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.

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.

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.

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.

Pyfastx: a robust Python package for fast random access to sequences from plain and gzipped FASTA/Q files.

FASTA and FASTQ are the most widely used biological data formats that have become the de facto standard to exchange sequence data between bioinformatics tools. With the avalanche of next-generation sequencing data, the amount of sequence data being deposited and accessed in FASTA/Q formats is increasing dramatically. However, the existing tools have very low efficiency at random retrieval of subsequences due to the requirement of loading the entire index into memory. In addition, most existing tools have no capability to build index for large FASTA/Q files because of the limited memory. Furthermore, the tools do not provide support to randomly accessing sequences from FASTA/Q files compressed by gzip, which is extensively adopted by most public databases to compress data for saving storage. In this study, we developed pyfastx as a versatile Python package with commonly used command-line tools to overcome the above limitations. Compared to other tools, pyfastx yielded the highest performance in terms of building index and random access to sequences, particularly when dealing with large FASTA/Q files with hundreds of millions of sequences. A key advantage of pyfastx over other tools is that it offers an efficient way to randomly extract subsequences directly from gzip compressed FASTA/Q files without needing to uncompress beforehand. Pyfastx can easily be installed from PyPI (https://pypi.org/project/pyfastx) and the source code is freely available at https://github.com/lmdu/pyfastx.

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 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, and 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 related to hypoxia with 3 and 2 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 contribute to the phylogeny of Perdix and the underlying adaptation strategies of the Tibetan partridge to a high-altitude environment.

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.

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.

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-ß, 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.

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.

Transcriptome Analysis Reveals the Alternative Splicing Changes in the Immune-Related Genes of the Giant Panda (Ailuropoda melanoleuca), in Response to the Canine Distemper Vaccine.

Canine distemper virus (CDV) is a highly fatal virus to the giant panda (Ailuropoda melanoleuca). Although vaccination is a key preventative measure in captive giant pandas, the immune response of giant pandas after vaccination remains unclear. Therefore, this study focuses on differential alternative splicing (DAS) events of giant pandas before and after vaccination to investigate the role of alternative splicing in the immune response of giant pandas after CDV vaccination. In this study, we identified 1113 DAS genes, which had 1288 DAS events. The KEGG functional enrichment analysis of DAS genes showed enrichment of some DNA damage repair and immune-related pathways. In the combined analysis of DAS and differentially expressed genes (from our previous research), we identified 66 differentially expressed genes with a DAS event, and found that some important immune-related genes, such as IL15, IL18, IL18RAP, CHUK, IFI44, CD40, and CD46 underwent DAS events and were involved in the immune response of giant pandas after CDV vaccination. We describe here the alternative splicing events of giant pandas after CDV vaccination for the first time and show that the results indicated that alternative splicing has an important role in regulating the immune response of giant pandas after vaccination.

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.

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.

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.

Immune profiles of male giant panda (Ailuropoda melanoleuca) during the breeding season.

BACKGROUND: The giant panda (Ailuropoda melanoleuca) is a threatened endemic Chinese species and a flagship species of national and global conservation concern. Life history theory proposes that reproduction and immunity can be mutually constraining and interrelated. Knowledge of immunity changes of male giant pandas during the breeding season is limited. RESULTS: Here, we researched peripheral blood gene expression profiles associated with immunity. Thirteen captive giant pandas, ranging from 9 to 11 years old, were divided into two groups based on their reproductive status. We identified 318 up-regulated DEGs and 43 down-regulated DEGs, which were enriched in 87 GO terms and 6 KEGG pathways. Additionally, we obtained 45 immune-related genes with altered expression, mostly up-regulated, and identified four hub genes HSPA4, SUGT1, SOD1, and IL1B in PPI analysis. These 45 genes were related to pattern recognition receptors, autophagy, peroxisome, proteasome, natural killer cell, antigen processing and presentation. SUGT1 and IL1B were related to pattern recognition receptors. HSP90AA1 was the most up-regulated gene and is a member of heat shock protein 90 family. HSP90 contributes to the translocation of extracellular antigen. KLRD1 encodes CD94, whose complex is an inhibitor of the cytotoxic activity of NK cells, was down-regulated. IGIP, which has the capability of inducing IgA production by B cells, was down-regulated, suggesting low concentration of IgA in male giant pandas. Our results suggest that most immune-related genes were up-regulated and more related to innate immune than adaptive immune. CONCLUSIONS: Our results indicated that breeding male giant pandas presented an immunoenhancement in innate immunity, enhanced antigen presentation and processing in cellular immunity compared to non-breeding males. The humoral immunity of male giant pandas may show a tendency to decrease during the breeding season. This study will provide a foundation for further studies of immunity and reproduction in male giant pandas.

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.

Age-related gene expression and DNA methylation changes in rhesus macaque.

Aging is a very complicated biological process that can change gene expressions. The Chinese rhesus macaque (Macaca mulatta lasiota; CR) is closely related to humans. We explored gene expression with increasing age and DNA methylation changes in young and old CRs. Results showed blood transcriptome and DNA methylome significantly changed from young to old CRs. The age-associated differentially expressed genes (DEGs) and differentially methylated regions (DMRs) were associated with age-related biological features, such as immunity, blood coagulation, and biosynthetic process. The measurements of coagulation indicators confirmed old CRs had shorter coagulation time than young CRs, and the activities of coagulation factor II (FII) and factor VIII (FVIII) were enhanced in old CRs. Humans and CRs exhibited the same enhanced blood coagulation with age phenotype. Our study found aging is a critical factor affecting gene expression in CRs, and also provided new insights into the blood coagulation changes in non-human primates.

Genome-wide analysis sheds light on the high-altitude adaptation of the buff-throated partridge (Tetraophasis szechenyii).

The buff-throated partridge (Tetraophasis szechenyii) is a hypoxia-tolerant bird living in an extremely inhospitable high-altitude environment, which has high ultraviolet (UV) radiation as well as a low oxygen supply when compared with low-altitude areas. To further understand the molecular genetic mechanisms of the high-altitude adaptation of the buff-throated partridges, we de novo assembled the complete genome of the buff-throated partridge. Comparative genomics revealed that positively selected hypoxia-related genes in the buff-throated partridge were distributed in the HIF-1 signaling pathway (map04066), response to hypoxia (GO:0001666), response to oxygen-containing compound (GO:1901700), ATP binding (GO:0005524), and angiogenesis (GO:0001525). Of these positively selected hypoxia-related genes, one positively selected gene (LONP1) had one buff-throated partridge-specific missense mutation which was classified as deleterious by PolyPhen-2. Moreover, positively selected genes in the buff-throated partridge were enriched in cellular response to DNA damage stimulus (corrected P value: 0.028006) and DNA repair (corrected P value: 0.044549), which was related to the increased exposure of the buff-throated partridge to UV radiation. Compared with other avian genomes, the buff-throated partridge showed expansion in genes associated with steroid hormone receptor activity and contractions in genes related to immune and olfactory perception. Furthermore, comparisons between the buff-throated partridge genome and red junglefowl genome revealed a conserved genome structure and provided strong evidence of the sibling relationship between Tetraophasis and Lophophorus. Our data and analysis contributed to the study of Phasianidae evolutionary history and provided new insights into the potential adaptation mechanisms to the high altitude employed by the buff-throated partridge.

Comprehensive analysis of lncRNA and mRNA expression changes in Tibetan chicken lung tissue between three developmental stages.

The Tibetan chicken is a native Chinese breed that lives at high elevations and has adapted to the extreme environmental conditions of the Tibetan Plateau. However, its hypoxic adaptation at the gene expression level is unclear. Here, we sequenced nine lung transcriptomes of the Tibetan chicken at three developmental stages (5 and 42 weeks and 4.5 years). A total of 1.02 billion clean reads were obtained. We identified 16 012 mRNAs and 6898 lncRNAs. The expression of mRNA showed that nine samples were significantly divided into three clusters, with higher correlation and closer relationship between the 5 and 42 week groups. We identified 399 differentially expressed genes (DEGs) between the 5 and 42 week groups, 3532 DEGs between the 5 week and 4.5 year groups, and 3909 DEGs between the 42 week and 4.5 year groups. The up-regulated DEGs in the 5 week group, compared with 42 week and 4.5 year groups, were enriched in GO terms associated with growth and development, whereas the up-regulated DEGs in the 4.5 year group were mainly enriched in many metabolic-related categories. Moreover, the enrichment results with up-regulated DEGs in the 5 and/or 42 week groups, compared with the 4.5 year group, were associated with hypoxic adaptation, such as oxygen transport, oxygen binding and oxygen carrier activity, and calcium signaling pathway. In addition, we identified 978 high-correlation lncRNA and protein-coding gene pairs, and 524 significant neighboring protein-coding genes were also DEGs. Our results provide new insights into gene expression of lung tissue in Tibetan chickens during the aging process.

Behavioral heterogeneity in quorum sensing can stabilize social cooperation in microbial populations.

BACKGROUND: Microbial communities are susceptible to the public goods dilemma, whereby individuals can gain an advantage within a group by utilizing, but not sharing the cost of producing, public goods. In bacteria, the development of quorum sensing (QS) can establish a cooperation system in a population by coordinating the production of costly and sharable extracellular products (public goods). Cooperators with intact QS system and robust ability in producing public goods are vulnerable to being undermined by QS-deficient defectors that escape from QS but benefit from the cooperation of others. Although microorganisms have evolved several mechanisms to resist cheating invasion in the public goods game, it is not clear why cooperators frequently coexist with defectors and how they form a relatively stable equilibrium during evolution. RESULTS: We show that in Pseudomonas aeruginosa, QS-directed social cooperation can select a conditional defection strategy prior to the emergence of QS-mutant defectors, depending on resource availability. Conditional defectors represent a QS-inactive state of wild type (cooperator) individual and can invade QS-activated cooperators by adopting a cheating strategy, and then revert to cooperating when there are abundant nutrient supplies irrespective of the exploitation of QS-mutant defector. Our mathematical modeling further demonstrates that the incorporation of conditional defection strategy into the framework of iterated public goods game with sound punishment mechanism can lead to the coexistence of cooperator, conditional defector, and defector in a rock-paper-scissors dynamics. CONCLUSIONS: These findings highlight the importance of behavioral heterogeneity in stabilizing the population structure and provide a potential reasonable explanation for the maintenance and evolution of cooperation in microbial communities.