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分子遗传学阅读文献：基因组学与分子遗传之一
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Leafing through the genomes of our major crop plants: strategies for capturing unique information
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
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.
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
https://blog.sciencenet.cn/blog-39731-36898.html
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