Analysis of genetic diversity in the endangered Hucho taimen from China

Hucho taimen are listed as endangered in China. The population size has declined recently, prompting an increase in the level of listing from grade three in 2002 to grade five in 2006. We analyzed the genetic diversity of wild populations using 17 microsatellite markers to establish a scientific basis for conservation of this species. We collected tissue samples from four populations in the Heilongjiang River basin: Huma River (HM), Hutou (HT), Haiqing (HQ), and Zhuaji (ZJ). A total of 21 loci were amplified, 18 of which were polymorphic. The number of alleles per locus ranged from 2 to 9 (mean: 4.1905). There were 13 highly polymorphic loci and 5 moderately polymorphic loci. Analysis of five genetic diversity parameters (Na, Ne, Ho, He, and PIC) suggested moderate levels of diversity within the populations. The populations were ranked HT > HQ > ZJ > HM, but the differences in diversity were not statistically significant (P > 0.05). A comparison of variation among all four populations suggested Hardy–Weinberg disequilibrium at 20% of the loci. Genetic differentiation (Fst) was 0.0644 and the gene flow among populations was estimated at 3.36 individuals per generation. The majority of diversity (93.88%) occurred among individuals within a population. In contrast, relatively little (6.12%) of the genetic diversity was distributed between the populations. An analysis of genetic differentiation and genetic distance between pairs of populations revealed that both parameters were higher in comparisons of the HM population to the HT, HQ, and ZJ populations than among the three latter populations. This suggests that the HM population has a distinct genetic structure. We hypothesize that habitat degradation and excessive fishing, not low genetic diversity, has caused the decline in H. taimen populations. However, this species should be protected from further declines in genetic diversity.     

Analysis of genetic diversity in the endangered Hucho taimen from China

Hucho taimen are listed as endangered in China. The population size has declined recently, prompting an increase in the level of listing from grade three in 2002 to grade five in 2006. We analyzed the genetic diversity of wild populations using 17 microsatellite markers to establish a scientific basis for conservation of this species. We collected tissue samples from four populations in the Heilongjiang River basin: Huma River (HM), Hutou (HT), Haiqing (HQ), and Zhuaji (ZJ). A total of 21 loci were amplified, 18 of which were polymorphic. The number of alleles per locus ranged from 2 to 9 (mean: 4.1905). There were 13 highly polymorphic loci and 5 moderately polymorphic loci. Analysis of five genetic diversity parameters (Na, Ne, Ho, He, and PIC) suggested moderate levels of diversity within the populations. The populations were ranked HT > HQ > ZJ > HM, but the differences in diversity were not statistically significant (P > 0.05). A comparison of variation among all four populations suggested Hardy–Weinberg disequilibrium at 20% of the loci. Genetic differentiation (Fst) was 0.0644 and the gene flow among populations was estimated at 3.36 individuals per generation. The majority of diversity (93.88%) occurred among individuals within a population. In contrast, relatively little (6.12%) of the genetic diversity was distributed between the populations. An analysis of genetic differentiation and genetic distance between pairs of populations revealed that both parameters were higher in comparisons of the HM population to the HT, HQ, and ZJ populations than among the three latter populations. This suggests that the HM population has a distinct genetic structure. We hypothesize that habitat degradation and excessive fishing, not low genetic diversity, has caused the decline in H. taimen populations. However, this species should be protected from further declines in genetic diversity.     

Genetic diversity and differentiation of masu salmon (Oncorhynchus masou masou) between and within cultured populations inferred from microsatellite DNA analysis

Masu salmon,Oncorhynchus masou masou,is one of the most valuable fishery species that has been introduced to China,though to date no studies on the genetic diversity and genetic relationship among hatchery populations has been performed with molecular markers.We undertook such a study and sampled 120 individuals from three hatchery stocks and analyzed 20 microsatellite loci.All loci were polymorphic and a total of 91 alleles were detected.A relatively low level of genetic diversity was revealed with effective number of allele of 3.1094,3.3299 and 3.1894 and expected heterozygosity of 0.6600,0.6648 and 0.6638 in the three stocks,respectively.Deviations from Hardy-Weinberg equilibrium were found due to heterozygote deficit.Accordingly,evidence of genetic bottlenecks were found in the three stocks.An individual assignment test demonstrated that 85% of individuals were correctly assigned into their original stocks.Pairwise Fst revealed that significant differentiation occurred between these three stocks.The results of the study indicated that disequilibrium of genetic structure and differentiation has occurred in all three stocks.This information collectively provides a basis for measures to avoid of loss of genetic diversity and introgression in Chinese aquaculture.     

Genetic diversity of the endangered species Rosa rugosa Thunb. in China and implications for conservation strategies

Rosa rugosa Thunb. is one of the dominant and important shrub species in estuary dunes and shingle beaches of northern China. However, its area of distribution, the number of populations, and the size of each population have decreased rapidly in the past two decades because of habitat degradation and loss. Random amplified polymorphic DNA markers were used to determine the genetic diversity of four remaining large natural populations of R. rugosa and to discuss an effective conservation strategy for this endangered species in China. High genetic variations were detected in R. rugosa populations in China. The mean percentage of polymorphic loci （P%） within four local populations was 57.99%, with the P% of the total population being 75.30%. Mean Shannon＇s information index （H0） was 0.2826, whereas total Ho was 0.3513. The genetic differentiation among populations was 0.1878, which indicates that most genetic diversity occurs within populations. Population Tumenjiang （TMJ） showed the highest genetic diversity （P% = 66.27%; H0 = 0.3117） and contained two exclusive bands. Population Changshandao （CSD） showed higher genetic diversity （P% =59.04%; H0 = 0.3065）. Populations TMJ and CSD contained 95.33% and 99.33%, respectively, of loci with moderate to high frequency （P〉0.05） of the total population. These results indicate that populations TMJ and CSD should be given priority for in situ conservation and regarded as seed or propagule sources for ex situ conservation. The results of the present study also suggest that R. rugosa in China has become endangered as a result of human actions rather than genetic depression of populations; thus, human interference should be absolutely forbidden in R. rugosa habitats.     

Clonal diversity of Clintonia udensis Trautv. et Mey. populations and its correlation with ecological factors

The clonal diversity of Clintonia udensis Trautv.et Mey.was detected by ISSR markers among 16 populations,and its correlation with ecological factors was analyzed as well in this work.Results showed that individuals(clonal ramets)per genotype were 1.12 and 1.149 at population and species levels,respectively,and that the 16 populations were all multiclonal.The detected genotypes were localized,without exception,within populations but demonstrated relatively high clonal differentiation among populations.The clonal diversity of the studied populations was high,with the average Simpson's index of 0.975,while the genets showed a clonal architecture of"guerilla".The population genetic diversities revealed by genet were consistent with those by ramet,further confirming their genetic differentiation among populations.And its genotype diversity within populations probably resulted largely from the frequent seedling regeneration and self-compatibility.In addition,the correlation analysis further revealed that,among the ecological factors,Simpson's index of C.udensis had a significant positive correlation(P<0.05)with pH values in the soil but not others.     

Examining the genetic diversity of Stipa grandis under various grazing pressures

The Stipa grandis steppe in the Inner Mongolia Autonomous Region occupies an area of 2798081 hm2. On the basis of the genetic variation, it was found that its adaptability to the environmental conditions under grazing pressure was significant. Using the Inter-Simple Sequence Repeat (ISSR) procedure, the changes to the genetic diversity of the Stipa grandis population under different grazing pressures were observed. Plant samples were collected from a series of grazing gradients of the Stipa grandis steppe in Dalinuoer National Nature Reserve in the Inner Mongolia (located at 116°38′–116°41′E and 43°25′–43°27′N.), which has the following vegetation types in abundance: Leymus chinensis is the constructive species; the dominant species include Stipa grandis, Cleistogenes squarrosa, and Artemisia frigida; the companion species is Potentilla acaulis and others. According to the grazing pressure, the following four grazing gradients were identified from the dwellings of the herdsmen to the enclosure site: (1) no grazing (CK enclosure site); (2) light grazing (LG); (3) moderate grazing (MG); (4) heavy grazing (HG). Young leaves of each Stipa grandis were collected during the growing season. The results showed that the Stipa grandis showed abundant genetic diversity despite the fact that certain polymorphic loci were lost; at the same time, new polymorphic loci emerged when grazing pressure increased; a total of 10 primers were used, and 74 bands were produced in total, of which 65 bands were polymorphic; the total percentage of polymorphism was 89%; the percentage of polymorphic loci of the Stipa grandis population decreased with the increase of grazing pressure; the percentage of polymorphic loci was 62.2% in the no-grazing (CK) population, 64.9% in the light-grazing (LG) population, 58.1% in the moderate-grazing (MG) population, and 56.8% in the heavy-grazing (HG) population; the genetic diversity of the population in the descending order using the Shannon's information index is as follows: (1) light grazing (0.3486); (2) no grazing (0.3339); (3) moderate grazing (0.3249); (4) heavy grazing (0.2735) with the same distributional pattern as the Nei's genetic diversity index. The test showed the following: As the grazing pressures increased, the change of genetic diversity decreased; the genetic differentiation coefficient among the population (Gst) was 0.1984, which showed the presence of small partial genetic diversity (19.8%) among populations; gene flow (Nm*) between primers varied from 0.9806 to 3.4463, and the mean gene flow (Nm*) was 2.0202; the UPGMA cluster figure that was constructed on the basis of the genetic distance matrix showed four populations that became genetically closer at each step: (1) The first group was the moderate-grazing (MG) population and the heavy- grazing (HG) population; (2) The second group consisted of the no-grazing (CK) population and the light-grazing (LG) population; (3) The two groups gathered together.     

Examining the genetic diversity of Stipa grandis under various grazing pressures

The Stipa grandis steppe in the Inner Mongolia Autonomous Region occupies an area of 2798081 hm2. On the basis of the genetic variation, it was found that its adaptability to the environmental conditions under grazing pressure was significant. Using the Inter-Simple Sequence Repeat (ISSR) procedure, the changes to the genetic diversity of the Stipa grandis population under different grazing pressures were observed. Plant samples were collected from a series of grazing gradients of the Stipa grandis steppe in Dalinuoer National Nature Reserve in the Inner Mongolia (located at 116°38′–116°41′E and 43°25′–43°27′N.), which has the following vegetation types in abundance: Leymus chinensis is the constructive species; the dominant species include Stipa grandis, Cleistogenes squarrosa, and Artemisia frigida; the companion species is Potentilla acaulis and others. According to the grazing pressure, the following four grazing gradients were identified from the dwellings of the herdsmen to the enclosure site: (1) no grazing (CK enclosure site); (2) light grazing (LG); (3) moderate grazing (MG); (4) heavy grazing (HG). Young leaves of each Stipa grandis were collected during the growing season. The results showed that the Stipa grandis showed abundant genetic diversity despite the fact that certain polymorphic loci were lost; at the same time, new polymorphic loci emerged when grazing pressure increased; a total of 10 primers were used, and 74 bands were produced in total, of which 65 bands were polymorphic; the total percentage of polymorphism was 89%; the percentage of polymorphic loci of the Stipa grandis population decreased with the increase of grazing pressure; the percentage of polymorphic loci was 62.2% in the no-grazing (CK) population, 64.9% in the light-grazing (LG) population, 58.1% in the moderate-grazing (MG) population, and 56.8% in the heavy-grazing (HG) population; the genetic diversity of the population in the descending order using the Shannon's information index is as follows: (1) light grazing (0.3486); (2) no grazing (0.3339); (3) moderate grazing (0.3249); (4) heavy grazing (0.2735) with the same distributional pattern as the Nei's genetic diversity index. The test showed the following: As the grazing pressures increased, the change of genetic diversity decreased; the genetic differentiation coefficient among the population (Gst) was 0.1984, which showed the presence of small partial genetic diversity (19.8%) among populations; gene flow (Nm*) between primers varied from 0.9806 to 3.4463, and the mean gene flow (Nm*) was 2.0202; the UPGMA cluster figure that was constructed on the basis of the genetic distance matrix showed four populations that became genetically closer at each step: (1) The first group was the moderate-grazing (MG) population and the heavy- grazing (HG) population; (2) The second group consisted of the no-grazing (CK) population and the light-grazing (LG) population; (3) The two groups gathered together.     

Temporal changes in SSR allelic diversity of major rice cultivars in China

Forty simple sequence repeats （SSRs） were used to assess the changes of diversity in 310 major Chinese rice cultivars grown during the 1950s-1990s. Of the 40 SSR loci, 39 were polymorphic. A total of 221 alleles were detected with an average of 5.7 alleles per locus （Na）. The Nei＇s genetic diversity index （He） varied drastically among the loci （0.207 to 0.874, mean 0.625）. Comparing the temporal changes in Na and He, the cultivars from the 1950s had more alleles and higher He scores than the cultivars from the other four decades. Analysis of molecular variance （AMOVA） indicated that the genetic differentiation among the five decades was not significant in the whole set, but significant within indica and japonica. More changes among the decades were revealed in indica cultivars than in japonica cultivars. Some alleles had been lost in current rice cultivars in the 1990s, occurring more frequently in indica. These results suggest that more elite alien genetic resources should be explored to widen the genetic backgrounds of rice cultivars currently grown in China.     

Analysis of genetic diversity and phylogenetic relationships among red jungle fowls and Chinese domestic fowls

Genetic diversity and phylogenetic relationships among 568 individuals of two red jungle fowl subspe- cies (Gallus gallus spadiceus in China and Gallus gallus gallus in Thailand) and 14 Chinese domestic chicken breeds were evaluated with 29 microstaellite loci, the genetic variability within population and genetic differentiation among population were estimated, and then genetic diversity and phylogenetic relationships were analyzed among red jungle fowls and Chinese domestic fowls. A total of 286 alleles were detected in 16 population with 29 microsatellite markers and the average number of the alleles observed in 29 microsatellite loci was 9.86±6.36. The overall expected heterozygosity of all population was 0.6708±0.0251, and the number of population deviated from Hardy-Weinberg equilibrium per locus ranged from 0 to 7. In the whole population, the average of genetic differentiation among population, measured as FST value, was 16.7% (P<0.001), and all loci contributed significantly (P<0.001) to this differentiation. It can also be seen that the deficit of heterozygotes was very high (0.015) (P<0.01). Reynolds' distance values varied between 0.036 (Xiaoshan chicken-Luyuan chicken pair) and 0.330 (G. gallus gallus-Gushi chicken pair). The Nm value ranged from 0.533 (between G. gallus gallus and Gushi chicken) to 5.833 (between Xiaoshan chicken and Luyuan chicken). An unrooted consensus tree was constructed using the neighbour-joining method and the Reynolds' genetic distance. The heavy-body sized chicken breeds, Luyuan chicken, Xiaoshan chicken, Beijing Fatty chicken, Henan Game chicken, Huainan Partridge and Langshan chicken formed one branch, and it had a close genetic relationship between Xiaoshan chicken-Luyuan chicken pair and Chahua chicken-Tibetan chicken pair. Chahua chicken and Tibetan chicken had closer genetic relationship with these two subspecies of red jungle fowl than other domestic chicken breeds. G. gallus spadiceus showed closer phylogenetic relationship with Chinese domestic chicken breeds than G. gallus gallus. All 29 microstaellite loci in this study showed high levels of polymorphism and significant genetic differentiation was observed among two subspecies of red jungle fowl and 14 Chinese domestic chicken breeds. The evolutional dendrogram is as follows: evolutional breeds→primitive breeds (Chahua chicken and Tibetan)→red jungle fowl in China (G. gallus spadiceus)→red jungle fowl in Thailand (G. gallus gallus). The results supported the theory that the domestic fowls might originate from different subspecies of red jungle fowl and Chinese domestic fowls had independent origin.     

RAPD diversity of Stipa grandis populations and its relationship with some ecological factors

The genetic diversity of Stipa grandis P.Smirn and its relationship with the climatic variables were studied using the RAPD technique for 90 genes from five natural populations sampled in the Xilingol steppe, China. Sixteen oligonucleotides screened from 100 random primers were used to amplify 310 trackable RAPD loci, which were all polymorphic. By analyzing the RAPD data using POPGENE software, different geographic S. grandis populations were studied, which indicated a high level of genetic diversity, and the maximum variation was observed within the populations with a 28% variation observed among the populations. Using Pearson correlation analysis, significant (P < 0.05) or highly significant (P < 0.01) relationships were found between gene diversity indexes and temperature factors (≥10°C cumulative temperature in a year, annual mean temperature and mean temperature in January). Mantel's tests showed that there was no significant correlation between Nei's unbiased genetic distance and the geographic distance of S. grandis populations (r = 0.184, P = 0.261). However, there were significant or highly significant correlations between Nei's genetic distance and the several climatic divergences in pairwise S. grandis populations. All results indicated that natural selection resulting from variations in water and temperature was responsible for the adaptive eco-geographical differentiation indicated by the RAPD markers of different S. grandis populations, and that immigration and gene drift did not play an important role in affecting the differentiation of S. grandis populations.     

A Unique Protease Cleavage Site Predicted in the Spike Protein of the Novel Pneumonia Coronavirus (2019-nCoV) Potentially Related to Viral Transmissibility

正Dear Editor,In December 2019, a novel human coronavirus caused an epidemic of severe pneumonia(Coronavirus Disease 2019,COVID-19) in Wuhan, Hubei, China(Wu et al. 2020; Zhu et al. 2020). So far, this virus has spread to all areas of China and even to other countries. The epidemic has caused 67,102 confirmed infections with 1526 fatal cases     

Curcuminoids as inhibitors of thioredoxin reductase: A receptor based pharmacophore study with distance mapping of the active site

Curcumin is the yellow pigment of turmeric that interacts irreversibly forming an adduct with thioredoxin reductase (TrxR), an enzyme responsible for redox control of cell and defence against oxidative stress. Docking at both the active sites of TrxR was performed to compare the potency of three naturally occurring curcuminoids, namely curcumin, demethoxy curcumin and bis-demethoxy curcumin. Results show that active sites of TrxR occur at the junction of E and F chains. Volume and area of both cavities is predicted. It has been concluded by distance mapping of the most active conformations that Se atom of catalytic residue SeCYS498, is at a distance of 3.56 from C13 of demethoxy curcumin at the E chain active site, whereas C13 carbon atom forms adduct with Se atom of SeCys 498. We report that at least one methoxy group in curcuminoids is necessary for interation with catalytic residues of thioredoxin. Pharmacophore of both active sites of the TrxR receptor for curcumin and demethoxy curcumin molecules has been drawn and proposed for design and synthesis of most probable potent antiproliferative synthetic drugs.     

The structure, reproduction and taxonomy of Vidalia and Osmundaria (Rhodophyta, Rhodomelaceae)

Comprises species occurring mostly in subtidal habitats in tropical, subtropical and warm-temperate areas of the world. An analysis of the type species, V. spiralis (Sonder) Lamouroux ex J. Agardh, a species from Australia, establishes basic characters for distinguishing species in the genus. These characters are (1) branching patterns of thalli, (2) flat blades that may be spiralled on their axis, (3) width of the blade, (4) primary or secondary derivation of sterile and fertile branchlets and (5) position of sterile and fertile branchlets on the thalli. Application of the latter two characters provides an important basic method for separation of species into three major groups. Osmundaria , a genus known only in southern Australia, was studied in relation to Vidalia , and its separation from the Vidalia assemblage is not accepted. Species of Vidalia therefore are transferred to the older genus name, Osmundaria. Two new species, Osmundaria papenfussii and Osmundaria oliveae are described from Natal. Confusion in the usage of the epithet, Vidalia fimbriala Brown ex Turner has been clarified, and Vidalia gregaria Falkenberg, described as an epiphyte on Osmundaria pro/ifera Lamouroux, is revealed to be young branches of the host, Osmundaria prolifera.     

New or rare chromosome counts in Artemisia L. (Asteraceae, Anthemideae) and related genera from Kazakhstan

Fifteen chromosome counts of six Artemisia taxa and one species of each of the genera Brachanthemum, Hippolytia, Kaschgaria, Lepidolopsis and Turaniphytum are reported from Kazakhstan. Three of them are new reports, two are not consistent with previous counts and the remainder are confirmations of very scarce (one to four) earlier records. All the populations studied have the same basic chromosome number, x = 9, with ploidy levels ranging from 2x to 6x. Some correlations between ploidy level, morphological characters and distribution are noted.     

肝癌中HBV和HCV基因和抗原的分布及意义

采用原位分子杂交方法检测HCV RNA及HBV X基因;采用免疫组织化学方法研究HCV核心抗原,非结构区C33c抗原及HBxAg在肝细胞肝癌中的定位及分布.结果表明(1)HCV RNA、HBV X基因在肝细胞肝癌组织检出率分别为40%(55/136)和82%(112/136).HCV RNA定位于癌细胞的胞浆内,阳性细胞呈散在、灶状及弥漫分布三种形式;HBV X基因在肝癌细胞中的分布呈胞浆型、核型及核浆型,阳性细胞也呈上述三种分布形式;(2)HCV C33c抗原、核心抗原在肝细胞肝癌中的阳性率为81%(133/164)及86%(141/164).C33c抗原定位于癌细胞及肝细胞的胞浆内;核心抗原既定位于癌细胞核中,又可定位于胞浆中.C33c抗原阳性细胞以灶状分布为主;而核心抗原阳性细     

Comparative morphology of the carpel in the Liliaceae: Hewardieae, Petrosavieae, and Tricyrteae

The young pistils in the melanthioid tribes, Hewardieae, Petrosavieae and Tricyrteae, are uniformly tricarpellate and syncarpous. They lack raphide idioblasts. All are multiovulate, with bitegmic ovules. The Petrosavieae are marked by the presence of septal glands and incomplete syncarpy. Tepals and stamens adhere to the ovary in the Hewardieae and the Petrosavieae but not in the Tricyrteae. Two vascular bundles occur in the stamens of the Hewartlieae and Tricyrtis latifolia. Ventral bundles in the upper part of the ovary of the Hewardieae are continuous with compound septal bundles and placental bundles in the lower part. Putative ventral bundles occur in the alternate position in the Tricyrteae and putative placental bundles in the opposite. position in the Petrosavieae. The dichtomously branched stigma in each carpel of the Tricyrteae is supplied by a bifurcated dorsal bundle.