Transcriptomes of Lolium/Schedonorus/Festuca species

Authors: Dinkins, Randy; HESSE, ULJANA - University Of Kentucky; ARNAOUDOVA, ELISSAVETA - University Of Kentucky; NAGABHYRU, PADMAJA - University Of Kentucky; MOORE, NEIL - University Of Kentucky; LIU, JINGE - University Of Kentucky; JAROMCZYK, JOLANDA - University Of Kentucky; ZENG, ZHENG - University Of Kentucky; LIU, JINZE - University Of Kentucky; DAI, XINBIN - Nobel Foundation; ZHAO, PATRICK - Nobel Foundation; Scheffler, Brian; JAROMCZYK, JERZY - University Of Kentucky; SCHARDL, CHRISTOPHER - University Of Kentucky

Submitted to: International Symposium on Fungal Endophytes of Grasses
Publication Type: Book / Chapter
Publication Acceptance Date: 2/13/2012
Publication Date: 6/1/2012
Citation: Dinkins, R.D., Hesse, U., Arnaoudova, E., Nagabhyru, P., Moore, N., Liu, J., Jaromczyk, J., Zeng, Z., Liu, J., Dai, X., Zhao, P.X., Scheffler, B.E., Jaromczyk, J., Schardl, C.L. 2012. Transcriptomes of Lolium/Schedonorus/Festuca species. International Symposium on Fungal Endophytes of Grasses. ISBNL 978-0-9754303-6-1.

Interpretive Summary: Molecular tools for forage grasses are presently sparse. In order to make available these tools for the community, a large scale sequencing effort has been conducted. Roughly 140,000 cDNA clones from normalized libraries obtained from meadow fescue/Epichloe festucae inflorescences and stromata and tall fescue root RNA have been sequenced. Presently 128,189 EST sequences have been submitted to the National Center for Biotechnology Information database, making this resource available to the community. Assembly of the non- Epichloe cDNAs resulted in 42,154 unigenes, or unique genes. These will serve as the basis for plant genomic analysis and further molecular tool development in forage grasses. The assembly was used to anchor sequencing done using the Next Generation Illumina sequencing technology comparing expression of genes of meadow fescue in inflorescences and stromata. Of the 63.3 million (M) Illumina reads approximately 10.4 M matched the fungal genome, and 18.8 M matched 27,780 plant unigenes. Comparison of the expression between the stromata and inflorescence found that approximately half of the unigenes were differentially expressed. Roughly 800 unigenes were ten-fold more highly expressed in one tissue over the other and will be further evaluated. The Illumina sequencing results demonstrated that specific unigenes are targeted utilizing the new Next Generation sequencing technologies and provide a framework to anchor these sequences. The sequencing of the Lolium/Schedonorus/Festuca ESTs thus provides species specific sequences to evaluate expression and provides a molecular tool in the study of these important forage and turf grasses.

Technical Abstract: ESTs from normalized cDNA libraries of tall fescue with Neotyphodium coenophialum and meadow fescue with Epichloë festucae have been sequenced. The meadow fescue libraries were from RNA isolated from immature tillers of meadow fescue symbiotic with E. festucae, displaying normal inflorescences and from inflorescences exhibiting the fruiting structures (stromata) of E. festucae. The tall fescue sequencing was from a normalized cDNA library from tall fescue (symbiotic with N. coenophialum) root mRNA that was isolated from combined plants subjected to differing drought stress treatments. A total of 128,189 EST sequences were obtained and have been submitted to NCBI. Following the removal of the sequences that mapped to the E. festucae genome, assembly of the plant reads, together with those of Festuca and Lolium spp from NCBI, resulted in 42,154 unigenes. The sequences were annotated by BLASTX against 1) the Gene Ontology (http://www.geneontology.org/) sequence database and 2) the uniprot trembl database (http://www.ebi.ac.uk/uniprot/). We have used the database to annotate and compare whole genome expression in meadow fescue infected with E. festucae with normal inflorescences and from inflorescences containing stromata using Illumina high throughput sequencing.