多倍体植物的表观遗传现象

表观遗传现象是指基因表达发生改变但不涉及DNA序列的变化, 它存在于许多植物的多倍体化过程中,而且能够在代与代之间传递。表观遗传变异包括基因沉默、DNA甲基化、核仁显性、休眠转座子激活和基因组印记等方面。这种现象可能是由于基因组间的相互作用直接诱发基因沉默或基因表达改变所致;也可能由DNA甲基化之外的组蛋白编码的改变引起;或者与甲基化不足、染色质重组或转座子激活等有关。表观遗传变异在提高基因表达的多样性,引起遗传学和细胞学上的二倍化,以及促进基因组间的相互协调等方面起着重要作用。文章综述了植物多倍体化过程中的表观遗传现象及其在多倍体植物基因组进化中的作用,并在此基础上提出了今后在这方面的研究途径。     

植物转座子与基因表达调控

植物转座子是植物基因组中可移动的DNA重复序列,在植物基因组进化、基因表达调控、系统发育和遗传多样性评价方面具有重要作用。综述了植物转座子分类、起源和转座机制以及转座子与宿主基因组间的表观遗传互作,阐述了不同转座子对基因表达调控方式,并对今后研究前景进行了展望,旨为全面了解植物转座子的功能提供参考。     

Mutator转座子及MULE在植物基因与基因组进化中的作用

Mutator（Mu）转座子是植物中已发现的转座最活跃的转座子,其高的转座频率及趋向于单拷贝功能基因转座的特性,使该转座子成为玉米功能基因克隆的主要方法.Mu转座子的同源类似因子广泛存在于被子植物基因组中,而且同一基因组中往往具有多种变异类型.它不仅具有其他DNA转座子在基因和基因组进化中的普遍作用,而且具有能够承载基因组内功能基因和基因片段的载体功能,这种载体Mu转座子（Pack-MuLEs）能够在基因组内移动众多的基因片段,从而对基因和基因组进化产生作用.Mu转座子的同源序列发生在水稻与狗尾草之间的水平转移提供了高等植物核基因水平转移的首个例证.对Mu转座子的了解促进了我们对动态基因组概念的认识.文章对Mutator转座子的发现、转座特征、基因标签应用等的研究进展进行了综述,对Mu转座子家族的同源序列进行了分类,讨论了该转座子在基因组进化中的作用,分析了应加强研究的问题.     

高等植物helitron转座子的研究进展

作为重复序列的一种主要类型,转座子在高等植物基因组中具有相当丰富的DNA含量,在改变基因结构、调节基因表达、影响基因组进化,以及创造新基因的过程中扮演着重要的角色。Helitron转座子是DNA转座子的一种,在转座过程中经常捕获基因或基因片段,以及插入到基因附近或基因内部,因此在改变基因组构成、影响基因组的进化过程以及改变基因型和表型等方面起着重要作用。该文对国内外近年来有关植物基因组中helitron转座子的结构特征、鉴定和分类方法、基因组中的含量和在染色体上的分布,以及转座扩增和基因片段的捕获等方面的研究进展进行了综述,并对helitron转座子研究过程中存在的问题进行了讨论,对今后helitron相关的研究进行了展望。     

稻属植物的基因组进化

水稻所在的稻属(Oryza)共有24个左右的物种。由于野生稻含有大量的优良农艺性状基因, 在水稻遗传学研究中日益受到重视。随着国际稻属基因组计划的开展, 越来越多的稻属基因组序列被测定, 稻属成为进行比较、功能和进化基因组学研究的模式系统。近期开展的一系列研究对稻属不同基因组区段以及全基因组序列的比较分析, 揭示了稻属在基因组大小、基因移动、多倍体进化、常染色质到异染色质的转化以及着丝粒区域的进化等方面的分子机制。转座子的活性以及转座子因非均等重组或非法重组而造成的删除, 对稻属基因组的扩增和收缩具有重要作用。DNA双链断裂修复介导的基因移动, 特别是非同源末端连接, 是稻属基因组非共线性基因形成的主要来源。稻属基因组从常染色质到异染色质的转换过程, 伴随着转座子的大量扩增、基因片段的区段性和串联重复以及从基因组其他位置不断捕获异染色质基因。对稻属不同物种间基因拷贝数、特异基因和重要农艺性状基因的进化等研究, 可揭示稻属不同物种间表型和适应性差异的分子基础, 将加速水稻的育种和改良。     

类Tc1转座子研究进展

转座子广泛存在于各种生物基因组中,能在染色体不同位点间转座,并在基因组中大量扩增.转座子的活动能引起生物基因组或基因的重组和变异,加速生物多样性及其进化速率,被视为生物基因组进化的内在驱动.转座子分2类：反转座子和DNA转座子.类Tc1转座子是DNA转座子超级家族中种类最多、分布最广的一类.本文简要概述了类Tc1转座子的结构特征,及其扩增、转座和迸发的机制,并展望了其应用和研究方向.     

昆虫转座子在转基因技术中的应用

转座子是基因组中一段可移动的DNA重复片段。越来越多的研究表明,转座子是真核生物基因组的主要组成成分,是基因组和表型进化的主要动力之一,并且对基因表达调控网络的进化具有重要的贡献。由于转座子在基因组内具有可移动性,使其在生物技术和分子生物学领域备受重视,尤其在转基因技术上得到了广泛应用。本文综述了转座子在昆虫中的分布、类型及功能,重点阐述不同昆虫转座子在转基因技术中的应用,并对转基因安全性和转座子稳定性进行了讨论。     

基因倍增研究进展

基因倍增是指DNA片段在基因组中复制出一个或更多的拷贝,这种DNA片段可以是一小段基因组序列、整条染色体,甚至是整个基因组。基因倍增是基因组进化最主要的驱动力之一,是产生具有新功能的基因和进化出新物种的主要原因之一。本文综述了脊椎动物、模式植物和酵母在进化过程中基因倍增研究领域的最新进展,并讨论了基因倍增研究的发展方向。     

转座子衍生基因的演变途径及对生物生长发育的影响

转座子(transposable elements,TEs)是指在基因组上能从同一条染色体的一个位置转移到另一个位置或者从一条染色体转移到另一条染色体上的一段DNA序列。广泛存在于基因组中的转座子通过复制、动员、重组基因片段以及修改原基因结构形成的新基因,被称为转座子衍生基因。该文综述了转座子衍生基因与转座子和常规基因的异同以及转座子衍生基因的演变途径,归纳了转座子衍生基因对宿主基因进化,以及对生物生长发育的影响。     

昆虫的转座子及其功能

转座子是一类散布在基因组中序列重复的DNA片段,它们可以通过特定转座酶在基因组中移动.目前测序的真核生物基因组的结果都显示转座子占基因组中相当大的一部分.目前对于转座子功能的研究主要集中在产生新功能、修饰染色质、保护生殖细胞,以及参与基因组的协同进化上.随着对其功能研究的深入,利用转座子转座能力开发的转基因系统可以改造物种的遗传性状.此外转座子还可以作为一个标尺用以分析物种进化关系.     

Repeated big bangs and the expanding universe: Directionality in plant genome size evolution

The lack of correlation between genome size and organismal complexity has long been a topic of great interest. Over the last decade it has become clear that transposable elements play a dominant role in genome size growth, and that most of the observed genome size variation in plants can be ascribed to differential accumulation of transposable elements, particularly long terminal repeat retrotransposons, which often massively proliferate over exceptionally short evolutionary time-scales. In the absence of one or more counterbalancing forces, Bennetzen and Kellogg previously suggested that growth via transposable element accumulation would create a “one-way ticket to genomic obesity”. Phylogenetic evidence, however, indicates that lineages may experience genomic downsizing, notwithstanding the relative paucity of experimental evidence on mechanisms capable of eliminating massive amounts of DNA. Thus, genome size evolution in plants may involve both feast and famine. Here we review recent insights into the molecular mechanisms and evolutionary dynamics of genome size evolution in plants. These include mechanisms that contribute to genome size expansion, i.e. polyploidy and transposable element proliferation, in addition to the counteracting forces that act to remove DNA, particularly intra-strand homologous recombination and illegitimate recombination. We argue that extant genome sizes reflect myriad competing forces of genomic expansion and contraction, but that current evidence pertaining to rates and amounts of DNA loss prove insufficient to overcome transposable element proliferation in most lineages. Accordingly, the directionality of plant genome size evolution in most cases is biased toward growth, with mechanisms of DNA loss acting to attenuate (but not reverse) the march toward obesity.     

Mechanisms and rates of genome expansion and contraction in flowering plants

Plant genomes are exceptional for their great variation in genome size, an outcome derived primarily from their frequent polyploid origins and from the amplification of retrotransposons. Although most studies of plant genome size variation have focused on developmental or physiological effects of nuclear DNA content that might influence plant fitness, more recent studies have begun to investigate possible mechanisms for plant genome expansion and contraction. Analyses of relatively neutral genome components, like transposable elements, have been particularly fruitful, largely due to the enormous growth in genomic sequence information from many different plant species. Current data suggest that unequal recombination can slow the growth in genome size caused by retrotransposon amplification, but that illegitimate recombination and other deletion processes may be primarily responsible for the removal of non-essential DNA from small genome plants.     

The sunflower (Helianthus annuus L.) genome reflects a recent history of biased accumulation of transposable elements

Aside from polyploidy, transposable elements are the major drivers of genome size increases in plants. Thus, understanding the diversity and evolutionary dynamics of transposable elements in sunflower (Helianthus annuus L.), especially given its large genome size (～3.5 Gb) and the well‐documented cases of amplification of certain transposons within the genus, is of considerable importance for understanding the evolutionary history of this emerging model species. By analyzing approximately 25% of the sunflower genome from random sequence reads and assembled bacterial artificial chromosome (BAC) clones, we show that it is composed of over 81% transposable elements, 77% of which are long terminal repeat (LTR) retrotransposons. Moreover, the LTR retrotransposon fraction in BAC clones harboring genes is disproportionately composed of chromodomain‐containing Gypsy LTR retrotransposons (‘chromoviruses’), and the majority of the intact chromoviruses contain tandem chromodomain duplications. We show that there is a bias in the efficacy of homologous recombination in removing LTR retrotransposon DNA, thereby providing insight into the mechanisms associated with transposable element (TE) composition in the sunflower genome. We also show that the vast majority of observed LTR retrotransposon insertions have likely occurred since the origin of this species, providing further evidence that biased LTR retrotransposon activity has played a major role in shaping the chromatin and DNA landscape of the sunflower genome. Although our findings on LTR retrotransposon age and structure could be influenced by the selection of the BAC clones analyzed, a global analysis of random sequence reads indicates that the evolutionary patterns described herein apply to the sunflower genome as a whole.     

Recombination drives vertebrate genome contraction

Selective and/or neutral processes may govern variation in DNA content and, ultimately, genome size. The observation in several organisms of a negative correlation between recombination rate and intron size could be compatible with a neutral model in which recombination is mutagenic for length changes. We used whole-genome data on small insertions and deletions within transposable elements from chicken and zebra finch to demonstrate clear links between recombination rate and a number of attributes of reduced DNA content. Recombination rate was negatively correlated with the length of introns, transposable elements, and intergenic spacer and with the rate of short insertions. Importantly, it was positively correlated with gene density, the rate of short deletions, the deletion bias, and the net change in sequence length. All these observations point at a pattern of more condensed genome structure in regions of high recombination. Based on the observed rates of small insertions and deletions and assuming that these rates are representative for the whole genome, we estimate that the genome of the most recent common ancestor of birds and lizards has lost nearly 20% of its DNA content up until the present. Expansion of transposable elements can counteract the effect of deletions in an equilibrium mutation model; however, since the activity of transposable elements has been low in the avian lineage, the deletion bias is likely to have had a significant effect on genome size evolution in dinosaurs and birds, contributing to the maintenance of a small genome. We also demonstrate that most of the observed correlations between recombination rate and genome contraction parameters are seen in the human genome, including for segregating indel polymorphisms. Our data are compatible with a neutral model in which recombination drives vertebrate genome size evolution and gives no direct support for a role of natural selection in this process.     

The mitochondrial genome of Malus domestica and the import-driven hypothesis of mitochondrial genome expansion in seed plants

Mitochondrial genomes of spermatophytes are the largest of all organellar genomes. Their large size has been attributed to various factors; however, the relative contribution of these factors to mitochondrial DNA (mtDNA) expansion remains undetermined. We estimated their relative contribution in Malus domestica (apple). The mitochondrial genome of apple has a size of 396 947 bp and a one to nine ratio of coding to non-coding DNA, close to the corresponding average values for angiosperms. We determined that 71.5% of the apple mtDNA sequence was highly similar to sequences of its nuclear DNA. Using nuclear gene exons, nuclear transposable elements and chloroplast DNA as markers of promiscuous DNA content in mtDNA, we estimated that approximately 20% of the apple mtDNA consisted of DNA sequences imported from other cell compartments, mostly from the nucleus. Similar marker-based estimates of promiscuous DNA content in the mitochondrial genomes of other species ranged between 21.2 and 25.3% of the total mtDNA length for grape, between 23.1 and 38.6% for rice, and between 47.1 and 78.4% for maize. All these estimates are conservative, because they underestimate the import of non-functional DNA. We propose that the import of promiscuous DNA is a core mechanism for mtDNA size expansion in seed plants. In apple, maize and grape this mechanism contributed far more to genome expansion than did homologous recombination. In rice the estimated contribution of both mechanisms was found to be similar.     

DNA methylome analysis provides evidence that the expansion of the tea genome is linked to TE bursts

DNA methylation is essential for gene regulation, imprinting and silencing of transposable elements (TEs). Although bursts of transposable elements are common in many plant lineages, how plant DNA methylation is related to transposon bursts remains unclear. Here we explore the landscape of DNA methylation of tea, a species thought to have experienced a recent transposon burst event. This species possesses more transposable elements than any other sequenced asterids (potato, tomato, coffee, pepper and tobacco). The overall average DNA methylation levels were found to differ among the tea, potato and tomato genomes, and methylation at CHG sequence sites was found to be significantly higher in tea than that in potato or tomato. Moreover, the abundant TEs resulting from burst events not only resulted in tea developing a very large genome size, but also affected many genes involved in importantly biological processes, including caffeine, theanine and flavonoid metabolic pathway genes. In addition, recently transposed TEs were more heavily methylated than ancient ones, implying that DNA methylation is proportionate to the degree of TE silencing, especially on recent active ones. Taken together, our results show that DNA methylation regulates transposon silencing and may play a role in genome size expansion.     

LTR retrotransposons and flowering plant genome size: emergence of the increase/decrease model

Long Terminal Repeat (LTR) retrotransposons are ubiquitous components of plant genomes. Because of their copy-and-paste mode of transposition, these elements tend to increase their copy number while they are active. In addition, it is now well established that the differences in genome size observed in the plant kingdom are accompanied by variations in LTR retrotransposon content, suggesting that LTR retrotransposons might be important players in the evolution of plant genome size, along with polyploidy. The recent availability of large genomic sequences for many crop species has made it possible to examine in detail how LTR retrotransposons actually drive genomic changes in plants. In the present paper, we provide a review of the recent publications that have contributed to the knowledge of plant LTR retrotransposons, as structural components of the genomes, as well as from an evolutionary genomic perspective. These studies have shown that plant genomes undergo genome size increases through bursts of retrotransposition, while there is a counteracting process that tends to eliminate the transposed copies from the genomes. This process involves recombination mechanisms that occur either between the LTRs of the elements, leading to the formation of solo-LTRs, or between direct repeats anywhere in the sequence of the element, leading to internal deletions. All these studies have led to the emergence of a new model for plant genome evolution that takes into account both genome size increases (through retrotransposition) and decreases (through solo-LTR and deletion formation). In the conclusion, we discuss this new model and present the future prospects in the study of plant genome evolution in relation to the activity of transposable elements.     

Mechanisms of recent genome size variation in flowering plants

BACKGROUND AND AIMS: Plant nuclear genomes vary tremendously in DNA content, mostly due to differences in ancestral ploidy and variation in the degree of transposon amplification. These processes can increase genome size, but little is known about mechanisms of genome shrinkage and the degree to which these can attenuate or reverse genome expansion. This research focuses on characterizing DNA removal from the rice and Arabidopsis genomes, and discusses whether loss of DNA has effectively competed with amplification in these species. METHODS: Retrotransposons were analyzed for sequence variation within several element families in rice and Arabidopsis. Nucleotide sequence changes in the two termini of individual retrotransposons were used to date their time of insertion. KEY RESULTS: An accumulation of small deletions was found in both species, caused by unequal homologous recombination and illegitimate recombination. The relative contribution of unequal homologous recombination compared to illegitimate recombination was higher in rice than in Arabidopsis. However, retrotransposons are rapidly removed in both species, as evidenced by the similar apparent ages of intact elements (most less than 3 million years old) in these two plants and all other investigated plant species. CONCLUSIONS: Differences in the activity of mechanisms for retrotransposon regulation or deletion generation between species could explain current genome size variation without any requirement for natural selection to act on this trait, although the results do not preclude selection as a contributing factor. The simplest model suggests that significant genome size variation is generated by lineage-specific differences in the molecular mechanisms of DNA amplification and removal, creating major variation in nuclear DNA content that can then serve as the substrate for fitness-based selection.     

Genome sequence comparison of Col and Ler lines reveals the dynamic nature of Arabidopsis chromosomes

Large differences in plant genome sizes are mainly due to numerous events of insertions or deletions (indels). The balance between these events determines the evolutionary direction of genome changes. To address the question of what phenomena trigger these alterations, we compared the genomic sequences of two Arabidopsis thaliana lines, Columbia (Col) and Landsberg erecta (Ler). Based on the resulting alignments large indels (>100bp) within these two genomes were analysed. There are ~8500 large indels accounting for the differences between the two genomes. The genetic basis of their origin was distinguished as three main categories: unequal recombination (Urec)-derived, illegitimate recombination (Illrec)-derived and transposable elements (TE)-derived. A detailed study of their distribution and size variation along chromosomes, together with a correlation analyses, allowed us to demonstrate the impact of particular recombination-based mechanisms on the plant genome evolution. The results show that unequal recombination is not efficient in the removal of TEs within the pericentromeric regions. Moreover, we discovered an unexpectedly high influence of large indels on gene evolution pointing out significant differences between the various gene families. For the first time, we present convincing evidence that somatic events do play an important role in plant genome evolution.