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

Abstract

This manuscript has been released on bioRxiv (Qiu et al., 2020b). AbstractBackground: 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 seed head tissues. We obtained 59,510 full-length transcripts, of which 38,595 were non-redundant full-length transcripts. The longest and shortest transcripts were 11,487 and 58 bp, respectively. To test the polyploid origin of F. brevipila, we sequenced three additional transcriptomes using closely related species on an Illumina platform. The results of our phylotranscriptomic analysis supported the allopolyploid origin of F. brevipila. Conclusions:Overall, the F. brevipila Pacbio Isoseq reference transcriptome provided the foundation for transcriptome studies and allowed breeders for gene discovery in this important turfgrass species.

Evaluating the Effects of Propiconazole on Hard Fescue (Festuca brevipila) via RNA sequencing and Liquid Chromatography–Mass Spectrometry

“…Trinity program parameters were set as max memory 200G, 24 CPU cores, and bflyCalculateCPU, with minimum contig size of 200 bp. To improve assembly quality, a previously published F. brevipila Pacbio Isoform sequencing transcriptome (Qiu, Yang et al 2020) was used and combined with the de novo assembly generated in this study. To merge and remove redundant transcripts in the combined transcriptome, ‘cd-hit-est’ from the CD-HIT (v 4.8.1) package was used to cluster redundant sequences with 95% sequence identity (Li and Godzik 2006).…”

“…A single genotype of F. brevipila (SPHD15-3), from the University of Minnesota turfgrass breeding program, which was used to generate a F. brevipila reference transcriptome (Qiu et al, 2020) was vegetatively propagated into individual 5-tiller plants in soilless media (BRK Promix soil, Premier Tech, USA). This genotype was previously confirmed as endophyte free using a commercial Phytoscreen Immunoblot Kit [ENDO797-3, Agrinostics, http://www.agrinostics.com ].…”