Gene Exchange Research Articles

Genomic analysis of sugar transporter genes in peanut (Arachis hypogaea): Characteristic, evolution and expression profiles during development and stress

Peanut (Arachis hypogaea L.) is an economically significant crop with aerial cleistogamous flowers and subterranean geocarpic fruit (pods). The formation of peanut pod requires movement of the embryo from air to ground and then development in the soil, which is a complex biological process involving transport and accumulation of sugars. Sugar transport proteins (STP) mediate the transport of monosaccharides in various physiological processes, including fertilization, ovary formation, and seed development. In this study, a total of 36 AhSTP genes (AhSTP1–36) containing the conserved sugar_tr motif were identified in the A. hypogaea genome. Phylogenetic analysis revealed that AhSTP genes were classified into four clades, and the arrangement of motifs in AhSTP proteins was similar within clades. Synteny analysis revealed that segmental duplication events have played an important role in the expansion of STP genes in peanut, and chromosome rearrangements might have facilitated the exchange of STP genes between the A and B sub-genomes. Transcriptome analyses revealed that the expression patterns of AhSTP genes varied among tissues. Hormone and abiotic stress treatments could up-regulate or down-regulate the expression of AhSTP genes, and low temperature had a major effect on the expression of most AhSTP genes. Four AhSTP genes (AhSTP3, AhSTP9, AhSTP19, and AhSTP28) were specifically expressed in the pod, indicating that these genes might be involved in pod formation and development in peanut. The unique expression of these four genes during pod construction and development was confirmed in two different type cultivars using quantitative real-time PCR analysis. Our findings provide new insights into the STP gene family in peanut and will aid future functional studies of AhSTP genes.

Development of EST-SSR markers and population genetic structure and genetic diversity of the Malus transitoria (Batalin) C. K. Schneider in Qinghai-Tibetan Plateau

Malus transitoria (Batalin) C. K. Schneider is a shrub or small tree species native to in and around the Qinghai-Tibetan Plateau (QTP). Using 18 pairs of EST-SSR markers, we examined 142 samples from 8 wild populations of M. transitoria obtained from the QTP. Genetic diversity had been high at the species level and showed the mean expected heterozygosity (He) and Shannon's information index (I) per population were 0.573 and 0.921, as well as the genetic diversity of the WD population (He = 0.595, I = 0.974) had been the greatest, whereas that of the BS population (He = 0.541, I = 0.870) was the lowest. The MKH population had the lowest genetic diversity (Nm = 5.034), while the mean Gene Flow (Nm) was 6.076. Molecular variance analysis (AMOVA) demonstrated moderate genetic differentiation among populations, that Within Populations variation (95%) had been significantly higher than Among Populations variation (5%), which complies to the genetic differentiation coefficient (Fst = 0.057). Two clusters grouped similar to the Unweighted Pair Group Method with Arithmetic (UPGMA) clustering and principal coordinates analysis (PCoA) as per the STRUCTURE analysis. We speculate that long-term orogeny prevents gene exchange across populations, leading to limited gene flow and loss of genetic resources. This research investigated the genetic diversity as well as structure of natural populations of M. transitoria in order to provide a scientific basis of the conservation, breeding, and rational utilization of this tree species germplasm resources in QTP. The lowest Gene Flow population may be preserved by a combination of in-situ conservation and ex-situ conservation (MKH population). Expanding the number of populations and ex-site conservation could preserve the smallest population (XQ population). The other population s could in-situ conserved in order to protect genetic resources.

Polyploidization and speciation: patterns of natural hybridization and gene flow in basil (Ocimum spp.)

The genus Ocimum maintains rich diversity of species through natural and artificial outcrossing. Africa is named as one of the epicentres of plant diversity including numerous Ocimum species. Cytological evidence has attributed such diversity to extensive genome augmentation through selection, speciation, polyploidy and hybridization. This study identified polyploidy as the major natural phenomenon that drives successful hybridization programs or otherwise, within and among four Ocimum species studied and showed rate of gene exchange among the concerned species. All Ocimum species and variants used were grown for two generations before hybridization experiments were carried out. Interspecific and intraspecific reciprocal crossing was done. The crossed flowers were monitored for flower abortion and fruit formation. The resulting progenies from successful crosses were raised along with their parents and evaluated for all identifiable agronomic character differences and similarities. All viable seeds resulted from crosses involving at least one polyploid parent (tetraploids O. basilicum, O. canum and O. americanum). The intra- and interspecific hybridization programs recorded success within O. basilicum and between O. basilicum and tetraploid O. canum. Hybridization within O. canum was difficult due to differences in ploidy levels of O. canum parents used. Hybrid progenies obtained within O. basilicum parents (b1 and b2) and between b2 and tetraploid O. canum possessed morphological characters related to b2 parent while offspring from crosses between b1 and c1 combined characters from both parents. Pollen fertility in both O. basilicum and O. canum parents and their reciprocal crosses was more than 50 percent. O. basilicum displayed higher gene exchange capacity than other species. O. kilimandscharicum and O. americanum parents exhibited allopatric behaviour and low crossability with other seemingly sympatric species used in the study. Genome imbalance and incompatibility were associated with some of the possible causes of sterility.

Comparative transcriptional analysis and identification of hub genes associated with wing differentiation of male in Aphis gossypii

BackgroundAphis gossypii Glover (Hemiptera: Aphididae), a worldwide polyphagous phloem-feeding agricultural pest, has three wing morphs (winged parthenogenetic female, gynopara, and male) in the life cycle. The exclusive males could fly from summer hosts to winter hosts, which are essential for gene exchanges of cotton aphid populations from different hosts or regions. However, the molecular mechanism of wing differentiation of male in A. gossypii remains unclear.ResultsMorphological observation of male A. gossypii showed that there is no distinct difference in the external morphologies of the 1st and 2nd instar nymphs. The obvious differentiation of wing buds started in the 3rd instar nymph and was visible via naked eyes in the 4th instar nymphal stage, then adult male emerged with full wings. According to morphological dynamic changes, the development of wings in males were divided into four stages: preliminary stage (the 1st instar to 2nd instar), prophase (the 3rd instar), metaphase (the 4th instar), anaphase (the 5th instar). Results of feeding behavior monitoring via EPG (electrical penetration graph) technology indicated that although the male cotton aphids had strong desire to feed (longer duration of C 55.24%, F 5.05% and Pd waves 2.56%), its feeding efficiency to summer host cotton was low (shorter E1 3.56% and E2 waves 2.63%). Dynamic transcriptome analysis of male aphid at 5 different developmental periods showed that in the 3rd instar nymph, the number of up-regulated DEGs was significant increased, and time-course gene transcriptional pattern analyses results also showed that numerous genes categorized in clusters 3, 5, and 8 had the highest expressed levels, which were consistent with morphological changes of wing buds. These results indicate that the 3rd instar nymph is the critical stage of wing bud differentiation in males. Furthermore, through pathway enrichment analysis of DEGs and WGCNA, it revealed that the neuroactive ligand-receptor interaction, Ras signaling pathway, dopaminergic synapse, circadian entrainment and the corresponding hub genes of PLK1, BUB1, SMC2, TUBG, ASPM, the kinesin family members (KIF23, KIF20, KIF18-19) and the novel subfamily of serine/threonine (Aurora kinase A and Aurora kinase B) probably played an important role in the critical stage of wing bud differentiation.ConclusionThis study explored morphological changes and genes transcriptional dynamics males in cotton aphid, revealed the phenomenon of low feeding efficiency of winged males on summer host cotton, and identified key signaling pathways and potential hub genes potentially involved in wing bud differentiation of male in A. gossypii.

Loss of the Rhodobacter capsulatus Serine Acetyl Transferase Gene, cysE1, Impairs Gene Transfer by Gene Transfer Agents and Biofilm Phenotypes.

ABSTRACTBiofilms are widespread in the environment, where they allow bacterial species to survive adverse conditions. Cells in biofilms are densely packed, and this proximity is likely to increase the frequency of horizontal gene transfer. Gene transfer agents (GTAs) are domesticated viruses with the potential to spread any gene between bacteria. GTA production is normally restricted to a small subpopulation of bacteria, and regulation of GTA loci is highly coordinated, but the environmental conditions that favor GTA production are poorly understood. Here, we identified a serine acetyltransferase gene, cysE1, in Rhodobacter capsulatus that is required for optimal receipt of GTA DNA, accumulation of extracellular polysaccharide, and biofilm formation. The cysE1 gene is directly downstream of the core Rhodobacter-like GTA (RcGTA) structural gene cluster and upregulated in an RcGTA overproducer strain, although it is expressed on a separate transcript. The data we present suggest that GTA production and biofilm are coregulated, which could have important implications for the study of rapid bacterial evolution and understanding the full impact of GTAs in the environment.IMPORTANCE Direct exchange of genes between bacteria leads to rapid evolution and is the major factor underlying the spread of antibiotic resistance. Gene transfer agents (GTAs) are an unusual but understudied mechanism for genetic exchange that are capable of transferring any gene from one bacterium to another, and therefore, GTAs are likely to be important factors in genome plasticity in the environment. Despite the potential impact of GTAs, our knowledge of their regulation is incomplete. In this paper, we present evidence that elements of the cysteine biosynthesis pathway are involved in coregulation of various phenotypes required for optimal biofilm formation by Rhodobacter capsulatus and successful infection by the archetypal RcGTA. Establishing the regulatory mechanisms controlling GTA-mediated gene transfer is a key stepping stone to allow a full understanding of their role in the environment and wider impact.

Genetic Evaluation in Natural Populations of the Threatened Conifer Amentotaxus argotaenia (Hance) Pilg. (Taxaceae) Using Microsatellites

Amentotaxus argotaenia (Hance) Pilg. is a threatened conifer with a wide distribution range from North to Central Vietnam due to habitat loss and over-exploitation. To provide information for its conservation and sustainable management, in the present study, genetic diversity and population genetic structure for 200 trees from eight populations, representing the natural distribution range of this species were estimated using nuclear microsatellites. The results showed a moderate genetic diversity of A. argotaenia (HO = 0.331, HE = 0.358). Significant heterozygosity deficits were detected in three populations in the Northeast area. Genetic differentiation was low in the same distribution area and high in different areas. However, the gene flow among the studied populations was relatively high (Nm = 1.17). Habitat fragmentation, geographical distance and high mountain range can be the major factors that reduce gene exchange between different areas. Various clustering analyses distinguished three major genetic groups related to the three distribution areas of this species in Vietnam. Based on the study results, we propose that some populations could be prioritized for in situ conservation due to their high genetic diversity with high allelic richness or private alleles, meanwhile other populations should be collected for ex situ conservation as genetic resources in the future.

Biofilm formation by ESBL-producing uropathogenic E. coli

Introduction: E. coli is considered to be the leading cause of urinary tract infections. (UTIs) and is responsible for both community acquired and hospital acquired UTIs. The ability of this bacterium to form biofilm on various devices like catheters plays an important role in progression of the disease. Biofilm production in extended spectrum beta lactamases (ESBLs) producing organisms provides a favourable environment for the exchange of resistance genes and may also facilitate widespread dissemination.
 Methods: The urine samples were collected from the suspected cases of urinary tract infections and were cultured on cystine lactose electrolyte deficient (CLED) agar plates to isolate the desired UPEC strains. All the isolated E. coli strains were subjected to ESBL detection by double disk approximation method and to biofilm formation by tissue culture plate method of biofilm detection. All the results were statistically analysed using k2 test with p value at <0.05 level of significance.
 Results: Out of all the gram negative bacilli isolated from urine samples, E. coli alone accounted for 90% of the isolates. Of all the UPEC isolates subjected to ESBL detection 50% of the strains turned out to be the ESBL producers and 35% of the strains showed biofilm formation.
 Conclusion:
 
 The majority of the work in literature sites the data samples collected from indoor patients, where these isolates coli strains which produced ESBLs were mainly a strong biofilm former as compared to non-ESBL producer strains.
 In this study in spite of all the coli strains being outpatient isolates still the correlation between ESBL production and biofilm formation holds true.
 We found a significant correlation between biofilm formation and ESBL production. The detection of ESBL production and biofilm formation pattern will help in development of newer and more effective treatment.

Identification and Evolutionary Relationship of Corynebacterium striatum Clinical Isolates.

Corynebacterium striatum has developed into a new community-acquired and hospital-acquired multi-drug resistance (MDR) bacterium, and is a potential target pathogen for infection control and antibacterial management projects. In this study, non-duplicate samples of inpatients were collected from a local central hospital. Mass spectrometry showed that 54 C. striatum isolates mainly appeared in secretion and sputum from 14 departments. Protein fingerprint cluster analysis showed that the isolates were divided into four groups, most of which appeared in summer. The drug resistance test showed that all strains had multi-drug resistance, with high resistance rates to lincosamides, quinolones and tetracycline detected. Further analysis of the phylogenetic tree of C. striatum was conducted by cloning the 16S rRNA gene. It was found that isolates in the same department had high homology and tended to be located in the same branch or to be crossed in the same main branch. The strains in the same evolutionary branch group had the same drug resistance. Screening of site-specific recombinant elements revealed that 18 strains had integrase genes with the same sequence. This study shows that there may be mobile genetic elements in clinical isolates that drive gene exchange among strains, thus causing the cross-infection, spread and evolution of pathogenic bacteria in the hospital.

Spatial-temporal dynamics and evolution of ecological security in a rapid urbanization city, Southwest China

The main goal of constructing ecological security patterns (ESPs) is to identify ecological sources, corridors and nodes that play significant roles in sustainable development on a regional scale. Although there are many studies on the construction of ESPs, there is no consensus in terms of research methodology and systematic frameworks for integrated landscape management. Based on land use data from 2000, 2010, and 2020 of Chongqing Municipality in southwest China, we evaluated the spatial-temporal variation of ESPs by integrating InVEST and Circuit Theory. Results showed that: (a) Habitat quality varied through space, with habitat quality being lower in the western and central regions and higher in the southeastern and northeastern regions. (b) The area of lower quality habitat across different time periods was more than 46%, and habitat quality over the last two decades has generally been low with no significant improvement. (c) From 2000 to 2020, ecological sources were primarily distributed in the mountainous areas with high habitat quality and fractional vegetation coverage in the northeast and southeast. The regions identified ecological sources in 2000, 2010, and 2020 accounted for 31.37, 33.53, and 32.7% of Chongqing Municipality, respectively. (d) The ESPs were composed of ecological sources dominated by forests, connected by continuous ecological corridors. The current ESPs of Chongqing Municipality included 20 ecological nodes, 17 continuous ecological corridors and 23 ecological sources. We strongly suggest the local governments strengthen the protection of the identified ecological nodes, ecological corridors, ecological sources, and protection gaps, and focus on strengthening the construction and management of the ecological corridor network system to promote species diffusion and gene exchange. Our findings are helpful for policy makers to introduce appropriate measures to objectively guide urban expansion via rational and sustainable development of land resources and improve the level of ecological security for Chongqing Municipality.

Study on the Genetic Variation of Triadica sebifera (Linnaeus) Small Populations Based on SSR Markers

Triadica sebifera (Linnaeus) Small is a tree species native to China. The seeds of T. sebifera are rich in oil and are widely used in industrial fields. To explore the genetic diversity and genetic differentiation of T. sebifera germplasm resources, 10 pairs of microsatellite markers were applied to 203 samples collected from eight populations. Forty-three alleles were detected. The average expected heterozygosity (He = 0.491) revealed a low level of genetic diversity. The genetic differentiation among T. sebifera populations was low (Fst = 0.026), which might be related to high gene flow (average Nm = 11.151). Genetic distance and structure results further confirmed that the genetic compositions of the eight populations were quite similar. One of the possible reasons for this phenomenon is that the early introduction and cultivation of T. sebifera were common, so gene exchange was frequent among populations. However, UPGMA clustering results indicated that the eight T. sebifera populations could still be divided into three categories. The classification was related to their geographical location: the southwestern group (ZY), central group (HG and XY) and eastern group (LS, HS, LX, XZ and LY). The reason for this differentiation might be severe deforestation following the decline in T. sebifera economic status. In addition, the central XY population had the largest number of rare alleles (4). In conclusion, although T. sebifera germplasm resources had a low level of genetic diversity, several rare alleles were detected in the central populations, which are valuable for breeding. These resources should be conserved to maintain genetic diversity in the T. sebifera populations. Moreover, geographical distances were important reasons for the limited genetic variations among the populations.

Genetic Diversity of Nanmu (Phoebe zhennan S. Lee. et F. N. Wei) Breeding Population and Extraction of Core Collection Using nSSR, cpSSR and Phenotypic Markers

Genetic characterization is vital for tree germplasm utilization and conservation. Nanmu (Phoebe zhennan S. Lee. et F. N. Wei) is an extremely valuable tree species that can provide logs for many industrial products. This study aimed to assess the genetic diversity of a Nanmu breeding population using nine nSSR, five newly-developed cpSSR markers, and nine phenotypic traits, and extract a core collection. In general, the Na, Ne, and PIC for each nSSR/cpSSR were 2–37/2–3, 1.160–11.276/1.020–1.940, and 0.306–0.934/0.109–0.384, respectively. Fifteen chlorotype haplotypes were detected in 102 germplasms. The breeding population exhibited a relatively high level of genetic diversity for both nSSR (I = 1.768), cpSSR (I = 0.440, h = 0.286), and phenotypic traits (H′ = 1.98). Bayesian and cluster analysis clustered these germplasms into three groups. The germplasms revealed a high level of admixture between clusters, which indicated a relatively high level of gene exchange between germplasms. The F value (0.124) also showed a moderate genetic differentiation in the breeding population. A core collection consisting of 64 germplasms (62.7% of the whole germplasm) was extracted from phenotypic and molecular data, and the diversity parameters were not significantly different from those of the whole germplasm. Thereafter, a molecular identity was made up for each core germplasm. These results may contribute to germplasm management and conservation in the Nanmu breeding program, as well as genetics estimation and core collection extraction in other wood production rare species.

Human Colonization with Antibiotic-Resistant Bacteria from Nonoccupational Exposure to Domesticated Animals in Low- and Middle-Income Countries: A Critical Review.

Data on community-acquired antibiotic-resistant bacterial infections are particularly sparse in low- and middle-income countries (LMICs). Limited surveillance and oversight of antibiotic use in food-producing animals, inadequate access to safe drinking water, and insufficient sanitation and hygiene infrastructure in LMICs could exacerbate the risk of zoonotic antibiotic resistance transmission. This critical review compiles evidence of zoonotic exchange of antibiotic-resistant bacteria (ARB) or antibiotic resistance genes (ARGs) within households and backyard farms in LMICs, as well as assesses transmission mechanisms, risk factors, and environmental transmission pathways. Overall, substantial evidence exists for exchange of antibiotic resistance between domesticated animals and in-contact humans. Whole bacteria transmission and horizontal gene transfer between humans and animals were demonstrated within and between households and backyard farms. Further, we identified water, soil, and animal food products as environmental transmission pathways for exchange of ARB and ARGs between animals and humans, although directionality of transmission is poorly understood. Herein we propose study designs, methods, and topical considerations for priority incorporation into future One Health research to inform effective interventions and policies to disrupt zoonotic antibiotic resistance exchange in low-income communities.

Origin and Phylogeography of Chinese Cereal Cyst Nematode Heterodera avenae Revealed by Mitochondrial COI Sequences.

Heterodera avenae, a globally distributed plant-parasitic nematode, is one of the most significant pests on cereal crops. In China, it is widely distributed in cereal-growing areas of 16 provinces and causes serious yield losses. In the present study, a total of 98 populations of H. avenae were collected from major wheat-growing regions in China and six other countries. The mitochondrial COI genes were amplified and analyzed. Forty-one mitochondrial COI haplotypes were identified, suggesting a high genetic diversity and endemism level of H. avenae in China. Phylogenetic analysis showed that H. avenae populations in China were divided into four clades. Significant evolutionary and genetic differences were found between Chinese (except Hubei) and foreign populations. Hap1, the most widely distributed haplotype, was considered to be a separate evolutionary origin in China. The gene flow of H. avenae from the northwestern region to the north China region and Huang-Huai-Hai region was significant, so as the direction between north China and Huang-Huai-Hai region. We speculate that water flowing from the Yellow River and mechanical harvesters promoted gene exchange among these groups. A distance-based redundancy analysis showed that genetic distances observed among H. avenae populations were explained foremost not only by geographic distance but also by temperature and precipitation. This study provides theoretical support for the origin and spread of H. avenae populations in China and elsewhere in the world.

Persistent versus transient, and conventional plastic versus biodegradable plastic? —Two key questions about microplastic-water exchange of antibiotic resistance genes

The ubiquitous microplastics (MPs) in water environment play an important role in the dissemination of antibiotic resistance genes (ARGs) due to their exchange between floating MPs and receiving waters. However, whether the ARG exchange is persistent or transient and what are the differences in ARG exchange between conventional plastics and biodegradable plastics are the two key issues to be addressed. In this study, biodegradable PBAT and non-biodegradable PET MPs were chosen to explore the MP-water ARG exchange after the MPs floated to the receiving waters. The results demonstrated that the active exchange of ARGs between MPs and receiving waters occurred, which, however, were transient for most of ARGs. The relative abundance of ARGs both on the MPs and in the waters rapidly decreased to the initial or lower levels within 4 weeks. Approximately 25–50% (ARG subtype number ratio) of studied ARG subtypes were introduced into the receiving waters by MPs, and 35–65% of studied ARG subtypes went through fluctuation in terms of abundance on MPs and in the receiving water. ARGs tended to converge between MPs and the receiving waters with time. Furthermore, the ARG exchange between MPs and waters facilitated horizontal gene transfer (HGT). IntI1 and tnpA05 played the crucial roles in HGT, which was indicated by their correlated change with most ARGs; in contrast, tnpA04 showed the obvious lagging responses. The biodegradable MP of PBAT generally accumulated higher levels of most ARGs including multidrug resistant genes than the non-biodegradable MP of PET. The transient exchange of most ARGs between MPs and water implies that the on-off hitchhiking of ARGs on MPs in aquatic environment may not exert significant influence on ARG transmission. However, compared with the conventional plastics, the biodegradable MPs might pose much higher ARG dissemination risks due to the higher enrichment of ARGs particularly with people's ever-increasingly usage. Enough attention must be paid to this emerging issue.

Genetic diversity and population structure of pigeonpea (Cajanus cajan [L.] Millspaugh) landraces grown in Benin revealed by Genotyping-By-Sequencing.

Genetic diversity studies provide important details on target trait availability and its variability, for the success of breeding programs. In this study, GBS approach was used to reveal a new structuration of genetic diversity and population structure of pigeonpea in Benin. We used a total of 688 high-quality Single Nucleotide Polymorphism markers for a total of 44 pigeonpea genotypes. The distribution of SNP markers on the 11 chromosomes ranged from 14 on chromosome 5 to 133 on chromosome 2. The Polymorphism Information Content and gene diversity values were 0.30 and 0.34 respectively. The analysis of population structure revealed four clear subpopulations. The Weighted Neighbor Joining tree agreed with structure analyses by grouping the 44 genotypes into four clusters. The PCoA revealed that genotypes from subpopulations 1, 2 and 3 intermixed among themselves. The Analysis of Molecular Variance showed 7% of the total variation among genotypes while the rest of variation (93%) was within genotypes from subpopulations indicating a high gene exchange (Nm = 7.13) and low genetic differentiation (PhiPT = 0.07) between subpopulations. Subpopulation 2 presented the highest mean values of number of different alleles (Na = 1.57), number of loci with private alleles (Pa = 0.11) and the percentage of polymorphic loci (P = 57.12%). We discuss our findings and demonstrate how the genetic diversity and the population structure of this specie can be used through the Genome Wide Association Studies and Marker-Assisted Selection to enhance genetic gain in pigeonpea breeding programs in Benin.

Genetic and Pathogenic Characterization of Avian Influenza Virus in Migratory Birds between 2015 and 2019 in Central China.

ABSTRACTActive surveillance of avian influenza virus (AIV) in wetlands and lakes is important for exploring the gene pool in wild birds. Through active surveillance from 2015 through 2019, 10,900 samples from wild birds in central China were collected, and 89 AIVs were isolated, including 2 subtypes of highly pathogenic AIV and 12 of low-pathogenic AIV; H9N2 and H6Ny were the dominant subtypes. Phylogenetic analysis of the isolates demonstrated that extensive intersubtype reassortments and frequent intercontinental gene exchange occurred in AIVs. AIV gene segments persistently circulated in several migration seasons, but interseasonal persistence of the whole genome was rare. The whole genomes of one H6N6 and polymerase basic 2 (PB2), polymerase acidic (PA), hemagglutinin (HA), neuraminidase (NA), M, and nonstructural (NS) genes of one H9N2 virus were found to be of poultry origin, suggesting a spillover of AIVs from poultry to wild birds. Importantly, one H9N2 virus only bound to human-type receptor, and one H1N1, four H6, and seven H9N2 viruses possessed dual receptor-binding capacity. Nineteen of 20 representative viruses tested could replicate in the lungs of mice without preadaptation, which poses a clear threat of infection in humans. Together, our study highlights the need for intensive AIV surveillance.IMPORTANCE Influenza virus surveillance in wild birds plays an important role in the early recognition and control of the virus. However, the AIV gene pool in wild birds in central China along the East Asian-Australasian flyway has not been well studied. Here, we conducted a 5-year AIV active surveillance in this region. Our data revealed the long-term circulation and prevalence of AIVs in wild birds in central China, and we observed that intercontinental gene exchange of AIVs is more frequent and continuous than previously thought. Spillover events from poultry to wild bird were observed in H6 and H9 viruses. In addition, in 20 representative viruses, 12 viruses could bind human-type receptors, and 19 viruses could replicate in mice without preadaption. Our work highlights the potential threat of wild bird AIVs to public health.

Differentiation and Temperature Adaptation of Pampus Echinogaster Based on Genome-Wide SNPs

Climate change and overfishing have led to the degradation of the quality and stock of Pampus echinogaster. Exploring the genetic structure and local adaptive evolutionary mechanisms of P. echinogaster is crucial for the management of this species. This population genomic study of nine geographical populations of P. echinogaster in China was conducted by specific-locus amplified fragment sequencing (SLAF-seq). A total of 935,215 SLAF tags were obtained, and the average sequencing depth of the SLAF tags was 20.80×. After filtering, a total of 46,187 high-consistency genome-wide single nucleotide polymorphisms (SNPs) were detected. Based on all SNPs, the population size of the nine P. echinogaster geographical populations was large. The Shantou population had the lowest genetic diversity, and the Tianjin population had the highest. Moreover, the population genetic structure based on all SNPs revealed significant gene exchange and no significant genetic differentiation among the nine P. echinogaster geographical populations, probably because of the population expansion after the last glacial period, the lack of balance between migration and genetic drift, and the long-distance diffusion of eggs and larvae. We suspect that variation of material metabolism, ion transfer, breeding, stress response, and inflammatory reactions-related genes were critical for adaptation to spatially heterogeneous temperature selection in natural P. echinogaster populations.

Discovery of archaeal fusexins homologous to eukaryotic HAP2/GCS1 gamete fusion proteins

Sexual reproduction consists of genome reduction by meiosis and subsequent gamete fusion. The presence of genes homologous to eukaryotic meiotic genes in archaea and bacteria suggests that DNA repair mechanisms evolved towards meiotic recombination. However, fusogenic proteins resembling those found in gamete fusion in eukaryotes have so far not been found in prokaryotes. Here, we identify archaeal proteins that are homologs of fusexins, a superfamily of fusogens that mediate eukaryotic gamete and somatic cell fusion, as well as virus entry. The crystal structure of a trimeric archaeal fusexin (Fusexin1 or Fsx1) reveals an archetypical fusexin architecture with unique features such as a six-helix bundle and an additional globular domain. Ectopically expressed Fusexin1 can fuse mammalian cells, and this process involves the additional globular domain and a conserved fusion loop. Furthermore, archaeal fusexin genes are found within integrated mobile elements, suggesting potential roles in cell-cell fusion and gene exchange in archaea, as well as different scenarios for the evolutionary history of fusexins.

Interspecific Hybridization Is an Important Driving Force for Origin and Diversification of Asian Cultivated Rice Oryza sativa L.

As one of the most important crops, Asian cultivated rice has evolved into a complex group including several subgroups adapting various eco-climate-systems around the globe. Here, we pictured a comprehensive view of its original domestication, divergences, and the origin of different subgroups by integrating agriculture, archeology, genetics, nuclear, and cytoplasm genome results. Then, it was highlighted that interspecific hybridization-introgression has played important role in improving the genetic diversity and adaptation of Oryza sativa during its evolution process. Natural hybridization-introgression led to the origin of indica, aus, and basmatic subgroups, which adapted to changing cultivated environments, and produced feral weedy rice coexisting and competing with cultivars under production management. Artificial interspecific hybridization-introgression gained several breakthroughs in rice breeding, such as developing three-line hybrid rice, new rice for Africa (NERICA), and some important pest and disease resistance genes in rice genetic improvement, contributing to the stable increase of rice production to meet the expanding human population. We proposed a series to exploit the virtues of hybridization-introgression in the genetic improvement of Asian cultivated rice. But some key issues such as reproductive barriers especially hybrid sterility should be investigated further, which are conducive to gene exchange between cultivated rice and its relatives, and even is beneficial to exploiting interspecific hybrid vigor. New technologies help introduce favorable genes from distant wild species to Asian cultivated rice, such as transgenic and genome editing systems. Rising introgression lines in a wider range with multi-donor benefits allele mining, understanding genetic network of rice growth and development, yield formation, and environmental adaptation. Then, integration of new tools and interspecific hybridization can be a future direction to develop more usable breeding populations which can make Asian cultivated rice more resilient to the changing climate and world.

Colonization of White-Tailed Deer (Odocoileus virginianus) from Urban and Suburban Environments with Cephalosporinase- and Carbapenemase-Producing Enterobacterales.

Wildlife play a role in the acquisition, maintenance, and dissemination of antimicrobial resistance (AMR). This is especially true at the human-domestic animal-wildlife interface, like urbanized areas, where interactions occur that can promote the cross-over of AMR bacteria and genes. We conducted a 2-year fecal surveillance (n = 783) of a white-tailed deer (WTD) herd from an urban park system in Ohio to identify and characterize cephalosporin-resistant and carbapenemase-producing bacteria using selective enrichment. Using generalized linear mixed models we found that older (OR = 2.3, P < 0.001), male (OR = 1.8, P = 0.001) deer from urbanized habitats (OR = 1.4, P = 0.001) were more likely to harbor extended-spectrum cephalosporin-resistant Enterobacterales. In addition, we isolated two carbapenemase-producing Enterobacterales (CPE), a Klebsiella quasipneumoniae harboring blaKPC-2 and an Escherichia coli harboring blaNDM-5, from two deer from urban habitats. The genetic landscape of the plasmid carrying blaKPC-2 was unique, not clustering with other reported plasmids encoding KPC-2, and only sharing 78% of its sequence with its nearest match. While the plasmid carrying blaNDM-5 shared sequence similarity with other reported plasmids encoding NDM-5, the intact IS26 mobile genetic elements surrounding multiple drug resistant regions, including the blaNDM-5, has been reported infrequently. Both carbapenemase genes were successfully conjugated to a J53 recipient conferring a carbapenem-resistant phenotype. Our findings highlight that urban environments play a significant role on the transmission of AMR bacteria and genes to wildlife and suggest WTD may play a role in the dissemination of clinically and epidemiologically relevant antimicrobial resistant bacteria. IMPORTANCE The role of wildlife in the spread of antimicrobial resistance is not fully characterized. Some wildlife, including white-tailed deer (WTD), can thrive in suburban and urban environments. This may result in the exchange of antimicrobial resistant bacteria and resistance genes between humans and wildlife, and lead to their spread in the environment. We found that WTD living in an urban park system carried antimicrobial resistant bacteria that were important to human health and resistant to antibiotics used to treat serious bacterial infections. This included two deer that carried bacteria resistant to carbapenem antibiotics which are critically important for treatment of life-threatening infections. These two bacteria had the ability to transfer their AMR resistance genes to other bacteria, making them a threat to public health. Our results suggest that WTD may contribute to the spread of antimicrobial resistant bacteria in the environment.