Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants

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.

Figure 1.

Dendrogram Depicting Phylogenetic Relationships of Higher Plant Taxa. Common names are given in parentheses. Species in red are those used on the garden blot. (Figure reprinted from Ku et al. [2000], based on a figure in Chase et al. [1993].)

Figure 2.

Relative Distribution of COS Markers over Functional Role Categories. Assignments of COS markers to specific subcategories on the Solanaceae Genome Network online database (http://sgn.cornell.edu).

Figure 3.

Microsynteny between Tomato and Arabidopsis Genomes. (A) A region of tomato chromosome 6 showing conservation of synteny with a region of Arabidopsis chromosome 2. (B) A region of tomato chromosome 3 showing conservation of synteny with a region of Arabidopsis chromosome 5.

Figure 4.

Autoradiographs from the Hybridization of Garden Blots with COS Markers. T, tomato (Lycopersicon esculentum); P, garden pepper (Capsicum annuum); E, eggplant (Solanum melongena); Sn, sunflower (Helianthus annuus); L, lettuce (Lactuca sativa); M, melon (Cucumis melon); Al, alfalfa (Medicago sativa); B, field bean (Phaseolus vulgaris); Ap, apple (Malus domestica); C, cotton (Gossypium hirsutum); At, Arabidopsis thaliana; Sp, spinach (Spinacia oleracea); and R, rice (Oryza sativa). (A) A garden blot filter probed with COS1039 tomato probe. (B) The same filter probed with the Arabidopsis counterpart of COS1039. (C) A garden blot filter probed with COS1263 tomato probe. (D) The same filter probed with the Arabidopsis counterpart of COS1263.

Figure 5.

Alignment of Protein Sequences of COS1335 and Its M. truncatula and Arabidopsis Counterparts (A), COS1358 and its M. truncatula and Arabidopsis Counterparts (B), and COS94 and its M. truncatula and Arabidopsis Counterparts (C). The consensus sequences are given at top. Triangles indicate approximate positions of Arabidopsis introns according to the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/).