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 ABC’s 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 ABC’s 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

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