植物复杂基因组与泛基因组研究现状与展望

基因组是指一个生物体内遗传物质的总和,是生物学研究的关键之一.自2000年拟南芥基因组被测序发表以来,已有超过800个植物基因组相继被破解,极大促进了植物分子生物学、遗传学等领域的发展.即便如此,植物基因组学研究仍然面临一系列挑战,包括高杂合、高重复度、高倍性等复杂基因组的组装和泛基因组的构建等.本文从植物基因组学的发展概况、基因组测序技术、组装算法等三个方面,全面展示了植物基因组的快速发展.其中,介绍了简单基因组装和复杂基因组装的相关策略,总结了“端粒到端粒”(telomere-to-telomere或称T2T)的组装和泛基因组构建方法以及其重要性.最后,对未来植物基因组的发展进行了展望,认为随着技术的不断进步,基因组解析技术和方法将会更加完善,为植物基因组的深入研究提供更多支持.本文为植物T2T、复杂基因组组装和泛基因组的构建方法研究提供了参考依据.     

植物基因组测序的研究进展

近年来,随着测序技术的不断发展,基因组测序技术渐趋成熟并在动物和植物基因组上获得了越来越多的成功,大量植物的基因组的草图和精细图不断地被公布出来。比较和分析了三代测序技术各自的特点,对测序前的准备、基因组组装、注释和比较基因组学等方面的研究进展进行了详细的评述,阐明了植物基因组研究的特点和难点。通过植物的全基因组测序,研究者不仅可以获得该植物基因组和重要功能基因的序列信息,为从分子水平研究植物的分子进化、基因组成和基因调控等提供了一定的依据,而且还对即将测序的植物基因组研究具有重要的借鉴意义。     

内蒙古草原不同基因组大小植物对氮水添加的响应

被子植物基因组大小的种间差异巨大,约为2400倍.基因组大小与植物从细胞核到个体水平的一系列性状密切相关,进而影响植物对环境变化的响应.作为水分和养分共同限制的生态系统,内蒙古草原植物群落对氮素、水分有效性变化的响应具有明显的种间差异,这种差异可能与种间基因组大小不同有关.本研究利用流式细胞术测定了内蒙古典型草原水分、氮素添加实验平台植物的基因组大小,研究了不同基因组大小植物地上净初级生产力(ANPP)和物种丰富度对水分、氮素添加及其交互作用的响应.结果表明:基因组大小显著影响了不同植物ANPP对水分的响应,小基因组植物ANPP对氮水添加响应更敏感,加水和氮水共同添加显著增加了小基因组植物ANPP,而大基因组植物ANPP对所有处理响应均不显著.加氮对大小基因组植物ANPP都无显著影响.大小基因组植物的物种丰富度对氮水添加的响应也均不显著.基因组大小影响内蒙古草原不同植物ANPP对水分增加的响应.作为植物细胞核水平上十分稳定且种间差异巨大的物种性状,将基因组大小引入生态学研究将对全球变化背景下生态系统结构与功能变化研究起到重要作用.     

植物功能基因组研究进展

随着植物基因组计划的深入,植物基因组学研究的重点已经转变为基因组功能的研究,即利用基因组序列的信息和高通量的系统分析技术,在基因组水平研究植物结构和组织与植物功能在细胞、有机体和进化上的关系.对功能基因组学研究的内容、方法以及最新研究进展进行了综述.     

植物古基因组学研究进展

植物古基因组学是基因组学一个新兴分支,从现存物种中重建其祖先基因组,推断在古历史中导致形成现存物种的进化或物种形成事件。高通量测序技术的不断革新使测序读长更长、更准确,加快了植物参考基因组序列的组装进程,为古基因组学研究提供了大批量可靠的现存物种的基因组序列资源。全基因组复制(whole-genome duplication, WGD)亦称古多倍化,使植物基因组快速重组,丢失大量基因,增加结构变异,对植物进化极其重要。本文综述了植物基因组测序与组装研究进展、植物古基因组学的原理、植物基因组WGD事件以及植物祖先基因组进化场景,并对未来植物古基因组学研究进行了展望。     

泛基因组及其在植物功能基因组学研究中的应用

参考基因组是现代功能基因组学的核心框架,以此为基础的现代基因组学技术在过去20年对植物遗传变异发掘、功能基因克隆等研究起了巨大的推动作用。然而,越来越多的研究发现,单一或少数参考基因组不能完整代表和呈现物种或特定群体内的所有基因组变异,因此其在功能基因组学研究中应用存在很大的局限性,甚至会导致错误的结果。泛基因组是指物种或特定群体内全部基因或基因组序列的总和。泛基因组通过完整捕获和呈现群体内全部的基因或基因组序列,代替单一参考基因组应用于功能基因组学研究,可以突破单一参考基因组的局限性。泛基因组在植物功能基因组学研究中有广泛的应用,以泛基因组为基础,结合最新的基因组学技术可以高效、精准鉴定种质资源中的遗传变异。泛基因组研究是目前植物基因组学研究的前沿和热点。本文综述了泛基因组概念的起源和发展,泛基因组组装的技术和策略,以及泛基因组在植物基因组学研究和分子育种方面的应用和最新进展,最后对植物泛基因组研究目前存在的问题和今后研究方向进行了展望。本综述可为植物泛基因组研究和应用提供参考。     

基因组原位杂交技术及其在园艺植物基因组研究中的应用

基因组原位杂交(GISH)技术可以鉴定植物多倍体物种起源、杂种亲本染色体来源和组成,分析栽培种与其近缘野生种的亲缘关系,研究减数分裂染色体行为等。基因组原位杂交包括多色基因组原位杂交、比较基因组原位杂交和自身基因组原位杂交等。基因组原位杂交技术的关键步骤是染色体制片、探针制备及长度优化、探针与封阻的浓度比例和杂交后洗脱强度。该文对近年来国内外有关基因组原位杂交技术的发展及其在园艺植物基因组研究中的应用现状进行了综述,并指出随着多种园艺植物全基因组的测定,未来应从基因组信息中寻找更多的染色体特异性标记,结合荧光显带及荧光原位杂交技术,为深入研究园艺植物的起源以及遗传关系鉴定等提供技术支持。     

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。     

植物病原生物基因组测序进展

随着基因组学的迅猛发展,越来越多的生物全基因组序列已经测定完成或正在进行之中。植物病原生物基因组序列的测定为理解植物与病原物互作分子机制有重要意义,并为植物病理学的发展作出了重要贡献。目前已有9种病原细菌和1种病原真菌的基因组序列彻底完成,另外还有更多的基因组草图正在组装或测序工作正在进行之中。对NCBI上主要的植物病原真菌和细菌全基因组测序进展作了整理和概述。     

基因组编辑技术在植物中的研究进展与应用前景

外源DNA导入细胞并与基因组靶基因发生同源重组可以精确修饰或替换靶基因,但在植物中产生自发同源重组的概率很低.近几年出现的人工改造核酸酶可以大幅提高同源重组的效率,实现基因组的精确、定向改造.其中,归巢核酸酶、锌指核酸酶和TALE核酸酶已在植物基因工程中得到成功应用,最近开发出来的基于CRISPR/Cas系统的基因组编辑技术则更具有高效方便等特点.这些人工核酸酶的应用为植物基因工程的发展呈现了更加美好的前景.首先介绍了基因组编辑技术及其发展历程,随后详细阐述了提高植物基因组定点编辑效率的策略,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.     

Munich information center for protein sequences plant genome resources: a framework for integrative and comparative analyses 1(W)

With several plant genomes sequenced, the power of comparative genome analysis can now be applied. However, genome-scale cross-species analyses are limited by the effort for data integration. To develop an integrated cross-species plant genome resource, we maintain comprehensive databases for model plant genomes, including Arabidopsis (Arabidopsis thaliana), maize (Zea mays), Medicago truncatula, and rice (Oryza sativa). Integration of data and resources is emphasized, both in house as well as with external partners and databases. Manual curation and state-of-the-art bioinformatic analysis are combined to achieve quality data. Easy access to the data is provided through Web interfaces and visualization tools, bulk downloads, and Web services for application-level access. This allows a consistent view of the model plant genomes for comparative and evolutionary studies, the transfer of knowledge between species, and the integration with functional genomics data.     

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.     

DNA-binding protein prediction using plant specific support vector machines: validation and application of a new genome annotation tool

There are currently 151 plants with draft genomes available but levels of functional annotation for putative protein products are low. Therefore, accurate computational predictions are essential to annotate genomes in the first instance, and to provide focus for the more costly and time consuming functional assays that follow. DNA-binding proteins are an important class of proteins that require annotation, but current computational methods are not applicable for genome wide predictions in plant species. Here, we explore the use of species and lineage specific models for the prediction of DNA-binding proteins in plants. We show that a species specific support vector machine model based on Arabidopsis sequence data is more accurate (accuracy 81%) than a generic model (74%), and based on this we develop a plant specific model for predicting DNA-binding proteins. We apply this model to the tomato proteome and demonstrate its ability to perform accurate high-throughput prediction of DNA-binding proteins. In doing so, we have annotated 36 currently uncharacterised proteins by assigning a putative DNA-binding function. Our model is publically available and we propose it be used in combination with existing tools to help increase annotation levels of DNA-binding proteins encoded in plant genomes.     

Deciphering the evolutionary interplay between subgenomes following polyploidy: A paleogenomics approach in grasses

How did plant species emerge from their most recent common ancestors (MRCAs) 250 million years ago? Modern plant genomes help to address such key questions in unveiling precise species genealogies. The field of paleogenomics is undergoing a paradigm shift for investigating species evolution from the study of ancestral genomes from extinct species to deciphering the evolutionary forces (in terms of duplication, fusion, fission, deletion, and translocation) that drove present‐day plant diversity (in terms of chromosome/gene number and genome size). In this review, inferred ancestral karyotype genomes are shown to be powerful tools to (1) unravel the past history of extant species by recovering the variations of ancestral genomic compartments and (2) accelerate translational research by facilitating the transfer of genomic information from model systems to species of agronomic interest.     

Mining the genomes of plant pathogenic bacteria: how not to drown in gigabases of sequence

Hundreds of bacterial genomes including the genomes of dozens of plant pathogenic bacteria have been sequenced. These genomes represent an invaluable resource for molecular plant pathologists. In this review, we describe different approaches that can be used for mining bacterial genome sequences and examples of how some of these approaches have been used to analyse plant pathogen genomes so far. We review how genomes can be mined one by one and how comparative genomics of closely related genomes releases the true power of genomics. Databases and tools useful for genome mining that are publicly accessible on the Internet are also described. Finally, the need for new databases and tools to efficiently mine today's plant pathogen genomes and hundreds more in the near future is discussed.     

Genomic architectural variation of plant mitochondria—A review of multichromosomal structuring

Since the endosymbiont origin from α-Proteobacteria, mitochondrial genomes have undergone extremely divergent evolutionary trajectories among eukaryotic lineages. Compared with the relatively compact and conserved animal mitochondrial genomes, plant mitochondrial genomes have many unique features, especially their large and complex genomic arrangements. The sizes of fully sequenced plant mitochondrial genomes span over a 100-fold range from 66 kb in Viscum scurruloideum to 11 000 kb in Silene conica. In addition to the typical circular structure, some species of plants also possess linear, and even multichromosomal, architectures. In contrast with the thousands of fully sequenced animal mitochondrial genomes and plant plastid genomes, only around 200 fully sequenced land plant mitochondrial genomes have been published, with many being only draft assemblies. In this review, we summarize some of the known novel characteristics found in plant mitochondrial genomes, with special emphasis on multichromosomal structures described in recent publications. Finally, we discuss the future prospects for studying the inheritance patterns of multichromosomal plant mitochondria and examining architectural variation at different levels of taxonomic organization—including at the population level.     

Cucumber: a model angiosperm for mitochondrial transformation?

Plants possess three major genomes, carried in the chloroplast, mitochondrion, and nucleus. The chloroplast genomes of higher plants tend to be of similar sizes and structure. In contrast both the nuclear and mitochondrial genomes show great size differences, even among closely related species. The largest plant mitochondrial genomes exist in the genus Cucumis at 1500 to 2300 kilobases, over 100 times the sizes of the yeast or human mitochondrial genomes. Biochemical and molecular analyses have established that the huge Cucumis mitochondrial genomes are due to extensive duplication of short repetitive DNA motifs. The organellar genomes of almost all organisms are maternally transmitted and few methods exist to manipulate these important genomes. Although chloroplast transformation has been achieved, no routine method exists to transform the mitochondrial genome of higher plants. A mitochondrial-transformation system for a higher plant would allow geneticists to use reverse genetics to study mitochondrial gene expression and to establish the efficacy of engineered mitochondrial genes for the genetic improvement of the mitochondrial genome. Cucumber possesses three unique attributes that make it a potential model system for mitochondrial transformation of a higher plant. Firstly, its mitochondria show paternal transmission. Secondly, microspores possess relatively few, huge mitochondria. Finally, there exists in cucumber unique mitochondrial mutations conditioning strongly mosaic (msc) phenotypes. The msc phenotypes appear after regeneration of plants from cell culture and sort with specific rearranged and deleted regions in the mitochondrial genome. These mitochondrial deletions may be a useful genetic tool to develop selectable markers for mitochondrial transformation of higher plants.     

In silico archeogenomics unveils modern plant genome organisation, regulation and evolution

Increasing access to plant genome sequences as well as high resolution gene-based genetic maps have recently offered the opportunity to compare modern genomes and model their evolutionary history from their reconstructed founder ancestors on an unprecedented scale. In silico paleogenomic data have revealed the evolutionary forces that have shaped present-day genomes and allowed us to gain insight into how they are organised and regulated today.     

植物基因组比较作图研究进展

基因组比较作图是基因组研究的重要内容。植物比较作图研究表明,在长期的进化过程中,基因的组成表现出高度的保守性。随着植物遗传图谱和物理图谱的迅速发展,为植物比较作图奠定了重要的基础。现就植物基因组遗传图和物理图以及比较作图的最新研究进展作一介绍。