tropiTree: an NGS-based EST-SSR resource for 24 tropical tree species
Autor: | 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. |
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Rok vydání: | 2014 |
Předmět: |
Range (biology)
Plant Genomes Plant Science Plant Genetics Gene flow Trees Sequencing techniques Databases Genetic Plant Genomics DNA libraries Genetics Expressed Sequence Tags Genetic Fingerprinting Expressed sequence tag Agroforests Multidisciplinary Sequence analysis High-Throughput Nucleotide Sequencing Agriculture Forestry RNA sequencing Genomics Genomic Databases Sequence tagged site analysis Conservation Genetics Medicine Sequence databases Tree species Research Article Biotechnology Crops Agricultural Resource (biology) Science Computational biology Genetic Fingerprinting and Footprinting Biology Genes Plant Genome sequencing DNA sequencing Molecular Genetics DNA sequence analysis Sequence (medicine) Base Sequence Biology and life sciences Population Biology RNA sequence analysis Ecology and Environmental Sciences Online database Sequence Analysis DNA DNA Genome Analysis Genomic Libraries Research and analysis methods Molecular biology techniques Genetic Polymorphism Plant Biotechnology Population Genetics Expressed sequence tags analysis Microsatellite Repeats |
Zdroj: | PLoS ONE PLoS ONE, Vol 9, Iss 7, p e102502 (2014) |
ISSN: | 1932-6203 |
Popis: | 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. |
Databáze: | OpenAIRE |
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