Reviews and Recommendations in Comparative Studies on Quality of Wild and Cultivated Chinese Crude Drugs / 中国实验方剂学杂志

By reviewing the research history on quality comparison between wild and cultivated Chinese crude drugs， this paper systematically combed the relevant research reports since the 1950s， and summarized and analyzed the results of existing comparative studies， and found that the existing comparative research on the quality of wild and cultivated Chinese crude drugs were mainly focused on several aspects， including characteristics， microstructures， chemical compositions， pharmacodynamic effects， and genetic diversity. Among these， comparative studies of chemical compositions have been the dominant approach， with a particular emphasis on comparing the contents of index components. However， research on pharmacodynamic effects remained relatively limited. Due to various factors such as sample quantity， sample origin， growth period and cultivation methods， the differences in quality between wild and cultivated Chinese crude drugs vary significantly. In general， most wild Chinese crude drugs exhibited higher quality than cultivated products， with significant differences in their characteristics. The contents and proportions of some chemical components underwent noticeable changes， particularly with a marked increase in the proportion of primary metabolites after cultivation. The quality of cultivated Chinese crude drugs is closely related to the cultivation practices employed. Chinese crude drugs produced through wild nurturing， simulated wild planting， ecological cultivation， and other similar methods demonstrate quality levels comparable to those of wild Chinese crude drugs. Based on the analysis results， it is recommended to explicitly specify the cultivation practices and cultivation period of cultivated Chinese crude drugs in comparative studies of the quality between wild and cultivated Chinese crude drugs. Multiple technical approaches， including characteristics， microscopy， non-targeted metabolomics combined with quantitative analysis of differential components， and bioefficacy evaluation， should be employed to comprehensively assess the quality disparities between wild and cultivated Chinese crude drugs. Moreover， research efforts should be intensified to investigate the changes in pharmacodynamic effects resulting from differences in plant cell wall composition， primary metabolites， and secondary metabolites， in order to guide the production of high-quality Chinese crude drugs.

Mitochondrial DNA diversity and maternal origins of Pakistani donkey / Diversidade de DNA mitocondrial e origens maternas do burro do Paquistão

Domestic donkey plays a key role as a draft animal in rural economy of Pakistan where its population is increasing every year. The complete mtDNA control region of forty randomly sampled donkeys was PCR- amplified and sequenced bi-directionally using specific primers. Distinct mtDNA haplotypes obtained in the current study (KY446001−KY446011) were subjected to haplotype (h) and nucleotide diversity (π) measures using DnaS as well as to phylogenetic, Network, and AMOVA analyses. There were a total 27 polymorphic sites present within 11 unique mtDNA haplotypes from the studied 40 animals from different regions. Neighbor-joining network and median-joining network both illustrated the splitting of all these haplotypes into two well-defined Nubian and Somali lineages, confirming African maternal origin of Pakistani domestic donkey. Diversity parameters h (0.967± 0.037) and π (0.02917± 0.00307) were found to reveal high levels of genetic diversity in Pakistani donkeys. AMOVA demonstrated only 1% of genetic differences between two mtDNA maternal lineages, pointing to lack of population substructure in Pakistani donkeys as is the case with worldwide domestic donkey population. Pakistani donkeys have African maternal origin and high levels of mtDNA diversity. High genetic diversity may be due to non-selective breeding and heteroplasmy. We herein provide the first report on mtDNA diversity of control region in Pakistani domestic donkey.

O burro doméstico possui um papel fundamental como animal de tração na economia rural do Paquistão, onde a população desse animal está aumentando a cada ano. A região de controle de mtDNA completa de 40 burros amostrados aleatoriamente foi ampliada por PCR e sequenciada bidirecionalmente por intermédio de primers específicos. Haplótipos distintos de mtDNA obtidos no estudo atual (KY446001 − KY446011) foram submetidos a medidas de haplótipo (h) e diversidade de nucleotídeos (π) por meio de DnaS, bem como análises filogenéticas, de rede e AMOVA. Havia um total de 27 sítios polimórficos presentes em 11 haplótipos de mtDNA exclusivos dos 40 animais estudados de diferentes regiões. A rede de união de vizinhos e a rede de união mediana ilustram a divisão de todos esses haplótipos em duas linhagens núbias e somalis bem definidas, confirmando a origem materna africana do burro doméstico do Paquistão. Os parâmetros de diversidade h (0,967 ± 0,037) e π (0,02917 ± 0,00307) revelaram altos níveis de diversidade genética em burros paquistaneses. AMOVA demonstrou apenas 1% de diferenças genéticas entre as duas linhagens maternas de mtDNA, apontando a falta de subestrutura populacional em burros paquistaneses, como é o caso da população mundial de burros domésticos. Os burros paquistaneses têm origem materna africana e altos níveis de diversidade de mtDNA. A alta diversidade genética pode ser por causa da reprodução não seletiva e de heteroplasmia. Aqui, fornecemos o primeiro relatório sobre a diversidade do mtDNA da região de controle em burros domésticos do Paquistão

Genetic diversity analysis and fingerprinting of 175 Chimonanthus praecox germplasm based on SSR molecular marker / 生物工程学报

The elucidation of resources pertaining to the Chimonanthus praecox varieties and the establishment of a fingerprint serve as crucial underpinnings for advancing scientific inquiry and industrial progress in relation to C. praecox. Employing the SSR molecular marker technology, an exploration of the genetic diversity of 175 C. praecox varieties (lines) in the Yanling region was conducted, and an analysis of the genetic diversity among these varieties was carried out using the UPDM clustering method in NTSYSpc 2.1 software. We analyzed the genetic structure of 175 germplasm using Structure v2.3.3 software based on a Bayesian model. General linear model (GLM) association was utilized to analyze traits and markers. The genetic diversity analysis revealed a mean number of alleles (Na) of 6.857, a mean expected heterozygosity (He) of 0.496 3, a mean observed heterozygosity (Ho) of 0.503 7, a mean genetic diversity index of Nei՚s of 0.494 9, and a mean Shannon information index of 0.995 8. These results suggest that the C. praecox population in Yanling exhibits a rich genetic diversity. Additionally, the population structure and the UPDM clustering were examined. In the GLM model, a total of fifteen marker loci exhibited significant (P < 0.05) association with eight phenotypic traits, with the explained phenotypic variation ranging from 14.90% to 36.03%. The construction of fingerprints for C. praecox varieties (lines) was accomplished by utilizing eleven primer pairs with the highest polymorphic information content, resulting in the analysis of 175 SSR markers. The present study offers a thorough examination of the genetic diversity and SSR molecular markers of C. praecox in Yanling, and establishes a fundamental germplasm repository of C. praecox, thereby furnishing theoretical underpinnings for the selection and cultivation of novel and superior C. praecox varieties, varietal identification, and resource preservation and exploitation.

Genetic Diversity Analysis and Molecular ID Card Construction of Pinellia ternata Based on Phenotypic Traits and SSR Markers / 中国实验方剂学杂志

ObjectiveTo study the genetic diversity and genetic relationship of Pinellia ternata germplasm resources and provide the basis for germplasm identification， variety breeding， and resource conservation. MethodIn this study， 27 P. ternata were used as experimental materials to determine seven phenotypic characters， such as plant height， leaf length， and leaf width. Simple sequence repeats （SSR） primers were designed based on P. ternata transcriptome data， and polymerase chain reaction （PCR） amplification was performed on 27 P. ternata samples. The genetic diversity of P. ternata germplasm was analyzed by POPGENE32， PowerMarker V3.25， and NTSYS-PC 2.10e software. ResultA total of 10 pairs of highly polymorphic primers （PIC>0.5） and four pairs of moderately polymorphic primers （0.25<PIC<0.5） were selected. The average number of alleles detected was 3.928 6， and the average Nei's diversity index （H） and Shannon's index （I） were 0.557 8 and 1.002 9， respectively， indicating a high level of genetic diversity. Cluster analysis divided the Pinellia ternata into seven categories， and P. ternata in the same province were in the same categories. The SSR molecular ID cards of 27 P. ternata germplasm were constructed with 14 pairs of primers， and the rapid identification of P. ternata in each region was realized. ConclusionThe results of this study can lay a foundation for the genetic diversity and population structure of P. ternata and provide a scientific basis for the identification of P. ternata germplasm resources， map construction， and molecular-assisted breeding.

Specific DNA barcodes screening, germplasm resource identification, and genetic diversity analysis of Platycodon grandiflorum / 药学学报

Platycodonis Radix is the dry root of Platycodon grandiflorum of Campanulaceae, which has a variety of pharmacological effects and is a commonly used bulk Chinese medicine. In this study, the chloroplast genome sequences of six P. grandiflorum from different producing areas has been sequenced with Illumina HiSeq X Ten platform. The specific DNA barcodes were screened, and the germplasm resources and genetic diversity were analyzed according to the specific barcodes. The total length of the chloroplast genome of 6 P. grandiflorum samples was 172 260-172 275 bp, and all chloroplast genomes showed a typical circular tetrad structure and encoded 141 genes. The comparative genomics analysis and results of amplification efficiency demonstrated that trnG-UCC and ndhG_ndhF were the potential specific DNA barcodes for identification the germplasm resources of P. grandiflorum. A total of 305 P. grandiflorum samples were collected from 15 production areas in 9 provinces, for which the fragments of trnG-UCC and ndhG_ndhF were amplificated and the sequences were analyzed. The results showed that trnG-UCC and ndhG_ndhF have 5 and 11 mutation sites, respectively, and 5 and 7 haplotypes were identified, respectively. The combined analysis of the two sequences formed 13 haplotypes (named Hap1-Hap13), and Hap4 is the main genotype, followed by Hap1. The unique haplotypes possessed by the three producing areas can be used as DNA molecular tags in this area to distinguish from the germplasm resources of P. grandiflorum from other areas. The haplotype diversity, nucleotide diversity and genetic distance were 0.94, 4.79×10-3 and 0.000 0-0.020 3, respectively, suggesting that the genetic diversity was abundant and intraspecific kinship was relatively close. This study laid a foundation for the identification of P. grandiflorum, the protection and utilization of germplasm resources, and molecular breeding.

Hypothesis of Genetic Diversity Selection in the Occurrence and Development of Lung Cancer: Molecular Evolution and Clinical Significance / 中国肺癌杂志

So far, the monoclonal hypothesis of tumor occurrence and development cannot be justified. The genetic diversity selection hypothesis for the occurrence and development of lung cancer links Mendelian genetics with Darwin's theory of evolution, suggesting that the genetic diversity of tumor cell populations with polyclonal origins-monoclonal selection-subclonal expansion is the result of selection pressure. Normal cells acquire mutations in oncogenic driver genes and have a selective advantage over other cells, becoming tumor initiating cells; In the interaction with the tumor microenvironment (TME), the vast majority of initiating cells are recognized and killed by the human immune system. If immune escape occurs, the incidence of malignant tumors will greatly increase, and subclonal expansion, intratumour heterogeneity, etc. will occur. This article proposed the hypothesis of genetic diversity selection and analyzed its clinical significance.
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Reduced genetic diversity and the success of the invasive peacock bass (Cichliformes: Cichlidae)

Abstract Several species of Cichla successfully colonized lakes and reservoirs of Brazil, since the 1960s, causing serious damage to local wildlife. In this study, 135 peacock bass were collected in a reservoir complex in order to identify if they represented a single dominant species or multiple ones, as several Cichla species have been reported in the basin. Specimens were identified by color pattern, morphometric and meristic data, and using mitochondrial markers COI, 16S rDNA and Control Region (CR). Overlapping morphological data and similar coloration patterns prevented their identification using the taxonomic keys to species identification available in the literature. However, Bayesian and maximum likelihood from sequencing data demonstrated the occurrence of a single species, Cichla kelberi. A single haplotype was observed for the 16S and CR, while three were detected for COI, with a dominant haplotype present in 98.5% of the samples. The extreme low diversity of the transplanted C. kelberi evidenced a limited number of founding maternal lineages. The success of this colonization seems to rely mainly on abiotic factors, such as increased water transparency of lentic environments that favor visual predators that along with the absence of predators, have made C. kelberi a successful invader of these reservoirs.

Resumo Muitas espécies de Cichla colonizaram com sucesso lagos e reservatórios do Brasil desde os anos 1960, causando graves prejuízos à vida selvagem nesses locais. Neste estudo, 135 tucunarés foram coletados em um complexo de reservatórios a fim de identificar se representavam uma espécie dominante ou múltiplas espécies, uma vez que diversas espécies de Cichla foram registradas na bacia. Os espécimes foram identificados com base na coloração, dados morfométricos e merísticos, e por marcadores mitocondriais COI, 16S rDNA e Região Controle (RC). A sobreposição dos dados morfométricos e o padrão similar de coloração impediram a identificação utilizando as chaves de identificação disponíveis na literatura. Entretanto, as análises bayesiana e de máxima verossimilhança de dados moleculares demonstraram a ocorrência de uma única espécie, Cichla kelberi. Um único haplótipo foi observado para o 16S e RC, enquanto três foram detectados para o COI, com um haplótipo dominante presente em 98,5% das amostras. A baixa diversidade nos exemplares introduzidos de C. kelberi evidenciou um número limitado de linhagens maternas fundadoras. O sucesso da invasão parece depender de fatores abióticos, como a maior transparência da água de ambientes lênticos que favorece predadores visuais que, atrelado à ausência de predadores, fez do C. kelberi um invasor bem-sucedido nesses reservatórios.

Mitochondrial DNA diversity and maternal origins of Pakistani donkey

Abstract Domestic donkey plays a key role as a draft animal in rural economy of Pakistan where its population is increasing every year. The complete mtDNA control region of forty randomly sampled donkeys was PCR- amplified and sequenced bi-directionally using specific primers. Distinct mtDNA haplotypes obtained in the current study (KY446001KY446011) were subjected to haplotype (h) and nucleotide diversity () measures using DnaS as well as to phylogenetic, Network, and AMOVA analyses. There were a total 27 polymorphic sites present within 11 unique mtDNA haplotypes from the studied 40 animals from different regions. Neighbor-joining network and median-joining network both illustrated the splitting of all these haplotypes into two well-defined Nubian and Somali lineages, confirming African maternal origin of Pakistani domestic donkey. Diversity parameters h (0.967± 0.037) and (0.02917± 0.00307) were found to reveal high levels of genetic diversity in Pakistani donkeys. AMOVA demonstrated only 1% of genetic differences between two mtDNA maternal lineages, pointing to lack of population substructure in Pakistani donkeys as is the case with worldwide domestic donkey population. Pakistani donkeys have African maternal origin and high levels of mtDNA diversity. High genetic diversity may be due to non-selective breeding and heteroplasmy. We herein provide the first report on mtDNA diversity of control region in Pakistani domestic donkey.

Resumo O burro doméstico possui um papel fundamental como animal de tração na economia rural do Paquistão, onde a população desse animal está aumentando a cada ano. A região de controle de mtDNA completa de 40 burros amostrados aleatoriamente foi ampliada por PCR e sequenciada bidirecionalmente por intermédio de primers específicos. Haplótipos distintos de mtDNA obtidos no estudo atual (KY446001 KY446011) foram submetidos a medidas de haplótipo (h) e diversidade de nucleotídeos () por meio de DnaS, bem como análises filogenéticas, de rede e AMOVA. Havia um total de 27 sítios polimórficos presentes em 11 haplótipos de mtDNA exclusivos dos 40 animais estudados de diferentes regiões. A rede de união de vizinhos e a rede de união mediana ilustram a divisão de todos esses haplótipos em duas linhagens núbias e somalis bem definidas, confirmando a origem materna africana do burro doméstico do Paquistão. Os parâmetros de diversidade h (0,967 ± 0,037) e (0,02917 ± 0,00307) revelaram altos níveis de diversidade genética em burros paquistaneses. AMOVA demonstrou apenas 1% de diferenças genéticas entre as duas linhagens maternas de mtDNA, apontando a falta de subestrutura populacional em burros paquistaneses, como é o caso da população mundial de burros domésticos. Os burros paquistaneses têm origem materna africana e altos níveis de diversidade de mtDNA. A alta diversidade genética pode ser por causa da reprodução não seletiva e de heteroplasmia. Aqui, fornecemos o primeiro relatório sobre a diversidade do mtDNA da região de controle em burros domésticos do Paquistão.

Reduced genetic diversity and the success of the invasive peacock bass (Cichliformes: Cichlidae) / Diversidade genética reduzida e o sucesso da espécie invasora tucunaré (Cichliformes: Cichlidae)

Abstract Several species of Cichla successfully colonized lakes and reservoirs of Brazil, since the 1960's, causing serious damage to local wildlife. In this study, 135 peacock bass were collected in a reservoir complex in order to identify if they represented a single dominant species or multiple ones, as several Cichla species have been reported in the basin. Specimens were identified by color pattern, morphometric and meristic data, and using mitochondrial markers COI, 16S rDNA and Control Region (CR). Overlapping morphological data and similar coloration patterns prevented their identification using the taxonomic keys to species identification available in the literature. However, Bayesian and maximum likelihood from sequencing data demonstrated the occurrence of a single species, Cichla kelberi. A single haplotype was observed for the 16S and CR, while three were detected for COI, with a dominant haplotype present in 98.5% of the samples. The extreme low diversity of the transplanted C. kelberi evidenced a limited number of founding maternal lineages. The success of this colonization seems to rely mainly on abiotic factors, such as increased water transparency of lentic environments that favor visual predators that along with the absence of predators, have made C. kelberi a successful invader of these reservoirs.

Resumo Muitas espécies de Cichla colonizaram com sucesso lagos e reservatórios do Brasil desde os anos 1960, causando graves prejuízos à vida selvagem nesses locais. Neste estudo, 135 tucunarés foram coletados em um complexo de reservatórios a fim de identificar se representavam uma espécie dominante ou múltiplas espécies, uma vez que diversas espécies de Cichla foram registradas na bacia. Os espécimes foram identificados com base na coloração, dados morfométricos e merísticos, e por marcadores mitocondriais COI, 16S rDNA e Região Controle (RC). A sobreposição dos dados morfométricos e o padrão similar de coloração impediram a identificação utilizando as chaves de identificação disponíveis na literatura. Entretanto, as análises bayesiana e de máxima verossimilhança de dados moleculares demonstraram a ocorrência de uma única espécie, Cichla kelberi. Um único haplótipo foi observado para o 16S e RC, enquanto três foram detectados para o COI, com um haplótipo dominante presente em 98,5% das amostras. A baixa diversidade nos exemplares introduzidos de C. kelberi evidenciou um número limitado de linhagens maternas fundadoras. O sucesso da invasão parece depender de fatores abióticos, como a maior transparência da água de ambientes lênticos que favorece predadores visuais que, atrelado à ausência de predadores, fez do C. kelberi um invasor bem-sucedido nesses reservatórios.

Variabilidad genética del pez Lutjanus guttatus (Perciformes: Lutjanidae) mediante el uso de microsatélites en Costa Rica / Genetic variability of the fish Lutjanus guttatus (Perciformes: Lutjanidae) using microsatellites in Costa Rica

Introducción: El pargo mancha es un pez marino de alto consumo e interés comercial en Costa Rica que está sometido a una fuerte presión pesquera, la cual puede afectar la diversidad genética y generar problemas por depresión endogámica. Objetivo: Evaluar el estado genético de la población de Lutjanus guttatus mediante el uso microsatélites. Métodos: Se recolectaron muestras entre el 2018 y 2019 y se estudiaron 44 individuos de cada una de las localidades del Golfo de Nicoya y Golfo Dulce. Se realizó la extracción de ADN y la amplificación de diez loci con microsatélites mediante PCR, para la determinación del genotipo, análisis de diversidad genética y estructura poblacional. Resultados: Los parámetros de diversidad indican un elevado polimorfismo asociado con un alto número de alelos obtenidos por locus, pero con bajos niveles de heterocigosidad observada en comparación con la esperada (Ho= 0.774 y 0.800 y He= 0.948 y 0.954 para Golfo de Nicoya y Golfo Dulce, respectivamente). No hay evidencia suficiente para decir que las dos poblaciones son distintas (FST= 0.00264, P > 0.05). La desviación del Equilibrio de Hardy-Weinberg indica la posible mezcla de organismos de origen distinto a los del medio silvestre. Conclusiones: L. guttatus tiene niveles altos de diversidad genética, no hay evidencia de diferenciación en subpoblaciones genéticas, lo que en manejo pesquerías se considera una sola población panmíctica. La posible mezcla de individuos de origen distinto al silvestre sugiere la presencia de organismos de un programa de repoblación o de cultivos comerciales en la región. El uso de marcadores genéticos se recomienda para el monitoreo, además, en programas de repoblación y evaluar su efecto.

Introduction: The spotted snapper is a high-consumption and commercially important marine fish in Costa Rica, subjected to heavy fishing pressures, which can affect genetic diversity and generate problems due to inbreeding depression. Objective: To evaluate the genetic status of the population of Lutjanus guttatus using microsatellites. Methods: Samples were collected between 2018 and 2019, and 44 individuals from each of the localities of the Gulf of Nicoya and the Gulf of Dulce were studied. DNA extraction and amplification of ten loci with microsatellites using PCR were performed, followed by genotyping, analysis of genetic diversity, and population structure. Results: Diversity parameters indicate a high polymorphism associated with a high number of alleles obtained per locus, but with low levels of observed heterozygosity compared to expected (Ho= 0.774 and 0.800, and He= 0.948 and 0.954 for the Gulf of Nicoya and Gulf of Dulce, respectively). There is not enough evidence to say that the two populations are distinct (FST= 0.00264, P > 0.05). Deviation from Hardy-Weinberg equilibrium was recorded, indicating possible mixing of organisms of different origin from the wild environment. Conclusions: L. guttatus presents high levels of genetic diversity, without evidence of differentiation in genetic subpopulations. For fisheries management purposes, they would be considered a single panmictic population. The possible mixing with wild individuals suggests the presence of organisms derived from a restocking or commercial cultivation program carried out in the region. The use of genetic markers is recommended to maintain monitoring, follow up on restocking programs and evaluate their effect.

Genetic diversity of Mycobacterium leprae in the state of São Paulo, an area of low-leprosy incidence in Brazil

ABSTRACT Background: Brazil has the second largest number of leprosy cases worldwide, and the state of São Paulo has been considered non-endemic since 2006. Methods: We analyzed 16 variable number tandem repeats loci and three single nucleotide polymorphisms loci of Mycobacterium leprae (M. leprae) in 125 clinical isolates from patients in different municipalities in the state. Results: The clustering pattern of M. leprae indicated that the transmission of leprosy persisted in the state and included scenarios of intra-extra-familial transmission in areas with low endemicity. Conclusions: A significantly active circulation of M. leprae was observed. Therefore, surveillance and control measures must be implemented.

Genetic diversity, phylogenetic and phylogeographic analyses of Oncideres impluviata (Germar, 1823) (Coleoptera: Cerambycidae) in Rio Grande do Sul state, Brazil

ABSTRACT The Cerambycidae Oncideres impluviata (Germar, 1823) is an important insect pest for Acacia mearnsii De Wild in Southern Brazil. The damage caused by their girdling behavior reduces tree productivity, specially in the early years of plant establishment, when girdling is performed on the main trunk of trees. Here, we used a fragment of the mtDNA COI gene to analyze the genetic diversity, population structure and demography of O. impluviata in Southern Brazil, as well as to present the first hypothesis of phylogenetic relationships among species of the genus Oncideres. Our results identified five distinct haplotypes among the populations of O. impluviata, with the most common haplotype identified as O.imp_COI_01. The phylogenetic inferences corroborated the monophyly of O. impluviata with maximum statistical support. In addition, the phylogeny recovered three main population strains that are largely congruent with the haplotype network, which includes two lineages that are found in different edaphic regions of Rio Grande do Sul (Serra do Sudeste and Encosta Inferior do Nordeste). This is the first molecular phylogenetic assessment of O. impluviata. Our findings provide insights into the evolution of a significant species for the Brazilian forestry sector, as well as new resources for planning of pest management strategies.

Chloroplast DNA reveals genetic population structure in Sinomenium acutum in subtropical China / 中草药·英文版

OBJECTIVE@#The population density and diversity of Sinomenium acutum (Menispermaceae) have been greatly reduced recently by overharvesting for medicinal purposes in China. Therefore, it is urgent that the remaining populations are investigated, and that strategies for the utilization and conservation of this species are developed. This study aimed to find the possible glacial refugia and define the genetic diversity of S. acutum for its proper utilization and conservation.@*METHODS@#A total of 77 S. acutum samples were collected from four locations, Qinling Mountains, Daba Mountains, Dalou Mountains, and Xuefeng Mountains, in subtropical China. Genetic diversity among and between these populations were phylogenetically analyzed using four chloroplast DNA molecular markers (atpI-atpH, trnQ-5'rps16, trnH-psbA and trnL-trnF).@*RESULTS@#A total of 14 haplotypes (C1 to C14) were found in collected samples. Haplotypes C1 and C3 were shared among all populations, with C3 as the ancestral haplotype. Haplotypes C11 and C12 diverged the most from C3 and other haplotypes. No obvious phylogeographic structure was found in four locations using the GST/NST test. There is no evidence of rapid demographic expansion in S. acutum based on the mismatch distribution, and the results of Tajima's D test, and Fu's FS test. Our analyses of molecular variance revealed a high level of genetic variation within populations. In contrast, the genetic differentiation among S. acutum populations was low, indicating frequent gene flow.@*CONCLUSION@#Xuefeng, Dalou, and Daba Mountains were possible glacial refugia for the populations of S. acutum. C1, C3, C11 and C12 haplotypes of S. acutum should be carefully preserved and managed for their genetic value.

Genetic diversity and Kdr mutations of natural Aedes (Stegomyia) aegypti (Diptera: Culicidae) populations of Brazil

ABSTRACT Aedes (Stegomyia) aegypti is an important vector of dengue, yellow fever, chikungunya and Zika virus. It is well known that resistance monitoring and genetic diversity data help designing the vector control programs. This study aimed to evaluate resistance to pyrethroids (PYs) through the frequency of kdr mutations Val1016IIe and F1534C, and the genetic variation of the mitochondrial gene ND4 in six natural populations of A. aegypti from Paraná - Brazil. Adults were obtained from eggs collected from Alvorada do Sul, Marilena, Maringá, Nova Londrina, Paranavaí and São Carlos do Ivaí. From these adults, 345 were used to identify the 1016 and 1534 sites, and 120 were used to perform the ND4 gene analysis. The studied populations from Paraná showed PYs resistance, low gene flow and genetic diversity. Additionally, a relationship was observed among the haplotypes of populations from the Amazon and Southeastern Brazil, Peru, Mexico, and North America.

High prevalence of hepatitis A and E viruses in environmental and clinical samples from West Argentina

ABSTRACT Environmental surveillance of water sources is important to monitoring viral hepatitis transmission in clinical settings. This study investigated the circulation of hepatitis A (HAV) and E (HEV) viruses in sewage and clinical samples from Argentina. Between 2016 and 2017, 80 raw sewage samples and 86 clinical samples (stool and serum) from suspected cases of hepatitis A and hepatitis E were obtained. HAV and HEV were tested by both real-time and nested PCR. Positive samples were sequenced for genotype determination and phylogenetic analysis. Overall, HAV was recovered in 39% of sewage samples and 61.1% of clinical samples. HEV was detected in 22.5% of sewage samples and 15.9% of clinical samples. HAV was found more frequently in sewage during the winter and in clinical samples in spring; HEV was more prevalent in sewage during summer and in clinical samples in autumn. All HAV isolates belonged to genotype IA and HEV isolates belonged to genotype 3, the most prevalent genotypes in South America. High prevalence of HAV and HEV in environmental and clinical samples in Mendoza, Argentina was observed. These findings reinforce the importance of environmental surveillance and implementation of health strategies to control the spread of HAV and HEV in developing countries.

Genetic variability of cocoa from the amazon basin: implications for genetic conservation

The cocoa and chocolate production chain involves US$60 billion annually and three million farmers around the world, in an area exceeding nine million hectares. The use of wild germplasm will enable to generate new disease- and pest-resistant cultivars and ability to adapt to changing environments. Here we evaluated 145 cocoa accessions, originated from nine Amazonian basins, based on eight fruit traits. Univariate anova showed significant differences (p<0.05) for all traits. For seven traits, the variance component within basins was higher (81.5%, on average). Therefore, it is recommended that the collection of wild accessions prioritize a larger number of plants from a few populations of the most divergent basins. The multivariate analyses revealed a greater divergence between the Ji-Paraná-RO and Solimões/Amazonas-PA basins (27.69) and a greater similarity between Alien clones-PER and Solimões/Amazonas-AM (0.66) in relation to their populations. They also revealed that the accessions differentiation occurred according to the river basin system. These results allowed elucidate the genetic structure and distribution of cacao populations. In addition, strengthen the importance of collecting and conserving germplasm to preserve genetic resources.

Common but not connected: high genetic structure and cryptic genetic diversity in the ubiquitous biting midge Culicoides peregrinus Kieffer

@#The biting midge Culicoides peregrinus Kieffer is a significant pest and vector species, and knowledge of its genetic diversity and genetic structure is critically important for designing an effective control program. However, such information is limited to only small sample-size DNA barcoding studies. Therefore, in this study, we used mitochondrial cytochrome c oxidase I (COI) to examine genetic structure and diversity of C. peregrinus from northeastern Thailand. In addition, we also inferred genetic relationships between C. peregrinus from Thailand and those reported from other countries across the geographic range of the species. Maximum intraspecific genetic divergence (3.83%) within Thai specimens was relatively high compared to other Culicoides species. Genetic structure analysis revealed that 71% (32 from 45) of population comparisons were highly significantly different. A high level of genetic structure among populations, even between those in close geographic proximity (22 km geographic distance) suggested that there has been little or no movement between local populations. This is possibly due to the ability to exploit diverse types of breeding site and a generalist feeding habit which enables C. peregrinus to complete its life cycle within cattle pens. Genetic relationships between Thai C. peregrinus and those reported from other countries revealed three genetically divergent lineages (A, B and C) associated with geographic origins. Specimens from Thailand + China formed lineage A, those from Australia formed lineage B and India + Bangladesh belonged to lineage C. These genetically divergent lineages also agree with morphological variation of the wing pale marking spots. Further investigation using independent genetic loci from nuclear genes will be very useful to resolve taxonomic status of these divergent lineages.

Exploration of transcriptome SSR markers and its application in genetic diversity assessment of Asarum sieboldii / 中国中药杂志

To explore the genetic diversity of Asarum sieboldii this study developed SSR markers based on transcriptome sequencing results and five populations of A.sieboldii from different regions were used as samples for genetic diversity assessment using software such as GenALEx 6.5, NTSYS 2.1, and Structure 2.3.4. The results showed that 16 SSR markers with high polymorphism and good repeatability were selected from the A.sieboldii transcriptome. Primers designed based on the flanking sequences of these markers successfully amplified 56 polymorphic fragments from 150 individual samples of the five A.sieboldii populations. On average, each primer amplified 3.5 polymorphic fragments, ranging from 2 to 8. The mean values of expected heterozygosity(H_e), Shannon's diversity index(I), Nei's gene diversity index(H), and the polymorphic information content(PIC) were 0.172, 0.281, 0.429, and 0.382, respectively. The mean population differentiation coefficient(F_(ST)) was 0.588, consistent with the analysis of molecular variance(AMOVA) results, which indicated greater genetic variation among A.sieboldii populations(69%) than that within populations(31%). The percentage of polymorphic loci(PPL) ranged from highest to lowest as SNJ>LN>SY>SZ>TB. Principal coordinate analysis(PCoA) and UPGMA clustering analysis further revealed genetic clustering of A.sieboldii individuals based on their geographical distribution, consistent with the results of the structure clustering analysis. In summary, the SSR markers developed from the transcriptome effectively assessed the genetic differentiation and population structure of natural A.sieboldii populations, revealing a relatively low genetic diversity in A.sieboldii, with genetic variation primarily observed at the population level and a correlation between population differentiation and geographic distance.

Genetic variations in four geographical isolates of Gohieria fusca based on cytochrome b and internal transcribed spacer genes / 中国血吸虫病防治杂志

Objective To investigate the genetic diversity and genetic differentiation of different geographical isolates of Gohieria fusca.. Methods G. fusca isolates were sampled from Wuhu (WH), Bengbu (BB) and Bozhou cities (BZ) of Anhui Province and Jiaxing City of Zhejiang Province (JX). Mitochondrial cytochrome b (Cytb) and ribosomal internal transcribed spacer (ITS) genes were amplified in WH, BB, BZ and JX isolates of G. fusca using PCR assay. The gene sequences were edited and aligned using the software Chromas 2 and DNASTAR 1.00, and the haplotype, haplotype diversity (Hd) and nucleotide polymorphism (Pi) of each isolate were calculated using the software DnaSP 5.10.00. The genetic differentiation among isolates (Fst) and gene flow value (Nm) were estimated using the software MEGA 10.2, and a phylogenetic tree was built. Tests of neutrality and analysis of molecular variance (AMOVA) were performed using the software Arlequin 3.1 and a haplotype network was built based on the Median-Joining network using the software Network 10.2. Results PCR assay showed that the sizes of the Cytb and ITS genes were 372 bp and 1 301 to 1 320 bp, respectively. All four isolates of G. fusca presented high genetic diversity based on mitochondrial Cytb and ITS genes (Hd = 0.804, Pi = 0.006 91). AMOVA showed genetic differentiation among geographical isolates of G. fusca (Fst = 0.202 40, P < 0.05), and the genetic variation was mainly caused by intra-population variations (79.76%). Gene flow analysis showed a high level of gene flow among G. fusca isolates (Nm > 1). Tests of neutrality based on Cytb gene measured a Tajima’s D value of −1.796 31 (P < 0.05) and a Fu’s FS value of −3.293 98 (P < 0.05) in WH isolate of G. fusca, indicating population expansion in WH isolate of G. fusca. Haplotype network analysis and phylogenetic analysis revealed no remarkable geographical distribution pattern among different geographical isolates of G. fusca. All four isolates of G. fusca presented high genetic diversity (Hd = 0.985, Pi = 0.011 97). AMOVA showed moderate level of genetic differentiation between four isolates (Fst = 0.104 62, P < 0.05). The tests of neutrality based on ITS genes measured a Tajima’s D value of −6.088 20 and a Fu’s FS value of −1.935 99 (both P > 0.05) in the whole isolate of G. fusca, indicating no obviously population expansion. Conclusions The four geographical isolates of G. fusca have high genetic diversity and remarkable genetic differentiation. Since a high level of gene flow is detected among different geographical isolates of G. fusca, no obvious geographical distribution pattern of G. fusca is found.

Excellent appearance of Dao-di Ginseng Radix et Rhizoma and interaction mechanism between genetic and environmental factors: a review / 中国中药杂志

Dao-di medicinal materials produced in a specific environment always present excellent appearance and high quality. Because of the unique appearance, Ginseng Radix et Rhizoma is regarded as a paradigm in the research on excellent appearance. This paper systematically summarized the research progress in the genetic and environmental factors influencing the formation of the excellent appearance of Ginseng Radix et Rhizoma, aiming to provide reference for the quality improvement of Ginseng Radix et Rhizoma and the scientific connotation of Dao-di Chinese medicinal materials. The Ginseng Radix et Rhizoma with high quality generally has a robust and long rhizome, a large angle between branch roots, and the simultaneous presence of a robust basal part of rhizome, adventitious roots, rhizome bark with circular wrinkles, and fibrous roots with pearl points. The cultivated and wild Ginseng Radix et Rhizoma have significant differences in the appearance and no significant difference in the population genetic diversity. The differences in the appearance are associated with cell wall modification, transcriptional regulation of genes involved in plant hormone transduction, DNA methylation, and miRNA regulation. The rhizosphere soil microorganisms including Fusarium and Alternaria, as well as the endophytes Trichoderma hamatum and Nectria haematococca, may be the key microorganisms affecting the growth and development of Panax ginseng. Cultivation mode, variety, and root exudates may be the main factors influencing the stability of rhizosphere microbial community. Ginsenosides may be involved in the formation of the excellent appearance. However, most of the available studies focus on the partial or single factors in the formation of Dao-di medicinal materials, ignoring the relationship within the complex ecosystems, which limits the research on the formation mechanism of Dao-di medicinal materials. In the future, the experimental models for the research involving genetic and environmental factors should be established and mutant materials should be developed to clarify the internal relationship between factors and provide scientific support for the research on Dao-di medicinal materials.