Transcriptome analysis of two buffalograss cultivars
1 Department of Biology and School of Interdisciplinary Informatics, University of Nebraska at Omaha, Omaha, NE 68182, USA
2 Department of Entomology, University of Nebraska at Lincoln, Lincoln, NE 68583, USA
3 Department of Agronomy & Horticulture, University of Nebraska at Lincoln, Lincoln, NE 68583, USA
4 Department of Biology, University of Nebraska at Kearney, Kearney, NE 68849, USA
5 Department of Biology, University of San Diego, San Diego, CA 92110, USA
BMC Genomics 2013, 14:613 doi:10.1186/1471-2164-14-613Published: 11 September 2013
Buffalograss [Buchloë dactyloides (Nutt.) Engel. syn. Bouteloua dactyloides (Nutt.) Columbus] is a United States native turfgrass species that requires less irrigation, fungicides and pesticides compared to more commonly used turfgrass species. In areas where water is limited, interest in this grass species for lawns is increasing. While several buffalograss cultivars have been developed through buffalograss breeding, the timeframe for new cultivar development is long and is limited by a lack of useful genetic resources. Two high throughput next-generation sequencing techniques were used to increase the genomic resources available for buffalograss.
Total RNA was extracted and purified from leaf samples of two buffalograss cultivars. ‘378’ and ‘Prestige’ cDNA libraries were subjected to high throughput sequencing on the Illumina GA and Roche 454 Titanium FLX sequencing platforms. The 454 platform (3 samples) produced 1,300,885 reads and the Illumina platform (12 samples) generated approximately 332 million reads. The multiple k-mer technique for de novo assembly using Velvet and Oases was applied. A total of 121,288 contigs were assembled that were similar to previously reported Ensembl commelinid sequences. Original Illumina reads were also mapped to the high quality assembly to estimate expression levels of buffalograss transcripts. There were a total of 325 differentially expressed genes between the two buffalograss cultivars. A glycosyl transferase, serine threonine kinase, and nb-arc domain containing transcripts were among those differentially expressed between the two cultivars. These genes have been previously implicated in defense response pathways and may in part explain some of the performance differences between ‘Prestige’ and ‘378’.
To date, this is the first high throughput sequencing experiment conducted on buffalograss. In total, 121,288 high quality transcripts were assembled, significantly expanding the limited genetic resources available for buffalograss genetic studies. Additionally, 325 differentially expressed sequences were identified which may contribute to performance or morphological differences between ‘Prestige’ and ‘378’ buffalograss cultivars.