灰毡毛忍冬主栽品种的遗传多样性及其亲缘关系分析

目的:研究灰毡毛忍冬主栽品种的遗传多样性及其亲缘关系.方法:以灰毡毛忍冬的5个主栽品种为试材,采用ISSR和SRAP分子标记技术,利用Treeconw软件分析处理数据,UPGMA法聚类,构建亲缘关系系统图.结果:20条ISSR引物共得到186条扩增条带,其中有103条呈现多态性,占54.63％,遗传距离0.058 4～0.230 8,平均值为0.1902.58个SRAP引物组合共得到591条扩增条带,其中有347条呈现多态性,占55.46％,遗传距离在0.1071～0.261 1,平均值为0.212 2.2种标记均表明灰毡毛忍冬主栽品种的遗传多样性仅居中等水平.2种标记系统得到了相似但并不完全相同的聚类图.结论:灰毡毛忍冬主栽品种有中等水平的遗传多样性,ISSR与SRAP标记均适用于其遗传多样性的分析.     

ISSR分析3种类型黄连的遗传多样性和遗传结构

目的 研究3种类型黄连的遗传多样性和遗传结构.方法 对3种类型黄连的90个单株进行ISSR分析,运用POPGENE 1.31软件计算相关参数.结果 22个引物共检测到164个位点,其中108个为多态位点;黄连3种类型具有较丰富的遗传多样性,在物种水平上,多态位点百分率(PPB)为65.85％,有效等位基因数(Ne)为1.229 8,Nei's基因多样度指数(H)为0.1440,物种水平Shannon's多样性信息指数(Hsp)为0.2302;在类型水平上,PPB为55.08％,Ne为1.2189,H为0.1360,类型水平Shannon’s多样性信息指数(Hpop)为0.2151.Nei's基因多样性指数计算的类型间遗传分化系数与Shannon’s类型分化系数分别为0.0561和0.0652,均说明大部分遗传变异存在于类型内;ISSR标记检测到类型间存在着广泛的基因流(Nm=8.4054),遗传分化程度较低;两两类型间的Nei's遗传一致度(I)的范围为0.9831～0.9897;根据Nei's遗传距离进行各类型间的UPGMA聚类,基于ISSR分子标记的聚类结果与形态分类基本一致.结论 3种类型的黄连遗传多样性较高,为新品种的培育提供了丰富的遗传基础.     

不同重楼变种间内生真菌群落多样性差异及生物标记物初探

目的通过对不同变种重楼内生真菌群落多样性研究及生物标记物分析,为中药材重楼多基源质量等同性及鉴别溯源技术的开发研究奠定基础。方法采用Illmina Hiseq高通量测序技术对3个变种的重楼内生真菌群落基因进行扩增子序列测定,同时对菌群多样性、真菌群落差异进行生物信息学分析。结果对不同变种重楼内生真菌进行多样性分析结果显示,七叶一枝花Paris polyphylla Smith var. chinensis (Franch.) Hara、长药隔重楼Paris polyphylla Sm. var. thibetica (Franch.) Hara、具柄重楼Paris fargesii Franch. var. petiolate (Baker ex C. H. Wright) Wang et Tang三者的内生真菌的α多样性存在差异,但β多样性无显著性差异,具柄重楼中特有的OTU仅为0.27%。真菌群落注释结果表明,3个变种分别注释到6个相同的门,但组成比率不同。另外,通过LEfSe分析,初步探索了3个变种的生物标记物差异,七叶一枝花中Rhizophagus irregularis与其他2变种有显著性差异。结论 3个变种重楼内生真菌群落β多样性变化不显著,但组成比率有很大的差异性。该研究结果中药材重楼多基源质量等同性及鉴别溯源技术的开发研究提供研究基础。     

白芷种质资源遗传多样性的ISSR研究

目的 应用ISSR分子标记技术分析中药白芷的遗传多样性。方法 对4大类商品白芷及白芷近缘野生种兴安白芷共20个居群的白芷种质进行ISSR分析,利用NTSYS2.1e软件分析遗传相似系数,UPGMA方法聚类,构建亲缘关系系统图。结果 9条引物共得到97条扩增条带,其中多态性条带37条,占38%;20个居群的样品聚为两大类。结论 不同产地栽培白芷的遗传多样性水平较低,种质间的亲缘关系较近;而兴安白芷与4大类商品白芷存在遗传差异。     

多花黄精内生菌群落结构多样性及其与有效成分含量相关性研究

目的 通过分析多花黄精Polygonatum cyrtonema内生菌菌群结构多样性及其与主要有效成分含量之间的相关性,探讨多花黄精内生菌对其药材品质的影响.方法 收集不同产地多花黄精样品,采用高通量测序对内生菌群落结构进行分析,并测定多糖、总皂苷等有效成分含量,通过双因素关联分析探究菌群多样性及其与有效成分之间的关系...     

Relationship of prevalence of non-insulin-dependent diabetes mellitus to Amerindian admixture in the Mexican Americans of San Antonio, Texas

A genetic and epidemiological survey of non-insulin-dependent diabetes mellitus (NIDDM) was conducted among the Mexican Americans residing in three socioeconomically distinct areas of San Antonio, Texas: a low socioeconomic (SES) traditional area (barrio), a middle SES, ethnically balanced area (transitional), and a high SES, predominantly Anglo area (suburb). Seventeen polymorphic markers were used to relate the prevalences of NIDDM with the extent of Amerindian ancestry of 1,237 Mexican Americans of these three residential areas. While only the RH and haptoglobin loci showed evidence of association with NIDDM, an admixture analysis of the combined allele frequency data revealed a pattern of decreasing NIDDM prevalence with increasing socioeconomic status (as approximated by neighborhood of residence) and a parallel decrease in Amerindian ancestry. The rank-order correlation between NIDDM prevalence and Amerindian admixture is 0.943 (P less than .001) for the crude prevalence rate and 0.829 (P less than .02) for the age-adjusted rate. Nested gene diversity analysis revealed that the heterogeneity of allele frequencies is more pronounced when individuals were classified by their NIDDM disease status as compared to the classification by neighborhood. Estimation of Amerindian ancestry of each individual did not reveal any significant change in the shape of the distributions of individual admixture proportions in diabetics as compared to the controls. Nevertheless, the results suggest that genetic factors partially explain the differences in NIDDM prevalence observed between the Mexican American and Anglo populations in the southwestern United States.     

变异链球菌F-ATPase亚基β基因多态性及表达研究

目的研究变异链球菌（Streptococcus燃，简称变链菌）临床分离株耐酸因子F-AT—Pase亚基B结构基因uncD的遗传多态性和mRNA表达水平差异，探讨其与细菌耐酸力的关系。方法实验株包括18株高耐酸和20株低耐酸变链菌临床株，以特异引物从细菌组DNA扩增uncD，行限制性内切酶长度多态性分析（RFLP）和测序比较；应用半定量RT-PCR两步法和凝胶成像系统定量软件，对20株不同基因型和不同耐酸力变链菌uncD基因的mRNA表达水平进行评价和比较。结果AluI—RFLP产生A、B基因型，测序证实导致多态出现的基因变异不在uncD的功能区和催化结构域；这两种基因型在不同耐酸力菌株的分布不同（P〈0．05），高耐酸性菌株中A型基因uncD的检出高于低耐酸力菌株。不同耐酸力菌株uncD的mRNA表达水平不同（P〈0．05），但A、B两基因型菌株uncD的mRNA表达差异没有统计学意义（P〉0．05）。结论F-ATPase的β亚基基因具有明显的遗传多态性，基因型和mRNA表达水平的多态性与菌株的耐酸力有一定的关系，虽然β亚基基因功能区高度保守，但在酸耐受适应中，仍表现为F—ATPase较活跃上调的亚基基因。     

The analysis of codon bias of foot-and-mouth disease virus and the adaptation of this virus to the hosts

The synonymous codon usage patterns of open reading frame (ORF) in foot-and-mouth disease virus (FMDV), the similarity degree of the synonymous codon usage between this virus and the hosts and the genetic diversities of FMDV ORFs and the viral functional genes in viral ORF have been investigated by some simply statistical analyses. As for the synonymous codon usage of FMDV, some over-represented and under-represented codons have a similar usage in all seven serotypes. 33 out of 59 synonymous codons are similarly selected between FMDV ORF and the hosts. It is interesting that the overall codon usage pattern of the strains of serotype O isolated from pigs is different with that of strains of the same serotype isolated from non-pig origin, suggesting that the factor of pigs takes part in the formation of codon usage of FMDV serotype O. Projection of codon usage of nine viral functional genes onto the two-dimensional map represents that even though viral functional genes have various genetic diversities and each gene is not separated from each other based on seven serotypes, the codon usage patterns of VP2, 2C, 3A, 3C and 3D genes belonging to serotype O strains isolated from pigs are different with those of the same serotype strains from non-pig origin. In addition, the interaction between GC₁₂% and GC₃% of viral functional genes indicates that the codon usage patterns of VP1, VP2, 2B, 3A, 3C and 3D genes are influenced by mutation pressure from virus. Furthermore, distribution plots of ENC value vs. GC₃% for viral function genes indicate that mutation pressure is not the only factor in the formation of codon usage of these genes. The results suggest that both the mutation pressure from virus and the translation selection from the hosts take part in the evolution process of viral functional genes of FMDV.     

Multilocus sequence typing of Enterocytozoon bieneusi: Lack of geographic segregation and existence of genetically isolated sub-populations

The population structure of Enterocytozoon bieneusi was examined by multilocus sequence typing (MLST) of 64 specimens from AIDS patients in Peru, Nigeria, and India and five specimens from captive baboons in Kenya using a combination of the ribosomal internal transcribed spacer (ITS) and four microsatellite and minisatellite markers. Parasites in different geographic locations (Peru, India, and Nigeria) all had strong and significant linkage disequilibrium (LD) and only limited recombination, indicative of a clonal population structure in E. bieneusi from each location. When isolates of various geographical areas were treated as a single population, phylogenetic analysis and substructural analysis using STRUCTURE found no evidence for the existence of geographically segregated sub-populations. Nevertheless, both analyses revealed the presence of two major genetically isolated groups of E. bieneusi: one (sub-population 1) contained all isolates of the anthroponotic ITS genotype A, whereas the other (sub-population 2) harbored isolates of multiple ITS genotypes with zoonotic potential. This was also supported by F_ST analysis. The measurement of LD and recombination rates indicated that sub-population 2 had a clonal population structure, whereas sub-population 1 had an epidemic population structure. The data confirmed the existence of genetic sub-populations in E. bieneusi that may be transmitted differently in humans.     

Whole-genome,deep pyrosequencing analysis of a duck influenza A virus evolution in swine cells

We studied the sub-population level evolution of a duck influenza A virus isolate during passage in swine tracheal cells. The complete genomes of the A/mallard/Netherlands/10-Nmkt/1999 strain and its swine cell-passaged descendent were analysed by 454 pyrosequencing with coverage depth ranging from several hundred to several thousand reads at any point. This allowed characterization of defined minority sub-populations of gene segments 2, 3, 4, 5, 7, and 8 present in the original isolate. These minority sub-populations ranged between 9.5% (for segment 2) and 46% (for segment 4) of their respective gene segments in the parental stock. They were likely contributed by one or more viruses circulating within the same area, at the same period and in the same or a sympatric host species. The minority sub-populations of segments 3, 4, and 5 became extinct upon viral passage in swine cells, whereas the minority sub-populations of segments 2, 7 and 8 completely replaced their majority counterparts. The swine cell-passaged virus was therefore a three-segment reassortant and also harboured point mutations in segments 3 and 4. The passaged virus was more homogenous than the parental stock, with only 17 minority single nucleotide polymorphisms present above 5% frequency across the whole genome. Though limited here to one sample, this deep sequencing approach highlights the evolutionary versatility of influenza viruses whereby they exploit their genetic diversity, predilection for mixed infection and reassortment to adapt to a new host environmental niche.