Paucity of genes on the Drosophila X chromosome showing male-biased expression

Sex chromosomes are primary determinants of sexual dimorphism in many organisms. These chromosomes are thought to arise via the divergence of an ancestral autosome pair and are almost certainly influenced by differing selection in males and females. Exploring how sex chromosomes differ from autosomes is highly amenable to genomic analysis. We examined global gene expression in Drosophila melanogaster and report a dramatic underrepresentation of X-chromosome genes showing high relative expression in males. Using comparative genomics, we find that these same X-chromosome genes are exceptionally poorly conserved in the mosquito Anopheles gambiae. These data indicate that the X chromosome is a disfavored location for genes selectively expressed in males.     

Rarity of males in pea aphids results in mutational decay

When females can reproduce without males, do males become an evolutionarily weaker sex whose genes experience mutational decay? We addressed this hypothesis in aphids, whose reproduction alternates between parthenogenetic and sexual forms: Over the course of a year, there can be 10 to 20 generations of asexual females but only a single, if any, generation with males. We used microarray analyses to identify male-biased, asexual female-biased, and neutral genes. Interspecific comparisons reveal accelerated evolution of male-biased genes, and intraspecific polymorphisms exhibit a significant excess of nonsynonymous coding variation in male-biased genes. We conclude that the ability of females to reproduce asexually without males reduces selection constraints on male-based genes, resulting in their mutational decay.     

Genome-wide detection of selective signatures in a Jinhua pig population

The aim of this study was to detect evidence for signatures of recent selection in the Jinhua pig genome. These results can be useful to better understand the regions under selection in Jinhua pigs and might shed some lights on groups of genes that control production traits. In the present study, we performed extended haplotype homozygosity(EHH) tests to identify significant core regions in 202 Jinhua pigs. A total of 26 161 core regions spanning 636.42 Mb were identified, which occupied approximately 28% of the genome across all autosomes, and 1 158 significant(P0.01) core haplotypes were selected. Genes in these regions were related to several economically important traits, including meat quality, reproduction, immune responses and exterior traits. A panel of genes including ssc-mir-365-2, KDM8, RABEP2, GSG1L, RHEB, RPH3AL and a signal pathway of PI3K-Akt were detected with the most extreme P-values. The findings in our study could draw a comparatively genome-wide map of selection signature in the pig genome, and also help to detect functional candidate genes under positive selection for further genetic and breeding research in Jinhua and other pigs.     

Positive natural selection in the human lineage

Positive natural selection is the force that drives the increase in prevalence of advantageous traits, and it has played a central role in our development as a species. Until recently, the study of natural selection in humans has largely been restricted to comparing individual candidate genes to theoretical expectations. The advent of genome-wide sequence and polymorphism data brings fundamental new tools to the study of natural selection. It is now possible to identify new candidates for selection and to reevaluate previous claims by comparison with empirical distributions of DNA sequence variation across the human genome and among populations. The flood of data and analytical methods, however, raises many new challenges. Here, we review approaches to detect positive natural selection, describe results from recent analyses of genome-wide data, and discuss the prospects and challenges ahead as we expand our understanding of the role of natural selection in shaping the human genome.     

Human genome ultraconserved elements are ultraselected

Ultraconserved elements in the human genome are defined as stretches of at least 200 base pairs of DNA that match identically with corresponding regions in the mouse and rat genomes. Most ultraconserved elements are noncoding and have been evolutionarily conserved since mammal and bird ancestors diverged over 300 million years ago. The reason for this extreme conservation remains a mystery. It has been speculated that they are mutational cold spots or regions where every site is under weak but still detectable negative selection. However, analysis of the derived allele frequency spectrum shows that these regions are in fact under negative selection that is much stronger than that in protein coding genes.     

春小麦黄绿色突变系的遗传及叶绿体结构的分析

本文对化学诱变剂EMS处理春小麦获得的一个黄绿色突变系的叶绿素含量、遗传机制及叶绿体的超微结构进行了分析。结果表明:黄绿色突变系的叶绿素a和b的含量均比正常植株低,其总含量为正常植株的41.8％。该突变性状的遗传属于细胞核遗传,由一对隐性基因控制,其叶绿休的形状为椭圆形和不规则形,而且结构简单,缺乏丰富和高度组织化的内膜系统,但基质较丰富。     

Kinetic path of genes undergoing selection

As natural populations approach genetic equilibrium, the various genes in the population are capable of assuming intermediate distributions that might not be anticipated from either the rate of the process or the final distribution of the genes. Since it is possible that many populations have not reached genetic equilibrium, the distribution of genes in natural populations may be a reflection of the kinetic path by which the genes approach equilibrium. Attention to kinetic path provides an explanation for an apparent discrepancy in recent studies of selection in man.     

Transitions to asexuality result in excess amino acid substitutions

Theory predicts that linkage between genetic loci reduces the efficiency of purifying selection. Because of the permanent linkage of all heritable genetic material, asexual lineages may be exceptionally prone to deleterious-mutation accumulation in both nuclear and organelle genes. Here, we show that the ratio of the rate of amino acid to silent substitution (Ka/Ks) in mitochondrial protein-coding genes is higher in obligately asexual lineages than in sexual lineages of the microcrustacean Daphnia pulex. Using a phylogeny-based approach to quantify the frequency of mutational-effect classes, we estimate that mitochondrial protein-coding genes in asexual lineages accumulate deleterious amino acid substitutions at four times the rate in sexual lineages. These results support the hypothesis that sexual reproduction plays a prominent role in reducing the mutational burden in populations.     

Hitchhiking Effect Mapping： A New Approach for Discovering Agronomic Important Genes

Besides the natural selection, the crops cultivated today have experienced two episodes of strong artificial selection, domestic and modern breeding. Domestication led to giant genetic structure differentiation between cultivars and their wild species, while modern breeding made further genetic structure differentiation between the modern varieties and the landraces. In a population, diversity of the loci under strong selection is significantly lower than that of other loci. At the same time, diversity in the genomic regions flanking these selected loci also declines in the process of selection. This phenomenon is called hitchhiking effects or selection sweep in genetics. Genomic regions with selection sweep （haplotype block） could be detected after draft genome scanning （genome typing） with molecular markers in a number of released varieties or natural populations. Marker/trait association analysis in these regions would detect the loci （or QTLs） even the favored alleles （genes） in breeding or natural adaptation. Fine scanning of these genomic regions would help to determine the sizes of haplotype blocks and to discover the key genes, thereby providing very valuable information for isolation of the key genes and molecular design of new varieties. Establishment of high density genetic linkage maps in the major crops and availability of high throughput genotyping platform make it possible to discover agronomic important genes through marker/trait association analysis. On the basis of available publications, we give a brief introduction of the hitchhiking effect mapping approach in this paper using plant height, 1 000-grain weight, and phosphorus-deficiency tolerance as examples in wheat.     

关于自然选择单位的四种学说的内在统一(英文)

[目的]探讨关于自然选择单位的4种学说的内在联系。[方法]通过建立数学模型,探讨遗传群体杂合子适合度取值范围,阐明自然选择单位的4种学说的内在联系。[结果]根据研究中建立的数学模型,发现突变基因必须在纯和杂2方面都满足自然选择的要求,而且能在杂合状态下表现出高适合度,才更容易被保留下来,这就兼顾到个体的适应与集体的适应。从而在理论上统一了个体选择,集体选择,基因选择及木村资生的中性学说。[结论]该研究结果显示关于自然选择单位的4种学说是可共存的,彼此间分享了一个共同的前提。     

The mutational landscape of head and neck squamous cell carcinoma

Head and neck squamous cell carcinoma (HNSCC) is a common, morbid, and frequently lethal malignancy. To uncover its mutational spectrum, we analyzed whole-exome sequencing data from 74 tumor-normal pairs. The majority exhibited a mutational profile consistent with tobacco exposure; human papillomavirus was detectable by sequencing DNA from infected tumors. In addition to identifying previously known HNSCC genes (TP53, CDKN2A, PTEN, PIK3CA, and HRAS), our analysis revealed many genes not previously implicated in this malignancy. At least 30% of cases harbored mutations in genes that regulate squamous differentiation (for example, NOTCH1, IRF6, and TP63), implicating its dysregulation as a major driver of HNSCC carcinogenesis. More generally, the results indicate the ability of large-scale sequencing to reveal fundamental tumorigenic mechanisms.     

矮败小麦轮回双向交替选择育种技术研究

为育成适合沧州地区生产的小麦突破性品种,利用矮败材料和优异抗旱耐盐亲本材料,建立盐碱圃和优良圃的双向交替选择,从而构建轮回选择群体,创新了矮败小麦轮回双向交替选择育种技术,实现了品种大量聚集有效的主效基因和微效基因,使之充分重组累加,产生更多遗传变异。利用自然选择的方法加大逆境选择压力,培育品种的多抗性,并通过人工选择和自然选择的方法选择培育出不同类型区的品种,培育出了沧核036等小麦品种,是一种行之有效的育种方法。     

芍药花色调控基因的密码子使用模式及其影响因素分析

【目的】芍药花色的优劣影响其观赏价值和商业价值,研究芍药花色调控基因的密码子使用偏好性和密码子使用模式的影响因素,为芍药花色调控基因在m RNA翻译、转基因设计、新基因表达与功能预测以及分子生物进化研究提供参考。【方法】根据前期芍药花色嵌合体品种‘金辉’转录组测序筛选的6 345个芍药花色调控基因,并根据CDS序列特征和大于300 bp原则进行过滤后最终获得的2 234个基因序列作为研究对象,利用Mobyle软件计算GC含量、第1与2位密码子的平均GC含量(GC12)、第3位密码子的GC含量(GC3s)、有效密码子数ENC、密码子适应指数CAI、相对同义密码子使用度RSCU等密码子偏性指标,其次进行中性绘图(GC12 vs.GC3)、ENC-GC3s绘图以及PR2(Parity Rule 2)绘图分析,并运用多元统计分析方法探讨突变压力和选择作用对密码子使用模式的影响程度,最后以5%CAI值作为高、低表达样本组,计算这两个样本组的同义密码子相对使用度,利用卡方检验Chi-square test分析两组之间的显著性差异来确定最优密码子。【结果】芍药花色相关基因的密码子GC3s含量为46.37%,大部分基因GC含量主要分布在30%—55%;中性绘图分析表明GC3s与GC12呈极显著的正相关(R2=0.202,P0.01);ENC-GC3s绘图表明大部分基因分布在标准曲线周围,也有一部分基因分布在标准曲线下方较远的位置,同时大部分基因(ENCexp-ENCobs)/ENCexp比值集中分布在0.0—0.4;PR2绘图分析显示密码子第三位T的使用频率高于A,C使用频率高于G,表明嘌呤(A和G)与嘧啶(T和C)的使用频率并不均衡;对应性分析COA(Correspondence Analysis)表明,第一轴上显示了38.09%的差异,其他3个轴分别为18.42%、15.09%、14.59%,表明芍药花色调控基因的密码子使用模式评价以第一轴(Axis 1)为主;突变压力和选择作用分析发现,第一主轴与GC3s、CAI的相关系数均达到极显著正相关(R2=0.736,P0.01;R2=0.286,P0.01);利用△RSCU和卡方显著性检验的方法,确定了21个为芍药花色调控相关基因的最优密码子,其中18个以G或C结尾,仅CGU、GGU等2个密码子以U结尾。【结论】芍药花色调控基因的最优密码子多数以G/C结尾,并且密码子使用模式主要受到碱基差异(R2=0.736)和基因表达水平(R2=0.286)共同作用的影响,其中碱基差异占主导因素。本研究了解了芍药花色调控基因的密码子使用模式情况,为通过密码子改造开展芍药花色遗传改良以及分子进化研究提供了一定的理论依据。     

野生稻种质资源优异基因定位和利用的研究进展

野生稻由于长期处于野生状态,经受了各种灾害和不良环境的自然选择,保存着栽培稻不具有的或已经消失了的特异基因,抗逆性较强,是天然的基因库。综述了野生稻种质资源中产量性状、抗病虫性和抗逆性优异基因定位及其在育种、生物技术利用方面的研究进展,以便为作物育种开发和利用野生稻资源提供理论依据。     

Sexual recombination and the power of natural selection

Theory predicts that recombination will increase the effectiveness of natural selection. A Drosophila melanogaster model system was developed that increased experimental power with the use of high experimental replication, explicit tracking of individual genes, and high but natural levels of background selection. Each of 34 independent experiments traced the fate of a newly arisen mutation located within genome-wide, synthetic chromosomes that were propagated with or without recombination. An intrinsic advantage to recombination was demonstrated by the finding that the realized strength of selection on new mutations was markedly increased when recombination was present.     

影响伪狂犬病病毒同义密码子用法特点的因素分析

为了充分了解伪狂犬病病毒基因组结构和病毒进化机制,计算伪狂犬病病毒各基因(组)Nc值、RSCU值、GC3s含量和双核苷酸组成,分析伪狂犬痛病毒密码子用法特点.采用目前最普遍使用的多变量统计分析方法(对应分析)分析影响伪狂犬病病毒基因组同义密码子用法偏爱性的因素.结果表明:①在GC含量丰富的伪狂犬病病毒基因组中,所有基因都偏爱于以G或C结尾的密码子;②伪狂犬病病毒对CpG、CpC、GpC和GpG 4种双核苷酸具有显著偏爱性,而较少使用ApA、ApT、TpA和TpT 4种双核苷酸;③碱基组成限制、碱基突变压力、翻译选择和基因功能是形成伪狂犬病病毒密码子用法特点的4种因素.伪狂犬病病毒所有基因Nc-GC3s分布图显示有些基因如LLT ORF1、LLT ORF2等的偏向性完全是由于碱基的组成限制.GC3s-GC12s散点图则显示碱基突变和自然选择都是PRV密码子偏向性的形成因素.根据RSCU值进行的对应分析表明伪狂犬病病毒大多数基因密码子用法受基因表达水平和基因功能影响.综上所述,伪狂犬病病毒偏爱于G或C结尾的密码子,且碱基组成限制、碱基突变、翻译选择和基因功能是影响伪狂犬病病毒同义密码子用法特点的主要因素.     

Natural selection shapes genome-wide patterns of copy-number polymorphism in Drosophila melanogaster

The role that natural selection plays in governing the locations and early evolution of copy-number mutations remains largely unexplored. We used high-density full-genome tiling arrays to create a fine-scale genomic map of copy-number polymorphisms (CNPs) in Drosophila melanogaster. We inferred a total of 2658 independent CNPs, 56% of which overlap genes. These include CNPs that are likely to be under positive selection, most notably high-frequency duplications encompassing toxin-response genes. The locations and frequencies of CNPs are strongly shaped by purifying selection, with deletions under stronger purifying selection than duplications. Among duplications, those overlapping exons or introns, as well as those falling on the X chromosome, seem to be subject to stronger purifying selection.     

选择牵连效应分析：发掘重要基因的新思路

作物在长期进化过程中，除自然选择外，还经历了两次大的人工选择，即人工驯化选择和育种选择，使栽培种与野生种之间、现代品种与古老的地方品种之间在群体遗传结构及性状上形成了很大的差异；在基因组中，一些承受强选择作用的基因在群体中的多样性显著降低，同时这些基因附近区域的遗传多样性也明显下降。在遗传学中将这种对个别基因的选择导致其侧翼区域遗传多样性降低的现象称之为选择牵连效应（Hitchhiking effect，也称选择搭载效应）。通过大群体多位点的扫描分析，可找到一些发生选择牵连效应的基因组区段，利用标记/性状关联分析（Marker/Trait association analysis），就可发现这些区段所控制的重要性状；对这些区段进行精细扫描和分析，即可找到一些决定重要农艺性状的基因，并发现优异等位变异，从而为重要基因的克隆和作物品种的分子设计奠定基础。各大作物高密度分子标记连锁图谱的绘制完成、高通量基因型分析技术体系的建立，为利用选择牵连效应分析、通过标记/性状之间的关联，寻找和定位一些重要基因奠定了基础。本文在查阅文献的基础上，结合作者的研究，以小麦株高、千粒重、磷的吸收和利用等性状为例，就选择牵连效应分析的基本思路、方法进行了讨论，以起到抛砖引玉之作用。