基因组学技术大发展助力园艺植物研究取得新进展

园艺植物包括花卉、蔬菜、果树、部分瓜类(如西瓜(Citrulluslanatus)和甜瓜(Cucumismelo))和茶树(Camellia sinensis),在植物分类上涉及大量物种。园艺植物的基因组学和遗传学研究具有重要的理论价值和经济意义。基因组测序技术及相关生物信息学工具的发展为园艺植物基因组和分子生物学研究注入了新的活力。睡莲是一种重要的花卉植物,除了具有观赏价值,其进化地位也非常特殊,属于一种早期被子植物类群。最近,蓝星睡莲(N. colorata)的高质量基因组图谱绘制完成。通过系统分析和比较睡莲基因组与其它被子植物的基因组,研究者阐明了睡莲的进化位置及相关进化事件。所获得的高质量基因组序列将有助于园艺植物研究者开展深入的分子遗传学研究,鉴定到控制和调控花器官、花色花香及品质等众多性状的功能基因,从而推动基础研究的快速发展和加快新品种创制。     

被子植物小热激蛋白家族的比较基因组学分析

小热激蛋白(sHSP)是一类重要的响应外界环境变化以及调控植物生长发育的蛋白家族。基于在睡莲(Nymphaea colorata)、水稻(Oryza sativa)、拟南芥(Arabidopsis thaliana)和葡萄(Vitis vinifera)中分别鉴定到的33个NcsHSPs、24个OssHSPs、17个AtsHSPs和47个VvsHSPs, 表明sHSP家族可分为12个亚家族, 不同亚家族包含不同的sHSP成员数目、保守基序、基因结构以及复制基因数目。在4种模式被子植物的sHSP成员中共鉴定到12个基因复制事件, 片段复制事件和串联复制事件均与sHSP成员的扩增有关, 且片段复制事件发生的时间早于串联复制事件。在所有sHSP成员中, 拟南芥和葡萄的sHSP成员的同源性最高, 其次为睡莲和葡萄的sHSP成员。sHSP家族在被子植物中可能向更短的氨基酸长度、更小的分子量、更简单的基因结构以及更集中的染色体分布进化。此外, 在睡莲、水稻、拟南芥和葡萄中鉴定了一些可能与调控植物生长发育相关的候选基因。研究结果为4种模式被子植物sHSP家族的比较基因组学研究奠定了重要基础, 并为其它被子植物sHSP家族的研究提供重要参考。     

荧光原位杂交技术在植物多倍体起源与进化研究中的应用

多倍化是植物物种形成与多样化的重要原动力。研究植物特别是一些重要经济作物和园艺植物多倍体的起源与进化,不仅对于揭示多倍体形成过程中性状变异的分子机制具有重要意义,而且可为植物遗传资源的保护与利用提供理论和技术支持。作为连接基因组序列片段到染色体组的桥梁,荧光原位杂交技术长期被广泛用来研究多倍体形成与进化过程中相关特异基因或序列的表达定位、外源染色体检测和鉴定、基因组结构变异等科学问题。因此,在简单介绍荧光原位杂交技术发展历史和植物多倍体主要类型的基础上,主要总结了荧光原位杂交技术在植物多倍体起源与进化相关研究上的应用。     

濒危植物坡垒的叶绿体基因组特征及系统发育分析

了解濒危植物坡垒(Hopea hainanensis)的叶绿体基因组结构,对揭示龙脑香科植物的系统进化关系具有重要意义.本研究通过高通量测序技术对坡垒叶绿体基因组的结构特征及与其近缘种的系统进化关系进行了分析.结果 表明:坡垒叶绿体基因组具有典型被子植物叶绿体基因组的四分体结构,基因组全长151 795 bp,共注释得到124个基因,其中包括77个蛋白质编码蛋白基因(5个基因在反向重复区重复)、39个转运RNA(tRNA)基因和8个核糖体RNA(rRNA)基因.生物信息学分析表明,坡垒叶绿体基因组的密码子有19 662个,其中编码亮氨酸Leu的密码子数量最多,同义密码子使用度最高的是UUA/GCU/UCU.坡垒叶绿体基因组中鉴定得到94个SSR位点,其中3个以上核苷酸、三核苷酸、二核苷酸和单核苷酸的数目分别为7、4、24、59个.坡垒与龙脑香科其他植物叶绿体基因组全序列比较分析表明,其基因组大小、基因组成及排列特征相近,但也存在ycf1基因缺失现象.通过MEGA软件最大似然法分析比较锦葵目17种植物的叶绿体基因组,构建系统进化树发现,坡垒与龙脑香科新棒果香木(Neobalanocarpus heimii)亲缘关系相对较近,整个龙脑香科植物聚为一支.该研究丰富了坡垒的遗传信息,为构建龙脑香科植物的系统进化提供了新的材料,也为解决龙脑香科植物的分类问题提供参考.     

基于Ks分布的被子植物演化的时间尺度研究

物种演化时间估算是生命演化研究的重要部分。近年来,许多研究发现由于不同基因和不同物种的进化速率差异显著,因此需要新的方法对进化事件发生时间进行重新估计。为了对被子植物演化时间的重新估计,该研究基于共享多倍化事件或共享分歧事件应该有共同同义突变率(Ks)峰值的理念,建立了基于基因组数据的进化速率矫正模型。结果表明:(1)对获取Ks分布三种常见方式进行比较分析,明确了通过提取共线性区块上Ks值的中位数的方式最优。(2)模拟了Ks值随时间累积系数(v)变化过程下的Ks分布,当假设v服从正态分布时,Ks分布出现了长尾现象。(3)将矫正方法应用到被子植物中,发现不同谱系的被子植物具有同步的辐射进化和适应性进化现象。并且,被子植物的进化速率虽然差异显著,但不同分支间的进化速率仍具有部分一致性,如木兰类植物进化速率最慢,真双子叶植物次之,单子叶植物进化速率最快。最终得到了相对可靠的物种同义突变率演化时间轴,为植物研究提供了系统发育和演化的支撑。     

被子植物异型花柱及其进化意义

异型花柱(heterostyly)是被子植物中一种特殊的花多态现象和雌雄异位形式, 包括二型花柱(distyly)和三型花柱(tristyly) 2种类型。据报道, 在被子植物的约31个科中有异型花柱植物。该类型植物的花部特征在避免自交、促进准确的异交传粉以及通过降低雌雄功能干扰以提高亲本适合度等方面具有重要的进化意义。该文从以下3个方面总结和分析了异型花柱及其进化意义: (1)异型花柱植物的类型和花部特征、附属多态性和种群结构; (2)异型花柱植物在被子植物中的分布、起源和演化; (3) 异型花柱植物的进化适应意义。结合目前作者开展的有关工作, 对异型花柱植物研究中存在的一些问题进行讨论和展望, 希望能为国内工作者开展该领域的研究提供一些参考。     

被子植物异型花柱及其进化意义

异型花柱(heterostyly)是被子植物中一种特殊的花多态现象和雌雄异位形式,包括二型花柱(distyly)和三型花柱(tristyly)2种类型.据报道,在被子植物的约31个科中有异型花柱植物.该类型植物的花部特征在避免自交、促进准确的异交传粉以及通过降低雌雄功能干扰以提高亲本适合度等方面具有重要的进化意义.该文从以下3个方面总结和分析了异型花柱及其进化意义:(1)异型花柱植物的类型和花部特征、附属多态性和种群结构:(2)异型花柱植物在被子植物中的分布、起源和演化:(3)异型花柱植物的进化适应意义.结合目前作者开展的有关工作,对异型花柱植物研究中存在的一些问题进行讨论和展望,希望能为国内工作者开展该领域的研究提供一些参考.     

植物泛基因组研究进展与展望

随着测序技术和生物信息学的快速发展,已有数百种植物的参考基因组被测序,极大地促进了植物功能基因组学、进化遗传学和分子育种学等领域的蓬勃发展.然而,随着研究的深入,越来越多的证据表明来自单一个体的参考基因组远不能代表整个物种的遗传多样性,由此催生了泛基因组(Pan-genome)的概念,并已成功应用于20余种植物的研究,...     

非损伤性取样样品中富集宿主DNA的研究进展

非损伤性取样被广泛应用在动物保护遗传学、分子生态学和分子进化等研究领域。随着基因组测序技术的发展和基因组学时代的到来,如何从非损伤性取样样品中获取能够用于进行基因组测序的高质量DNA是研究者面临的难题。本文总结和比较了非损伤性取样中最常用的粪便样品和考古材料或博物馆标本两类样品中富集宿主DNA的方法及应用,以期为非损伤性取样在动物基因组学的研究和应用提供重要参考。     

植物内生固氮菌系统发育进化新进展

在植物内生固氮菌系统发育进化关系研究中,常用的方法有形态学与蛋白质水平法、数值分类和自动化鉴定法、化学分类法、分子遗传学方法等。本文简要介绍了常用方法的关键技术,并归纳了它们的优缺点。生物学的研究进入基因组时代后,随着高通量DNA测序技术在微生物学领域应用的迅速发展,全基因组测序被应用到微生物系统发育进化研究中,然而目前并未发现对已测全基因组序列的植物内生固氮菌进行系统总结。本文在对已测序植物内生固氮菌进行归纳的基础上,又详细研究了基于基因组数据的几种具有代表性的新方法(ANI分析法、最大唯一匹配指数法、核心基因组分析、组分矢量法、基因流动性分析),并结合目前系统发育进化研究常用方法,对植物内生固氮菌系统发育进化研究趋势进行总结和展望,旨在使植物内生固氮菌的系统发育进化关系研究在精确度、可靠性等方面有所突破。     

Exploring plant biodiversity: the Physcomitrella genome and beyond

For decades, plant molecular biology has focused on only a few angiosperm species. Recently, the approximately 500mega base pairs (Mb) of the haploid Physcomitrella patens genome were sequenced and annotated. Mosses such as P. patens occupy a key evolutionary position halfway between green algae and flowering plants. This draft genome, in comparison to existing genome data from other plants, allows evolutionary insights into the conquest of land by plants and the molecular biodiversity that land plants exhibit. As a model organism, P. patens provides a well-developed molecular toolbox, including efficient gene targeting in combination with the morphologically simple moss tissues. We describe current as well as future tools for P. patens research and the prospects they offer for plant research in general.     

Evolutionary Dynamics of Microsatellite Distribution in Plants: Insight from the Comparison of Sequenced Brassica,Arabidopsis and Other Angiosperm Species

Despite their ubiquity and functional importance, microsatellites have been largely ignored in comparative genomics, mostly due to the lack of genomic information. In the current study, microsatellite distribution was characterized and compared in the whole genomes and both the coding and non-coding DNA sequences of the sequenced Brassica, Arabidopsis and other angiosperm species to investigate their evolutionary dynamics in plants. The variation in the microsatellite frequencies of these angiosperm species was much smaller than those for their microsatellite numbers and genome sizes, suggesting that microsatellite frequency may be relatively stable in plants. The microsatellite frequencies of these angiosperm species were significantly negatively correlated with both their genome sizes and transposable elements contents. The pattern of microsatellite distribution may differ according to the different genomic regions (such as coding and non-coding sequences). The observed differences in many important microsatellite characteristics (especially the distribution with respect to motif length, type and repeat number) of these angiosperm species were generally accordant with their phylogenetic distance, which suggested that the evolutionary dynamics of microsatellite distribution may be generally consistent with plant divergence/evolution. Importantly, by comparing these microsatellite characteristics (especially the distribution with respect to motif type) the angiosperm species (aside from a few species) all clustered into two obviously different groups that were largely represented by monocots and dicots, suggesting a complex and generally dichotomous evolutionary pattern of microsatellite distribution in angiosperms. Polyploidy may lead to a slight increase in microsatellite frequency in the coding sequences and a significant decrease in microsatellite frequency in the whole genome/non-coding sequences, but have little effect on the microsatellite distribution with respect to motif length, type and repeat number. Interestingly, several microsatellite characteristics seemed to be constant in plant evolution, which can be well explained by the general biological rules.     

Conservation and diversity in flower land

During the past decade, enormous progress has been made in understanding the molecular regulation of flower development. In particular, homeotic genes that determine the identity of the floral organs have been characterised from different flowering plants, revealing considerable conservation among angiosperm species. On the other hand, evolutionary diversification has led to enormous variation in flower morphology. Increasing numbers of reports have described differences in the regulation, redundancy and function of homeotic genes from various species. These fundamentals of floral organ specification are therefore an ideal subject for comparative analyses of flower development, which will lead to a better understanding of plant evolution, plant development and the complexity of molecular mechanisms that control flower development and morphology.     

Genomic resources in fruit plants: an assessment of current status

The availability of many genomic resources such as genome sequences, functional genomics resources including microarrays and RNA-seq, sufficient numbers of molecular markers, express sequence tags (ESTs) and high-density genetic maps is causing a rapid acceleration of genetics and genomic research of many fruit plants. This is leading to an increase in our knowledge of the genes that are linked to many horticultural and agronomically important traits. Recently, some progress has also been made on the identification and functional analysis of miRNAs in some fruit plants. This is one of the most active research fields in plant sciences. The last decade has witnessed development of genomic resources in many fruit plants such as apple, banana, citrus, grapes, papaya, pears, strawberry etc.; however, many of them are still not being exploited. Furthermore, owing to lack of resources, infrastructure and research facilities in many lesser-developed countries, development of genomic resources in many underutilized or less-studied fruit crops, which grow in these countries, is limited. Thus, research emphasis should be given to those fruit crops for which genomic resources are relatively scarce. The development of genomic databases of these less-studied fruit crops will enable biotechnologists to identify target genes that underlie key horticultural and agronomical traits. This review presents an overview of the current status of the development of genomic resources in fruit plants with the main emphasis being on genome sequencing, EST resources, functional genomics resources including microarray and RNA-seq, identification of quantitative trait loci and construction of genetic maps as well as efforts made on the identification and functional analysis of miRNAs in fruit plants.     

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。     

An everlasting pioneer: the story of Antirrhinum research

Despite the tremendous success of Arabidopsis thaliana, no single model can represent the vast range of form that is seen in the approximately 250,000 existing species of flowering plants (angiosperms). Here, we consider the history and future of an alternative angiosperm model--the snapdragon Antirrhinum majus. We ask what made Antirrhinum attractive to the earliest students of variation and inheritance, and how its use led to landmark advances in plant genetics and to our present understanding of plant development. Finally, we show how the wide diversity of Antirrhinum species, combined with classical and molecular genetics--the two traditional strengths of Antirrhinum--provide an opportunity for developmental, evolutionary and ecological approaches. These factors make A. majus an ideal comparative angiosperm.     

Deciding among green plants for whole genome studies

Recent comparative DNA-sequencing studies of chloroplast, mitochondrial and ribosomal genes have produced an evolutionary tree relating the diversity of green-plant lineages. By coupling this phylogenetic framework to the explosion of information on genome content, plant-genomic efforts can and should be extended beyond angiosperm crop and model systems. Including plant species representative of other crucial evolutionary nodes would produce the comparative information necessary to understand fully the organization, function and evolution of plant genomes. The simultaneous development of genomic tools for green algae, bryophytes, ‘seed-free’ vascular plants and gymnosperms should provide insights into the bases of the complex morphological, physiological, reproductive and biochemical innovations that have characterized the successful transition of green plants to land.     

The evolutionary dynamics of plant duplicate genes

Given the prevalence of duplicate genes and genomes in plant species, the study of their evolutionary dynamics has been a focus of study in plant evolutionary genetics over the past two decades. The past few years have been a particularly exciting time because recent theoretical and experimental investigations have led to a rethinking of the classic paradigm of duplicate gene evolution. By combining recent advances in genomic analysis with a new conceptual framework, researchers are determining the contributions of single-gene and whole-genome duplications to the diversification of plant species. This research provides insights into the roles that gene and genome duplications play in plant evolution.     

Phylogenomics of Fargesia and Yushania reveals a history of reticulate evolution

Reticulate evolution is a common and important driving force in angiosperm evolution. In this study, we analyzed the phylogenetic signals of genomic regions with different inheritance patterns to understand the evolutionary process of organisms using species-rich Himalaya–Hengduan taxa of bamboos (Fargesia Franchet and Yushania Keng). We constructed phylogenetic trees using different sampling strategies and reconstruction methods based on genome skimming and double digest restriction-site-associated DNA sequencing data. We assessed the congruence of topologies generated from different datasets and employed several approaches to reveal the causes of phylogenetic incongruence, including the detection of hybridization and introgression using PhyloNetworks and the D-statistic test (ABBA-BABA test). We found that, in the plastome-based phylogeny, Fargesia bamboos can be clustered into three groups and Yushania was nested within one of them, which contradicts the nuclear–double digest restriction-site-associated DNA sequencing-based phylogeny. Moreover, the genetic variation of chloroplast DNA is significantly correlated with geographical distribution. The strong signal of incomplete lineage sorting, hybridization, introgression, and cytoplasmic gene flow found among genera and species suggests that reticulate evolution is the main cause for the phylogenetic incongruence between nuclear and chloroplast datasets. Our results add evidence that genomes with different inheritance patterns can reveal distinct evolutionary histories of species and suggest that reticulate evolution is prevalent in rapidly diversifying groups.     

Phylogenetic footprint of the plant clock system in angiosperms: evolutionary processes of <Emphasis Type="Italic">Pseudo-Response Regulator</Emphasis>s

Background  

Plant circadian clocks regulate many photoperiodic and diurnal responses that are conserved among plant species. The plant circadian clock system has been uncovered in the model plant, Arabidopsis thaliana, using genetics and systems biology approaches. However, it is still not clear how the clock system had been organized in the evolutionary history of plants. We recently revealed the molecular phylogeny of LHY/CCA1 genes, one of the essential components of the clock system. The aims of this study are to reconstruct the phylogenetic relationships of angiosperm clock-associated PRR genes, the partner of the LHY/CCA1 genes, and to clarify the evolutionary history of the plant clock system in angiosperm lineages.