Large-scale gene discovery has led to the production of 13,964 expressed sequence tags (ESTs) collectively from the grass endophytes Neotyphodium coenophialum, N. lolii and Epichloë festucae

Edwards, D.

Erwin, T. A.

Felitti, S. A.

Logan, E. G.

Love, C. G.

Ramsperger, M.

Shields, K.

Singh, D.

Spangenberg, G. C.

English

University of Kentucky

University of Kentucky UKnowledge International Grassland Congress Proceedings XX International Grassland Congress Endophyte ASTRA: a Web-Based Resource for Neotyphodium and Epichloë EST Analysis K. Shields Molecular Plant Breeding Cooperative Research Centre, Australia M. Ramsperger La Trobe University, Australia S. A. Felitti La Trobe University, Australia C. G. Love La Trobe University, Australia T. A. Erwin La Trobe University, Australia See next page for additional authors Follow this and additional works at: https://uknowledge.uky.edu/igc  Part of the Agricultural Science Commons, Agronomy and Crop Sciences Commons, Plant Biology Commons, Plant Pathology Commons, Soil Science Commons, and the Weed Science Commons This document is available at https://uknowledge.uky.edu/igc/20/satellitesymposium5/90 The XX International Grassland Congress took place in Ireland and the UK in June-July 2005. The main congress took place in Dublin from 26 June to 1 July and was followed by post congress satellite workshops in Aberystwyth, Belfast, Cork, Glasgow and Oxford. The meeting was hosted by the Irish Grassland Association and the British Grassland Society. Proceedings Editor: D. A. McGilloway Publisher: Wageningen Academic Publishers, The Netherlands © Wageningen Academic Publishers, The Netherlands, 2005 The copyright holder has granted the permission for posting the proceedings here. This Event is brought to you for free and open access by the Plant and Soil Sciences at UKnowledge. It has been accepted for inclusion in International Grassland Congress Proceedings by an authorized administrator of UKnowledge. For more information, please contact UKnowledge@lsv.uky.edu. Presenter Information K. Shields, M. Ramsperger, S. A. Felitti, C. G. Love, T. A. Erwin, D. Singh, E. G. Logan, D. Edwards, and G. C. Spangenberg This event is available at UKnowledge: https://uknowledge.uky.edu/igc/20/satellitesymposium5/90 Molecular breeding for the genetic improvement of forage crops and turf 207Endophyte ASTRA: a web-based resource for Neotyphodium and Epichloë EST analysis  K. Shields1,2, M. Ramsperger1,2, S.A. Felitti1,2, C.G. Love1,3, T.A. Erwin1,3, D. Singh1,3, E.G. Logan1,3, D. Edwards1,2,3 and G.C. Spangenberg1,2,3 1Primary Industries Research Victoria, Plant Biotechnology Centre, La Trobe University, Bundoora, Victoria 3086, Australia 2Molecular Plant Breeding Cooperative Research Centre, Australia 3Victorian Bioinformatics Consortium, Australia Email: kate.shields@dpi.vic.gov.au  Keywords: grass endophytes, expressed sequence tags (ESTs), gene annotation, bioinformatics ASTRA database, simple sequence repeats (SSRs), single nucleotide polymorphisms (SNPs)  Introduction Large-scale gene discovery has led to the production of 13,964 expressed sequence tags (ESTs) collectively from the grass endophytes Neotyphodium coenophialum, N. lolii and Epichloë festucae.   Materials and methods A total of 9,783 ESTs were generated from fungal tissue grown in vitro, while 4,181 ESTs were generated from tissue grown in planta. Each of these sequences was annotated by comparison to the GenBank and SwissProt public sequence databases. Automated intermediate Gene Ontology (GO) annotation was also determined.  Results and conclusions Sequence annotation was determined for 38%, 45% and 43% of sequences using GenBank, SwissProt and GO annotation respectively, with 43% of sequences were determined to have no comparative annotation and thus appear to be unique to grass endophytes (Fig 1). EST redundancy was resolved through assembly with CAP3, identifying at total of 7,585 unigenes within this dataset, comprised of 5,846 singletons and 1,739 contigs. All sequences and annotation are maintained within an ASTRA format MySQL database, with web based access for text searching, BLAST sequence comparison and Gene Ontology hierarchical tree browsing.   In total, 1,047 endophyte simple sequence repeat molecular markers (SSRs) have been identified using SSRPrimer and specific PCR amplification primers were designed. A total of 1,636 candidate single nucleotide polymorphism (SNP) molecular markers and 326 insertion deletions (InDels) were also identified across 300 loci using AutoSNP. The integration of different analysis tools and the resulting data within a central resource allow users to identify novel candidate genes for functional genomics and design of novel endophyte-grass associations.                       Figure 1 Annotation of endophyte genes within the ASTRA database 26% GenBank 38% SwissProt Gene  Ontology 14% 45% 43% 2% 1% No annotation 43% 

Endophyte ASTRA: a Web-Based Resource for Neotyphodium and Epichloë EST Analysis

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Endophyte ASTRA: a Web-Based Resource for Neotyphodium and Epichloë EST Analysis

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