植物多倍体基因组的形成与进化

多倍化是植物进化变异的自然现象,也是促进植物发生进化改变的重要力量。在被子植物中,约 70％的种类在进化史中曾发生过一次或多次多倍化的过程。目前的研究结果表明,自然界绝大多数多倍体是通过未减数配子的融合而形成的,并且很多多倍体种是通过多次独立的多倍化过程而重复发生的。由多倍化所导致的重复基因在多倍体基因组中可能有三种不同的命运,即：保持原有的功能、基因沉默或分化并执行新的功能。多倍化以后,重复基因组的进化动态则主要表现在染色体重排和“染色体二倍化”、不同基因组之间的相互渗透、以及核-质之间的相互作用等方面。     

A BAC Library Constructed to the Rice Cultivar

"Minghui 63" is the restorer line for a number of the most important commercial rice hybrids varieties in China. To facilitate long-term commitment in genetic analysis and molecular cloning of the superior genes in the genome of "Minghui 63", the authors have constructed a largeinsert genomic DNA library using the bacterial artificial chromosome (BAC) cloning vector (pBe- loBAC 11). Size fractionated Hind m digest of genomic DNA was ligated to the BAC vector, and the ligation mixture was used to transform the bacterial strain DH10B. A total of over 26 000 clones were obtained with the average insert size of about 150 kb, ranging from 90 to 240 kb. These clones thus represent 9 x rice haploid genome equivalents. The library is now being used for physical mapping of several genomic regions for map-based gene cloning.     

Insight into Trichoderma reesei's genome content, organization and evolution revealed through BAC library characterization

Trichoderma reesei is an important industrial fungus known for its ability to efficiently secrete large quantities of protein as well as its wide variety of biomass degrading enzymes. Past research on this fungus has primarily focused on extending its protein production capabilities, leaving the structure of its 33 Mb genome essentially a mystery. To begin to address these deficiencies and further our knowledge of T. reesei's secretion and cellulolytic potential, we have created a genomic framework for this fungus. We constructed a BAC library containing 9216 clones with an average insert size of 125 kb which provides a coverage of 28 genome equivalents. BAC ends were sequenced and annotated using publicly available software which identified a number of genes not seen in previously sequenced EST datasets. Little evidence was found for repetitive sequence in T. reesei with the exception of several copies of an element with similarity to the Podospora anserina transposon, PAT. Hybridization of 34 genes involved in biomass degradation revealed five groups of co-located genes in the genome. BAC clones were fingerprinted and analyzed using fingerprinted contigs (FPC) software resulting in 334 contigs covering 28 megabases of the genome. The assembly of these FPC contigs was verified by congruence with hybridization results.     

GENOMICS IN THE LIGHT OF EVOLUTIONARY TRANSITIONS

Molecular biology has entrenched the gene as the basic hereditary unit and genomes are often considered little more than collections of genes. However, new concepts and genomic data have emerged, which suggest that the genome has a unique place in the hierarchy of life. Despite this, a framework for the genome as a major evolutionary transition has not been fully developed. Instead, genome origin and evolution are frequently considered as a series of neutral or nonadaptive events. In this article, we argue for a Darwinian multilevel selection interpretation for the origin of the genome. We base our arguments on the multilevel selection theory of hypercycles of cooperative interacting genes and predictions that gene‐level trade‐offs in viability and reproduction can help drive evolutionary transitions. We consider genomic data involving mobile genetic elements as a test case of our view. A new concept of the genome as a discrete evolutionary unit emerges and the gene–genome juncture is positioned as a major evolutionary transition in individuality. This framework offers a fresh perspective on the origin of macromolecular life and sets the scene for a new, emerging line of inquiry—the evolutionary ecology of the genome.     

基因编辑技术在斑马鱼中的应用及研究进展

基因编辑技术通过对特定DNA片段的插入、敲除、修饰或替换等,实现对生物体中目标基因的编辑。与早期基因工程技术将遗传物质随机插入宿主基因组中的方式不同的是,基因编辑技术能够定点需要插入的位置,从而实现对生物体基因组特定位点的准确修饰、人为地改造生物体的遗传信息,目前广泛应用于斑马鱼的基因组学、遗传发育和基因功能研究中。其方法包括诱变技术、Tol2转座子、Morpholino、ZFNs、TALEN和CRISPR/Cas系统等。本研究主要介绍了基因编辑技术的作用机理与发展概况。作为一种精准而高效的基因工程方法,基因编辑技术在近年来得到了飞速地发展。它既可以采用对特定基因的靶向突变来研究基因的功能,也可以通过将功能性基因插入并替代缺陷基因而用于某些遗传性疾病的基因治疗。可以肯定的是,基因编辑技术未来将在基础生物学、医学、生物技术等多个领域具有重要的研究价值和应用价值。     

Non-LTR retrotransposons with unique integration preferences downstream of Dictyostelium discoideum tRNA genes

Retrotransposable elements are genetic entities which move and replicate within host cell genomes. We have previously reported on the structures and genomic distributions of two non-long terminal repeat (non-LTR) retrotransposons, DRE and Tdd-3, in the eukaryotic microorganism Dictyostelium discoideum. DRE elements are found inserted upstream, and Tdd-3 elements downstream, of transfer RNA (tRNA) genes with remarkable position and orientation specificities. The data set currently available from the Dictyostelium Genome Project led to the characterisation of two repetitive DNA elements which are related to the D. discoideum non-LTR retrotransposon Tdd-3 in both their structural properties and genomic distributions. It appears from our data that in the D. discoideum genome tRNA genes are major targets for the insertion of mobilised non-LTR retrotransposons. This may be interpreted as the consequence of a process of coevolution, allowing a viable population of retroelements to transpose without being deleterious to the small microbial host genome which carries only short intergenic DNA sequences. A new nomenclature is introduced to designate all tRNA gene-targeted non-LTR retrotransposons (TREs) in the D. discoideum genome. TREs inserted 5′ and 3′ of tRNA genes are named TRE5 and TRE3, respectively. According to this nomenclature DRE and Tdd-3 are renamed TRE5-A and TRE3-A, respectively. The new retroelements described in this study are named TRE3-B (formerly RED) and TRE3-C. Received: 27 May 1999 / Accepted: 23 July 1999     

以BAC为基础的疱疹病毒感染性克隆技术

疱疹病毒（HPVs）庞大而复杂的基因组一直使得HPVs的遗传分析颇具挑战性。近几年发展起来的以细菌人工染色体（BAC）为基础的HPVs全长感染性克隆是全新的技术,促进了在HPVs整个基因组中对单个基因功能的研究。本文以EB病毒为例,介绍了该技术的原理、建立、突变方法及应用。     

Integration of genetic and genomic methods for identification of genes and gene variants encoding QTLs in the nonhuman primate

We have developed an integrated approach, using genetic and genomic methods, in conjunction with resources from the Southwest National Primate Research Center (SNPRC) baboon colony, for the identification of genes and their functional variants that encode quantitative trait loci (QTL). In addition, we use comparative genomic methods to overcome the paucity of baboon specific reagents and to augment translation of our findings in a nonhuman primate (NHP) to the human population. We are using the baboon as a model to study the genetics of cardiovascular disease (CVD). A key step for understanding gene–environment interactions in cardiovascular disease is the identification of genes and gene variants that influence CVD phenotypes. We have developed a sequential methodology that takes advantage of the SNPRC pedigreed baboon colony, the annotated human genome, and current genomic and bioinformatic tools. The process of functional polymorphism identification for genes encoding QTLs involves comparison of expression profiles for genes and predicted genes in the genomic region of the QTL for individuals discordant for the phenotypic trait mapping to the QTL. After comparison, genes of interest are prioritized, and functional polymorphisms are identified in candidate genes by genotyping and quantitative trait nucleotide analysis. This approach reduces the time and labor necessary to prioritize and identify genes and their polymorphisms influencing variation in a quantitative trait compared with traditional positional cloning methods.     

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...     

The evolutionary mechanism of cancer

Identification of the general molecular mechanism of cancer is the Holy Grail of cancer research. Since cancer is believed to be caused by a sequential accumulation of cancer gene mutations, the identification, characterization, and targeting of common genetic alterations and their defined pathways have dominated the field for decades. Despite the impressive data accumulated from studies of gene mutations, epigenetic dysregulation, and pathway alterations, an overwhelming amount of diverse molecular information has offered limited understanding of the general mechanisms of cancer. To solve this paradox, the newly established genome theory is introduced here describing how somatic cells evolve within individual patients. The evolutionary mechanism of cancer is characterized using only three key components of somatic cell evolution that include increased system dynamics induced by stress, elevated genetic and epigenetic heterogeneity, and genome alteration mediated natural selection. Cancer progression represents a macro‐evolutionary process where karyotype change or genome replacement plays the key dominant role. Furthermore, the recently identified relationship between the evolutionary mechanism and a large number of diverse individual molecular mechanisms is discussed. The total sum of all the individual molecular mechanisms is equal to the evolutionary mechanism of cancer. Individual molecular mechanisms including all the molecular mechanisms described to date are stochastically selected and unpredictable and are therefore clinically impractical. Recognizing the fundamental importance of the underlying basis of the evolutionary mechanism of cancer mandates the development of new strategies in cancer research. J. Cell. Biochem. 109: 1072–1084, 2010. © 2010 Wiley‐Liss, Inc.     

Protozoan genomes: gene identification and annotation

The draft sequence of several complete protozoan genomes is now available and genome projects are ongoing for a number of other species. Different strategies are being implemented to identify and annotate protein coding and RNA genes in these genomes, as well as study their genomic architecture. Since the genomes vary greatly in size, GC-content, nucleotide composition, and degree of repetitiveness, genome structure is often a factor in choosing the methodology utilised for annotation. In addition, the approach taken is dictated, to a greater or lesser extent, by the particular reasons for carrying out genome-wide analyses and the level of funding available for projects. Nevertheless, these projects have provided a plethora of material that will aid in understanding the biology and evolution of these parasites, as well as identifying new targets that can be used to design urgently required drug treatments for the diseases they cause.     

Cancer progression by non-clonal chromosome aberrations

The establishment of the correct conceptual framework is vital to any scientific discipline including cancer research. Influenced by hematologic cancer studies, the current cancer concept focuses on the stepwise patterns of progression as defined by specific recurrent genetic aberrations. This concept has faced a tough challenge as the majority of cancer cases follow non-linear patterns and display stochastic progression. In light of the recent discovery that genomic instability is directly linked to stochastic non-clonal chromosome aberrations (NCCAs), and that cancer progression can be characterized as a dynamic relationship between NCCAs and recurrent clonal chromosome aberrations (CCAs), we propose that the dynamics of NCCAs is a key element for karyotypic evolution in solid tumors. To support this viewpoint, we briefly discuss various basic elements responsible for cancer initiation and progression within an evolutionary context. We argue that even though stochastic changes can be detected at various levels of genetic organization, such as at the gene level and epigenetic level, it is primarily detected at the chromosomal or genome level. Thus, NCCA-mediated genomic variation plays a dominant role in cancer progression. To further illustrate the involvement of NCCA/CCA cycles in the pattern of cancer evolution, four cancer evolutionary models have been proposed based on the comparative analysis of karyotype patterns of various types of cancer.     

The genome‐centric concept: resynthesis of evolutionary theory

Modern biology has been heavily influenced by the gene‐centric concept. Paradoxically, this very concept – on which bioresearch is based – is challenged by the success of gene‐based research in terms of explaining evolutionary theory. To overcome this major roadblock, it is essential to establish new theories, to not only solve the key puzzles presented by the gene‐centric concept, but also to provide a conceptual framework that allows the field to grow. This paper discusses a number of paradoxes and illustrates how they can be addressed by the genome‐centric concept in order to further resynthesize evolutionary theory. In particular, methodological breakthroughs that analyze genome evolution are discussed. The multiple interactions among different levels of a complex system provide the key to understanding the relationship between self‐organization and natural selection. Darwinian natural selection applies to the biological level due to its unique genetic and heterogeneous features, but does not simply or directly apply to either the lower non‐living level or higher intellectual society level. At the complex bio‐system level, the genome context (the entire package of genes and their genomic physical relationship or genomic topology), not the individual genes, defines the system and serves as the principle selection platform for evolution.     

Building the sugarcane genome for biotechnology and identifying evolutionary trends

Background

Sugarcane is the source of sugar in all tropical and subtropical countries and is becoming increasingly important for bio-based fuels. However, its large (10 Gb), polyploid, complex genome has hindered genome based breeding efforts. Here we release the largest and most diverse set of sugarcane genome sequences to date, as part of an on-going initiative to provide a sugarcane genomic information resource, with the ultimate goal of producing a gold standard genome.

Results

Three hundred and seventeen chiefly euchromatic BACs were sequenced. A reference set of one thousand four hundred manually-annotated protein-coding genes was generated. A small RNA collection and a RNA-seq library were used to explore expression patterns and the sRNA landscape. In the sucrose and starch metabolism pathway, 16 non-redundant enzyme-encoding genes were identified. One of the sucrose pathway genes, sucrose-6-phosphate phosphohydrolase, is duplicated in sugarcane and sorghum, but not in rice and maize. A diversity analysis of the s6pp duplication region revealed haplotype-structured sequence composition. Examination of hom(e)ologous loci indicate both sequence structural and sRNA landscape variation. A synteny analysis shows that the sugarcane genome has expanded relative to the sorghum genome, largely due to the presence of transposable elements and uncharacterized intergenic and intronic sequences.

Conclusion

This release of sugarcane genomic sequences will advance our understanding of sugarcane genetics and contribute to the development of molecular tools for breeding purposes and gene discovery.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-540) contains supplementary material, which is available to authorized users.     

水稻基因组测序的研究进展

水稻是最重要的粮食作物之一,世界上大约有一半的人口以水稻为主要粮食。作为基因组研究的模式植物,水稻基因组的测序工作已在世界范围内展开。此项研究工作不仅能破译水稻全基因组序列,还将有助于了解其他禾本科植物的基因组信息。本对水稻基因组测序工作进展作一综述。     

Structure and regulation of human troponin genes

The recent completion of a first draft of the human genome has allowed "in silico" genome browsing to become routine. Such computer-based research is now a useful adjunct to experiments based at the bench, and is accelerating gene discovery and the analysis and understanding of genes in their genomic contexts. This review summarises recent findings on genes encoding proteins of the troponin complex. We describe the organization of the three pairs of genes which encode isoforms of troponins I and T, and discuss how this relates to their evolution and regulation. Detailed analysis of the chromosomal context of the cardiac troponin I and slow skeletal troponin T genes reveals a region of densely packed differentially expressed genes, including new genes identified by automatic genome annotation. This information is discussed within the context of detailed analysis of the best-studied gene in this region, cardiac troponin I. In this way, we illustrate the uses to which a combination of conventional bench experiments and "in silico" analyses may be put in understanding the relationship between structure and function within the genome.     

New tools for the high throughput characterization of rat genomic DNA samples

Linkage studies and positional cloning projects for the identification of disease related genes require the genetic characterization of large numbers of genomic DNA samples. The application of spotting robots enables the production of high density filters representing several thousand DNA probes. To take full advantage of the potential of these filters we have established a new, hybridization based Interspersed Repetitive Sequence (IRS-)marker system for the rat genome. This marker panel was shown to be useful for rapid genotyping of many multigenic crosses as well as high throughput characterization of large insert genomic libraries.     

Unraveling the effect of genomic structural changes in the rhesus macaque - implications for the adaptive role of inversions

Background

By reshuffling genomes, structural genomic reorganizations provide genetic variation on which natural selection can work. Understanding the mechanisms underlying this process has been a long-standing question in evolutionary biology. In this context, our purpose in this study is to characterize the genomic regions involved in structural rearrangements between human and macaque genomes and determine their influence on meiotic recombination as a way to explore the adaptive role of genome shuffling in mammalian evolution.

Results

We first constructed a highly refined map of the structural rearrangements and evolutionary breakpoint regions in the human and rhesus macaque genomes based on orthologous genes and whole-genome sequence alignments. Using two different algorithms, we refined the genomic position of known rearrangements previously reported by cytogenetic approaches and described new putative micro-rearrangements (inversions and indels) in both genomes. A detailed analysis of the rhesus macaque genome showed that evolutionary breakpoints are in gene-rich regions, being enriched in GO terms related to immune system. We also identified defense-response genes within a chromosome inversion fixed in the macaque lineage, underlying the relevance of structural genomic changes in evolutionary and/or adaptation processes. Moreover, by combining in silico and experimental approaches, we studied the recombination pattern of specific chromosomes that have suffered rearrangements between human and macaque lineages.

Conclusions

Our data suggest that adaptive alleles – in this case, genes involved in the immune response – might have been favored by genome rearrangements in the macaque lineage.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-530) contains supplementary material, which is available to authorized users.