Building a Reference Transcriptome for the Hexaploid Hard Fescue Turfgrass (Festuca brevipila) Using a Combination of PacBio Isoseq and Illumina Sequencing

Abstract

Background: Hard fescue (Festuca brevipila Tracey, 2n=6x=42) is a cool season turfgrass with a fine leaf texture that performs well under low-input management. Breeding and genetics studies of F. brevipila have been limited due to the complexity of its hexaploid genome. To advance our knowledge of F. brevipila genomics, we used PacBio isoform sequencing to develop a reference transcriptome for this species. Results: Here, we report the F. brevipila reference transcriptome generated from root, crown, leaf, and inflorescence tissues. We obtained 59,510 full-length transcripts, of which 38,556 were non-redundant full-length transcripts. The longest and shortest transcripts were 11,487 and 58 bp, respectively. Distribution of synonymous distances among paralogs within F. brevipila suggested highly similar subgenomes that are difficult to distinguish from sequencing errors. To evaluate the phylogenetic relationships among F. brevipila and close relatives, we sequenced three additional transcriptomes using closely related species on an Illumina platform. The results of our phylotranscriptomic analysis supported the close relationships among F. brevipila (6x), Festuca ovina (4x), Festuca ovina subsp. ovina (2x), and Festuca valesiaca (2x), with high levels of discordance among gene trees. Conclusions: Overall, the F. brevipila PacBio Isoseq reference transcriptome provided the foundation for transcriptome studies and allowed breeders a resource for gene discovery in this important turfgrass species.