and development or even death. Being globally distributed, it causes considerable economic losses to the animal husbandry industry. Here, using Illumina, PacBio and BioNano techniques, we obtain a high-quality genome assembly of M. expansa, which has a total length of 142 Mb, a scaffold N50 length of 7.27 Mb and 8,104 coding genes. M. expansa has a very high body fat content and a specific type of fatty acid metabolism. It cannot synthesize any lipids due to the loss of some key genes involved in fatty acid synthesis, and it may can metabolize most lipids via the relatively complete fatty acid β-oxidation pathway. The M. expansa genome encodes multiple lipid transporters and lipid binding proteins that enable the utilization of lipids in the host intestinal fluid. Although many of its systems are degraded (with the loss of homeobox genes), its reproductive system is well developed. PL10, AGO, Nanos and Pumilio compose a reproductive stem cell regulatory network. The results suggest that the high body lipid content of M. expansa provides an energy source supporting the high fecundity of this parasite. Our study provides insight into host interaction, adaptation, nutrient acquisition, strobilization, and reproduction in this parasite and this is also the first genome published in Anoplocephalidae.

Sex-specific gene expression in the blood of four primates

Blood is an important non-reproductive tissue, but little is known about the sex-specific gene expressions in the blood. Therefore, we investigated sex-specific gene expression differences in the blood tissues of four primates, rhesus macaques (Macaca mulatta), Tibetan macaques (M. thibetana), yellow baboons (Papio cynocephalus), and humans. We identified seven sex-specific differentially expressed genes (SDEGs) in each non-human primate and 31 SDEGs in humans. The four primates had only one common SDEG, MAP7D2. In humans, immune-related SDEGs were identified as up-regulated, but also down-regulated in females. We also found that most of the X-Y gene pairs had similar expression levels between species, except pair EIF1AY/EIF1AX. The expression level of X-Y gene pairs of rhesus and Tibetan macaques showed no significant differential expression levels, while humans had six significant XY-biased and three XX-biased X-Y gene pairs. Our observed sex differences in blood should increase understanding of sex differences in primate blood tissue.

Metabolic cold adaptation in the Asiatic toad: intraspecific comparison along an altitudinal gradient

The metabolic cold adaptation (MCA) hypothesis predicts an increase in metabolic rate and thermal sensitivity of poikilotherms from cold environments as compared to those from warm environments, when measured under standardized conditions. This compensatory response is also expected to evolve in life history and behavioral traits if the reductions in these phenotypic traits at low temperature involves in a reduction in fitness. We investigated the extent to which the level of energy intake (measured as feeding rate), energy turnover (measured as standard metabolic rate, SMR) and the energy budget (energy allocation to growth and physical activity) are influenced by climatic conditions in three populations of the Asiatic toad (Bufo gargarizans) distributed across an altitudinal gradient of 1350 m in the Qionglai Mountains of Western China. We found a similar thermal reaction norm of SMR at both population and individual levels; therefore, the data did not support the MCA hypothesis. However, there was a co-gradient variation (CoGV) for mass change rate in which the high and medium altitudinal populations displayed slower mass change rates than their counterparts from low altitudes. Moreover, this CoGV pattern was accompanied by a low feeding rate and high physical activity for the high- and medium-altitude populations. Our results highlight that adjustments in energy intake and energy allocation to behaviors, but not energy allocation to metabolism of maintenance, could act as an energetic strategy to accommodate the varied growth efficiency in Asiatic toads along an altitudinal gradient.

Brain size variation along altitudinal gradients in the Asiatic Toad (Bufo gargarizans)

Size changes in brain and brain regions along altitudinal gradients provide insight into the trade-off between energetic expenditure and cognitive capacity. We investigated the brain size variations of the Asiatic Toad (Bufo gargarizans) across altitudes from 700 m to 3,200 m. A total of 325 individuals from 11 sites and two transects were sampled. To reduce confounding factors, all sampling sites within each transect were within a maximum distance of 85 km and an altitudinal difference close to 2,000 m. Brains were dissected, and five regions were both measured directly and with 3D CT scan. There is a significant negative correlation between the relative whole-brain volume (to snout-vent length) and altitude. Furthermore, the relative volumes (to whole-brain volume) of optic tectum and cerebellum also decrease along the altitudinal gradients, while the telencephalon increases its relative volume along the gradients. Therefore, our results are mostly consistent with the expensive brain hypothesis and the functional constraint hypothesis. We suggest that most current hypotheses are not mutually exclusive and data supporting one hypothesis are often partially consistent with others. More studies on mechanisms are needed to explain the brain size evolution in natural populations.

De novo transcriptome assemblies of Epicauta tibialis provide insights into the sexual dimorphism in the production of cantharidin

Blister beetles have medicinal uses for their defensive secretion cantharidin, which has curative effects on many cancers and other diseases. It was demonstrated that sexual dimorphism exists in the production of cantharidin between male and female adults. This study performed a de novo assembly of Epicauta tibialis transcriptomes and analyzed the differentially expressed genes (DEGs) between male and female adults to help to find genes and pathways associated with cantharidin biosynthesis. A total of 99,295,624 paired reads were generated, and more than 7 Gb transcriptome data for each sample were obtained after trimming. The clean data were used to de novo assemble and then cluster into 27,355 unigenes, with a mean length of 1442 bp and an N50 of 2725 bp. Of these, 14,314 (52.33%) unigenes were annotated by protein databases. Differential expression analysis identified 284 differentially expressed genes (DEGs) between male and female adults. Nearly 239 DEGs were up-regulated in male adults than in female adults, while 45 DEGs were down-regulated. The Kyoto Encyclopedia of Gene and Genomes pathway enrichment manifested that seven up-regulated DEGs in male adults were assigned to the terpenoid biosynthesis pathway, to which 19 unigenes were annotated. The DEGs in the terpenoid biosynthesis pathway between male and female adults may be responsible for the sexual dimorphism in cantharidin production. The up-regulated genes assigned to the pathway in male adults may play a significant role in cantharidin biosynthesis, and its biosynthesis process is probably via the mevalonate pathway. The results would be helpful to better understand and reveal the complicated mechanism of the cantharidin biosynthesis.