Gene Exchange Research Articles

Population genetics analysis of Tolai hares (Lepus tolai) in Xinjiang, China using genome-wide SNPs from SLAF-seq and mitochondrial markers.

The main topic of population genetics and evolutionary biology is the influence of the ecological environment, geographical isolation, and climatic factors on population structure and history. Here, we estimated the genetic diversity, genetic structure, and population history of two subspecies of Tolai hares (Lepus tolai Pallas, 1778), L. t. lehmanni inhabiting Northern and Northwest Xinjiang and L. t. centrasiaticus inhabiting Central and Eastern Xinjiang using SNP of specific-length amplified fragment sequencing (SLAF-seq) and four mitochondrial DNA (mtDNA). Our results showed a relatively high degree of genetic diversity for Tolai hares, and the diversity of L. t. lehmanni was slightly higher than that of L. t. centrasiaticus, likely due to the more favorable ecological environment, such as woodlands and plains. Phylogenetic analysis from SNP and mtDNA indicated a rough phylogeographical distribution pattern among Tolai hares. Strong differentiation was found between the two subspecies and the two geographical groups in L. t. centrasiaticus, possibly due to the geographical isolation of mountains, basins, and deserts. However, gene flow was also detected between the two subspecies, which might be attributed to the Tianshan Corridor and the strong migration ability of hares. Tolai hare population differentiation occurred at approximately 1.2377 MYA. Population history analysis based on SNP and mtDNA showed that the Tolai hare population has a complex history and L. t. lehmanni was less affected by the glacial event, possibly because its geographic location and terrain conditions weaken the drastic climate fluctuations. In conclusion, our results indicated that the joint effect of ecological environment, geographic events, and climatic factors might play important roles in the evolutionary process of L. t. lehmanni and L. t. centrasiaticus, thus resulting in differentiation, gene exchange, and different population history.

Genetic Diversity and Population Structure Analysis in the Chinese Endemic Species Michelia crassipes Based on SSR Markers

Michelia crassipes Y. W. Law (Magnoliaceae) is endemic to China and is the only species with purple flowers in the genus Michelia. It is commonly used as an important parent for flower color improvement and hybrid breeding. M. crassipes is recognized as an endangered plant. An urgent need exists to explore the genetic diversity of M. crassipes to efficiently select hybrid parents and develop efficient conservation strategies. In this study, a total of 128 samples were selected from seven natural populations of M. crassipes to explore their genetic diversity and structure. A total of 14 microsatellite (SSR) markers with high polymorphism and repeatability were developed, and 218 alleles were detected. This study mainly revealed three results: (1) The parameters of expected heterozygosity (He = 0.536) and mean Shannon’s information index (I = 1.121) revealed moderately high levels of genetic diversity for the M. crassipes natural population; (2) The genetic differentiation coefficient (Fst = 0.108) showed that there was a low level of genetic differentiation, and AMOVA indicated that genetic variation existed mainly within populations and that there was frequent gene exchange between populations; and (3) The population genetic structure analysis showed that seven natural populations originated from two ancestral groups, and the Mantel test revealed that genetic and geographical distances between populations were significantly correlated. Our study is the first to explore the genetic diversity and structure of the M. crassipes natural population, which provides an important reference for the collection, conservation and utilization of Michelia crassipes germplasm resources.

Molecular insights into the dynamics of species invasion by hybridisation in Tasmanian eucalypts.

In plants where seed dispersal is limited compared with pollen dispersal, hybridisation may enhance gene exchange and species dispersal. We provide genetic evidence of hybridisation contributing to the expansion of the rare Eucalyptus risdonii into the range of the widespread Eucalyptus amygdalina. These closely related tree species are morphologically distinct, and observations suggest that natural hybrids occur along their distribution boundaries and as isolated trees or in small patches within the range of E.amygdalina. Hybrid phenotypes occur outside the range of normal dispersal for E.risdonii seed, yet in some hybrid patches small individuals resembling E.risdonii occur and are hypothesised to be a result of backcrossing. Using 3362 genome-wide SNPs assessed from 97 individuals of E.risdonii and E.amygdalina and 171 hybrid trees, we show that (i) isolated hybrids match the genotypes expected of F1 /F2 hybrids, (ii) there is a continuum in the genetic composition among the isolated hybrid patches from patches dominated by F1 /F2 -like genotypes to those dominated by E.risdonii-backcross genotypes, and (iii) the E.risdonii-like phenotypes in the isolated hybrid patches are most-closely related to proximal larger hybrids. These results suggest that the E.risdonii phenotype has been resurrected in isolated hybrid patches established from pollen dispersal, providing the first steps in its invasion of suitable habitat by long-distance pollen dispersal and complete introgressive displacement of E.amygdalina. Such expansion accords with the population demographics, common garden performance data, and climate modelling which favours E.risdonii and highlights a role of interspecific hybridisation in climate change adaptation and species expansion.

Subspecies-level genome comparison of Lactobacillus delbrueckii

Lactobacillus delbrueckii comprises six subspecies, L. delbrueckii subsp. bulgaricus, L. delbrueckii subsp. lactis, L. delbrueckii subsp. jakobsenii, L. delbrueckii subsp. delbrueckii, L. delbrueckii subsp. sunkii, and L. delbrueckii subsp. indicus. We investigated the evolution of the six subspecies of L. delbrueckii using comparative genomics. While the defining feature of the species was the gene number increment driven by mobile elements and gene fragmentation, the repertoire of subspecies-specific gene gains and losses differed among the six subspecies. The horizontal gene transfer analyses indicated that frequent gene transfers between different subspecies had occurred when the six subspecies first diverged from the common ancestor, but recent gene exchange was confined to a subspecies implying independent evolution of the six subspecies. The subspecies bulgaricus is a homogeneous group that diverged from the other subspecies a long time ago and underwent convergent evolution. The subspecies lactis, jakobsenii, delbrueckii, and sunkii were more closely related to each other than to other subspecies. The four subspecies commonly show increasing genetic variability with increasing genome size. However, the four subspecies were distinguished by specific gene contents. The subspecies indicus forms a branch distant from the other subspecies and shows an independent evolutionary trend. These results could explain the differences in the habitat and nutritional requirements of the subspecies of L. delbrueckii.

Mate Choice in Molluscs of the Genus Littorina (Gastropoda: Littorinidae) from White Sea

We studied the reproductive behaviour associated with mate choice by size in three species of White Sea molluscs of the genus Littorina—L. saxatilis, L. obtusata and L. fabalis. Three behavioural patterns were revealed after a comparative analysis of the behaviour of the male snails. The males of L. obtusata, regardless of their size, could mate with all females but preferred to mate with larger ones. The males of L. fabalis chose females of their own size or larger. The males of L. saxatilis mated with females of approximately their own size. In the first case (L. obtusata), there is a free exchange of genes between all the size groups in the population. In the second case (L. fabalis), the gene transfer from small males to females of any size is free but the gene transfer from large males to small females is limited. In the third case (L. saxatilis), the gene flow is limited between groups of individuals of dramatically different size. Thus, in the case of L. saxatilis and L. fabalis, to varying degrees restriction of random mating associated with size assortativity in choosing a mating partner was expressed, which under certain circumstances (divergence of individuals in different econiches, the presence of ecotypes differing in size, lack of stronger natural selection in the other direction) can favour sympatric speciation. The males of all the three periwinkles’ species preferred larger females but sexual selection in favour of larger females was found only in L. obtusata. In the other two species, there were no statistically significant size differences between copulating and non-copulating females. This appears to be due to the occurrence of size-assortative mating in these species, which limits the ability of males to choose larger female partners.

Ecology, more than antibiotics consumption, is the major predictor for the global distribution of aminoglycoside-modifying enzymes.

Antibiotic consumption and its abuses have been historically and repeatedly pointed out as the major driver of antibiotic resistance emergence and propagation. However, several examples show that resistance may persist despite substantial reductions in antibiotic use, and that other factors are at stake. Here, we study the temporal, spatial, and ecological distribution patterns of aminoglycoside resistance, by screening more than 160,000 publicly available genomes for 27 clusters of genes encoding aminoglycoside-modifying enzymes (AME genes). We find that AME genes display a very ubiquitous pattern: about 25% of sequenced bacteria carry AME genes. These bacteria were sequenced from all the continents (except Antarctica) and terrestrial biomes, and belong to a wide number of phyla. By focusing on European countries between 1997 and 2018, we show that aminoglycoside consumption has little impact on the prevalence of AME-gene-carrying bacteria, whereas most variation in prevalence is observed among biomes. We further analyze the resemblance of resistome compositions across biomes: soil, wildlife, and human samples appear to be central to understand the exchanges of AME genes between different ecological contexts. Together, these results support the idea that interventional strategies based on reducing antibiotic use should be complemented by a stronger control of exchanges, especially between ecosystems.

Genomic C-Value Variation Analysis in Jujube (Ziziphus jujuba Mill.) in the Middle Yellow River Basin

Chinese jujube (Ziziphus jujuba Mill.) originated in the Yellow River basin (YRB) of the Shanxi-Shaanxi region. The genomic C-value is a crucial indicator for plant breeding and germplasm evaluation. In this study, we used flow cytometry to determine the genomic C-values of jujube germplasms in the YRB of the Shanxi-Shaanxi region and evaluated their differences in different sub-regions. Of the 29 sub-regions, the highest and lowest variations were in Linxian and Xiaxian, respectively. The difference between jujube germplasms was highly significant (F = 14.89, p < 0.0001) in Linxian. Cluster analysis showed that both cluster 2 and 4 belonged to Linxian, which were clearly separated from other taxa but were cross-distributed in them. Linxian County is an important gene exchange center in the YRB of the Shanxi-Shaanxi region. Principal component analysis showed that cluster 1 had low genomic C-values and single-fruit weights and cluster 2 had high genomic C-values and vitamin C contents. The genomic C-value was correlated with single-fruit weight and vitamin C content. In addition, the genomic C-value was used to predict fruit agronomic traits, providing a reference for shortening the breeding cycle and genetic diversity-related studies of jujube germplasm.

Multilayer networks of plasmid genetic similarity reveal potential pathways of gene transmission

Antimicrobial resistance (AMR) is a significant threat to public health. Plasmids are principal vectors of AMR genes, significantly contributing to their spread and mobility across hosts. Nevertheless, little is known about the dynamics of plasmid genetic exchange across animal hosts. Here, we use theory and methodology from network and disease ecology to investigate the potential of gene transmission between plasmids using a data set of 21 plasmidomes from a single dairy cow population. We constructed a multilayer network based on pairwise plasmid genetic similarity. Genetic similarity is a signature of past genetic exchange that can aid in identifying potential routes and mechanisms of gene transmission within and between cows. Links between cows dominated the transmission network, and plasmids containing mobility genes were more connected. Modularity analysis revealed a network cluster where all plasmids contained a mobM gene, and one where all plasmids contained a beta-lactamase gene. Cows that contain both clusters also share transmission pathways with many other cows, making them candidates for super-spreading. In support, we found signatures of gene super-spreading in which a few plasmids and cows are responsible for most gene exchange. An agent-based transmission model showed that a new gene invading the cow population will likely reach all cows. Finally, we showed that edge weights contain a non-random signature for the mechanisms of gene transmission, allowing us to differentiate between dispersal and genetic exchange. These results provide insights into how genes, including those providing AMR, spread across animal hosts.

Knockdown resistance mutations distribution and characteristics of Aedes albopictus field populations within eleven dengue local epidemic provinces in China.

Aedes albopictus, commonly known as the tiger mosquito, has attracted global attention because its bite can transmit several viruses, such as dengue virus. With the absence of an effective therapy and vaccine, mosquito control is the sole method for dengue fever control. However, Ae. albopictus has developed resistance to most insecticides, especially pyrethroids. Many scholars have conducted thorough research for the target-site of pyrethroids. The main target-site is the voltage-gated sodium channel gene (VGSC) whose mutation causes knockdown resistance (kdr). The spatial distribution of three locus kdr mutations in Ae. albopictus has not been comprehensively analyzed nationwide in China. In addition, the relationship between the frequency of kdr mutations and dengue fever has not yet been explored. A total of 2,241 Ae. albopictus samples from 49 populations from 11 provinces of mainland China were collected in 2020 and analyzed for mutations in the VGSC gene. DNAstar 7.1. Seqman and Mega-X were used to compare the sequences and read the peak map to confirm the genotypes and alleles of each mutation. ArcGIS 10.6 software was used to make interpolation and extract meteorological data of collection sites and to conduct spatial autocorrelation analysis. R 4.1.2 software was used to conduct a chi-square test for kdr mutations and dengue area and to analyze the correlation between meteorological factors and kdr mutations. The overall frequencies of mutant alleles at 1016G, 1532T, and 1534S/C/L were 13.19%, 4.89%, and 46.90%, respectively. Mutations at the three loci were found at 89.80% (44/49), 44.90% (22/49), and 97.96% (48/49) of the field populations. At each of the loci V1016 and I1532, only one allele was detected, which was GGA(G) and ACC(T), respectively. Five mutant alleles were found at codon 1534: TCC/S (33.49%), TGC/C (11.96%), TTG/L (0.60%), CTC/L (0.49%), and TTA/L (0.58%). In total, 31 triple-locus genotype combinations were found, and the single locus mutation was the most common. We also found firstly triple-locus mutant individuals, whose genotypes were V/G+I/T+F/S and V/G+I/T+S/S. The 1016 and 1532 mutation rates were significantly negatively related to the annual average temperature (AAT), but the 1534 mutation rate was significantly positively related to AAT. The 1532 mutation rate was significantly positively related to the 1016 mutation rate but negatively related to the 1534 mutation rate. A relationship was observed between the 1534 codon mutation rate and dengue epidemic areas in this study. Furthermore, spatial autocorrelation analysis results showed that the mutation rates of different codons in different geographical areas had spatial aggregation and positive spatial correlation. This study showed that the multiple kdr mutations at codon 1016, 1532 and 1534 of Ae. albopictus were found in most areas of China. Two novel triple-locus genotype combinations, V/G+I/T+F/S and V/G+I/T+S/S, were detected in this study. In addition, the relationship between mosquito resistance and dengue fever outbreak should be further explored, especially considering the insecticide-usage history in different areas. The characteristic of spatial aggregation of VGSC gene mutation rates reminds us to notice the gene exchange and similarity of insecticide usage in the adjacent areas. The use of pyrethroids should be restricted to delay resistance development. New-type insecticides should be developed to adjust the changes in the resistance spectrum. Our study provides abundant data on the Ae. albopictus kdr gene mutation in China; these findings will be useful for the correlation analysis of molecular mechanism of insecticide resistance.

Genetic Diversity and Differentiation of Chinese Fir around Karst Landform in Guangxi

The karst geo-ecosystems are fragile environments. The largest karst region in the world is located in southwestern China, within which the Guangxi province is one of the main areas. Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.), an evergreen species, is an important fast-growing timber tree in southern China. In the present study, we examined the genetic diversity and spatial genetic differentiation of Chinese fir in sampling localities around the karst landform region of Guangxi by genotyping 330 individuals from 11 sampling localities with 22 novel polymorphic microsatellite loci. High levels of gene flow have homogenized Chinese fir in Rongshui, Nandan, and Tiane sites, which are speculated to be the primary center of gene exchange and diversity for Chinese fir around the karst landform in Guangxi. Significant isolation by distance pattern was found among nine sampling localities. A moderate level of genetic differentiation (FST = 0.089, Dest = 0.139) between sampling localities was detected. Structure analysis divided Chinese fir into three subgroups (K = 3). With higher differentiation and less genetic variation than in the central population, marginal populations of Cangwu and Pubei were identified in the south of the karst landform. An effective conservation strategy focusing on the maintenance of genetic variation for marginal populations of the species was proposed.

Rapid assessment of antibiotic susceptibility using a fully 3D-printed impedance-based biosensor

The sustained misuse and overuse of antibacterial agents is accelerating the emergence of antimicrobial resistance (AMR), which is becoming one of the major threats to public health. Abuse of antibiotics drives spontaneous evolution, bacterial mutation, and exchange of resistant genes through lateral gene transfer. Mitigating the worldwide impact of AMR requires enhanced antibiotic stewardship through faster diagnostic testing. In this work, we aim to tackle this issue via development of a fully 3D-printed electrochemical, gel-modified biosensor for rapid bacterial growth monitoring. By using electrochemical impedance spectroscopy, we have successfully identified growth profiles and confirmed antibiotic susceptibility of two ESKAPE pathogens, Escherichia coli and Pseudomonas aeruginosa, following overnight culture it was possible to determine antibiotic sensitivity in 90 min, altogether faster than the 24–48 h current gold standard of culture-based antimicrobial susceptibility testing with significant scope for optimisation. Results show a clear distinction between growth profiles in the presence and absence of amoxicillin, gentamicin, and fosfomycin, therefore demonstrating a rapid, cost-efficient platform for phenotypic antibiotic susceptibility testing within clinically relevant concentration ranges for conditions such as urinary tract infections and pneumonia.

Genetic Diversity of Jinshaia sinensis (Cypriniformes, Balitoridae) Distributed Upstream of the Yangtze River

The upper reaches of the Yangtze River (upper YR) are a biological zone with extremely rich fish diversity, especially endemic fish. However, long-term human interference, such as environmental pollution and cascade hydropower construction, has significantly changed the habitat of many fish and is threatening the number and genetic diversity of fish populations. Jinshaia sinensis is a typical small and endemic but rare fish that is found in the upper YR, and its genetic diversity and structure still need further study. To understand the current levels of genetic diversity in J. sinensis, we analyzed the genetic diversity, population history, genetic structure, etc., of three J. sinensis populations based on two mitochondrial genes (the cytochrome-c oxidase subunit I, COI, and cytochrome-b gene, Cytb) and two nuclear genes (recombination-activating protein 1, RAG1, and rhodopsin, RH). The genetic diversity analysis indicated that J. sinensis had high genetic diversity, with high haplotype diversity (h) and nucleotide diversity (Pi). Population pairwise FST analysis revealed a significant genetic divergence between the Lijiang and Luzhou populations for all genes and between the Panzhihua and Luzhou populations, except for the COI gene; however, analyses of molecular variance (AMOVA) showed no significant geographic genetic structure among populations, and gene flow analysis also indicated a certain degree of gene exchange among populations. Haplotype network structure analyses revealed low levels of shared haplotypes among populations. Neutrality test and mismatch distribution results indicated that only the Lijiang population had experienced obvious population expansion. Overall, these results indicate that J. sinensis is still a single evolutionarily significant unit, but when considering the threat of habitat disturbance to the population, it is still necessary to carry out long-term genetic monitoring on J. sinensis and on other endemic fishes with similar ecological habits in order to maintain the genetic diversity of fishes in the upper YR.

Analysis of Whole-Genome Sequences of Pathogenic Gram-Positive and Gram-Negative Isolates from the Same Hospital Environment to Investigate Common Evolutionary Trends Associated with Horizontal Gene Exchange, Mutations and DNA Methylation Patterning.

Hospital-acquired infections are a generally recognized problem for healthcare professionals. Clinical variants of Gram-negative and Gram-positive pathogens are characterized with enhanced antibiotic resistance and virulence due to mutations and the horizontal acquisition of respective genetic determinants. In this study, two Escherichia coli, two Klebsiella pneumoniae, three Pseudomonas aeruginosa, two Staphylococcus aureus, one Staphylococcus epidermidis and one Streptococcus pneumoniae showing broad spectra of antibiotic resistance were isolated from patients suffering from nosocomial infections in a local hospital in Almaty, Kazakhstan. The aim of the study was to compare general and species-specific pathways of the development of virulence and antibiotic resistance through opportunistic pathogens causing hospital-acquired infections. The whole-genome PacBio sequencing of the isolates allowed for the genotyping and identification of antibiotic resistance and virulence genetic determinants located in the chromosomes, plasmids and genomic islands. It was concluded that long-read sequencing is a useful tool for monitoring the epidemiological situation in hospitals. Marker antibiotic resistance mutations common for different microorganisms were identified, which were acquired due to antibiotic-selective pressure in the same clinical environment. The genotyping and identification of strain-specific DNA methylation motifs were found to be promising in estimating the risks associated with hospital infection outbreaks and monitoring the distribution and evolution of nosocomial pathogens.

Meloidogyne graminicola Population Structure in China Suggests a South-to-North Expansion.

The distribution range of root-knot nematode Meloidogyne graminicola is rapidly expanding, posing a severe threat to rice production. In this study, the sequences of cytochrome oxidase subunit I (COI) genes of rice M. graminicola populations from all reported provinces in China were amplified and sequenced by PCR. The distribution pattern and phylogenetic tree showed that all 54 M. graminicola populations in China have distinct geographical distribution characteristics; specifically, cluster 1 (southern China), cluster 2 (central south and southwest China), and cluster 3 (central and eastern China). The high haplotype diversity (Hd = 0.646) and low nucleotide diversity (π = 0.00682), combined with the negative value of Tajima's D (-1.252) and Fu's Fs (-3.06764), suggested that all nematode populations were expanding. The existence of high genetic differentiation (Fst = 0.5933) and low gene flow (Nm = 0.3333) indicated that there was a block of gene exchange between most populations. Mutation accumulation with population expansion might be directly responsible for the high genetic differentiation; therefore, the tested nematode population showed high within-group genetic variation (96.30%). The haplotype Hap8 was located at the bottom of the network topology, with the widest distribution and the highest frequency (59.26%), indicating that it was the ancestral haplotype. The populations in cluster 3 were newly invasive according to the lowest frequency of occurrence of Hap8, the highest number of endemic haplotypes, and the highest total haplotype frequency (60%). In contrast, cluster 1 having the highest genetic diversity (Hd = 0.772, π = 0.01127) indicated that it was the most primitive. Interestingly, the highest gene flow (Nm > 1), lowest genetic differentiation (Fst ≤ 0.33), and closest genetic distance (0.000) only occurred between the Guangdong/Hainan population and others, which suggested that there might be channels for gene exchange between them and that long-distance dispersal occurred. This suggestion is further confirmed by the weak correlation between genetic distance and geographical distance. Based on these data, a hypothesis can be drawn that M. graminicola populations in China were spreading from south to north, specifically from Guangdong and Hainan Provinces to other regions. Natural selection (including anthropogenic) and genetic drift were the main drivers of their evolution. Coincidentally, this hypothesis was consistent with the gradual warming trend and the chronological order of reporting these populations. The main factors influencing current M. graminicola population expansion and distribution patterns might be geography, climate, long-distance seedling transport, interregional operations of agricultural machinery, and rotation mode. It reminds human beings of the necessity to be vigilant about preventing nematode disease according to local conditions all year round.

Characterization and Application of EST-SSR Markers Developed from Transcriptome Sequences in Elymus breviaristatus (Poaceae: Triticeae).

Elymus L. is the largest genus in the Triticeae tribe. Most species in this genus are highly stress resistant, with excellent forage value. Elymus breviaristatus, a rare species endemic to the Qinghai-Tibet Plateau (QTP), is declining due to habitat fragmentation. However, genetic data for E. breviaristatus are limited, with expressed sequence tag (EST) markers being particularly rare, hampering genetic studies and protection measures. We obtained 9.06 Gb clean sequences from the transcriptome of E. breviaristatus, generating 171,522 unigenes, which were assembled and functionally annotated against five public databases. We identified 30,668 SSRs in the E. breviaristatus transcriptome, from which 103 EST-SSR primer pairs were randomly selected. Of these, 58 pairs of amplified products of the expected size, and 18 of the amplified products were polymorphic. Model-based Bayesian clustering, the unweighted pair group method with arithmetic average (UPGMA), and principal coordinate analysis (PCoA) of 179 wild E. breviaristatus in 12 populations using these EST-SSRs were generally consistent, grouping the 12 populations into two major clades. Analysis of molecular variance (AMOVA) found 70% of the genetic variation among the 12 populations and 30% within the populations, indicating a high level of genetic differentiation (or low gene exchange) among the 12 populations. The transferability of the 58 successful EST-SSR primers to 22 related hexaploid species was 86.2-98.3%. UPGMA analysis generally grouped species with similar genome types together. Here, we developed EST-SSR markers from the transcriptome of E. breviaristatus. The transferability of these markers was evaluated, and the genetic structure and diversity of E. breviaristatus were explored. Our results provide a basis for the conservation and management of this endangered species, and the obtained molecular markers represent valuable resources for the exploration of genetic relationships among species in the Elymus genus.

Dynamic properties of the pinyon pine syngameon.

This article is a Commentary on Buck et al. (2023), 237: 2435–2449.

Genetic diversity analysis and variety identification using SSR and SNP markers in melon

Melon is an important horticultural crop with a pleasant aromatic flavor and abundance of health-promoting substances. Numerous melon varieties have been cultivated worldwide in recent years, but the high number of varieties and the high similarity between them poses a major challenge for variety evaluation, discrimination, as well as innovation in breeding. Recently, simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs), two robust molecular markers, have been utilized as a rapid and reliable method for variety identification. To elucidate the genetic structure and diversity of melon varieties, we screened out 136 perfect SSRs and 164 perfect SNPs from the resequencing data of 149 accessions, including the most representative lines worldwide. This study established the DNA fingerprint of 259 widely-cultivated melon varieties in China using Target-seq technology. All melon varieties were classified into five subgruops, including ssp. agrestis, ssp. melo, muskmelon and two subgroups of foreign individuals. Compared with ssp. melo, the ssp. agrestis varieties might be exposed to a high risk of genetic erosion due to their extremely narrow genetic background. Increasing the gene exchange between ssp. melo and ssp. agrestis is therefore necessary in the breeding procedure. In addition, analysis of the DNA fingerprints of the 259 melon varieties showed a good linear correlation (R2 = 0.9722) between the SSR genotyping and SNP genotyping methods in variety identification. The pedigree analysis based on the DNA fingerprint of ‘Jingyu’ and ‘Jingmi’ series melon varieties was consistent with their breeding history. Based on the SNP index analysis, ssp. agrestis had low gene exchange with ssp. melo in chromosome 4, 7, 10, 11and 12, two specific SNP loci were verified to distinguish ssp. agrestis and ssp. melon varieties. Finally, 23 SSRs and 40 SNPs were selected as the core sets of markers for application in variety identification, which could be efficiently applied to variety authentication, variety monitoring, as well as the protection of intellectual property rights in melon.

Adaptive Evolution Compensated for the Plasmid Fitness Costs Brought by Specific Genetic Conflicts.

New Delhi metallo-β-lactamase (NDM)-carrying IncX3 plasmids is important in the transmission of carbapenem resistance in Escherichia coli. Fitness costs related to plasmid carriage are expected to limit gene exchange; however, the causes of these fitness costs are poorly understood. Compensatory mutations are believed to ameliorate plasmid fitness costs and enable the plasmid's wide spread, suggesting that such costs are caused by specific plasmid-host genetic conflicts. By combining conjugation tests and experimental evolution with comparative genetic analysis, we showed here that the fitness costs related to ndm/IncX3 plasmids in E. coli C600 are caused by co-mutations of multiple host chromosomal genes related to sugar metabolism and cell membrane function. Adaptive evolution revealed that mutations in genes associated with oxidative stress, nucleotide and short-chain fatty acid metabolism, and cell membranes ameliorated the costs associated with plasmid carriage. Specific genetic conflicts associated with the ndm/IncX3 plasmid in E. coli C600 involve metabolism and cell-membrane-related genes, which could be ameliorated by compensatory mutations. Collectively, our findings could explain the wide spread of IncX3 plasmids in bacterial genomes, despite their potential cost.

Prediction Model for the Chemical Futures Price Using Improved Genetic Algorithm Based Long Short-Term Memory

In this paper, a new prediction model for accurately recognizing and appropriately evaluating the trends of domestic chemical products and for improving the forecasting accuracy of the chemical products’ prices is proposed. The proposed model uses the minimum forecasting error as the evaluation objective to forecast the settlement price. Active contracts for polyethylene and polypropylene futures on the Dalian Commodity Futures Exchange for the next five days were used, the data were divided into a training set and test set through normalization, and the time window, batch processing size, number of hidden layers, and rejection rate of a long short-term memory (LSTM) network were optimized by an improved genetic algorithm (IGA). In the experiments, with respect to the shortcomings of the genetic algorithm, the crossover location determination and some gene exchange methods in the crossover strategy were improved, and the predicted results of the IGA–LSTM model were compared with those of other models. The results showed that the IGA–LSTM model could effectively capture the characteristics and trends of time-series changes. The results showed that the proposed model obtained the minimum values (MSE = 0.00107, RMSE = 0.03268, and MAPE = 0.0691) in the forecasting of futures prices for two types of chemical products, showing excellent forecasting performance.

Analysis of the Genetic Diversity of Two Rhopalosiphum Species from China and Europe Based on Nuclear and Mitochondrial Genes.

Population genetic studies can reveal clues about the evolution of adaptive strategies of aphid species in agroecosystems and demonstrate the influence of environmental factors on the genetic diversity and gene flow among aphid populations. To investigate the genetic diversity of two Rhopalosiphum aphid species from different geographical regions, 32 populations (n = 535) of the bird cherry-oat aphid (Rhopalosiphum padi Linnaeus) and 38 populations (n = 808) of the corn leaf aphid (Rhopalosiphum maidis Fitch) from China and Europe were analyzed using one nuclear (elongation factor-1 alpha) and two mitochondrial (cytochrome oxidase I and II) genes. Based on the COI-COII sequencing, two obvious clades between Chinese and European populations and a low level of gene flow (Nm = 0.15) were detected in R. padi, while no geographical-associated genetic variation was found for EF-1α in this species. All genes in R. maidis had low genetic variation, indicating a high level of gene flow (Nm = 5.31 of COI-COII and Nm = 2.89 of EF-1α). Based on the mitochondrial result of R. padi, we concluded that the long distance between China and Europe may be interrupting the gene flow. The discordant results of nuclear gene analyses in R. padi may be due to the slower evolution of nuclear genes compared to mitochondrial genes. The gene exchange may occur gradually with the potential for continuous migration of the aphid. This study facilitates the design of control strategies for these pests.