Affiliations 

  • 1 Plant Functional Biology and Climate Change Cluster (C3), University of Technology, Sydney NSW, Australia
  • 2 Centro Andaluz de Biología del Desarrollo (CABD-CSIC), Universidad Pablo de Olavide Sevilla, Spain
  • 3 Centre for Research in Biotechnology for Agriculture and Institute of Biological Sciences, Faculty of Science, University of Malaya Kuala Lumpur, Malaysia
  • 4 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
  • 5 Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova Padova, Italy
  • 6 CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto Vila do Conde, Portugal
Front Plant Sci, 2016;7:878.
PMID: 27446111 DOI: 10.3389/fpls.2016.00878

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.

* Title and MeSH Headings from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.