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)

Get numbers of SSRs found by repeat type

This will return a summary table of the numbers of different types of repeat motifs discovered in each species.

Look up a transcript by name

If you know the ID of a transcript you can use this to go directly to it, or you can use wildcards to return a table of a subset of transcript IDs.

Wildcards accepted ('*' will return a list of every transcript in the species).
All transcript names are of the form 'comp110_c0_seq1'.

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.