Plant transposable elements,with an emphasis on grass species

Transposable elements are presents in all known genomes so far, and have the faculty of changing their genomic location and/or number of copies within the genome. They are mobile endogenous genetic elements, with a large variety of structure and transposition mechanism. In crops, they compose the major part of the nucleic DNA, up to 80% in some cereals like maize and wheat. Despite their omnipresence, they are largely unknown and uncharacterized within the Poaceae family. In this review, we describe a possible classification of the elements present in this family, some of their known transposition mechanism, their known activity and possible action in crops, and their possible origin.     

高等植物线粒体基因组进化分析

线粒体是进行呼吸代谢、为生命活动提供能量的细胞器;其基因组相对独立于核基因组,表现为半自主遗传特性。植物线粒体基因组较大,基因组重排、重复序列重组,以及基因获得/缺失/转移/重复等频繁发生,很大程度影响其基因的正常功能行使;同时,也增加了研究其基因功能及其基因组进化的难度。新一代测序技术降低了测序成本,数据库中测序基因组数据激增。其中,也包括大量已获得的植物细胞器——线粒体和叶绿体的基因组序列。本文使用公用数据库的线粒体基因组序列,通过对高等植物线粒体DNA序列、结构、功能基因丢失/迁入、DNA片段水平转移、重复序列及RNA编辑等方面比较分析,试图从某些侧面揭示植物线粒体基因组复杂的进化特征与过程,为解析植物线粒体基因组的进化、探讨细胞质雄性不育机制提供新证据。     

雷蒙德氏棉PIF-like转座元件鉴定与特征分析

PIF-like转座元件在植物基因组中含量丰富,是植物DNA转座子的重要组成部分。利用基因组学和生物信息学的研究手段,系统研究了雷蒙德氏棉全基因组水平PIF-like转座元件的数量、染色体分布、结构特征、表达模式及相邻基因的种类和功能等,共鉴定了440条包含转座酶且插入位置明确的PIF-like转座元件。这些元件几乎均匀地分布在13条染色体上,上下游2 kb内共有171个相邻编码蛋白的基因,其中132个基因注释到了GO数据库中,且这些基因的功能分布广泛;部分PIF-like转座元件表达,且具有组织特异性。这些遗传信息为深入研究棉花PIF-like转座元件介导的基因和基因组的进化规律以及棉花基因的功能奠定基础。     

流式细胞术测定5种苔藓植物的基因组大小

作为藻类和维管植物之间的过渡类群,苔藓植物不仅占有重要的进化地位,它同时可作为园艺上的观赏植物。目前对很多苔藓植物的培养条件、基因组大小等信息非常缺乏,且已进行基因组测序的苔藓物种较少,这些都严重制约了苔藓植物系统学的研究和资源利用。本研究以基因组大小为942 Mb的野生番茄(Solanum pennellii)为内标,采用流式细胞术对5种苔藓植物的基因组大小进行测定,结果表明,拟短月藓(Brachymeniopsis gymnostoma)的基因组大小约为391.40 Mb,绒叶青藓(Brachythecium velutinum)的基因组大小约为386.96 Mb,尖叶梨蒴藓(Entosthodon wichurae)的基因组大小约为441.01 Mb,桧叶白发藓(Leucobryum juniperoideum)的基因组大小约为493.21Mb,明叶藓(Vesicularia montagnei)的基因组大小约为337.94Mb。本研究为苔藓植物的全基因组测序、分子生物学研究、亲缘进化研究以及园艺苔藓品种开发和育种等方面提供重要信息。     

Chromosome-level de novo genome assemblies of over 100 plant species

Genome sequence analysis in higher plants began with the whole-genome sequencing of Arabidopsis thaliana. Owing to the great advances in sequencing technologies, also known as next-generation sequencing (NGS) technologies, genomes of more than 400 plant species have been sequenced to date. Long-read sequencing technologies, together with sequence scaffolding methods, have enabled the synthesis of chromosome-level de novo genome sequence assemblies, which has further allowed comparative analysis of the structural features of multiple plant genomes, thus elucidating the evolutionary history of plants. However, the quality of the assembled chromosome-level sequences varies among plant species. In this review, we summarize the status of chromosome-level assemblies of 114 plant species, with genome sizes ranging from 125 Mb to 16.9 Gb. While the average genome coverage of the assembled sequences reached up to 89.1%, the average coverage of chromosome-level pseudomolecules was 73.3%. Thus, further improvements in sequencing technologies and scaffolding, and data analysis methods, are required to establish gap-free telomere-to-telomere genome sequence assemblies. With the forthcoming new technologies, we are going to enter into a new genomics era where pan-genomics and the >1,000 or >1 million genomes’ project will be routine in higher plants.     

Genome size variation among sex types in dioecious and trioecious Caricaceae species

Caricaceae is a small family consisting of 35 species of varying sexual systems and includes economically important fruit crop, Carica papaya, and other species of “highland papayas”. Flow cytometry was used to obtain genome sizes for 11 species in three genera of Caricaceae to determine if genome size differences can be detected between sexes. Genome sizes ranged from 442.5 to 625.9 megabases (Mb) likely due to variation in the accumulation of retrotransposons in the genomes. The C. papaya genome size was estimated to be 442.5 Mb, larger than previously reported. Significant differences were detected between male and female samples in Jacaratia spinosa, Vasconcellea horovitziana, and V. stipulata, and between male and hermaphrodite samples of V. cundinamarcensis, suggesting the presence of sex chromosomes for these species. The small size differences between genomes of the papaya sexes were not detected using flow cytometry. Vasconcellea horovitziana was discovered to have a larger female genome size than male, suggesting the possibility of a ZW sex chromosome system in the family. The estimated genome sizes of these 11 species will be used in sequencing their genomes and in sex chromosome research for this family.     

利用高通量测序技术鉴定棉纤维发育相关miRNAs及其靶基因

miRNA (microRNA)是一类21～24个核酸长度的非编码小分子RNA(sRNA),它主要通过抑制或降解靶基因来调控植物生长发育等过程.试验利用在纤维长度上有显著差异的2个回交自交系BILs (Backcross inbred lines)的0DPA (Days post anthesis)、3 DPA的胚珠和10 DPA的纤维构建6个sRNA文库并进行Solexa 测序.以已公布的棉花D5基因组序列和棉属其他序列为参考,经分析共发现561个miRNAs,其中包括254个已知的miRNAs(属于40个miRNA家族),75个候选的miRNAs和232个新的miRNAs,研究结果极大地丰富了棉属miRNAs.通过miRNA靶基因预测分析发现多数miRNAs负调控其对应的靶基因,少数正调控.KEGG(Kyoto encyclopedia of genes and genomes)注释结果表明miRNA的靶基因在植物激素代谢途径中显著富集.     

Molecular markers: actual and potential contributions to wheat genome characterization and breeding

The demands for increasing global crop production have prompted the development of new approaches relying on molecular marker technologies to investigate and improve the plant genome. The merits of molecular markers make them valuable tools in a range of research areas. This review describes novel approaches based on modern molecular marker technologies for characterization and utilization of genetic variation for wheat improvement. Large-scale genome characterization by DNA-fingerprinting has revealed no declining trends in the molecular genetic diversity in wheat as a consequence of modern intensive breeding thus opposing the genetic ‘erosion’ hypothesis. A great number of important major genes and quantitative trait loci have been mapped with molecular markers. Marker-assisted selection based on a tight linkage between a marker allele and a gene(s) governing a qualitative or quantitative trait is gaining considerable importance as it facilitates and accelerates cultivar improvement through precise transfer of chromosome regions carrying the gene of interest. The implementations of molecular markers in wheat genotyping, mapping and breeding complemented by specific approaches associated with the complex polyploid nature of common wheat are analyzed and presented.     

Bulk pollen pollination in maize for efficient construction of introgression populations with high genome coverage

Introgression populations consist of a set of introgression lines or families, constructed by continuous backcrossing to the recurrent parent, while carrying a limited number of chromosome segments from a donor parent in their genomes. Increasing the genome coverage is an important aim when constructing introgression population. In this study, we proposed bulk pollen pollination (BPP) method and used it to increase the genome coverage of a maize introgression population. The results showed that the genome coverage of the introgression population constructed using BPP method reached 100% at BC₃ generation, which accorded with the simulation result. The BPP‐based BC₃F_1:2 population could identify most quantitative trait loci (QTL) detected using the F_2:3 population, especially major QTL. Simulation analysis showed that the genome coverage of introgression population increased with the increase of population size and the number of bulked plants, and decreased with the increase of backcross generation. Our results proved the reliability of the BPP‐based introgression population in increasing genome coverage and detecting QTL, and provided references for constructing high‐coverage introgression populations.     

FISHy Analysis of Tetrapioid Cotton Species

Fluorescent in situ hybridization (FISH) is an important technique in plant genome research,because it provides integrated information about DNA,chromosomes and genomes.Genomic in situ hybridization (GISH) is a modification of FISH that can be used to rapidly compare genorne content,relatedness,organization and/or behavior.GISH results often provide insight into genome evolution and species relationships.     

Molecular markers to assess genetic diversity

Molecular markers play an essential role today in all aspects of plant breeding, ranging from the identification of genes responsible for desired traits to the management of backcrossing programs. The emergence of marker systems has, for the last 30 years, closely tracked developments in biochemistry and molecular biology. Following the demonstration that retrotransposons are ubiquitous, active, and abundant in plant genomes, markers were developed that are based on the insertional polymorphism they create upon replication. They virtually all exploit the joint that is formed, during retrotransposon integration, between genomic DNA and the long terminal repeats at either end of retrotransposon. The various retrotransposon marker systems differ in the nature of the second primer used in the amplification reactions. All except one of these marker methods is dominant (RBIP is co-dominant). Hence, the availability of effective means to generate doubled haploid populations through gametophytic embryogenesis is valuable for the efficient use of these markers. Over the last eight years, retrotransposon-based markers have been developed for crop species and trees across the plant kingdom, as well as for fungi and insects. Many retrotransposons features make them appealing as the basis of molecular marker systems. They are usually dispersed throughout the genome and produce large genetic changes at the point of insertion that can be detected with family-specific amplification primers. The ancestral state of a retrotransposon insertion is known, and subsequent changes at the locus are not subject to homoplasy. Retrotransposon markers are useful in accelerating backcrossing programs, tagging genes of interest, tracking germplasm, verifying and producing pedigrees, and examining crop evolution.     

Recent advances in molecular genetics of forest trees

The use of molecular markers has greatly enhanced our understanding of the genome structure of forest trees. Conifers, in particular, have a relatively large genome, containing a very high proportion of repeated DNA, consisting of tandemly repetitive and dispersed repetitive DNA sequences. The nature of highly conserved tandemly repetitive rRNA genes has been investigated in a number of tree species, and their sites mapped on specific chromosomes by fluorescent in situ hybridization (FISH). Different families of retrotransposons (IFG, and TPE1) have been isolated and characterized from the dispersed repetitive DNA of pines. Genome maps have been constructed in a number of forest tree genera: Pinus, Picea, Pseudotsuga, Cryptomeria, Taxus, Populus, and Eucalyptus. EST databases have been established from cDNA clones of pines and poplars. The structure and maternal or paternal modes of inheritance of organelle genomes have been investigated in forest trees. Comparative mapping in conifers has shown that gene families are conserved across genera. Due to lack of polyploidy in conifers, the evolution of this group of trees may have occurred primarily by duplication and dispersal of genes, probably by retrotranspositions, to form complex gene families. The evolution of angiosperm tree species has presumably involved both gene duplication as well as genome duplication (polyploidy). Application of genetic engineering has shown that genes from phylogenetically unrelated organisms can be introduced and expressed in trees, thus offering prospects of genetic improvement of forest trees. This revised version was published online in August 2006 with corrections to the Cover Date.     

Genome-Wide Identification and Functional Prediction of Phytochelatin Synthase Gene in Upland Cotton

[Objective] Heavy metal stress rise advertise effects on growth and development in plant, from which phytochelatin synthase (PCS) plays key roles to protect plant cells. This article will present studies on the gene amount, structure, distribution and features. [Method] PCS gene family in cotton are analyzed based on completely global genome sequence cotton species including Gossypium hirsutum ((AD)1), G. raimondii (D5) and G. arboreum (A2), for further understanding of those genes and protein family features. In this study, we conducted the analysis involving in identification on PCS family members, special protein domain comparison, polygenetic analysis, gene structure prediction and Cysteine survey. [Result] 2, 2 and 4 PCS genes were identified out in G. raimondii (D5), G. arboreum (A2) and G. hirsutum ((AD)1), respectively. All these 8 PCS genes had phytochelatin and phytochelatin_C domains and strictly conserved amino acid residues related to catalytic activity. Cotton PCS protein family members could be divided into 2 sub-group, and these members belongs to sub-group I or sub-group II are close todicotyledon or nematode, respectively. What’s more, there are some difference in both gene structure and Cys distribution between those 2 sub-groups. Less integrity of exons in PCS genes in G. raimondii, comparing to G. hirsutum and G. arboreum. [Conclusion] Comparing to sub-group II, the PCS genes from sub-group I should be higher catalytic activity. G. hirsutum and its donor G. arboreum probably are more heavy metal tolerant than G. raimondii. Based on the results, this research will provide some insights on further functional study.     

植物中微型反向重复转座元件(MITEs)研究进展及其在作物遗传研究中的应用

MITEs(Miniature Inverted-repeat Transposable Elements),是最近发现的几乎在所有生物基因组中广泛分布的一类非自主型DNA转座元件,具有典型的TIR(Terminal Invert Repeat)和TSD(Target Sequence Duplication)结构,长度较短。MITEs主要分布在常染色质区,并有大量的拷贝分布在基因编码区附近。MITEs可能来源于自主转座元件的内部缺失;转座酶通过对TIR的识别和结合,激活MITEs的转录活性,使其在基因组中进行扩增。MITEs在基因组中不同的分布模式,使物种中形成了大量的遗传多态性,为自然选择或驯化提供了基础,对基因的表达模式也有重要的影响。随着研究的深入,逐渐揭示出MTIEs与农艺性状间的联系,MITEs在作物遗传研究和育种中的应用价值也逐渐体现。本文对以上内容做了简单的综述,并对进一步的研究做出展望。     

Recent developments in genome editing and applications in plant breeding

Increasing genetic variation beyond natural variation is an important aim in plant breeding. In the past 70 years, random mutagenesis by irradiation or by chemicals has created numerous mutants which have been frequently used in breeding. However, their application is hampered by the mutational load due to many background mutations. In the past 10 years, new techniques for site‐directed mutagenesis have been introduced to plant breeding which are commonly referred to as “genome editing.” Among these, the CRISPR/Cas9 system turned out to be the most efficient and easy to apply. DNA is cleaved by a nuclease precisely at a target site where a mutation is likely to be beneficial. The DNA is healed by the cellular repair system either by error‐prone non‐homologous end joining or by homologous recombination, by which small DNA fragments can be inserted at the target site. In this review, we describe the application of targeted mutagenesis to crop plants and the modification of agronomically important traits, which could have direct impacts on plant breeding.     

甘蔗栽培种单倍体基因组SSR位点的发掘与应用

甘蔗是世界上最重要的糖料作物之一,由于尚未完全破译栽培种基因组,导致SSR标记匮乏,难以覆盖全基因组,限制了甘蔗遗传研究的进展。本研究以栽培种R570的4660个BAC文库片段序列(累计总长为382 Mb,预测到25,316个编码蛋白基因)组装成的一套甘蔗单倍体基因组的模板,利用MISA (Microsatellite identification tool)软件,发掘SSR位点;并综合分析其与4种禾本科植物(高粱、玉米、水稻和二岁短柄草)SSR位点的分布特征;选取50对以TG和AG重复基序的SSR引物,分别利用4个甘蔗属材料(R570、ROC1、LA purple和SES208)和24个重要甘蔗亲本,对SSR引物进行扩增效率验证和多态性分析。共发掘到27,241个SSR位点,平均每个BAC片段有6.29个SSR位点,平均密度为71.33个SSR Mb?1,远低于高粱的平均密度(350.00个SSR Mb?1)。在重复基序中,占比前2位的分别为单核苷酸基序(11,079个)和三核苷酸重复基序(6447个),合计占总SSR位点数的64.33%。与甘蔗不同的是, 4种禾本科植物中的三核苷酸...     

Microsatellite markers: an overview of the recent progress in plants

In recent years, molecular markers have been utilized for a variety of applications including examination of genetic relationships between individuals, mapping of useful genes, construction of linkage maps, marker assisted selections and backcrosses, population genetics and phylogenetic studies. Among the available molecular markers, microsatellites or simple sequence repeats (SSRs) which are tandem repeats of one to six nucleotide long DNA motifs, have gained considerable importance in plant genetics and breeding owing to many desirable genetic attributes including hypervariability, multiallelic nature, codominant inheritance, reproducibility, relative abundance, extensive genome coverage including organellar genomes, chromosome specific location and amenability to automation and high throughput genotyping. High degree of allelic variation revealed by microsatellite markers results from variation in number of repeat-motifs at a locus caused by replication slippage and/or unequal crossing-over during meiosis. In spite of limited understanding of the functions of the SSR motifs within the plant genes, SSRs are being widely utilized in plant genome analysis. Microsatellites can be developed directly from genomic DNA libraries or from libraries enriched for specific microsatellites. Alternatively, microsatellites can also be found by searching public databases such as GenBank and EMBL or through cross-species transferability. At present, EST databases are an important source of candidate genes, as these can generate markers directly associated with a trait of interest and may be transferable in close relative genera. A large number of SSR based techniques have been developed and a quantum of literature has accumulated regarding the applicability of SSRs in plant genetics and genomics. In this review we discuss the recent developments (last 4–5 years) made in plant genetics using SSR markers.     

基于株高性状的玉米EST序列与水稻基因组的比较研究

从已公布的玉米分子标记中，挑选出均匀覆盖玉米全基因组、平均间距小于10 cM的224个SSR和RFLP分子标记，从NCBI上查找这些标记所在的玉米EST或基因的原始序列，逐一与水稻数据库的序列信息进行同源性比较。结果表明：在PN<1e-5水平上，从水稻数据库中共找到16 939段同源序列，平均每段玉米的序列可以在水稻数据库中找到75.6     

植物抗病基因特异性分子进化

病原物与寄主间长期的相互选择与适应，使得植物的抗病性具有丰富的表现形式。根据基因对基因模式，植物中存在的抗病基因和病原物中具备的无毒基因的互作进化可视为连续的步步适应的相互选择的过程。随着抗病基因的分离以及抗病性分子生物学研究的不断深入，抗病基因保持对无毒基因的识别从而不断进化的分子机制逐步得到阐明。本文综述了植物与病原物相互作用过程中，植物对病原物的特异性识别，由此获得的对于该病原物的专化抗性，并且随病原物的变异而进化的分子机制方面的研究进展，主要包括：抗病基因的结构特征，无毒基因的多样性，抗病基因的基因组结构，抗病基因之间在起源和进化上的关系以及重组、复制、删除、转座子等对植物保持对不断变化的无毒基因特异性识别所起的作用等方面。     

DaizuBase,an integrated soybean genome database including BAC-based physical maps

Soybean [Glycine max (L) Merrill] is one of the most important leguminous crops and ranks fourth after to rice, wheat and maize in terms of world crop production. Soybean contains abundant protein and oil, which makes it a major source of nutritious food, livestock feed and industrial products. In Japan, soybean is also an important source of traditional staples such as tofu, natto, miso and soy sauce. The soybean genome was determined in 2010. With its enormous size, physical mapping and genome sequencing are the most effective approaches towards understanding the structure and function of the soybean genome. We constructed bacterial artificial chromosome (BAC) libraries from the Japanese soybean cultivar, Enrei. The end-sequences of approximately 100,000 BAC clones were analyzed and used for construction of a BAC-based physical map of the genome. BLAST analysis between Enrei BAC-end sequences and the Williams82 genome was carried out to increase the saturation of the map. This physical map will be used to characterize the genome structure of Japanese soybean cultivars, to develop methods for the isolation of agronomically important genes and to facilitate comparative soybean genome research. The current status of physical mapping of the soybean genome and construction of database are presented.