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3.
Heredity (Edinb) ; 100(2): 141-9, 2008 Feb.
Article in English | MEDLINE | ID: mdl-17091126

ABSTRACT

Microarray technology is one of the key developments in recent years that has propelled biological research into the post-genomic era. With the ability to assay thousands to millions of features at the same time, microarray technology has fundamentally changed how biological questions are addressed, from examining one or a few genes to a collection of genes or the whole genome. This technology has much to offer in the study of genome evolution. After a brief introduction on the technology itself, we then focus on the use of microarrays to examine genome dynamics, to uncover novel functional elements in genomes, to unravel the evolution of regulatory networks, to identify genes important for behavioral and phenotypic plasticity, and to determine microbial community diversity in environmental samples. Although there are still practical issues in using microarrays, they will be alleviated by rapid advances in array technology and analysis methods, the availability of many genome sequences of closely related species and flexibility in array design. It is anticipated that the application of microarray technology will continue to better our understanding of evolution and ecology through the examination of individuals, populations, closely related species or whole microbial communities.


Subject(s)
Ecology , Evolution, Molecular , Genetics, Microbial , Genomics , Oligonucleotide Array Sequence Analysis/methods , Ecosystem , Gene Expression Profiling , Gene Regulatory Networks
4.
Sci STKE ; 2001(113): re22, 2001 Dec 18.
Article in English | MEDLINE | ID: mdl-11752632

ABSTRACT

Plant receptor-like kinases (RLKs) are transmembrane proteins with putative amino-terminal extracellular domains and carboxyl-terminal intracellular kinase domains, with striking resemblance in domain organization to the animal receptor tyrosine kinases such as epidermal growth factor receptor. The recently sequenced Arabidopsis genome contains more than 600 RLK homologs, representing nearly 2.5% of the annotated protein-coding genes in Arabidopsis. Although only a handful of these genes have known functions and fewer still have identified ligands or downstream targets, the studies of several RLKs such as CLAVATA1, Brassinosteroid Insensitive 1, Flagellin Insensitive 2, and S-locus receptor kinase provide much-needed information on the functions mediated by members of this large gene family. RLKs control a wide range of processes, including development, disease resistance, hormone perception, and self-incompatibility. Combined with the expression studies and biochemical analysis of other RLKs, more details of RLK function and signaling are emerging.


Subject(s)
Arabidopsis Proteins , Genes, Plant/physiology , Genetic Variation/physiology , Multigene Family/physiology , Plant Proteins/genetics , Protein Kinases/genetics , Signal Transduction/genetics , Animals , Humans , Multigene Family/genetics , Plant Proteins/physiology , Protein Kinases/physiology , Signal Transduction/physiology
5.
Proc Natl Acad Sci U S A ; 98(19): 10763-8, 2001 Sep 11.
Article in English | MEDLINE | ID: mdl-11526204

ABSTRACT

Plant receptor-like kinases (RLKs) are proteins with a predicted signal sequence, single transmembrane region, and cytoplasmic kinase domain. Receptor-like kinases belong to a large gene family with at least 610 members that represent nearly 2.5% of Arabidopsis protein coding genes. We have categorized members of this family into subfamilies based on both the identity of the extracellular domains and the phylogenetic relationships between the kinase domains of subfamily members. Surprisingly, this structurally defined group of genes is monophyletic with respect to kinase domains when compared with the other eukaryotic kinase families. In an extended analysis, animal receptor kinases, Raf kinases, plant RLKs, and animal receptor tyrosine kinases form a well supported group sharing a common origin within the superfamily of serine/threonine/tyrosine kinases. Among animal kinase sequences, Drosophila Pelle and related cytoplasmic kinases fall within the plant RLK clade, which we now define as the RLK/Pelle family. A survey of expressed sequence tag records for land plants reveals that mosses, ferns, conifers, and flowering plants have similar percentages of expressed sequence tags representing RLK/Pelle homologs, suggesting that the size of this gene family may have been close to the present-day level before the diversification of land plant lineages. The distribution pattern of four RLK subfamilies on Arabidopsis chromosomes indicates that the expansion of this gene family is partly a consequence of duplication and reshuffling of the Arabidopsis genome and of the generation of tandem repeats.


Subject(s)
Genes, Plant , Plant Proteins/genetics , Animals , Arabidopsis/enzymology , Eukaryotic Cells , Genetic Variation , Genome, Plant , Humans , Phylogeny
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