title: tropiTree: an NGS-based EST-SSR resource for 24 tropical tree species.
abstract: The development of genetic tools for non-model organisms has been hampered by cost, but advances in next-generation sequencing (NGS) have created new opportunities. In ecological research, this raises the prospect for developing molecular markers to simultaneously study important genetic processes such as gene flow in multiple non-model plant species within complex natural and anthropogenic landscapes. Here, we report the use of bar-coded multiplexed paired-end Illumina NGS for the de novo development of expressed sequence tag-derived simple sequence repeat (EST-SSR) markers at low cost for a range of 24 tree species. Each chosen tree species is important in complex tropical agroforestry systems where little is currently known about many genetic processes. An average of more than 5,000 EST-SSRs was identified for each of the 24 sequenced species, whereas prior to analysis 20 of the species had fewer than 100 nucleotide sequence citations. To make results available to potential users in a suitable format, we have developed an open-access, interactive online database, tropiTree (http://bioinf.hutton.ac.uk/tropiTree), which has a range of visualisation and search facilities, and which is a model for the efficient presentation and application of NGS data.
authors.affiliation: Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Scotland, United Kingdom.
authors.forename: Joanne R
authors.initials: JR
authors.lastname: Russell
authors.affiliation: Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Scotland, United Kingdom.
authors.forename: Peter E
authors.initials: PE
authors.lastname: Hedley
authors.affiliation: Information and Computational Sciences, James Hutton Institute, Invergowrie, Scotland, United Kingdom.
authors.forename: Linda
authors.initials: L
authors.lastname: Cardle
authors.affiliation: Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Scotland, United Kingdom; College of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom.
authors.forename: Siobhan
authors.initials: S
authors.lastname: Dancey
authors.affiliation: Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Scotland, United Kingdom.
authors.forename: Jenny
authors.initials: J
authors.lastname: Morris
authors.affiliation: Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Scotland, United Kingdom.
authors.forename: Allan
authors.initials: A
authors.lastname: Booth
authors.affiliation: Headquarters, Kenya Forestry Research Institute, Nairobi, Kenya; Centre for Ecology & Hydrology at Edinburgh, Centre for Ecology & Hydrology, Penicuik, Scotland, United Kingdom.
authors.forename: David
authors.initials: D
authors.lastname: Odee
authors.affiliation: Headquarters, World Agroforestry Centre, Nairobi, Kenya.
authors.forename: Lucy
authors.initials: L
authors.lastname: Mwaura
authors.affiliation: Headquarters, Kenya Forestry Research Institute, Nairobi, Kenya.
authors.forename: William
authors.initials: W
authors.lastname: Omondi
authors.affiliation: Headquarters, Kenya Forestry Research Institute, Nairobi, Kenya.
authors.forename: Peter
authors.initials: P
authors.lastname: Angaine
authors.affiliation: Headquarters, Kenya Forestry Research Institute, Nairobi, Kenya.
authors.forename: Joseph
authors.initials: J
authors.lastname: Machua
authors.affiliation: Headquarters, World Agroforestry Centre, Nairobi, Kenya.
authors.forename: Alice
authors.initials: A
authors.lastname: Muchugi
authors.affiliation: Information and Computational Sciences, James Hutton Institute, Invergowrie, Scotland, United Kingdom.
authors.forename: Iain
authors.initials: I
authors.lastname: Milne
authors.affiliation: Headquarters, World Agroforestry Centre, Nairobi, Kenya.
authors.forename: Roeland
authors.initials: R
authors.lastname: Kindt
authors.affiliation: Headquarters, World Agroforestry Centre, Nairobi, Kenya.
authors.forename: Ramni
authors.initials: R
authors.lastname: Jamnadass
authors.affiliation: Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Scotland, United Kingdom; Headquarters, World Agroforestry Centre, Nairobi, Kenya.
authors.forename: Ian K
authors.initials: IK
authors.lastname: Dawson
mesh_terms: D001483:Base Sequence; D018556:Crops, Agricultural / Q000235:genetics; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D017343:Genes, Plant; D059014:High-Throughput Nucleotide Sequencing; D018895:Microsatellite Repeats; D017422:Sequence Analysis, DNA; D014197:Trees / Q000235:genetics*