Conserved Ortholog Set II (COSII) markers

COSII markers are PCR-based markers developed from a set of single-copy conserved orthologous genes (COSII genes) in Asterid species. Each COSII gene (representing a group of Asterid unigenes) matches only one single-copy Arabidopsis gene. In comparison with COS markers reported by Fulton et al. (2002), COSII markers/genes have the following new properties:

  1. Multiple EST-assembled unigene databases, tomato, potato, pepper and coffee, as well as the Arabidopsis CDS database, were screened computationally and the method for establishing orthology was more robust.
  2. Phylogenetic analyses support their classification as orthologs.
  3. They occur as single-copy genes in these species.
  4. Designed "Universal Primers" were able to amplify orthologous counterparts (exons and/or introns) from other related solanaceous species including those lack of sequence data.

Therefore, this set of COSII genes as well as Universal Primers is a powerful tool for establishing a syntenic network between Solanaceae and Arabidopsis, and for elucidating phylogenies, genome evolution and genome organization of Solanaceae. Moreover, one can establish similar orthologs sets and Universal Primers for other plant families (especially dicots), and connect them with COSII genes by the common Arabidopsis orthologs.

The computational screen for identifying COSII genes is described in this diagram.

In this section of SGN, you will find sequence information of each COSII gene as well as the mapping information of those mapped COSII genes (so called COSII markers). We've mapped more than 300 COSII markers in tomato and will map more in the future, up to at least 500, and in the meanwhile, these COSII markers will be mapped in major solanaceous species (e.g. eggplant, pepper, Nicotiana, etc.). All the information in this section will be updated as new data are generated, so please come back and check from time to time.

Universal Primers developed from COSII genes (iUPA and eUPA)

Universal Primers for Asterid species (UPA) were designed on the consensus sequence of a COSII gene/group, which amplify both exonic and intronic regions in most, if not all, solanaceous species and related taxa in the Asterid I clade of dicot plant species, and which are therefore useful for comparative mapping and phylogenetics.

Intronic UPA (iUPA) amplify an intron with a short stretch of the flanking exons and hence are useful for genome/comparative mapping, and phylogenetics of closely related species. Many iUPAs have been tested in various solanaceous species as well as coffee, and primer sequences, PCR conditions and product sizes are available.

Exonic UPAS (eUPA) amplify at least 400bp exonic sequences with/without an intervening intron and hence are useful for phylogenetics of distantly related species. Some eUPAs have been tested in various solanaceous species as well as coffee, and primer sequences, PCR conditions and product sizes are available.

How to read COSII marker information pages

Arabidopsis CDS is not edited. The unigenes were edited based on their alignment with the CDS, by trimming the UTRs and correcting sequencing errors. Peptide sequence is translated from from edited sequence in frame 1 (for unigenes) or downloaded from TAIR (for Arabidopsis). Intron locations of unigenes were predicted from alignment with the Arabidopsis CDS, whose intron locations were downloaded from TAIR. "=====" indicates introns from TAIR (for Arabidopsis) or predicted intron location in the sequence (for unigenes).

Functional annotation of COSII genes

Each of the COSII genes was assigned a functional annotation based on the Gene Ontology (GO) annotation of the matching Arabidopsis gene member.

Mapping PCR-based COSII markers in major solanaceous species

All mapped COSII markers can be found in these marker search results.

Complete listing of COSII genes

Complete listings of COSII genes and markers can be found in our marker search results or in this .xls spreadsheet. The spreadsheet is sometimes more up-to-date than the search results. Sequence text files and other associated COSII data can be downloaded from our FTP site.

  1. Fulton T, van der Hoeven R, Eannetta N, Tanksley S (2002). Identification, Analysis and Utilization of a Conserved Ortholog Set (COS) Markers for Comparative Genomics in Higher Plants. The Plant Cell 14: 1457-1467
  2. Wu F, Mueller LA, Crouzillat D, Petiard V, Tanksley SD (2006). Combining Bioinformatics and Phylogenetics to Identify Large Sets of Single Copy, Orthologous Genes (COSII) for Comparative, Evolutinonary and Systematics Studies: A Test Case in the Euasterid Plant Clade (2006). Genetics, 2006 Nov;174(3):1407-20. Genetics | PubMed | [access supplement information on SGN FTP site]