The fine-scale structure of recombination rate variation in the human genome

The nature and scale of recombination rate variation are largely unknown for most species. In humans, pedigree analysis has documented variation at the chromosomal level, and sperm studies have identified specific hotspots in which crossing-over events cluster. To address whether this picture is representative of the genome as a whole, we have developed and validated a method for estimating recombination rates from patterns of genetic variation. From extensive single-nucleotide polymorphism surveys in European and African populations, we find evidence for extreme local rate variation spanning four orders in magnitude, in which 50% of all recombination events take place in less than 10% of the sequence. We demonstrate that recombination hotspots are a ubiquitous feature of the human genome, occurring on average every 200 kilobases or less, but recombination occurs preferentially outside genes.     

A fine-scale chimpanzee genetic map from population sequencing

To study the evolution of recombination rates in apes, we developed methodology to construct a fine-scale genetic map from high-throughput sequence data from 10 Western chimpanzees, Pan troglodytes verus. Compared to the human genetic map, broad-scale recombination rates tend to be conserved, but with exceptions, particularly in regions of chromosomal rearrangements and around the site of ancestral fusion in human chromosome 2. At fine scales, chimpanzee recombination is dominated by hotspots, which show no overlap with those of humans even though rates are similarly elevated around CpG islands and decreased within genes. The hotspot-specifying protein PRDM9 shows extensive variation among Western chimpanzees, and there is little evidence that any sequence motifs are enriched in hotspots. The contrasting locations of hotspots provide a natural experiment, which demonstrates the impact of recombination on base composition.     

High-resolution mapping of crossovers reveals extensive variation in fine-scale recombination patterns among humans

Recombination plays a crucial role in meiosis, ensuring the proper segregation of chromosomes. Recent linkage disequilibrium (LD) and sperm-typing studies suggest that recombination rates vary tremendously across the human genome, with most events occurring in narrow "hotspots." To examine variation in fine-scale recombination patterns among individuals, we used dense, genome-wide single-nucleotide polymorphism data collected in nuclear families to localize crossovers with high spatial resolution. This analysis revealed that overall recombination hotspot usage is similar in males and females, with individual hotspots often active in both sexes. Across the genome, roughly 60% of crossovers occurred in hotspots inferred from LD studies. Notably, however, we found extensive and heritable variation among both males and females in the proportion of crossovers occurring in these hotspots.     

Genetics. Motivating hotspots

Only recently have we begun to characterize fine-scale recombination rates in mammals. In her Perspective, Przeworski discusses the work by Myers et al. in which linkage disequilibrium data have been used to produce a high-resolution recombination map for most of the human genome. More than 25,000 putative hotspots have been identified, as well as the first motifs that appear to influence their intensity.     

Comparison of fine-scale recombination rates in humans and chimpanzees

We compared fine-scale recombination rates at orthologous loci in humans and chimpanzees by analyzing polymorphism data in both species. Strong statistical evidence for hotspots of recombination was obtained in both species. Despite approximately 99% identity at the level of DNA sequence, however, recombination hotspots were found rarely (if at all) at the same positions in the two species, and no correlation was observed in estimates of fine-scale recombination rates. Thus, local patterns of recombination rate have evolved rapidly, in a manner disproportionate to the change in DNA sequence.     

The structure of haplotype blocks in the human genome

Haplotype-based methods offer a powerful approach to disease gene mapping, based on the association between causal mutations and the ancestral haplotypes on which they arose. As part of The SNP Consortium Allele Frequency Projects, we characterized haplotype patterns across 51 autosomal regions (spanning 13 megabases of the human genome) in samples from Africa, Europe, and Asia. We show that the human genome can be parsed objectively into haplotype blocks: sizable regions over which there is little evidence for historical recombination and within which only a few common haplotypes are observed. The boundaries of blocks and specific haplotypes they contain are highly correlated across populations. We demonstrate that such haplotype frameworks provide substantial statistical power in association studies of common genetic variation across each region. Our results provide a foundation for the construction of a haplotype map of the human genome, facilitating comprehensive genetic association studies of human disease.     

A genetic map and recombination parameters of the human malaria parasite Plasmodium falciparum

Genetic investigations of malaria require a genome-wide, high-resolution linkage map of Plasmodium falciparum. A genetic cross was used to construct such a map from 901 markers that fall into 14 inferred linkage groups corresponding to the 14 nuclear chromosomes. Meiotic crossover activity in the genome proved high (17 kilobases per centimorgan) and notably uniform over chromosome length. Gene conversion events and spontaneous microsatellite length changes were evident in the inheritance data. The markers, map, and recombination parameters are facilitating genome sequence assembly, localization of determinants for such traits as virulence and drug resistance, and genetic studies of parasite field populations.     

CRISPR/Cas9系统在植物基因组定点编辑中的研究进展

当外源DNA通过转基因技术导入植物细胞后,会以同源重组或非同源重组两种不同的方式整合到基因组中,进而获得相应的目标性状。外源DNA与受体细胞序列相同或相近的位点发生重新组合,从而整合到受体细胞的染色体上称之为同源重组;当发生了DNA双链断裂的细胞为了避免DNA或染色体断裂而造成DNA降解或对生命力的影响,而强行将2个DNA断端彼此连接在一起时则为非同源重组。发生非同源重组的细胞其基因组常出现核苷酸片段的插入和/或缺失以及其他突变等多种情况,使得研究者无法得到精确控制的突变结果;而发生同源重组的细胞基因组序列通常不变,通过加入同源重组的供体DNA,可以实现对基因组的精确修饰和改造。由于在植物中产生自发同源重组的概率很低,对植物基因组进行精确修饰和改造非常困难,位点特异性核酸酶的出现和应用,大大提升了同源重组的效率,使基因组编辑变得更加高效和精确,从而使得对包括植物在内的任何物种进行基因组编辑都将成为可能。锌指核酸酶（ZFN）和TALE核酸酶（TALENs）是能够使DNA的靶位点产生DNA双链断裂进而实现基因组定点编辑的常用系统,但在具体应用中发现这两种系统存在着许多缺陷和不足,如脱靶效应、与基因组进行特异结合与染色体位置及邻近序列有关等,另外技术难度大、构建组装时间长也限制了其应用。CRISPR/Cas系统广泛存在于细菌及古生菌中, 是机体长期进化形成的RNA指导的降解入侵病毒或噬菌体DNA的适应性免疫系统。Ⅱ型CRISPR/Cas系统经过密码子优化等改造后已成为继锌指核酸酶ZFNs和TALENs后的新型高效定点编辑的新技术,具有突变效率高、制作简单、易操作及成本低的特点。目前,该技术成功应用于人类细胞、斑马鱼、小鼠以及细菌的基因组精确编辑,编辑的类型包括基因的定点插入、小片段的缺失、多个位点同时突变、基因定点的indel突变等。目前,CRISPR/Cas系统在植物中的应用还比较有限,但该技术为植物基因工程的发展呈现了美好的前景。文中首先简要介绍了CRISPR/Cas系统的组成和基本原理,进而详细综述了该技术在植物内源基因和外源基因定点编辑中的应用,主要列举了自CRISPR/Cas系统改造成功以来利用该系统对单子叶和双子叶植物进行基因组定点编辑的案例,最后对基因组编辑技术在农业和植物基因工程上的应用进行了展望,希望能够为开展该领域研究的科研工作者提供参考。     

The evolution of resistance gene in plants

Resistance genes enable plants to fight against plant pathogens. Plant resistance genes (R gene) are organized complexly in genome. Some resistance gene sequence data enable an insight into R gene structure and gene evolution. Some sites like Leucine-Rich Repeat (LRR) are of specific interest since homologous recombination can happen. Crossing over, transposon insertion and excision and mutation can produce new specificity. Three models explaining R gene evolution were discussed. More information needed for dissection of R gene evolution though some step can be inferred from genetic and sequence analysis.     

Virus population dynamics and acquired virus resistance in natural microbial communities

Viruses shape microbial community structure and function by altering the fitness of their hosts and by promoting genetic exchange. The complexity of most natural ecosystems has precluded detailed studies of virus-host interactions. We reconstructed virus and host bacterial and archaeal genome sequences from community genomic data from two natural acidophilic biofilms. Viruses were matched to their hosts by analyzing spacer sequences that occur among clustered regularly interspaced short palindromic repeats (CRISPRs) that are a hallmark of virus resistance. Virus population genomic analyses provided evidence that extensive recombination shuffles sequence motifs sufficiently to evade CRISPR spacers. Only the most recently acquired spacers match coexisting viruses, which suggests that community stability is achieved by rapid but compensatory shifts in host resistance levels and virus population structure.     

High direct estimate of the mutation rate in the mitochondrial genome of Caenorhabditis elegans

Mutations in the mitochondrial genome have been implicated in numerous human genetic disorders and offer important data for phylogenetic, forensic, and population genetic studies. Using a long-term series of Caenorhabditis elegans mutation accumulation lines, we performed a wide-scale screen for mutations in the mitochondrial genome that revealed a mutation rate that is two orders of magnitude higher than previous indirect estimates, a highly biased mutational spectrum, multiple mutations affecting coding function, as well as mutational hotspots at homopolymeric nucleotide stretches.     

Phylogeny and Homologous Recombination in Japanese Encephalitis Viruses

Japanese encephalitis virus (JEV) is a significant causative agent of arthropod-borne encephalitis and what is less clear that the factors cause the virus wide spread. The objective was to confirm whet...     

玉米骨干自交系京2416杂种优势及遗传重组解析

【目的】玉米骨干自交系京2416是以(京24×5237)×京24构建基础选系群体,利用高大严及同群优系聚合等选系技术选育的优良黄改群自交系。以其为父本育成的审定品种已有20多个,其中代表性品种京农科728,突破了黄淮海夏玉米籽粒机收技术瓶颈,成为中国首批通过国家审定的机收籽粒品种。通过分析京2416与X群种质的杂种优势,及其形成过程中的重组事件和黄早四基因组片段传递规律,解析京2416形成的遗传机制,以期为黄改系的进一步遗传改良提供参考。【方法】选用黄早四、京2416及其2个选系亲本(京24和5237)为材料,与5份X群代表性自交系根据NCII遗传设计组配杂交组合,利用F1产量相关性状单穗粒重的中亲优势、超高亲优势值和配合力效应值评估4份黄改系的杂种优势。对4份黄改系及5份X群自交系进行测序深度约为18×的全基因组重测序,用BWA、GATK等软件进行序列比对和变异检测,基于获得的SNP和InDel标记信息,利用GCTA和Treebest软件进行主成分分析和系统发生树构建,同源传递片段(identity-by-descent,IBD)使用IBDseq软件识别。【结果】通过比较分析黄早四、...     

鳞翅目昆虫线粒体DNA的研究进展*

 线粒体DNA（mtDNA）具有母性遗传,缺乏重组和进化速度快等特点,是研究鳞翅目昆虫系统学常用的分子标记。分析了鳞翅目昆虫线粒体DNA的结构特点,并就近年来对鳞翅目昆虫中进行过mtDNA研究的基因片段进行了简要综述,旨在为今后鳞翅目昆虫学研究提供参考。     

Copper-Controllable, Site-Specific DNA Excision in Transgenic Plants

A copper-inducible, Cre-loxP recombination-mediated DNA excision system has been developed in transgenic tobacco plants. The copper inducible system derived from yeast was used for the control of the expression of the Cre recombinase. Upon copper induction, the GUS reporter gene expression unit flanked by two direct lox sites was excised from the transgenic tobacco genome. Quantitative fluorometric GUS assays,Northern blot and PCR analyses showed a high-efficient, copper-dependent and Cre-loxP mediated DNA recombination in all the tested transgenic lines. The copper inducible foreign gene excision might be of great potential in genetic control of transgenic crops.     

The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization

We sequenced and annotated the genome of the filamentous fungus Fusarium graminearum, a major pathogen of cultivated cereals. Very few repetitive sequences were detected, and the process of repeat-induced point mutation, in which duplicated sequences are subject to extensive mutation, may partially account for the reduced repeat content and apparent low number of paralogous (ancestrally duplicated) genes. A second strain of F. graminearum contained more than 10,000 single-nucleotide polymorphisms, which were frequently located near telomeres and within other discrete chromosomal segments. Many highly polymorphic regions contained sets of genes implicated in plant-fungus interactions and were unusually divergent, with higher rates of recombination. These regions of genome innovation may result from selection due to interactions of F. graminearum with its plant hosts.     

Recombination and the nature of bacterial speciation

Genetic surveys reveal the diversity of bacteria and lead to the questioning of species concepts used to categorize bacteria. One difficulty in defining bacterial species arises from the high rates of recombination that results in the transfer of DNA between relatively distantly related bacteria. Barriers to this process, which could be used to define species naturally, are not apparent. Here, we review conceptual models of bacterial speciation and describe our computer simulations of speciation. Our findings suggest that the rate of recombination and its relation to genetic divergence have a strong influence on outcomes. We propose that a distinction be made between clonal divergence and sexual speciation. Hence, to make sense of bacterial diversity, we need data not only from genetic surveys but also from experimental determination of selection pressures and recombination rates and from theoretical models.     

侵染广西红宝石青柚的柑橘褪绿矮化相关病毒遗传进化分析

【目的】明确引起广西多地泰国红宝石青柚产生叶片变形、扭曲、皱缩、褪绿花叶和矮化症状的病原,为有效防治该病害提供理论依据。【方法】从广西多地采集疑似发病的红宝石青柚叶片样品,利用柑橘褪绿矮化相关病毒（Citrus chlorotic dwarf-associated virus,CCDaV）特异引物进行PCR检测,通过分段扩增、克隆等方法对样品进行鉴定并获取全长基因序列,运用RDP5和MEGA 7.0对所获得的全长基因序列进行重组及遗传多样性分析。【结果】PCR检测结果显示采集的红宝石青柚叶片样品可扩增出642 bp的目的条带,证实红宝石青柚受到CCDaV感染;采用分段克隆的方法获得LA-1、LA-2、WM-1、GG-1、GG-2、WZ-1和WZ-2等7个各地代表分离物的全长序列,序列长度分别为3641、3642、3642、3640、3642、3644和3644 bp;核苷酸相似性比对发现,7个分离物间的核苷酸相似性在98%以上,与GenBank已登录的CCDaV各分离物间的核苷酸相似性在99%以上,说明研究获得的病毒分离物为CCDaV的分离物;重组分析发现,7个分离物未发生重组。系统发育进化树分析结果显示,研究获得的WZ-1和WZ-2分离物分别与Tha1-19、Tha30处于同一个小分支,说明这2个分离物与Tha1-19和Tha30具有较近的亲缘关系;其余几个分离物则分处不同的小分支,说明CCDaV广西分离物间仍有一定的进化多样性。【结论】引起广西红宝石青柚叶片呈V字型、皱缩、卷曲、褪绿花叶和植株严重矮化等症状的病原为CCDaV,部分地区分离物存在地域多样性。     

QTL analysis for plant height and fine mapping of two environmentally stable QTLs with major effects in soybean

Plant height is an important agronomic trait, which is governed by multiple genes with major or minor effects. Of numerous QTLs for plant height reported in soybean, most are in large genomic regions, which results in a still unknown molecular mechanism for plant height. Increasing the density of molecular markers in genetic maps will significantly improve the efficiency and accuracy of QTL mapping. This study constructed a high-density genetic map using 4 011 recombination bin markers developed from whole genome re-sequencing of 241 recombinant inbred lines (RILs) and their bi-parents, Zhonghuang 13 (ZH) and Zhongpin 03-5373 (ZP). The total genetic distance of this bin map was 3 139.15 cM, with an average interval of 0.78 cM between adjacent bin markers. Comparative genomic analysis indicated that this genetic map showed a high collinearity with the soybean reference genome. Based on this bin map, nine QTLs for plant height were detected across six environments, including three novel loci (qPH-b_11, qPH-b_17 and qPH-b_18). Of them, two environmentally stable QTLs qPH-b_13 and qPH-b_19-1 played a major role in plant height, which explained 10.56–32.7% of the phenotypic variance. They were fine-mapped to 440.12 and 237.06 kb region, covering 54 and 28 annotated genes, respectively. Via the function of homologous genes in Arabidopsis and expression analysis, two genes of them were preferentially predicted as candidate genes for further study.     

Structural dynamics of eukaryotic chromosome evolution

Large-scale genome sequencing is providing a comprehensive view of the complex evolutionary forces that have shaped the structure of eukaryotic chromosomes. Comparative sequence analyses reveal patterns of apparently random rearrangement interspersed with regions of extraordinarily rapid, localized genome evolution. Numerous subtle rearrangements near centromeres, telomeres, duplications, and interspersed repeats suggest hotspots for eukaryotic chromosome evolution. This localized chromosomal instability may play a role in rapidly evolving lineage-specific gene families and in fostering large-scale changes in gene order. Computational algorithms that take into account these dynamic forces along with traditional models of chromosomal rearrangement show promise for reconstructing the natural history of eukaryotic chromosomes.