PlantFuncSSR: Integrating first and next generation transcriptomics for mining of SSR-functional domains markers

Sablok, G; Pérez-Pulido, AJ; Do, T; Seong, TY; Casimiro-Soriguer, CS; La Porta, N; Ralph, PJ; Squartini, A; Muñoz-Merida, A; Harikrishna, JA

PlantFuncSSR: Integrating first and next generation transcriptomics for mining of SSR-functional domains markers

Sablok, G

Pérez-Pulido, AJ Do, T Seong, TY Casimiro-Soriguer, CS La Porta, N Ralph, PJ

Squartini, A Muñoz-Merida, A Harikrishna, JA

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Publication Type:: Journal Article
Citation:: Frontiers in Plant Science, 2016, 7
Issue Date:: 2016-06-27

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Field	Value	Language
dc.contributor.author	Sablok, G https://orcid.org/0000-0002-4157-9405	en_US
dc.contributor.author	Pérez-Pulido, AJ	en_US
dc.contributor.author	Do, T	en_US
dc.contributor.author	Seong, TY	en_US
dc.contributor.author	Casimiro-Soriguer, CS	en_US
dc.contributor.author	La Porta, N	en_US
dc.contributor.author	Ralph, PJ https://orcid.org/0000-0002-3103-7346	en_US
dc.contributor.author	Squartini, A	en_US
dc.contributor.author	Muñoz-Merida, A	en_US
dc.contributor.author	Harikrishna, JA	en_US
dc.date.available	2016-06-03	en_US
dc.date.issued	2016-06-27	en_US
dc.identifier.citation	Frontiers in Plant Science, 2016, 7	en_US
dc.identifier.uri	http://hdl.handle.net/10453/117048
dc.description.abstract	© 2016 Sablok, Pérez-Pulido, Do, Seong, Casimiro-Soriguer, La Porta, Ralph, Squartini, Muñoz-Merida and Harikrishna. Analysis of repetitive DNA sequence content and divergence among the repetitive functional classes is a well-accepted approach for estimation of inter- and intrageneric 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.	en_US
dc.relation.ispartof	Frontiers in Plant Science	en_US
dc.relation.isbasedon	10.3389/fpls.2016.00878	en_US
dc.title	PlantFuncSSR: Integrating first and next generation transcriptomics for mining of SSR-functional domains markers	en_US
dc.type	Journal Article
utslib.citation.volume	7	en_US
utslib.for	0602 Ecology	en_US
utslib.for	0607 Plant Biology	en_US
pubs.embargo.period	Not known	en_US
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Engineering and Information Technology
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Strength - AAI - Advanced Analytics Institute Research Centre
pubs.organisational-group	/University of Technology Sydney/Strength - C3 - Climate Change Cluster
utslib.copyright.status	open_access
pubs.publication-status	Published	en_US
pubs.volume	7	en_US

Abstract:

© 2016 Sablok, Pérez-Pulido, Do, Seong, Casimiro-Soriguer, La Porta, Ralph, Squartini, Muñoz-Merida and Harikrishna. Analysis of repetitive DNA sequence content and divergence among the repetitive functional classes is a well-accepted approach for estimation of inter- and intrageneric 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.

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http://hdl.handle.net/10453/117048