tropiTree: an NGS-based EST-SSR resource for 24 tropical tree species

Prasad, Manoj; Russell, Joanne R.; Hedley, Peter E.; Cardle, Linda; Dancey, Siobhan; Morris, Jenny; Booth, Allan; Odee, David; Mwaura, Lucy; Omondi, William; Angaine, Peter; Machua, Joseph; Muchugi, Alice; Milne, Iain; Kindt, Roeland; Jamnadass, Ramni; Dawson, Ian K.. 2014 tropiTree: an NGS-based EST-SSR resource for 24 tropical tree species. PLoS ONE, 9 (7), e102502. 7, pp. 10.1371/journal.pone.0102502

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Abstract/Summary

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.

Item Type:	Publication - Article
Digital Object Identifier (DOI):	10.1371/journal.pone.0102502
UKCEH and CEH Sections/Science Areas:	Watt
ISSN:	1932-6203
Additional Information. Not used in RCUK Gateway to Research.:	This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Date made live:	18 Mar 2019 14:31 +0 (UTC)
URI:	https://nora.nerc.ac.uk/id/eprint/522576

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