- tropiTree - Tropical Tree Expressed Transcripts, SSR Markers and Primer Pairs
In this website you will find the assembled expressed transcripts from an RNA-seq study of a set of 24 important tropical tree species, along with the microsatellites discovered within them and primer pairs designed to the microsatellite markers.
For a full list of the 24 species used in this study and the numbers of SSRs and primers available for each please see the Table of SSRs by Species
If you have the sequence of a gene of interest you can use the BLAST facility
to search for homologous genes within the transcripts. If you have a gene name or keywords, you can search the annotation of the transcripts
to obtain a list of candidate transcripts.
Below you will find you can view lists of the total numbers of SSR motifs for each species, you can list a specific transcript, or subset of transcripts, using transcript IDs, and you can also go straight to a complete listing of the SSRs discovered in a species.
Finally, you can download all the data files
which went into creating the database from our server.
Details of the methods used to sequence tree species and the background to the construction of this database are provided in the following (open access) publication that should be cited by users of tropiTree:
Russell JR, Hedley PE, Cardle L, Dancey S, Morris J, Booth A, Odee D, Mwaura L, Omondi W, Angaine P, Machua J, Muchugi A, Milne I, Kindt R, Jamnadass R, Dawson IK (2014) tropiTree: an NGS-based EST-SSR resource for 24 tropical tree species. PLoS ONE, 9, e102502. doi:10.1371/journal.pone.0102502 (Link to article
List all SSRs ordered by longest SSR first
This will return a list of all transcripts containing at least one SSR, in order of the longest SSR first.