Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants.
Plant Cell, 2002/7;14(7):1457-67.
Fulton TM[1], Van der Hoeven R, Eannetta NT, Tanksley SD
Affiliations
PMID: 12119367
Impact factor: 12.085
Abstract
We have screened a large tomato EST database against the Arabidopsis genomic sequence and report here the identification of a set of 1025 genes (referred to as a conserved ortholog set, or COS markers) that are single or low copy in both genomes (as determined by computational screens and DNA gel blot hybridization) and that have remained relatively stable in sequence since the early radiation of dicotyledonous plants. These genes were annotated, and a large portion could be assigned to putative functional categories associated with basic metabolic processes, such as energy-generating processes and the biosynthesis and degradation of cellular building blocks. We further demonstrate, through computational screens (e.g., against a Medicago truncatula database) and direct hybridization on genomic DNA of diverse plant species, that these COS markers also are conserved in the genomes of other plant families. Finally, we show that this gene set can be used for comparative mapping studies between highly divergent genomes such as those of tomato and Arabidopsis. This set of COS markers, identified computationally and experimentally, may further studies on comparative genomes and phylogenetics and elucidate the nature of genes conserved throughout plant evolution.
MeSH terms
Amino Acid Sequence; Arabidopsis; Chromosome Mapping; Consensus Sequence; Conserved Sequence; Databases, Genetic; Expressed Sequence Tags; Genetic Markers; Genome, Plant; Genomic Library; Lycopersicon esculentum; Medicago; Molecular Sequence Data; Phylogeny; Plants; Sequence Alignment; Synteny
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