广东省一株新型肠道病毒EV-B83型的全基因组序列进化分析及重组分析

本研究对2001年广东省急性弛缓性麻痹(Acute flaccid paralysis,AFP)病例中分离到的一株肠道病毒AFP341_GD-CHN_2001株进行了高通量测序后,获取该全基因组序列,经鉴定该毒株为EV-B83。为了解该广东省首株EV-B83分离株的全基因组特征及其重组特点,本研究对AFP341_GD-CHN_2001毒株通过最大似然法构建系统进化树,利用bootscanning分析该毒株与其它型别肠道病毒的重组位点,最后根据该重组位点分区段构建系统进化树,进一步验证重组分析结果。全长VP1序列构建的分子进化树表明,AFP341_GD-CHN_2001毒株与EV-B83原型株及柬埔寨SEP025_KH_2012分离株形成一簇;初步构建P1、P2、P3编码区序列系统进化树,提示该分离株在其分子进化中可能存在基因重组,而bootscanning分析表明非结构蛋白编码区是其发生基因重组的区域。根据bootscanning分析的断裂点对该毒株的全基因组序列分成3段构建系统进化树,该系统进化分析结果进一步明确该分离株于2B、2C、3D非结构编码区存在型间重组,与AFP341_GD-CHN_2001发生重组的毒株为CV-A9分离株NSW-V20_AU_2008、CV-B2分离株NSW-V53_AU_2010以及CV-B3分离株SSM_JL-CHN_2006。当前GenBank数据库中仅有来自美国以及中国云南的两株EV-B83全基因组序列,缺乏对该基因型的分子进化特征描述,本研究中的AFP341_GD-CHN_2001毒株为广东省首株EV-B83分离株,扩展了EV-B83数据信息,为今后EV-B83的研究提供了基础性资料。     

植物基因组大小进化的研究进展

不同的真核生物之间基因组大小差异很大, 并与生物体复杂性不相关, 在基因组中存在大量的非编码DNA序列是造成这种差异的主要原因, 特别是转座子序列。文章综述了植物基因组大小差异以及引起这种差异的主要进化动力的最新研究进展。植物基因组多倍化和转座子积累是导致基因组增大的主要动力, 而同源不平等重组和非正规重组则是驱动基因组DNA丢失的潜在动力, 以制约基因组无限制地增大。文中还讨论了植物基因组大小进化方向, 即总体趋势是朝着增大的方向进化, 某些删除机制主要是削弱这种增大作用但不能逆转。     

梅花草属叶绿体基因组进化分析

叶绿体基因组序列变异和基因组成等特征可有效反映植物类群间的系统发育和进化关系。本研究利用Illumina高通量测序平台对梅花草属（Parnassia）及其近缘属5种植物的叶绿体基因组进行测序和组装,同时基于已发表的近缘种叶绿体基因组信息,对梅花草属叶绿体基因组结构特征、序列遗传变异和蛋白编码基因密码子偏好性比对分析。结果显示：梅花草属叶绿体基因组整体结构较为保守,均为四分体结构;梅花草多个基因出现假基因化,而本属其他物种叶绿体基因组成一致,均编码115个基因;与近缘属物种相比,本属所有物种均丢失rpl16基因的内含子;蛋白质编码基因的非同义/同义替代率比值较低,叶绿体基因可能经历纯化选择作用;密码子偏好性聚类结果与蛋白编码序列重建的系统发育关系结果一致。本研究表明选择压力可能在梅花草属叶绿体基因组蛋白编码基因进化过程中发挥作用,有助于进一步理解梅花草属植物的进化和适应机制。     

脊椎动物中微小RNA进化模式研究

微小RNA（microRNA,miRNA）是一类长度约为22个核苷酸的内源性非编码RNA．它们在植物、多细胞动物和病毒的基因组中广泛存在并起着重要的调控作用．到目前为止,人们对于这类重要调控因子的进化特性还知之甚少．大多数的miRNA被认为在进化上是高度保守的,但近期随着大量相对不保守的miRNA被相继发现并报道,人们发现在进化过程中不断有新的miRNA产生．在本文中通过研究一个微小RNA超家族,分析了miRNA在脊椎动物中的进化特性．发现新产生的miRNA在其出现后的一段时期内会经历一个近似中性进化的过程,在序列上快速演变,随后逐渐固定下来,并在进化上趋于保守．同时观察到miRNA有系特异性（1ineage—specific）的大规模复制现象,以及miRNA在串连复制后,同源的miRNA前体可能会选择其发卡环不同臂上的序列作为成熟体,从而大大增加了miRNA新功能产生的可能性．这些观察表明,miRNA这一类重要的调控因子在进化过程中是十分活跃的。     

叶绿体的遗传进化

叶绿体是半自主性细胞器,其生长和增殖受核基因组和自身的基因组2套遗传系统的控制、关于叶绿体的起源有2种学说,近年来．大量叶绿体基因组全序列被测定,以及分子生物学的研究结果为内共生起源学说提供了更多证据。相对于线粒体,叶绿体DNA的结构更趋于保守一,叶绿体与核基因组所编码的蛋白质互相协调来维持叶绿体的正常功能。在进化过程中,基因可能从叶绿体大量转移到细胞核中。叶绿体基因组的信息常常表现出“母性遗传”特征．因而,使之更具生物反应器的优势。     

动物线粒体遗传系统理论与应用研究进展

随着线粒体与人类疾病之间关系研究的不断深入,线粒体DNA及其编码的13个多肽的功能和进化引起了众多研究者的关注。作为有氧呼吸的后生动物主要的产能系统——线粒体电子传递系统(ETS)由线粒体和核基因组共同编码,自然选择被认为偏爱那些增强ETS功能的突变,此类突变可发生在线粒体或核编码的ETS蛋白中并引起积极的基因组间的相互作用,即"共适应"。线粒体DNA进化通常被认为遵循一种稳定的突变速率平衡中性模型,但有证据表明该假设可能并不可靠。对线粒体遗传系统研究的最新进展进行了综述,这对科学和合理地使用线粒体DNA分析技术具重要意义。     

假基因研究进展

假基因是功能基因的缺陷拷贝,它在序列结构上与功能基因非常相似,但已丧失了正常的蛋白质编码功能．假基因曾被认为是一类典型的非编码“垃圾DNA”,而如今人们发现假基因在基因表达调控和基因组进化过程中发挥着重要作用．从假基因的起源、序列结构特征、假基因的识别、假基因在染色体上的分布、分子进化规律,以及假基因功能等几个方面较为全面地介绍了该领域的最新研究进展．     

人类基因组中突变对紧邻碱基的依赖性与重组率

减数分裂重组通过基因转变、碱基替换等方式影响基因组进化。紧邻碱基对突变偏好性有很强的影响,但该“紧邻碱基效应”如何随重组率变化有待深入研究。本文提出基于条件互信息(Conditional mutual information)量化突变对紧邻碱基依赖性的方法,并利用人类SNP等相关数据,分析重组率如何影响突变对紧邻碱基的依赖性。结果表明:在全基因组水平上, SNP位点上的突变对紧邻碱基的依赖性(即平均条件互信息)随着重组率的增加而增加;具体而言,当SNPs两侧碱基为A/G、C/G或C/T时,随着重组率的增加突变偏向性增强,但两侧碱基为A/A或T/T时,重组率对SNP突变偏向性产生抑制作用;另外,重组率越高,外显子与基因间区SNP的突变偏好性越强;而内含子区域SNP的突变偏好受到高重组率的抑制。结果有助于深入理解减数分裂重组如何影响基因组进化。     

脊椎动物基因组与基因复制研究进展

脊椎动物的出现是动物进化历史上一次质的飞跃.由于所有的脊椎动物在其胚胎发育中都呈现连续的解剖学特征,因此过去很多学者都根据现存脊椎动物的形态特征和在其发育过程中的解剖学特征假想原始脊椎动物,并推导其进化过程和起源.近年来的研究表明,通过对脊椎动物和与之亲缘关系接近的物种之间进行基因家族、染色体结构分析,可以对脊椎动物进化提供很多线索和证据.更多的研究表明,脊椎动物在进化过程中很可能发生过整体基因组的复制, 基因和/或基因组的复制可能是引起脊椎动物形体结构复杂性增加的根本原因.因此,基因和基因组的复制正在成为生物进化研究的热点问题.但这两种复制方式中哪一种是产生动物形体结构和功能复杂性增加最重要的原因尚有争论.     

物种形成过程中的分化基因组岛及其形成机制

理解物种形成机制是生态和进化领域的重要任务。得益于测序技术的快速发展, 越来越多研究发现分化种群(亚种、物种)间的基因组常呈现异质性分化景观, 存在分化基因组岛, 这被认为是基因流存在下的歧化选择引起的, 支持基因流存在下的成种假说。然而, 基因渐渗、祖先多态性的差异分选、连锁选择等其他进化过程也可导致分化基因组岛的形成。现有实证研究在解析分化基因组岛的形成机制时, 往往忽略了上述其他进化过程的作用。为此, 本文在辨析分化基因组岛相关概念的基础上, 总结了利用种群基因组数据鉴定分化基因组岛的方法, 对比了不同进化过程形成分化基因组岛的特征, 指出在区分不同机制时联用基因渐渗程度、绝对分化指数(d_XY)、相对节点深度(RND)、重组率等多个指标的必要性, 归纳了物种形成过程中分化基因组岛形成机制解析的研究思路, 并对未来在生殖隔离机制上的深入探索以及实证研究的整合分析等方面进行了展望。     

The Correlation Between Recombination Rate and Dinucleotide Bias in Drosophila melanogaster

Revealing how recombination affects genomic sequence is of great significance to our understanding of genome evolution. The present paper focuses on the correlation between recombination rate and dinucleotide bias in Drosophila melanogaster genome. Our results show that the overall dinucleotide bias is positively correlated with recombination rate for genomic sequences including untranslated regions, introns, intergenic regions, and coding sequences. The correlation patterns of individual dinucleotide biases with recombination rate are presented. Possible mechanisms of interaction between recombination and dinucleotide bias are discussed. Our data indicate that there may be a genome-wide universal mechanism acting between recombination rate and dinucleotide bias, which is likely to be neighbor-dependent biased gene conversion.     

Prokaryotic evolution in light of gene transfer

Accumulating prokaryotic gene and genome sequences reveal that the exchange of genetic information through both homology-dependent recombination and horizontal (lateral) gene transfer (HGT) is far more important, in quantity and quality, than hitherto imagined. The traditional view, that prokaryotic evolution can be understood primarily in terms of clonal divergence and periodic selection, must be augmented to embrace gene exchange as a creative force, itself responsible for much of the pattern of similarities and differences we see between prokaryotic microbes. Rather than replacing periodic selection on genetic diversity, gene loss, and other chromosomal alterations as important players in adaptive evolution, gene exchange acts in concert with these processes to provide a rich explanatory paradigm-some of whose implications we explore here. In particular, we discuss (1) the role of recombination and HGT in giving phenotypic "coherence" to prokaryotic taxa at all levels of inclusiveness, (2) the implications of these processes for the reconstruction and meaning of "phylogeny," and (3) new views of prokaryotic adaptation and diversification based on gene acquisition and exchange.     

Human SNP variability and mutation rate are higher in regions of high recombination

Understanding the co-variation of nucleotide diversity and local recombination rates is important both for the mapping of disease-associated loci and in understanding the causes of sequence evolution. It is known that single nucleotide polymorphisms (SNPs) around protein coding genes show higher diversity in regions of high recombination. Here, we find that this correlation holds for SNPs across the entire human genome, the great majority of which are not near exons or control elements. Contrasting with results from coding regions, we provide evidence that the higher nucleotide diversity in regions of high recombination is most likely due, at least in part, to a higher mutation rate. One possible explanation for this is that recombination is mutagenic.     

The impact of recombination on nucleotide substitutions in the human genome

Unraveling the evolutionary forces responsible for variations of neutral substitution patterns among taxa or along genomes is a major issue for detecting selection within sequences. Mammalian genomes show large-scale regional variations of GC-content (the isochores), but the substitution processes at the origin of this structure are poorly understood. We analyzed the pattern of neutral substitutions in 1 Gb of primate non-coding regions. We show that the GC-content toward which sequences are evolving is strongly negatively correlated to the distance to telomeres and positively correlated to the rate of crossovers (R²=47%). This demonstrates that recombination has a major impact on substitution patterns in human, driving the evolution of GC-content. The evolution of GC-content correlates much more strongly with male than with female crossover rate, which rules out selectionist models for the evolution of isochores. This effect of recombination is most probably a consequence of the neutral process of biased gene conversion (BGC) occurring within recombination hotspots. We show that the predictions of this model fit very well with the observed substitution patterns in the human genome. This model notably explains the positive correlation between substitution rate and recombination rate. Theoretical calculations indicate that variations in population size or density in recombination hotspots can have a very strong impact on the evolution of base composition. Furthermore, recombination hotspots can create strong substitution hotspots. This molecular drive affects both coding and non-coding regions. We therefore conclude that along with mutation, selection and drift, BGC is one of the major factors driving genome evolution. Our results also shed light on variations in the rate of crossover relative to non-crossover events, along chromosomes and according to sex, and also on the conservation of hotspot density between human and chimp.     

The novel mitochondrial gene arrangement of the cattle tick, Boophilus microplus: fivefold tandem repetition of a coding region.

We sequenced across all of the gene boundaries in the mitochondrial genome of the cattle tick, Boophilus microplus, to determine the arrangement of its genes. The mtDNA of B. microplus has a coding region, composed of tRNA(Glu) and 60 bp of the 3' end of ND1, that is repeated five times. Boophilus microplus is the first coelomate animal known to have more than two copies of a coding sequence. The mitochondrial genome of B. microplus has other unusual features, including (1) reduced T arms in tRNAs, (2) an AT bias in codon use, (3) two control regions that have evolved in concert, (4) three gene rearrangements, and (5) a stem-loop between tRNA(Gln) and tRNA(Phe). The short T arms and small control regions (CRs) of B. microplus and other ticks suggest strong selection for small genomes. Imprecise termination of replication beyond its origin, which can account for the evolution of tandem repeats of coding regions in other mitochondrial genomes, cannot explain the evolution of the fivefold repeated sequence in the mitochondrial genome of B. microplus. Instead, slipped-strand mispairing or recombination are the most plausible explanations for the evolution of these tandem repeats.     

Integrating genomics,bioinformatics, and classical genetics to study the effects of recombination on genome evolution

This study presents compelling evidence that recombination significantly increases the silent GC content of a genome in a selectively neutral manner, resulting in a highly significant positive correlation between recombination and "GC3s" in the yeast Saccharomyces cerevisiae. Neither selection nor mutation can explain this relationship. A highly significant GC-biased mismatch repair system is documented for the first time in any member of the Kingdom Fungi. Much of the variation in the GC3s within yeast appears to result from GC-biased gene conversion. Evidence suggests that GC-biased mismatch repair exists in numerous organisms spanning six kingdoms. This transkingdom GC mismatch repair bias may have evolved in response to a ubiquitous AT mutational bias. A significant positive correlation between recombination and GC content is found in many of these same organisms, suggesting that the processes influencing the evolution of the yeast genome may be a general phenomenon. Nonrecombining regions of the genome and nonrecombining genomes would not be subject to this type of molecular drive. It is suggested that the low GC content characteristic of many nonrecombining genomes may be the result of three processes (1) a prevailing AT mutational bias, (2) random fixation of the most common types of mutation, and (3) the absence of the GC-biased gene conversion which, in recombining organisms, permits the reversal of the most common types of mutation. A model is proposed to explain the observation that introns, intergenic regions, and pseudogenes typically have lower GC content than the silent sites of corresponding open reading frames. This model is based on the observation that the greater the heterology between two sequences, the less likely it is that recombination will occur between them. According to this "Constraint" hypothesis, the formation and propagation of heteroduplex DNA is expected to occur, on average, more frequently within conserved coding and regulatory regions of the genome. In organisms possessing GC-biased mismatch repair, this would enhance the GC content of these regions through biased gene conversion. These findings have a number of important implications for the way we view genome evolution and suggest a new model for the evolution of sex.     

The analysis of nucleotide substitutions, gaps, and recombination events between RHD and RHCE genes through complete sequencing

We determined the entire nucleotide sequences of all introns within the RHD and RHCE genes by amplifying genomic DNA using long PCR methods. The RHD and RHCE genes were 57,295 and 57,831 bp in length, respectively. Aligning both genes revealed 138 gaps (insertions and deletions) below 100 bp, 1116 substitutions in all introns and all exons (coding region), and 5 gaps of over 100 bp. Homologies (%) between the RH genes were 93.8% over all introns and coding exons and 91.7% over all exons and introns. Various short tandem repeats (STRs) and many interspersed nuclear elements were identified in both genes. The proportions of Alu sequences in the RHD and RHCE genes were 25.9 and 25.7%, respectively and these Alu sequences were concentrated in several regions. We confirmed multiple recombinations in introns 1 and 2. Such multiple recombination, which probably arose due to the concentrations of Alu sequences and the high level of the homology (%), is one of most important factors in the formation and evolution of RH gene. The variability of the Rh system may be generated because of these features of RH genes. Apparent mutational hotspots and regions with low of K values (the numbers of substitutions per nucleotide site) caused by recombinations as well as true mutational hotspots may be found in human genome. Accordingly, in searching for and identifying single nucleotide polymorphisms (SNPs) especially in noncoding regions, apparent mutational hotspots and areas of low K values by recombination should be noted since the unequal distribution of SNPs will reduce the power of SNPs as genetic maker. Combining the complete sequences' data of both RH genes with serological findings will provide beneficial information with which to elucidate the mechanism of recombination, mutation, polymorphism, and evolution of other genes containing the RH gene as well as to analyze Rh variants and develop new methods of Rh genotyping.     

原核基因组的进化方向和癌／正常细胞的熵产生

本文评述了理论生物学的两个基础实验。一是用离子束辐照加速大肠杆菌进化的方法研究原核基因组的进化方向,证明进化中的缺失偏好性和编码信息量扩增律不矛盾。二是提出用导热法测量细胞的熵产生,比较研究了癌细胞和正常细胞的熵产生和外加电场的关系,证明在一定强度的电场作用下正常细胞的熵产生可以明显超过癌细胞,从而实现改变两类细胞间熵流方向的目的。     

Direct and indirect consequences of meiotic recombination: implications for genome evolution

There is considerable variation within eukaryotic genomes in the local rate of crossing over. Why is this and what effect does it have on genome evolution? On the genome scale, it is known that by shuffling alleles, recombination increases the efficacy of selection. By contrast, the extent to which differences in the recombination rate modulate the efficacy of selection between genomic regions is unclear. Recombination also has direct consequences on the origin and fate of mutations: biased gene conversion and other forms of meiotic drive promote the fixation of mutations in a similar way to selection, and recombination itself may be mutagenic. Consideration of both the direct and indirect effects of recombination is necessary to understand why its rate is so variable and for correct interpretation of patterns of genome evolution.     

Application of Motif-Based Tools on Evolutionary Analysis of Multipartite Single-Stranded DNA Viruses

Multipartite viruses contain more than one distinctive genome component, and the origin of multipartite viruses has been suggested to evolve from a non-segmented wild-type virus. To explore whether recombination also plays a role in the evolution of the genomes of multipartite viruses, we developed a systematic approach that employs motif-finding tools to detect conserved motifs from divergent genomic regions and applies statistical approaches to select high-confidence motifs. The information that this approach provides helps us understand the evolution of viruses. In this study, we compared our motif-based strategy with current alignment-based recombination-detecting methods and applied our methods to the analysis of multipartite single-stranded plant DNA viruses, including bipartite begomoviruses, Banana bunchy top virus (BBTV) (consisting of 6 genome components) and Faba bean necrotic yellows virus (FBNYV) (consisting of 8 genome components). Our analysis revealed that recombination occurred between genome components in some begomoviruses, BBTV and FBNYV. Our data also show that several unusual recombination events have contributed to the evolution of BBTV genome components. We believe that similar approaches can be applied to resolve the evolutionary history of other viruses.