Combining Bioinformatics and Phylogenetics to Identify Large Sets of Single-Copy Orthologous Genes (COSII) for Comparative, Evolutionary and Systematic Studies: A Test Case in the Euasterid Plant Clade

Abstract

We report herein the application of a set of algorithms to identify a large number (2869) of single-copy orthologs (COSII), which are shared by most, if not all, euasterid plant species as well as the model species Arabidopsis. Alignments of the orthologous sequences across multiple species enabled the design of ''universal PCR primers,'' which can be used to amplify the corresponding orthologs from a broad range of taxa, including those lacking any sequence databases. Functional annotation revealed that these conserved, single-copy orthologs encode a higher-than-expected frequency of proteins transported and utilized in organelles and a paucity of proteins associated with cell walls, protein kinases, transcription factors, and signal transduction. The enabling power of this new ortholog resource was demonstrated in phylogenetic studies, as well as in comparative mapping across the plant families tomato (family Solanaceae) and coffee (family Rubiaceae). The combined results of these studies provide compelling evidence that (1) the ancestral species that gave rise to the core euasterid families Solanaceae and Rubiaceae had a basic chromosome number of x ¼ 11 or 12.2) No whole-genome duplication event (i.e., polyploidization) occurred immediately prior to or after the radiation of either Solanaceae or Rubiaceae as has been recently suggested.

High resolution synteny maps allowing direct comparisons between the coffee and tomato genomes

“…Phylogenetically, the model species most closely related to coffee, for which significant genetics and genomic resources exist, is tomato. Both coffee and tomato belong to the Euasterid I clade of flowering plants and are likely derived from an ancestral species with a haploid number of ×=11 or 12 (Wu et al 2006).…”

“…This high level of conservation can be attributed, at least in part, to the absence of polyploidization in the ancestral genome that gave rise to the family Solanaceae (Wang et al 2008). Furthermore, recent studies suggest that the Solanaceae and Rubiaceae (which contains coffee) families descended from a diploid ancestor without any recent whole genome duplication (Wu et al 2006). Hence, one might expect a reasonable level of both macro and micro (Guyot et al 2009) synteny between the tomato and coffee genomes.…”

Genetic mapping and annotation of genomic microsatellites isolated from globe artichoke

“…As previously performed in the Solanaceae (Wu et al 2006(Wu et al , 2009, Fabaceae (Phan et al 2007;Hougaard et al 2008;Ellwood et al 2008) and Asteraceae (Chapman et al 2007) families, a COS marker approach may represent an effective mean for generating molecular markers. Our comparative analysis amongst the Asteraceae species showed similarity values up to 100% between sequences from globe artichoke and those from the yellow starthistle (Centaurea solstitialis) or safflower (Carthamus tinctorius); accordingly, an exploration of the Asteraceae dbEST seems very promising for new microsatellite markers mining as well as for synteny studies.…”

High resolution map of eggplant (Solanum melongena) reveals extensive chromosome rearrangement in domesticated members of the Solanaceae

“…Universal primers of COSII markers (Wu et al 2006) were used to amplify orthologous segments from the two parents as described in Wu et al (2009). COSII primers yielding amplicons of different size were then used to genotype the 58 F 2 individuals.…”

“…Thus, 110 conserved ortholog set (COSII) markers [developed from single copy genes conserved between the Solanaceae and Rubiaceae (Wu et al 2006)] were added to the Doganlar et al (2002a) eggplant map (Wu et al 2009). This augmented map improved the resolution of the previous map, bringing the average distance between framework markers down to 6.1 cM (from 7.6 cM) and allowing for a more complete characterization of the chromosomal rearrangements distinguishing the tomato and eggplant genomes (Wu et al 2009).…”