Towards an accurate sequence of the rice genome Delseny M. Towards an accurate sequence of the rice genome. Curr Opin Plant Biol. 2003 Apr; 6 (2): 101-5. Several more- or less-elaborated rice genome sequences have been produced recently using different strategies. It has become possible to compare them and to unravel the major features of the rice genome in terms of nucleotide composition, repeats, gene content and variability. It has also become possible to compare the rice and Arabidopsis genomes and to evaluate rice as a model genome. Towards an accurate sequence of the rice genome Comparing the whole-genome-shotgun and map-based sequences of the rice genome Yu J, Ni P, Wong GK. Comparing the whole-genome-shotgun and map-based sequences of the rice genome. Trends Plant Sci. 2006 Aug; 11 (8): 387-91. Epub 2006 Jul 13. The rice genome has now been sequenced using whole-genome-shotgun and map-based methods. The relative merits of the two methods are the subject of debate, as they were in the human genome project. In this Opinion article, we will show that the serious discrepancies between the resultant sequences are mostly found in the large transposable elements such as copia and gypsy that populate the intergenic regions of plant genomes. Differences in published gene counts and polymorphism rates are similarly resolved by considering how transposable elements affect the sequence analysis. Comparing the whole-genome-shotgun and map-based sequences of the rice genome Diversity in Oryza genus Vaughan DA, Morishima H, Kadowaki K. Diversity in the Oryza genus. Curr Opin Plant Biol. 2003 Apr; 6 (2): 139-46. The pan-tropical wild relatives of rice grow in a wide variety of habitats: forests, savanna, mountainsides, rivers and lakes. The completion of the sequencing of the rice nuclear and cytoplasmic genomes affords an opportunity to widen our understanding of the genomes of the genus Oryza. Research on the Oryza genus has begun to help to answer questions related to domestication, speciation, polyploidy and ecological adaptation that cannot be answered by studying rice alone. The wild relatives of rice have furnished genes for the hybrid rice revolution, and other genes from Oryza species with major impact on rice yields and sustainable rice production are likely to be found. Care is needed, however, when using wild relatives of rice in experiments and in interpreting the results of these experiments. Careful checking of species identity, maintenance of herbarium specimens and recording of Genbank accession numbers of material used in experiments should be standard procedure when studying wild relatives of rice. Diversity in Oryza genus Genome-wide intraspecific DNA-sequence variations in rice Han B, Xue Y. Genome-wide intraspecific DNA-sequence variations in rice. Curr Opin Plant Biol.2003 Apr; 6 (2): 134-8. Genome-wide comparative analysis of the DNA sequences of two major cultivated rice subspecies, Oryza sativa L. ssp indica and Oryza sativa L. ssp japonica, have revealed their extensive microcolinearity in gene order and content. However, deviations from colinearity are frequent owing to insertions or deletions. Intraspecific sequence polymorphisms commonly occur in both coding and non-coding regions. These variations often affect gene structures and may contribute to intraspecific phenotypic adaptations. Genome-wide intraspecific DNA-sequence variations in rice Sequencing the maize genome Martienssen RA, Rabinowicz PD, O'Shaughnessy A, McCombie WR. Sequencing the maize genome. Curr Opin Plant Biol. 2004 Apr; 7 (2): 102-7. Sequencing of complex genomes can be accomplished by enriching shotgun libraries for genes. In maize, gene-enrichment by copy-number normalization (high C(0)t) and methylation filtration (MF) have been used to generate up to two-fold coverage of the gene-space with less than 1 million sequencing reads. Simulations using sequenced bacterial artificial chromosome (BAC) clones predict that 5x coverage of gene-rich regions, accompanied by less than 1x coverage of subclones from BAC contigs, will generate high-quality mapped sequence that meets the needs of geneticists while accommodating unusually high levels of structural polymorphism. By sequencing several inbred strains, we propose a strategy for capturing this polymorphism to investigate hybrid vigor or heterosis. Sequencing the maize genome Genomic diversity in forest tree Savolainen O, Pyhjrvi T. Genomic diversity in forest trees. Curr Opin Plant Biol. 2007 Apr; 10 (2): 162-7. Epub 2007 Feb 9. Forest trees in general are out-crossing, long-lived, and at early stages of domestication. Molecular evolution at neutral sites is very slow because of the long generation times. Transferring information between closely related conifer species is facilitated by high sequence similarity. At the nucleotide level, trees have at most intermediate levels of variation relative to other plants. Importantly, in many species linkage disequilibrium within genes declines within less than 1000 bp. In contrast to the slow rate of neutral evolution, large tree populations respond rapidly to natural selection. Detecting traces of selection may be easier in tree populations than in many other species. Association studies between genotypes and phenotypes are proving to be useful tools for functional genomics. Genomic diversity in forest tree Complex gene families in pine genomes Jumping genes and maize genomics
Comparison of rice and Arabidopsis annotation Schoof H, Karlowski WM. Comparison of rice and Arabidopsis annotation. Curr Opin Plant Biol. 2003 Apr; 6 (2): 106-12. Several versions of the rice genome were published in 2002, providing a first overview of the genome content of this model monocot. At the same time, the genome of the model dicot, Arabidopsis thaliana, reached a new level of annotation as thousands of full-length cDNA sequences were integrated with the genome sequence. Comparison of rice and Arabidopsis annotation The ABCs of comparative genomics in the Brassicaceae: building blocks of crucifer genomes Schranz ME, Lysak MA, Mitchell-Olds T. The ABC's of comparative genomics in the Brassicaceae: building blocks of crucifer genomes. Trends Plant Sci. 2006 Nov; 11 (11): 535-42. Epub 2006 Oct 6. In this review we summarize recent advances in our understanding of phylogenetics, polyploidization and comparative genomics in the family Brassicaceae. These findings pave the way for a unified comparative genomic framework. We integrate several of these findings into a simple system of 24 conserved chromosomal blocks (labeled A-X). The naming, order, orientation and color-coding of these blocks are based on their positions in a proposed ancestral karyotype (n=8), rather than by their position in the reduced genome of Arabidopsis thaliana (n=5). We show how these crucifer building blocks can be rearranged to model the genome structures of A. thaliana, Arabidopsis lyrata, Capsella rubella and Brassica rapa. A framework for comparison between species is timely because several crucifer genome-sequencing projects are underway. The ABCs of comparative genomics in the Brassicaceae-building blocks of crucifer genomes Comparative biology comes into bloom: genomic and genetic comparision of flowering pathways in rice and Arabidopsis Izawa T, Takahashi Y, Yano M. Comparative biology comes into bloom: genomic and genetic comparison of flowering pathways in rice and Arabidopsis. Curr Opin Plant Biol. 2003 Apr; 6 (2): 113-20. Huge advances in plant biology are possible now that we have the complete genome sequences of several flowering plants. Now, genomes can be comprehensively compared and map-based cloning can be performed more easily. Association study is emerging as a powerful method for the functional identification of genes and molecular genetics has begun to reveal the basis of plant diversity. Taking the flowering pathways as an example, we discuss the potential of several approaches to comparative biology. Comparative biology comes into bloom-genomic and genetic comparision of flowering pathways in rice and Arabidopsis Unveiling the molecular arms race between two conflicting genomes in cytoplasmic male sterility Touzet P, Budar F. Unveiling the molecular arms race between two conflicting genomes in cytoplasmic male sterility? Trends Plant Sci. 2004 Dec; 9 (12): 568-70. Cytoplasmic male sterility can be thought of as the product of a genetic conflict between two genomes that have different modes of inheritance. Male sterilizing factors, generally encoded by chimeric mitochondrial genes, can be down-regulated by specific nuclear restorer genes. The recent cloning of a restorer gene in rice and its comparison with restorer genes cloned in petunia and radish could be regarded as the beginning of a general molecular scenario in this peculiar arms race. Unveiling the molecular arms race between two conflicting genomes in cytoplasmic male sterility
The genetic colinearty of rice and other cereals on the basis of genomic sequence analysis Bennetzen JL, Ma J. The genetic colinearity of rice and other cereals on the basis of genomic sequence analysis. Curr Opin Plant Biol. 2003 Apr; 6 (2): 128-33. Small segments of rice genome sequence have been compared with that of the model plant Arabidopsis thaliana and with several closer relatives, including the cereals maize, rice, sorghum, barley and wheat. The rice genome is relatively stable relative to those of other grasses. Nevertheless, comparisons with other cereals have demonstrated that the DNA between cereal genes is highly variable and evolves rapidly. Genic regions have undergone many more small rearrangements than have been revealed by recombinational mapping studies. Tandem gene duplication/deletion is particularly common, but other types of deletions, inversions and translocations also occur. The many thousands of small genic rearrangements within the rice genome complicate but do not negate its use as a model for larger cereal genomes. The genetic colinearty of rice and other cereals on the basis of genomic sequence analysis Updating the crop circle Devos KM. Updating the 'crop circle'. Curr Opin Plant Biol. 2005 Apr; 8 (2): 155-62. Comparative analyses unravel the relationships between genomes of related species. The most comprehensive comparative dataset obtained to date is from the grass family, which contains all of the major cereals. Early studies aimed to identify chromosomal regions that have remained conserved over long evolutionary time periods, but in recent years, researchers have focused more on the extent of colinearity at the DNA-sequence level. The latter studies have uncovered many small rearrangements that disturb colinearity in orthologous chromosome regions. In part, genomes derive their plasticity from genome- and gene-amplification processes. Duplicated gene copies are more likely to escape selective constraints and thus move to other regions of the genome, where they might acquire new functions or become deleted. These rearrangements will affect map applications. The most popular applications, especially since the complete rice genomic sequence has been available, are the use of comparative data in the generation of new markers to tag traits in other species and to identify candidate genes for these traits. The isolation of genes underlying orthologous traits is the first step in conducting comparative functional studies. Updating the crop circle Colinearty and gene density in grass genomes Keller B, Feuillet C. Colinearity and gene density in grass genomes. Trends Plant Sci. 2000 Jun; 5 (6): 246-51. Grasses are the single most important plant family in agriculture. In the past years, comparative genetic mapping has revealed conserved gene order (colinearity) among many grass species. Recently, the first studies at gene level have demonstrated that microcolinearity of genes is less conserved: small scale rearrangements and deletions complicate the microcolinearity between closely related species, such as sorghum and maize, but also between rice and other crop plants. In spite of these problems, rice remains the model plant for grasses as there is limited useful colinearity between Arabidopsis and grasses. However, studies in rice have to be complemented by more intensive genetic work on grass species with large genomes (maize, Triticeae). Gene-rich chromosomal regions in species with large genomes, such as wheat, have a high gene density and are ideal targets for partial genome sequencing. Colinearty and gene density in grass genomes Comparison of genes among cereals Ware D, Stein L. Comparison of genes among cereals. Curr Opin Plant Biol. 2003 Apr; 6 (2): 121-7. Comparison of partially sequenced cereal genomes suggests a mosaic structure consisting of recombinationally active gene-rich islands that are separated by blocks of high-copy DNA. Annotation of the whole rice genome suggests that most, but not all, cereal genes are present within the rice genome and that the high number of reported genes in this genome is probably due to duplications. Within the cereals, macrocolinearity is conserved but, at the level of individual genes, microcolinearity is frequently disrupted. Preliminary evidence from limited comparative analysis of sequenced orthologous genomic segments suggests that local gene amplification and translocation within a plant genome may be linked in some cases. Comparison of genes among cereals Patterns in grass genome evolution Bennetzen JL. Patterns in grass genome evolution. Curr Opin Plant Biol. 2007 Apr; 10 (2): 176-81. Epub 2007 Feb 8. Increasingly comprehensive, species-rich, and large-scale comparisons of grass genome structure have uncovered an even higher level of genomic rearrangement than originally observed by recombinational mapping or orthologous clone sequence comparisons. Small rearrangements are exceedingly abundant, even in comparisons of closely related species. The mechanisms of these small rearrangements, mostly tiny deletions caused by illegitimate recombination, appear to be active in all of the plant species investigated, but their relative aggressiveness differs dramatically in different plant lineages. Transposable element amplification, including the acquisition and occasional fusion of gene fragments from multiple loci, is also common in all grasses studied, but has been a much more major contributor in some species than in others. The reasons for these quantitative differences are not known, but it is clear that they lead to species that have very different levels of genomic instability. Similarly, polyploidy and segmental duplication followed by gene loss are standard phenomena in the history of all flowering plants, including the grasses, but their frequency and final outcomes are very different in different lineages. Now that genomic instability has begun to be characterized in detail across an array of plant species, it is time for comprehensive studies to investigate the relationships between particular changes in genome structure and organismal function or fitness. Patterns in grass genome evolution The rice genome and comparative genomics of higher plants The rice genome and comparative genomics of higher plants
Leafing through the genomes of our major crop plants: strategies for capturing unique information Paterson AH. Leafing through the genomes of our major crop plants: strategies for capturing unique information. Nat Rev Genet. 2006 Mar; 7 (3): 174-84. Crop plants not only have economic significance, but also comprise important botanical models for evolution and development. This is reflected by the recent increase in the percentage of publicly available sequence data that are derived from angiosperms. Further genome sequencing of the major crop plants will offer new learning opportunities, but their large, repetitive, and often polyploid genomes present challenges. Reduced-representation approaches - such as EST sequencing, methyl filtration and Cot-based cloning and sequencing - provide increased efficiency in extracting key information from crop genomes without full-genome sequencing. Combining these methods with phylogenetically stratified sampling to allow comparative genomic approaches has the potential to further accelerate progress in angiosperm genomics. Leafing through the genomes of our major crop plants-strategies for capturing unique information Genomics tools for QTL analysis and gene discovery Borevitz JO, Chory J. Genomics tools for QTL analysis and gene discovery. Curr Opin Plant Biol. 2004 Apr; 7 (2): 132-6. In recent years, several new genomics resources and tools have become available that will greatly assist quantitative trait locus (QTL) mapping and cloning of the corresponding genes. Genome sequences, tens of thousands of molecular markers, microarrays, and knock-out collections are being applied to QTL mapping, facilitating the use of natural accessions for gene discovery. Genomics tools for QTL analysis and gene discovery Tandem gene arrays: a challenge for functional genomics Jander G, Barth C. Tandem gene arrays: a challenge for functional genomics. Trends Plant Sci. 2007 May; 12 (5): 203-10. Epub 2007 Apr 9. In sequenced plant genomes, 15% or more of the identified genes are members of tandem-arrayed gene families. Because mutating only one gene in a duplicated pair often produces no measurable phenotype, this poses a particular challenge for functional analysis. To generate phenotypic knockouts, it is necessary to create deletions that affect multiple genes, select for rare meiotic recombination between tightly linked loci, or perform sequential mutant screens in the same plant line. Successfully implemented strategies include PCR-based screening for fast neutron-induced deletions, selection for recombination between herbicide resistance markers, and localized transposon mutagenesis. Here, we review the relative merits of current genetic approaches and discuss the prospect of site-directed mutagenesis for generating elusive knockouts of tandem-arrayed gene families. Tandem gene arrays-a challenge for functional genomics Re-valuating the relevance of ancenstral shared synteny as a tool for crop improvement Delseny M. Re-evaluating the relevance of ancestral shared synteny as a tool for crop improvement. Curr Opin Plant Biol. 2004 Apr; 7 (2): 126-31. In addition to the Arabidopsis and rice genomic sequences, numerous expressed sequence tags (ESTs) and sequenced tag sites are now available for many species. These tools have made it possible to re-evaluate the extent of synteny and collinearity not only between Arabidopsis and related crops or between rice and other cereals but also between Arabidopsis and rice, between Arabidopsis and other dicots, and between cereals other than rice. Major progress in describing synteny relies on statistical tests. Overall, the data point to the occurrence of ancestral genome fragments in which a framework of common markers can be recognised. Micro-synteny studies reveal numerous rearrangements, which are likely to complicate map-based cloning strategies that use information from a model genome. Re-valuating the relevance of ancenstral shared synteny as a tool for crop improvement Synteny: recent advances and future prospects Schmidt R. Synteny: recent advances and future prospects. Curr Opin Plant Biol. 2000 Apr; 3 (2): 97-102. Their small sizes have meant that the Arabidopsis and rice genomes are the best-studied of all plant genomes. Although even closely related plant species can show large variations in genome size, extensive genome colinearity has been established at the genetic level and recently also at the gene level. This allows the transfer of information and resources assembled for rice and Arabidopsis to be used in the genome analysis of many other plants. Synteny-recent advances and future prospects Synergy between sequence and size in large-scale genomics Gregory TR. Synergy between sequence and size in large-scale genomics. Nat Rev Genet. 2005 Sep; 6 (9): 699-708. Until recently the study of individual DNA sequences and of total DNA content (the C-value) sat at opposite ends of the spectrum in genome biology. For gene sequencers, the vast stretches of non-coding DNA found in eukaryotic genomes were largely considered to be an annoyance, whereas genome-size researchers attributed little relevance to specific nucleotide sequences. However, the dawn of comprehensive genome sequencing has allowed a new synergy between these fields, with sequence data providing novel insights into genome-size evolution, and with genome-size data being of both practical and theoretical significance for large-scale sequence analysis. In combination, these formerly disconnected disciplines are poised to deliver a greatly improved understanding of genome structure and evolution. Synergy between sequence and size in large-scale genomics Transposable elements and the plant pan-genomes Morgante M, De Paoli E, Radovic S. Transposable elements and the plant pan-genomes. Curr Opin Plant Biol. 2007 Apr; 10 (2): 149-55. Epub 2007 Feb 14. The comparative sequencing of several grass genomes has revealed that transposable elements are largely responsible for extensive variation in both intergenic and local genic content, not only between closely related species but also among individuals within a species. These observations indicate that a single genome sequence might not reflect the entire genomic complement of a species, and prompted us to introduce the concept of the plant pan-genome, which includes core genomic features that are common to all individuals and a dispensable genome composed of partially shared and/or non-shared DNA sequence elements. Uncovering the intriguing nature of the dispensable genome, namely its composition, origin and function, represents a step forward towards an understanding of the processes that generate genetic diversity and phenotypic variation. The developing view of transcriptional regulation as a complex and modular system, in which long-range interactions and the involvement of transposable elements are frequently observed, lends support to the possibility of an important functional role for the dispensable genome and could make it less dispensable than previously thought. Transposable elements and the plant pan-genomes Flux an important, but neglected, component of functional genomics Fernie AR , Geigenberger P, Stitt M. Flux an important, but neglected, component of functional genomics. Curr Opin Plant Biol. 2005 Apr; 8 (2): 174-82. Genomics approaches aimed at understanding metabolism currently tend to involve mainly expression profiling, although proteomics and steady-state metabolite profiling are increasingly being carried out as alternative strategies. These approaches provide rich information on the inventory of the cell. It is, however, of growing importance that such approaches are augmented by sophisticated integrative analyses and a higher-level understanding of cellular dynamics to provide insights into mechanisms that underlie biological processes. We argue the need for, and discuss theoretical and practical aspects of, the determination of metabolic flux as a component of functional genomics. Flux an important, but neglected, component of functional genomics Genomics of sex chromosomes Ming R, Moore PH. Genomics of sex chromosomes. Curr Opin Plant Biol. 2007 Apr ;10 (2): 123-30. Epub 2007 Feb 14. Sex chromosomes in plants and animals are distinctive, not only because of their gender-determining role but also for genomic features that reflect their evolutionary history. The genomic sequences in the ancient sex chromosomes of humans and in the incipient sex chromosomes of medaka, stickleback, papaya, and poplar exhibit unusual features as consequences of their evolution. These include the enormous palindrome structure in human MSY, a duplicated genomic fragment that evolved into a Y chromosome in medaka, and a 700 kb extra telomeric sequence of the W chromosome in poplar. Comparative genomic analysis of ancient and incipient sex chromosomes highlights common features that implicate the selection forces that shaped them, even though evolutionary origin, pace, and fate vary widely among individual sex-determining systems. Genomics of sex chromosomes And then there were many: MADS goes genomic De Bodt S, Raes J, Van de Peer Y, Theissen G. And then there were many: MADS goes genomic. Trends Plant Sci. 2003 Oct; 8 (10): 475-83. During the past decade, MADS-box genes have become known as key regulators in both reproductive and vegetative plant development. Traditional genetics and functional genomics tools are now available to elucidate the expression and function of this complex gene family on a much larger scale. Moreover, comparative analysis of the MADS-box genes in diverse flowering and non-flowering plants, boosted by bioinformatics, contributes to our understanding of how this important gene family has expanded during the evolution of land plants. Therefore, the recent advances in comparative and functional genomics should enable researchers to identify the full range of MADS-box gene functions, which should help us significantly in developing a better understanding of plant development and evolution. And then there were many-MADS goes genomic Plant functional genomics: beyond the parts list Stewart CN Jr. Plant functional genomics: beyond the parts list. Trends Plant Sci. 2005 Dec; 10 (12): 561-2. Epub 2005 Nov 14. Plant functional genomics-beyond the parts list Genomics-deeper and wider in order to understanding plant diversity Genomics-deeper and wider in order to understanding plant diversity The consequences of gene and genome duplication in plants The consequences of gene and genome duplication in plants
标签: 分子遗传
