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分子遗传学阅读文献：基因组学与分子遗传之二
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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.
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
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