30个祖先信息位点的筛选及应用

摘要：目的 筛选一组祖先信息SNPs位点（AIMs,Ancestry Informative Markers）,构建复合检测体系,用于东亚、欧洲和非洲人群遗传成分描述及个体种族来源推断。方法 以HapMap数据库9个人群的658份样本的分型数据为基础,从30个表型相关基因总共282个SNPs位点中筛选出30个AIMs位点,基于微测序-通用芯片技术构建复合检测体系,并建立人群等位基因频率数据库。使用这组位点分析HapMap数据库中658份人群样本,初步验证位点的区分效能;然后,使用研究构建的体系检验收集的5个人群194份无关个体的DNA样本。最后,通过Structure软件分析获取人群的成分构成以及个体的遗传成分,对个体样本进行种族来源推断。 结果 筛选的30个AIMs位点符合哈迪温伯格平衡（p>0.01）,位点之间没有连锁（r2<0.1）, 658份HapMap数据库样本和194份实验样本的祖先成分分析结果与已知结果完全一致。 结论 本文筛选并建立的30个AIMs位点复合检测体系,能够有效实现东亚、欧洲、非洲人群及混合人群的成分构成和个体遗传成分的分析,有效控制遗传连锁分析中由于人群分层现象带来的误差,也可以用于法医DNA检验中个体祖先来源推断。     

Signatures of hybridization and speciation in genomic patterns of ancestry*

Genomes sampled from hybrid zones between nascent species provide important clues into the speciation process. With advances in genome sequencing and single nucleotide polymorphism (SNP) genotyping, it is now feasible to measure variation in gene flow with high genomic resolution. This progress motivates the development of conceptual and analytical frameworks for hybrid zones that complement well‐established cline approaches. We extend the perspective that genomic distributions of ancestry are sensitive indicators of hybridization history. We use simulations to examine the behavior of the number of ancestry junctions—a simple summary of genomic patterns—in hybrid zones under increasingly realistic scenarios. Neutral simulations revealed that ancestry junction number is shaped by population structure, migration rate, and population size. Modeling multiple genetic architectures of hybrid dysfunction, with an emphasis on epistatic hybrid incompatibilities, showed that selection reduces junction number near loci that confer reproductive barriers. The magnitude of this signature was affected by the form of selection, dominance, and genomic location (autosome vs. sex chromosome) of incompatible loci. Our results suggest that researchers can identify loci involved in reproductive isolation by scanning hybrid genomes for local reductions in junction number. We outline necessary directions for future theory and method development to realize this goal.     

Functional analysis of the yeast genome

Just as Saccharomyces cerevisiae itself provides a model for so many processes essential to eukaryotic life, we anticipate that the methods and the mindset that have moved yeast biological research "beyond the genome" provide a prototype for making similar progress in other organisms. In this review I describe the experimental processes, results and utility of the current large-scale experimental approaches that use genomic data to provide a functional analysis of the yeast genome. Electronic Publication     

Isochores,GC3 and mutation biases in the human genome

In this work we re-examined the hypothesis that the variation in GC content in the human genome is due to different regional mutational biases. For this purpose we inferred the mutational pattern by using mutation databases that are available for many genes associated with human genetic diseases. The assumption of this approach is that such mutations reflect the actual frequency distribution of mutations as they arise in the population. Four classes of genes, classified according to their GC₃ level, were included in this study: GC₃-poor genes (GC₃<45%), genes with intermediate GC₃ content (45%3<60%), GC₃-rich genes (60%3<75%) and very GC₃-rich genes (GC₃>75%). Our results show that most genes are under AT mutational biases, with very little variation compared to the expectations of neutral GC level. It is noteworthy that the mutational patterns in the GC₃-rich genes do not appear to account for their GC₃-richness. Instead, GC₃-rich and very GC₃-rich genes exhibit patterns of mutations that yield expectations of neutral GC₃ content that are much lower than their actual GC₃.     

The distribution of surviving blocks of an ancestral genome

What is the chance that some part of a stretch of genome will survive? In a population of constant size, and with no selection, the probability of survival of some part of a stretch of map length y < 1 approaches y/log(yt/2) for log(yt) > or = 1. Thus, the whole genome is certain to be lost, but the rate of loss is extremely slow. This solution extends to give the whole distribution of surviving block sizes as a function of time. We show that the expected number of blocks at time t is 1+yt and give expressions for the moments of the number of blocks and the total amount of genome that survives for a given time. The solution is based on a branching process and assumes complete interference between crossovers, so that each descendant carries only a single block of ancestral material. We consider cases where most individuals carry multiple blocks, either because there are multiple crossovers in a long genetic map, or because enough time has passed that most individuals in the population are related to each other. For species such as ours, which have a long genetic map, the genome of any individual which leaves descendants (approximately 80% of the population for a Poisson offspring number with mean two) is likely to persist for an extremely long time, in the form of a few short blocks of genome.     

The promise of a protist: the Dictyostelium genome project

The genome of Dictyostelium discoideum is being sequenced by an international consortium and is scheduled for completion in the next few years. The sequence will accelerate research into a number of phenomena carried out by these versatile soil amoebae, providing insight into analogous processes that operate in a wide range of eukaryotes. These include the dynamic regulation of the cytoskeleton during chemotaxis, intercellular communication during multicellular development and the intracellular growth of bacterial pathogens. The current state of the genome project is summarized and the challenges of sequencing a genome with unusually low guanine and cytosine content and with a bimodal base composition distribution are discussed. The prospects for functional analyses at the genomic scale are also considered. Electronic Publication     

HLA-E, HLA-F, and HLA-G polymorphism: genomic sequence defines haplotype structure and variation spanning the nonclassical class I genes

Despite several studies that defined the polymorphism of the nonclassical human leukocyte antigen-E (HLA-E), HLA-F, and HLA-G genes, most polymorphisms thus far examined in correlative studies were derived from the coding sequences of these genes. In addition, some discrepancies and ambiguities in the available data have persisted in current databases. To expand the data available and to resolve some of the discrepant data, we have defined protocols that allow for the amplification of 6 to 7 kb of contiguous genomic sequence for each gene, including all of the coding and intron sequences, approximately 2 kb of 5' flanking promoter sequence, and 1 kb of 3' flanking sequence. Using long-range polymerase chain reaction (PCR) protocols, generating either one or two PCR products depending on the locus, amplified genomic DNA was directly sequenced to completion using a set of about 30 primers over each locus to yield contiguous sequence data from both strands. Using this approach, we sequenced 33 genomic DNAs, from Asian, African American, and Caucasian samples. The results of this analysis confirmed several previously reported coding sequence variants, identified several new allelic variants, and also defined extensive variation in intron and flanking sequences. It was possible to construct haplotype maps and to identify tagging single nucleotide polymorphisms that can be used to detect the composite variation spanning all three genes.     

Looking back, looking beyond: revisiting the ethics of genome generation

This paper will explore some of the ethical imperatives that have shaped strategic and policy frameworks for the use of new genetic technologies and how these play a role in shaping the nature of research and changing attitudes; with an attempt to conceptualize some theories of genetic determinism. I analyse why there is a need to put bioethical principles within a theoretical framework in the context of new technologies, and how, by doing so, their practical applications for agriculture, environment medicine and health care can be legitimized. There are several theories in favour of and against the use of genetic technologies that focus on genes and their role in our existence. In particular the theory of geneticisation is commonly debated. It highlights the conflicting interests of science, society and industry in harnessing genetic knowledge when the use of such knowledge could challenge ethical principles. Critics call it a ‘reductionist’ approach, based on arguments that are narrowed down to genes, often ignoring other factors including biological, social and moral ones. A parallel theory is that there is something special about genes, and it is this “genetic exceptionalism” that creates hopes and myths. Either way, the challenging task is to develop a common ground for understanding the importance of ethical sensitivities. As research agendas become more complex, ethical paradigms will need to be more influential. New principles are needed to answer the complexities of ethical issues as complex technologies develop. This paper reflects on global ethical principles and the tensions between ethical principles in legitimizing genetic technologies at the social and governance level.     

Comparison of different imputation methods from low- to high-density panels using Chinese Holstein cattle

Imputation of high-density genotypes from low- or medium-density platforms is a promising way to enhance the efficiency of whole-genome selection programs at low cost. In this study, we compared the efficiency of three widely used imputation algorithms (fastPHASE, BEAGLE and findhap) using Chinese Holstein cattle with Illumina BovineSNP50 genotypes. A total of 2108 cattle were randomly divided into a reference population and a test population to evaluate the influence of the reference population size. Three bovine chromosomes, BTA1, 16 and 28, were used to represent large, medium and small chromosome size, respectively. We simulated different scenarios by randomly masking 20%, 40%, 80% and 95% single-nucleotide polymorphisms (SNPs) on each chromosome in the test population to mimic different SNP density panels. Illumina Bovine3K and Illumina BovineLD (6909 SNPs) information was also used. We found that the three methods showed comparable accuracy when the proportion of masked SNPs was low. However, the difference became larger when more SNPs were masked. BEAGLE performed the best and was most robust with imputation accuracies >90% in almost all situations. fastPHASE was affected by the proportion of masked SNPs, especially when the masked SNP rate was high. findhap ran the fastest, whereas its accuracies were lower than those of BEAGLE but higher than those of fastPHASE. In addition, enlarging the reference population improved the imputation accuracy for BEAGLE and findhap, but did not affect fastPHASE. Considering imputation accuracy and computational requirements, BEAGLE has been found to be more reliable for imputing genotypes from low- to high-density genotyping platforms.     

Evaluating the effectiveness of landscape metrics in quantifying spatial patterns

The effectiveness of landscape metrics in quantifying spatial patterns is fundamental to metrics assessment. Setting 36 simulated landscapes as sample space and focusing on 23 widely used landscape metrics, their effectiveness in quantifying the complexity of such spatial pattern components as number of patch types, area ratio of patch types and patch aggregation level, were analyzed with the application of the multivariate linear regression analysis method. The results showed that all the metrics were effective in quantifying a certain component of spatial patterns, and proved that what the metrics quantified were not a single component but the complexity of several components of spatial patterns. The study also showed a distinct inconsistency between the performances of landscape metrics in simulated landscapes and the real urban landscape of Shenzhen, China. It was suggested that the inconsistency resulted from the difference of the correlation among spatial pattern components between simulated and real landscapes. After considering the very difference, the changes of all 23 landscape metrics against changing of number of patch types in simulated landscapes were consistent with those in the real landscape. The phenomenon was deduced as the sign effect of spatial pattern components on landscape metrics, which was of great significance to the proper use of landscape metrics.     

Haplotypes of single cancer driver genes and their local ancestry in a highly admixed long-lived population of Northeast Brazil

Admixed populations have not been examined in detail in cancer genetic studies. Here, we inferred the local ancestry of cancer-associated single nucleotide polymorphisms (SNPs) and haplotypes of a highly admixed Brazilian population. SNP array was used to genotype 73 unrelated individuals aged 80-102 years. Local ancestry inference was performed by merging genotyped regions with phase three data from the 1000 Genomes Project Consortium using RFmix. The average ancestry tract length was 9.12-81.71 megabases. Strong linkage disequilibrium was detected in 48 haplotypes containing 35 SNPs in 10 cancer driver genes. All together, 19 risk and eight protective alleles were identified in 23 out of 48 haplotypes. Homozygous individuals were mainly of European ancestry, whereas heterozygotes had at least one Native American and one African ancestry tract. Native-American ancestry for homozygous individuals with risk alleles for HNF1B, CDH1, and BRCA1 was inferred for the first time. Results indicated that analysis of SNP polymorphism in the present admixed population has a high potential to identify new ancestry-associated alleles and haplotypes that modify cancer susceptibility differentially in distinct human populations. Future case-control studies with populations with a complex history of admixture could help elucidate ancestry-associated biological differences in cancer incidence and therapeutic outcomes.     

Evaluating the accuracy of SHAPE-directed RNA secondary structure predictions

Recent advances in RNA structure determination include using data from high-throughput probing experiments to improve thermodynamic prediction accuracy. We evaluate the extent and nature of improvements in data-directed predictions for a diverse set of 16S/18S ribosomal sequences using a stochastic model of experimental SHAPE data. The average accuracy for 1000 data-directed predictions always improves over the original minimum free energy (MFE) structure. However, the amount of improvement varies with the sequence, exhibiting a correlation with MFE accuracy. Further analysis of this correlation shows that accurate MFE base pairs are typically preserved in a data-directed prediction, whereas inaccurate ones are not. Thus, the positive predictive value of common base pairs is consistently higher than the directed prediction accuracy. Finally, we confirm sequence dependencies in the directability of thermodynamic predictions and investigate the potential for greater accuracy improvements in the worst performing test sequence.     

Begin at the beginning: A BAC-end view of the passion fruit (Passiflora) genome

Background

The passion fruit (Passiflora edulis) is a tropical crop of economic importance both for juice production and consumption as fresh fruit. The juice is also used in concentrate blends that are consumed worldwide. However, very little is known about the genome of the species. Therefore, improving our understanding of passion fruit genomics is essential and to some degree a pre-requisite if its genetic resources are to be used more efficiently. In this study, we have constructed a large-insert BAC library and provided the first view on the structure and content of the passion fruit genome, using BAC-end sequence (BES) data as a major resource.

Results

The library consisted of 82,944 clones and its levels of organellar DNA were very low. The library represents six haploid genome equivalents, and the average insert size was 108 kb. To check its utility for gene isolation, successful macroarray screening experiments were carried out with probes complementary to eight Passiflora gene sequences available in public databases. BACs harbouring those genes were used in fluorescent in situ hybridizations and unique signals were detected for four BACs in three chromosomes (n = 9). Then, we explored 10,000 BES and we identified reads likely to contain repetitive mobile elements (19.6% of all BES), simple sequence repeats and putative proteins, and to estimate the GC content (~42%) of the reads. Around 9.6% of all BES were found to have high levels of similarity to plant genes and ontological terms were assigned to more than half of the sequences analysed (940). The vast majority of the top-hits made by our sequences were to Populus trichocarpa (24.8% of the total occurrences), Theobroma cacao (21.6%), Ricinus communis (14.3%), Vitis vinifera (6.5%) and Prunus persica (3.8%).

Conclusions

We generated the first large-insert library for a member of Passifloraceae. This BAC library provides a new resource for genetic and genomic studies, as well as it represents a valuable tool for future whole genome study. Remarkably, a number of BAC-end pair sequences could be mapped to intervals of the sequenced Arabidopsis thaliana, V. vinifera and P. trichocarpa chromosomes, and putative collinear microsyntenic regions were identified.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-816) contains supplementary material, which is available to authorized users.     

Tick genomics: the Ixodes genome project and beyond

Ticks and mites (subphylum Chelicerata; subclass Acari) include important pests of animals and plants worldwide. The Ixodes scapularis (black-legged tick) genome sequencing project marks the beginning of the genomics era for the field of acarology. This project is the first to sequence the genome of a blood-feeding tick vector of human disease and a member of the subphylum Chelicerata. Genome projects for other species of Acari are forthcoming and their genome sequences will likely feature significantly in the future of tick research. Parasitologists interested in advancing the field of tick genomics research will be faced with specific challenges. The development of genetic tools and resources, and the size and repetitive nature of tick genomes are important considerations. Innovative approaches may be required to sequence, assemble, annotate and analyse tick genomes. Overcoming these challenges will enable scientists to investigate the genes and genome organisation of this important group of arthropods and may ultimately lead to new solutions for control of ticks and tick-borne diseases.     

基因组测序分析广叶绣球菌SP-A菌株的遗传差异

广叶绣球菌Sparassis latifolia是一种极具开发潜力的食药用真菌,新品种的选育是其产业发展的迫切需求.绣球菌新品种'SP-A'是福建省农业科学院选育的绣球菌工厂化栽培新品种,但由于缺少基因组信息,严重阻碍了其相关基础研究.本研究利用高通量测序技术,对'SP-A'全基因组进行测序,获得了1.58Gb高质量测...     

多重耐药肺炎克雷伯菌噬菌体KP002的生物学特性及基因组学研究

以上海某些医院临床分离到的多重耐药肺炎克雷伯菌为宿主菌,从不同环境的污水中分离获得1株肺炎克雷伯菌噬菌体KP002。电子显微镜显示其为有尾噬菌体,头部直径约70nm,尾长约80nm,尾宽约20nm。对其生物学特性进行研究,结果显示此株噬菌体在pH 3~9及4~50℃的环境中具有较高活性;6min吸附率达95%以上;潜伏期为10min,爆发期为50min;裂解量为172pfu/cell。结果表明,该噬菌体对pH值和温度适应范围较宽。对其全基因组进行测序分析,结果显示其基因组为环状双链DNA,全长47 173bp,GC含量为48%。本研究筛选获得1株对pH值和温度适应范围较宽的耐药肺炎克雷伯菌烈性噬菌体KP002,为建立耐药肺炎克雷伯菌的噬菌体库以用于治疗临床多重耐药菌感染提供了新的思路。