Alkan, C., Sajjadian, S., and Eichler, E.E. (2011). Limitations of next-generation genome sequence assembly. Nature Methods 8, 61.
Bolger, A.M., Lohse, M., and Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114-2120.
Byrne, S.L., Nagy, I., Pfeifer, M., Armstead, I., Swain, S., Studer, B., Mayer, K., Campbell, J.D., Czaban, A., Hentrup, S. and Panitz, F., 2015. A synteny‐based draft genome sequence of the forage grass Lolium perenne. The Plant Journal, 84(4), pp.816-826.
Capella-Gutiérrez, S., Silla-Martínez, J.M., and Gabaldón, T. (2009). trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972-1973.
Carroll, J. (1943). Effects of drought, temperature and nitrogen on turf grasses. Plant Physiology 18, 19.
Chang, H.-X., and Hartman, G.L. (2017). Characterization of insect resistance loci in the USDA soybean germplasm collection using genome-wide association studies. Frontiers in Plant Science 8, 670.
Chao, Y., Yuan, J., Li, S., Jia, S., Han, L., and Xu, L. (2018). Analysis of transcripts and splice isoforms in red clover (Trifolium pratense L.) by single-molecule long-read sequencing. BMC Plant Biology 18, 300.
Chen, L.-Y., Morales-Briones, D.F., Passow, C.N., and Yang, Y. (2019). Performance of gene expression analyses using de novo assembled transcripts in polyploid species. Bioinformatics 35, 4314-4320.
Clayton, W.D., and Renvoize, S.A. (1986). Genera graminum. Grasses of the world. Genera graminum. Grasses of the World. 13.
Edgar, R.C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32, 1792-1797.
Edger, P.P., Poorten, T.J., Vanburen, R., Hardigan, M.A., Colle, M., Mckain, M.R., Smith, R.D., Teresi, S.J., Nelson, A.D., and Wai, C.M. (2019). Origin and evolution of the octoploid strawberry genome. Nature Genetics 51, 541-547.
Emms, D.M., and Kelly, S. (2019). OrthoFinder: phylogenetic orthology inference for comparative genomics. BioRxiv, 466201.
Grabherr, M.G., Haas, B.J., Yassour, M., Levin, J.Z., Thompson, D.A., Amit, I., Adiconis, X., Fan, L., Raychowdhury, R., and Zeng, Q. (2011). Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology 29, 644.
Gupta, P., Langridge, P., and Mir, R. (2010). Marker-assisted wheat breeding: present status and future possibilities. Molecular Breeding 26, 145-161.
Hand, M.L., Spangenberg, G.C., Forster, J.W., and Cogan, N.O. (2013). Plastome sequence determination and comparative analysis for members of the Lolium-Festuca grass species complex. G3: Genes, Genomes, Genetics, g3. 112.005264.
Hanson, A.A., and Juska, F.V. (1969). Turfgrass science. Turfgrass Science.
Hoang, N.V., Furtado, A., Mason, P.J., Marquardt, A., Kasirajan, L., Thirugnanasambandam, P.P., Botha, F.C., and Henry, R.J. (2017). A survey of the complex transcriptome from the highly polyploid sugarcane genome using full-length isoform sequencing and de novo assembly from short read sequencing. BMC Genomics 18, 395.
Huff, D.R., and Palazzo, A.J. (1998). Fine fescue species determination by laser flow cytometry. Crop Science 38, 445-450.
Jenkin, T., and Jenkin, T. (1955). Interspecific and intergeneric hybrids in herbage grasses-XIV. The breeding affinities of Festuca ovina. Journal of Genetics 53.
Kantar, M., Unver, T., and Budak, H. (2010). Regulation of barley miRNAs upon dehydration stress correlated with target gene expression. Functional & Integrative Genomics 10, 493-507.
Katoh, K., and Standley, D.M. (2013). MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution 30, 772-780.
Kozomara, A., and Griffiths-Jones, S. (2013). miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Research 42, D68-D73.
Langmead, B., and Salzberg, S.L. (2012). Fast gapped-read alignment with Bowtie 2. Nature Methods 9, 357.
Lassmann, T., Hayashizaki, Y., and Daub, C.O. (2010). SAMStat: monitoring biases in next generation sequencing data. Bioinformatics 27, 130-131.
Li, A., Zhang, J., and Zhou, Z. (2014). PLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme. BMC Bioinformatics 15, 311.
Li, H., and Durbin, R. (2009). Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754-1760.
Li, W., and Godzik, A. (2006). Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658-1659.
Ma, Y., Staub, J.E., Robbins, M.D., Johnson, P.G., and Larson, S.R. (2014). Phenotypic and genetic characterization of Kyrgyz fine-leaved Festuca valesiaca germplasm for use in semi-arid, low-maintenance turf applications. Genetic Resources and Crop Evolution 61, 185-197.
Mccormick, R.F., Truong, S.K., Sreedasyam, A., Jenkins, J., Shu, S., Sims, D., Kennedy, M., Amirebrahimi, M., Weers, B.D., and Mckinley, B. (2018). The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization. The Plant Journal 93, 338-354.
Mirarab, S., Reaz, R., Bayzid, M.S., Zimmermann, T., Swenson, M.S., and Warnow, T. (2014). ASTRAL: genome-scale coalescent-based species tree estimation. Bioinformatics 30, i541-i548.
Ozsolak, F., and Milos, P.M. (2011). RNA sequencing: advances, challenges and opportunities. Nature Reviews Genetics 12, 87-98.
Pastor-Corrales, M. (2003). Sources, genes for resistance and pedigrees of 52 rust and mosaic resistant dry bean germplasm lines released by the USDA Beltsville bean project in collaboration. Science 29, 834-835.
Phing Lau, W.C., Latif, M.A., Y. Rafii, M., Ismail, M.R., and Puteh, A. (2016). Advances to improve the eating and cooking qualities of rice by marker-assisted breeding. Critical Reviews in Biotechnology 36, 87-98.
Qiu, Y., Hamernick, S., Ortiz, J.B., and Watkins, E. (2020a). DNA content and ploidy estimation of Festuca ovina accessions by flow cytometry. Crop Science, https://doi.org/10.1002/csc2.20229
Qiu, Y., Hirsch, C.D., Yang, Y., and Watkins, E. (2019). Towards Improved Molecular Identification Tools in Fine Fescue (Festuca L., Poaceae) Turfgrasses: Nuclear Genome Size, Ploidy, and Chloroplast Genome Sequencing. Frontiers in Genetics 10.
Qiu, Y., Yang, Y., Hirsch, C.D., and Watkins, E. (2020b). Building a reference transcriptome for the hexaploid hard fescue turfgrass (Festuca brevipila) using a combination of Pacbio isoseq and illumina sequencing. biorxiv, 2020.2002.2026.966952.
Quevillon, E., Silventoinen, V., Pillai, S., Harte, N., Mulder, N., Apweiler, R., and Lopez, R. (2005). InterProScan: protein domains identifier. Nucleic Acids Research 33, W116-W120.
Team, R. C. (2013). R: A language and environment for statistical computing.
Rambaut, A. (2012). "FigTree v1. 4".).
Reiter, M., Friell, J., Horgan, B., Soldat, D., and Watkins, E. (2017). Drought Response of Fine Fescue Mixtures Maintained as a Golf Course Fairway. International Turfgrass Society Research Journal 13, 65-74.
Rhoads, A., and Au, K.F. (2015). PacBio sequencing and its applications. Genomics, Proteomics & Bioinformatics 13, 278-289.
Ruemmele, B., Brilman, L., and Huff, D. (1995). Fine fescue germplasm diversity and vulnerability. Crop Science 35, 313-316.
Salmela, L., and Rivals, E. (2014). LoRDEC: accurate and efficient long read error correction. Bioinformatics 30, 3506-3514.
Sanan-Mishra, N., Kumar, V., Sopory, S.K., and Mukherjee, S.K. (2009). Cloning and validation of novel miRNA from basmati rice indicates cross talk between abiotic and biotic stresses. Molecular Genetics and Genomics 282, 463.
Schmieder, R., and Edwards, R. (2011). Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PloS one 6, e17288.
Shan, Q., Wang, Y., Li, J., Zhang, Y., Chen, K., Liang, Z., Zhang, K., Liu, J., Xi, J.J., and Qiu, J.-L. (2013). Targeted genome modification of crop plants using a CRISPR-Cas system. Nature Biotechnology 31, 686.
Shi, G.-Q., Fu, J.-Y., Rong, L.-J., Zhang, P.-Y., Guo, C.-J., and Kai, X. (2018). TaMIR1119, a miRNA family member of wheat (Triticum aestivum), is essential in the regulation of plant drought tolerance. Journal of Integrative Agriculture 17, 2369-2378.
Simão, F.A., Waterhouse, R.M., Ioannidis, P., Kriventseva, E.V., and Zdobnov, E.M. (2015). BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210-3212.
Šmarda, P., Bureš, P., Horová, L., Foggi, B., and Rossi, G. (2008). Genome size and GC content evolution of Festuca: ancestral expansion and subsequent reduction. Annals of Botany 101, 421-433.
Smith, S.A., Moore, M.J., Brown, J.W., and Yang, Y. (2015). Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants. BMC Evolutionary Biology 15, 150.
Stamatakis, A. (2006). RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688-2690.
Suyama, M., Torrents, D., and Bork, P. (2006). PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Research 34, W609-W612.
Varshney, R.K., Graner, A., and Sorrells, M.E. (2005). Genomics-assisted breeding for crop improvement. Trends in Plant Science 10, 621-630.
Wang, B., Tseng, E., Regulski, M., Clark, T.A., Hon, T., Jiao, Y., Lu, Z., Olson, A., Stein, J.C., and Ware, D. (2016). Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing. Nature Communications 7, 11708.
Wang, D., Ling, L., Zhang, W., Bai, Y., Shu, Y., and Guo, C. (2018). Uncovering key small RNAs associated with gametocidal action in wheat. Journal of Experimental Botany 69, 4739-4756.
Wenger, A.M., Peluso, P., Rowell, W.J., Chang, P.-C., Hall, R.J., Concepcion, G.T., Ebler, J., Fungtammasan, A., Kolesnikov, A., and Olson, N.D. (2019). Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. Nature Biotechnology 37, 1155-1162.
Wang, X., Wang, J., Jin, D., Guo, H., Lee, T. H., Liu, T., & Paterson, A. H. (2015). Genome alignment spanning major Poaceae lineages reveals heterogeneous evolutionary rates and alters inferred dates for key evolutionary events. Molecular Plant, 8(6), 885-898.
Wilkinson, M.J., and Stace, C.A. (1991). A new taxonomic treatment of the Festuca ovina L. aggregate (Poaceae) in the British Isles. Botanical Journal of the Linnean Society 106, 347-397.
Wu, T.D., and Watanabe, C.K. (2005). GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 21, 1859-1875.
Zhang, B., Liu, J., Wang, X., and Wei, Z. (2018). Full-length RNA sequencing reveals unique transcriptome composition in bermudagrass. Plant Physiology and Biochemistry 132, 95-103.
Zhang, G., Sun, M., Wang, J., Lei, M., Li, C., Zhao, D., Huang, J., Li, W., Li, S., and Li, J. (2019). PacBio full‐length cDNA sequencing integrated with RNA‐seq reads drastically improves the discovery of splicing transcripts in rice. The Plant Journal 97, 296-305.
Zwaenepoel, A., & Van de Peer, Y. (2019). wgd—simple command line tools for the analysis of ancient whole-genome duplications. Bioinformatics, 35(12), 2153-2155.