tropiTree: an NGS-based EST-SSR resource for 24 tropical tree species.
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 s...
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2014
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oai:doaj.org-article:4a6dd7a649814d01a567abb63a899f7a2021-11-25T06:08:27ZtropiTree: an NGS-based EST-SSR resource for 24 tropical tree species.1932-620310.1371/journal.pone.0102502https://doaj.org/article/4a6dd7a649814d01a567abb63a899f7a2014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/25025376/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203The 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.Joanne R RussellPeter E HedleyLinda CardleSiobhan DanceyJenny MorrisAllan BoothDavid OdeeLucy MwauraWilliam OmondiPeter AngaineJoseph MachuaAlice MuchugiIain MilneIain MilneRoeland KindtRamni JamnadassIan K DawsonPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 7, p e102502 (2014) |
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Medicine R Science Q |
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Medicine R Science Q Joanne R Russell Peter E Hedley Linda Cardle Siobhan Dancey Jenny Morris Allan Booth David Odee Lucy Mwaura William Omondi Peter Angaine Joseph Machua Alice Muchugi Iain Milne Iain Milne Roeland Kindt Ramni Jamnadass Ian K Dawson tropiTree: an NGS-based EST-SSR resource for 24 tropical tree species. |
| description |
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. |
| format |
article |
| author |
Joanne R Russell Peter E Hedley Linda Cardle Siobhan Dancey Jenny Morris Allan Booth David Odee Lucy Mwaura William Omondi Peter Angaine Joseph Machua Alice Muchugi Iain Milne Iain Milne Roeland Kindt Ramni Jamnadass Ian K Dawson |
| author_facet |
Joanne R Russell Peter E Hedley Linda Cardle Siobhan Dancey Jenny Morris Allan Booth David Odee Lucy Mwaura William Omondi Peter Angaine Joseph Machua Alice Muchugi Iain Milne Iain Milne Roeland Kindt Ramni Jamnadass Ian K Dawson |
| author_sort |
Joanne R Russell |
| title |
tropiTree: an NGS-based EST-SSR resource for 24 tropical tree species. |
| title_short |
tropiTree: an NGS-based EST-SSR resource for 24 tropical tree species. |
| title_full |
tropiTree: an NGS-based EST-SSR resource for 24 tropical tree species. |
| title_fullStr |
tropiTree: an NGS-based EST-SSR resource for 24 tropical tree species. |
| title_full_unstemmed |
tropiTree: an NGS-based EST-SSR resource for 24 tropical tree species. |
| title_sort |
tropitree: an ngs-based est-ssr resource for 24 tropical tree species. |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2014 |
| url |
https://doaj.org/article/4a6dd7a649814d01a567abb63a899f7a |
| work_keys_str_mv |
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