植物多倍化与多倍体基因组进化研究进展

多倍化(polyploidization)是指细胞核中的染色体组发生加倍并以可遗传的方式传递至后代的现象.虽然已有研究揭示多倍化事件普遍出现于被子植物各类群的进化过程中,但其对物种多样化与基因组进化的作用始终都处于争论之中.近年来随着基因组测序的革命性进步与多种组学和分子生物学技术的应用,植物多倍化与多倍体基因组进化领域的研究已取得多方面的重要进展.本文首先系统地介绍了植物多倍化的研究历史、多倍体分类系统以及该领域目前存在的主要学术争论.在此基础上,侧重从染色体数目与结构、DNA和组蛋白表观遗传修饰以及RNA和蛋白质表达等多个层次,对在多倍体小麦、油菜与棉花等模式作物中所取得的研究成果进行了较详细的概括.期望本文通过对最新研究成果的总结与未来研究展望,进一步增进对多倍化在植物物种多样性形成与基因组进化过程中重要作用的理解,促进我国植物多倍化研究领域的发展.     

PNAS:科学家破解植物多倍化进化之谜

<正>中国农科院蔬菜花卉研究所王晓武团队和美国科学院院士迈克·菲林领导的团队合作,对植物基因组多倍化进化过程中基因分化和多基因组分化机理进行了研究。相关成果日前在线发表于美国《国家科学院院刊》。植物在进化过程中通过基因组加倍(多倍化)的扩增方式,进行自我进化和适应自然环境。随着DNA测序技术的快速发展,越来越多的植物基因组被公布,这使得通过比较基因组学阐明植物多倍化进化机制成为可能。     

水稻和其他禾本科植物基因组多倍体起源的证据

基因加倍(Gene duplication)被认为是进化的加速器。古老的基因组加倍事件已经在多个物种中被确定,包括酵母、脊椎动物以及拟南芥等。本研究发现水稻基因组同样存在全基因组加倍事件,大概发生在禾谷类作物分化之前,距今约7000万年。在水稻基因组中,共找到117个加倍区段(Duplicated block),分布在水稻的全部12条染色体,覆盖约60％的水稻基因组。在加倍区段,大约有20％的基因保留了加倍后的姊妹基因对(Duplicated pairs)。与此形成鲜明对照的是加倍区段的转录因子保留了60％的姊妹基因。禾本科植物全基因组加倍事件的确定对研究禾本科植物基因组的进化具有重要影响,暗示了多倍体化及随后的基因丢失、染色体重排等在禾谷类物种分化中扮演了重要角色。     

植物多倍体研究的回顾与展望

多倍化是促进植物进化的重要力量。多倍体主要是通过未减数配子融合,体细胞染色体加倍以及多精受精三种方式起源的。其中,不减数配子是多倍体形成的主要机制。三倍体可能在四倍体的进化中起了重要作用。过去认为多倍体只能是进化的死胡同,现在发现很多多倍体类群都是多元起源的而不是单元起源的。当多倍体形成后,基因组中的重复基因大部分保持原有的功能,也有相当比例的基因发生基因沉默。多倍体通常表现出不存在于二倍体祖先的表型,并且超出了其祖先的分布范围,因为在多倍体中发生了很多基因表达的变化。主要从多倍体的起源、影响多倍体发生的因素及多倍体基因组的进化等方面回顾并展望多倍体的研究。     

植物群落稀有种维持机制与土壤反馈的研究进展

自Janzen-Connell (J-C)假说提出后半个世纪以来, 生态学家在热带及亚热带森林对该假说开展的大量实证研究表明, 由专性天敌导致的J-C效应所引起的负密度制约是维持森林多样性和决定群落组成的重要驱动力, 该假说成功地解释了热带及亚热带森林的丰富多样性。土壤病原真菌所引起的植物-土壤负反馈是J-C效应最主要的表现形式。然而, 对于植物-土壤负反馈是否能够维持森林群落中的大量稀有种仍然存在许多争议。基于当代物种共存理论的“稀有种优势”假说认为, 只有在满足“可入侵准则” (即物种在稀有时具有种群增加的趋势)的前提下, 稀有种才能在群落中与其他物种长期共存。然而, 当前基于土壤反馈的实验结果与该理论预测相悖, 因此在稀有种的维持机制方面仍存在较大的分歧。本文通过介绍植物-土壤反馈理论, 整合了可能对稀有种维持有较大影响的因素, 包括共生菌根真菌、土壤养分以及植物细根性状等在影响土壤负反馈方面的相关研究, 并对这些因素如何影响群落中物种多度和稀有种在群落中的维持进行了探讨。最后, 我们也从其他角度探讨了一些对稀有种维持的研究。我们认为在未来对稀有种的研究中, 探讨使其长期存续的“优势”和制约其种群扩大的“限制”同等重要, 将当代物种共存理论与新技术、新方法相结合对于探究稀有种的维持机制具有重要的意义, 可为稀有种保护提供理论依据。     

染色体数据的挖掘及其在植物多样性进化研究中的利用

多倍化（或全基因组加倍）是植物物种形成的重要途径,现存的被子植物可能都发生过一次甚至多次多倍化事件。多倍化传统的定义是染色体数目相对于祖先类群呈整倍性增加。其中最常用的研究方法是核型分析,核型能够提供物种的基本细胞学参数,包括染色体数目、倍性水平、核型不对称性、核型变异系数等。目前核型研究的趋势表现出从物种基本核型参数分析逐渐演化到多类群、多学科交叉融合的特点：一方面植物核型分析从种群、物种、科属的类群到生命之树,探讨染色体核型在各支系的进化特征、趋势以及驱动植物系统进化的细胞学机制;另一方面探讨和分析区域或生态系统植物区系的染色体谱或倍性等细胞学特征,可以探究区域地质环境变化或生态环境对染色体倍性等的影响,或通过区域染色体谱的构建,分析区域植物区系的形成和进化历史。因而,植物核型研究为系统发育、分子系统进化、生命之树以及植物区系地理的起源和演化研究提供了新思路。越来越多的新方法、新手段在植物核型分析与多倍化研究中得到运用,从而揭示了植物类群或植物区系的染色体进化以及细胞地理特征。今后植物细胞学研究趋势会向多学科交叉融合,整合各研究领域证据,从不同水平角度综合分析植物核型多样性形成的原因及意义,从而更加全面地认识和理解植物物种多样化与物种形成原因。     

染色体数据的挖掘及其在植物多样性进化研究中的利用

多倍化(或全基因组加倍)是植物物种形成的重要途径,现存的被子植物可能都发生过一次甚至多次多倍化事件。多倍化传统的定义是染色体数目相对于祖先类群呈整倍性增加。其中最常用的研究方法是核型分析,核型能够提供物种的基本细胞学参数,包括染色体数目、倍性水平、核型不对称性、核型变异系数等。目前核型研究的趋势表现出从物种基本核型参数分析逐渐演化到多类群、多学科交叉融合的特点:一方面植物核型分析从种群、物种、科属的类群到生命之树,探讨染色体核型在各支系的进化特征、趋势以及驱动植物系统进化的细胞学机制;另一方面探讨和分析区域或生态系统植物区系的染色体谱或倍性等细胞学特征,可以探究区域地质环境变化或生态环境对染色体倍性等的影响,或通过区域染色体谱的构建,分析区域植物区系的形成和进化历史。因而,植物核型研究为系统发育、分子系统进化、生命之树以及植物区系地理的起源和演化研究提供了新思路。越来越多的新方法、新手段在植物核型分析与多倍化研究中得到运用,从而揭示了植物类群或植物区系的染色体进化以及细胞地理特征。今后植物细胞学研究趋势会向多学科交叉融合,整合各研究领域证据,从不同水平角度综合分析植物核型多样性形成的原因及意义,从而更加全面地认识和理解植物物种多样化与物种形成原因。     

植物边缘种群遗传多样性研究进展

边缘种群指地理分布边缘可检测到的一定数量的同种个体集合, 准确评价其遗传多样性对于理解第四纪冰期后气候变化对物种边缘扩展或收缩、遗传资源保护与利用以及物种形成等有重要意义。该文探讨了维持植物边缘种群遗传多样性的进化机制, 分析交配系统对物种边缘及其遗传多样性的影响, 比较了边缘与中心种群遗传多样性的差异及其形成的生态与进化过程, 并探讨了边缘种群遗传多样性与其所在的群落物种多样性的关系及理论基础。该文提出今后研究的重点是应用全基因组序列或转录组基因序列研究前缘-后缘种群之间或边缘-中心种群之间的适应性差异, 边缘种群与所在群落其他物种之间相互作用的分子机制, 深入解析边缘种群对环境的适应及边缘种群遗传多样性与群落物种多样性关系的生态与进化过程。     

植物边缘种群遗传多样性研究进展

边缘种群指地理分布边缘可检测到的一定数量的同种个体集合,准确评价其遗传多样性对于理解第四纪冰期后气候变化对物种边缘扩展或收缩、遗传资源保护与利用以及物种形成等有重要意义。该文探讨了维持植物边缘种群遗传多样性的进化机制,分析交配系统对物种边缘及其遗传多样性的影响,比较了边缘与中心种群遗传多样性的差异及其形成的生态与进化过程,并探讨了边缘种群遗传多样性与其所在的群落物种多样性的关系及理论基础。该文提出今后研究的重点是应用全基因组序列或转录组基因序列研究前缘-后缘种群之间或边缘-中心种群之间的适应性差异,边缘种群与所在群落其他物种之间相互作用的分子机制,深入解析边缘种群对环境的适应及边缘种群遗传多样性与群落物种多样性关系的生态与进化过程。     

植物多倍体中的基因组印记

植物多倍体在自然界中广泛存在,这说明拥有多套遗传物质使得多倍体的适应进化具有优势。新多倍体形成后,一些基因组范围的变化较迅速地发生在多倍体形成开端,另一些在长期进化中发生。由于受到遗传、表观等因素的影响,亲本对于新形成多倍体基因组的贡献不均衡。这种偏向于某个亲本基因组的显性优势,称为基因组印记。植物多倍体中的基因组印记表现为基因组偏向性的序列消除、不均衡基因表达、基因沉默,这些受到基因组合并及DNA甲基化、核仁显性等表观因素影响。本文旨在为多倍体基因组进化及育种的相关研究提供参考。     

Plant polyploidy and non-uniform effects on insect herbivores

Genomic duplication through polyploidy has played a central role in generating the biodiversity of flowering plants. Nonetheless, how polyploidy shapes species interactions or the ecological dynamics of communities remains largely unknown. Here we provide evidence from a 4 year study demonstrating that the evolution of polyploidy has reshaped the interactions between a widespread plant and three species of phytophagous moths. Our results show that polyploidy has produced non-uniform effects, with polyploids less attacked by one insect species, but significantly more attacked by two other species. These results suggest that the evolution of plant polyploidy may not generally confer uniform resistance to multiple species of insect herbivores. In the absence of such a uniform release, the extreme evolutionary success of polyploid plants is probably due to factors other than escape from herbivory. Together, these results suggest that a primary consequence of plant polyploidy may be to shape the ecological structure of plant-insect interactions, thereby providing opportunities for diversification in both plant and insect taxa.     

Dating and functional characterization of duplicated genes in the apple (<Emphasis Type="Italic">Malus domestica</Emphasis> Borkh.) by analyzing EST data

Background  

Gene duplication is central to genome evolution. In plants, genes can be duplicated through small-scale events and large-scale duplications often involving polyploidy. The apple belongs to the subtribe Pyrinae (Rosaceae), a diverse lineage that originated via allopolyploidization. Both small-scale duplications and polyploidy may have been important mechanisms shaping the genome of this species.     

KRAB型锌指蛋白的进化及在物种演化中的功能

C2H2型锌指蛋白家族是目前发现的哺乳动物中最大的转录/转录调控因子家族,由一小群古老的含有真核锌指结构的转录因子经过多次基因复制和功能分化演化而来。KRAB型锌指蛋白(KRAB-containing zinc finger proteins, KRAB-ZFPs)作为C2H2型锌指蛋白家族中最大的亚家族,最早出现在四足脊椎动物,并随物种的进化数量快速增长,在人类中占据C2H2型锌指蛋白的60%左右。在物种演化中,进化压力主要改变KRAB-ZFPs的DNA结合能力,而KRAB-ZFPs介导的转录抑制能力则稳定存在。同时,多种KRAB-ZFPs能够与KRAB相关蛋白1(KRAB-associated protein 1, KAP1)协同作用沉默哺乳动物中反转录元件的活性,并与之协同进化,严格限制反转录原件的跳跃能力。本文综述了KRAB-ZFPs的数量倍增、锌指结构的灵活多变、KRAB-ZFPs/KAP1的转录抑制能力和反转录元件的跳跃性在促进哺乳动物调控网络的差异、基因组稳定性的变化和物种进化中的作用,旨在进一步揭示KRAB-ZFPs在推动物种稳定演化中的特点和功能。     

Species interactions and plant polyploidy

Polyploidy is a common mode of speciation that can have far‐reaching consequences for plant ecology and evolution. Because polyploidy can induce an array of phenotypic changes, there can be cascading effects on interactions with other species. These interactions, in turn, can have reciprocal effects on polyploid plants, potentially impacting their establishment and persistence. Although there is a wealth of information on the genetic and phenotypic effects of polyploidy, the study of species interactions in polyploid plants remains a comparatively young field. Here we reviewed the available evidence for how polyploidy may impact many types of species interactions that range from mutualism to antagonism. Specifically, we focused on three main questions: (1) Does polyploidy directly cause the formation of novel interactions not experienced by diploids, or does it create an opportunity for natural selection to then form novel interactions? (2) Does polyploidy cause consistent, predictable changes in species interactions vs. the evolution of idiosyncratic differences? (3) Does polyploidy lead to greater evolvability in species interactions? From the scarce evidence available, we found that novel interactions are rare but that polyploidy can induce changes in pollinator, herbivore, and pathogen interactions. Although further tests are needed, it is likely that selection following whole‐genome duplication is important in all types of species interaction and that there are circumstances in which polyploidy can enhance the evolvability of interactions with other species.     

Rarely successful polyploids and their legacy in plant genomes

Polyploidy, or whole genome duplication, is recognized as an important feature of eukaryotic genome evolution. Among eukaryotes, polyploidy has probably had the largest evolutionary impact on vascular plants where many contemporary species are of recent polyploid origin. Genomic analyses have uncovered evidence of at least one round of polyploidy in the ancestry of most plants, fueling speculation that genome duplications lead to increases in net diversity. In spite of the frequency of ancient polyploidy, recent analyses have found that recently formed polyploid species have higher extinction rates than their diploid relatives. These results suggest that despite leaving a substantial legacy in plant genomes, only rare polyploids survive over the long term and most are evolutionary dead-ends.     

Molecular Evidence for Asymmetric Evolution of Sister Duplicated Blocks after Cereal Polyploidy

Polyploidy (genome duplication) is thought to have contributed to the evolution of the eukaryotic genome, but complex genome structures and massive gene loss during evolution has complicated detection of these ancestral duplication events. The major factors determining the fate of duplicated genes are currently unclear, as are the processes by which duplicated genes evolve after polyploidy. Fine-scale analysis between homologous regions may allow us to better understand post-polyploidy evolution. Here, using gene-by-gene and gene-by-genome strategies, we identified the S5 region and four homologous regions within the japonica genome. Additional phylogenomic analyses of the comparable duplicated blocks indicate that four successive duplication events gave rise to these five regions, allowing us to propose a model for this local chromosomal evolution. According to this model, gene loss may play a major role in post-duplication genetic evolution at the segmental level. Moreover, we found molecular evidence that one of the sister duplicated blocks experienced more gene loss and a more rapid evolution subsequent to two recent duplication events. Given that these two recent duplication events were likely involved in polyploidy, this asymmetric evolution (gene loss and gene divergence) may be one possible mechanism accounting for the diploidization at the segmental level. Supplementary material to this paper is available in electronic form at http://dx.doi.org/10.1007/s11103-005-4414-1     

Polyploidy and self-fertilization in flowering plants

Mating systems directly control the transmission of genes across generations, and understanding the diversity and distribution of mating systems is central to understanding the evolution of any group of organisms. This basic idea has been the motivation for many studies that have explored the relationships between plant mating systems and other biological and/or ecological phenomena, including a variety of floral and environmental characteristics, conspecific and pollinator densities, growth form, parity, and genetic architecture. In addition to these examples, a potentially important but poorly understood association is the relationship between plant mating systems and genome duplication, i.e., polyploidy. It is widely held that polyploid plants self-fertilize more than their diploid relatives, yet a formal analysis of this pattern does not exist. Data from 235 species of flowering plants were used to analyze the association between self-fertilization and ploidy. Phylogenetically independent contrasts and cross-species analyses both lend support to the hypothesis that polyploids self-fertilize more than diploids. Because polyploidy and self-fertilization are so common among angiosperms, these results contribute not only to our understanding of the relationship between mating systems and polyploidy in particular, but more generally, to our understanding of the evolution of flowering plants.     

The more the better? The role of polyploidy in facilitating plant invasions

Background

Biological invasions are a major ecological and socio-economic problem in many parts of the world. Despite an explosion of research in recent decades, much remains to be understood about why some species become invasive whereas others do not. Recently, polyploidy (whole genome duplication) has been proposed as an important determinant of invasiveness in plants. Genome duplication has played a major role in plant evolution and can drastically alter a plant''s genetic make-up, morphology, physiology and ecology within only one or a few generations. This may allow some polyploids to succeed in strongly fluctuating environments and/or effectively colonize new habitats and, thus, increase their potential to be invasive.

Scope

We synthesize current knowledge on the importance of polyploidy for the invasion (i.e. spread) of introduced plants. We first aim to elucidate general mechanisms that are involved in the success of polyploid plants and translate this to that of plant invaders. Secondly, we provide an overview of ploidal levels in selected invasive alien plants and explain how ploidy might have contributed to their success.

Conclusions

Polyploidy can be an important factor in species invasion success through a combination of (1) ‘pre-adaptation’, whereby polyploid lineages are predisposed to conditions in the new range and, therefore, have higher survival rates and fitness in the earliest establishment phase; and (2) the possibility for subsequent adaptation due to a larger genetic diversity that may assist the ‘evolution of invasiveness’. Alternatively, polyploidization may play an important role by (3) restoring sexual reproduction following hybridization or, conversely, (4) asexual reproduction in the absence of suitable mates. We, therefore, encourage invasion biologists to incorporate assessments of ploidy in their studies of invasive alien species.