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.
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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