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, Pyhäjärvi 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

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