title: PlantFuncSSR: Integrating First and Next Generation Transcriptomics for Mining of SSR-Functional Domains Markers.
abstract: Analysis of repetitive DNA sequence content and divergence among the repetitive functional classes is a well-accepted approach for estimation of inter- and intra-generic differences in plant genomes. Among these elements, microsatellites, or Simple Sequence Repeats (SSRs), have been widely demonstrated as powerful genetic markers for species and varieties discrimination. We present PlantFuncSSRs platform having more than 364 plant species with more than 2 million functional SSRs. They are provided with detailed annotations for easy functional browsing of SSRs and with information on primer pairs and associated functional domains. PlantFuncSSRs can be leveraged to identify functional-based genic variability among the species of interest, which might be of particular interest in developing functional markers in plants. This comprehensive on-line portal unifies mining of SSRs from first and next generation sequencing datasets, corresponding primer pairs and associated in-depth functional annotation such as gene ontology annotation, gene interactions and its identification from reference protein databases. PlantFuncSSRs is freely accessible at: http://www.bioinfocabd.upo.es/plantssr.
authors.affiliation: Plant Functional Biology and Climate Change Cluster (C3), University of Technology, Sydney NSW, Australia.
authors.forename: Gaurav
authors.initials: G
authors.lastname: Sablok
authors.affiliation: Centro Andaluz de Biología del Desarrollo (CABD-CSIC), Universidad Pablo de Olavide Sevilla, Spain.
authors.forename: Antonio J
authors.initials: AJ
authors.lastname: Pérez-Pulido
authors.affiliation: Plant Functional Biology and Climate Change Cluster (C3), University of Technology, Sydney NSW, Australia.
authors.forename: Thac
authors.initials: T
authors.lastname: Do
authors.affiliation: Centre for Research in Biotechnology for Agriculture and Institute of Biological Sciences, Faculty of Science, University of Malaya Kuala Lumpur, Malaysia.
authors.forename: Tan Y
authors.initials: TY
authors.lastname: Seong
authors.affiliation: Centro Andaluz de Biología del Desarrollo (CABD-CSIC), Universidad Pablo de Olavide Sevilla, Spain.
authors.forename: Carlos S
authors.initials: CS
authors.lastname: Casimiro-Soriguer
authors.affiliation: Department of Sustainable Agro-Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund MachTrento, Italy; MountFOR Project Centre, European Forest InstituteTrento, Italy; Consiglio Nazionale delle Ricerche, Istituto per la Valorizzazione del Legno e delle Specie ArboreeFlorence, Italy.
authors.forename: Nicola
authors.initials: N
authors.lastname: La Porta
authors.affiliation: Plant Functional Biology and Climate Change Cluster (C3), University of Technology, Sydney NSW, Australia.
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Ralph
authors.affiliation: Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova Padova, Italy.
authors.forename: Andrea
authors.initials: A
authors.lastname: Squartini
authors.affiliation: CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto Vila do Conde, Portugal.
authors.forename: Antonio
authors.initials: A
authors.lastname: Muñoz-Merida
authors.affiliation: Centre for Research in Biotechnology for Agriculture and Institute of Biological Sciences, Faculty of Science, University of Malaya Kuala Lumpur, Malaysia.
authors.forename: Jennifer A
authors.initials: JA
authors.lastname: Harikrishna
keywords: NGS; functional domains markers; gene ontology (GO); inter-pro; short tandem repeats (STRs)