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Orthology guided transcriptome assembly of Italian ryegrass and meadow fescue for single-nucleotide polymorphism discovery

(2016) PLANT GENOME. 9(3).
Author
Organization
Abstract
Single-nucleotide polymorphisms (SNPs) represent natural DNA sequence variation. They can be used for various applications including the construction of high-density genetic maps, analysis of genetic variability, genome-wide association studies, and mapbased cloning. Here we report on transcriptome sequencing in the two forage grasses, meadow fescue (Festuca pratensis Huds.) and Italian ryegrass (Lolium multiflorum Lam.), and identification of various classes of SNPs. Using the Orthology Guided Assembly (OGA) strategy, we assembled and annotated a total of 18,952 and 19,036 transcripts for Italian ryegrass and meadow fescue, respectively. In addition, we used transcriptome sequence data of perennial ryegrass (L. perenne L.) from a previous study to identify 16,613 transcripts shared across all three species. Large numbers of intraspecific SNPs were identified in all three species: 248,000 in meadow fescue, 715,000 in Italian ryegrass, and 529,000 in perennial ryegrass. Moreover, we identified almost 25,000 interspecific SNPs located in 5343 genes that can distinguish meadow fescue from Italian ryegrass and 15,000 SNPs located in 3976 genes that discriminate meadow fescue from both Lolium species. All identified SNPs were positioned in silico on the seven linkage groups (LGs) of L. perenne using the GenomeZipper approach. With the identification and positioning of interspecific SNPs, our study provides a valuable resource for the grass research and breeding community and will enable detailed characterization of genomic composition and gene expression analysis in prospective Festuca  Lolium hybrids.
Keywords
FESTUCA-PRATENSIS HUDS., DNA-SEQUENCING DATA, LOLIUM-PERENNE L., RNA-SEQ DATA, GENOME, CULTIVARS, FESTULOLIUM, MULTIFLORUM, HYBRID, RECOMBINATION

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Citation

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MLA
Stočes, Štěpán et al. “Orthology Guided Transcriptome Assembly of Italian Ryegrass and Meadow Fescue for Single-nucleotide Polymorphism Discovery.” PLANT GENOME 9.3 (2016): n. pag. Print.
APA
Stočes, Š., Ruttink, T., Bartoš, J., Studer, B., Yates, S., Zwierzykowski, Z., Abrouk, M., et al. (2016). Orthology guided transcriptome assembly of Italian ryegrass and meadow fescue for single-nucleotide polymorphism discovery. PLANT GENOME, 9(3).
Chicago author-date
Stočes, Štěpán, Tom Ruttink, Jan Bartoš, Bruno Studer, Steven Yates, Zbigniew Zwierzykowski, Michael Abrouk, et al. 2016. “Orthology Guided Transcriptome Assembly of Italian Ryegrass and Meadow Fescue for Single-nucleotide Polymorphism Discovery.” Plant Genome 9 (3).
Chicago author-date (all authors)
Stočes, Štěpán, Tom Ruttink, Jan Bartoš, Bruno Studer, Steven Yates, Zbigniew Zwierzykowski, Michael Abrouk, Isabel Roldàn-Ruiz, Tomasz Książczyk, Elodie Rey, Jaroslav Doležel, and David Kopecký. 2016. “Orthology Guided Transcriptome Assembly of Italian Ryegrass and Meadow Fescue for Single-nucleotide Polymorphism Discovery.” Plant Genome 9 (3).
Vancouver
1.
Stočes Š, Ruttink T, Bartoš J, Studer B, Yates S, Zwierzykowski Z, et al. Orthology guided transcriptome assembly of Italian ryegrass and meadow fescue for single-nucleotide polymorphism discovery. PLANT GENOME. 2016;9(3).
IEEE
[1]
Š. Stočes et al., “Orthology guided transcriptome assembly of Italian ryegrass and meadow fescue for single-nucleotide polymorphism discovery,” PLANT GENOME, vol. 9, no. 3, 2016.
@article{8508388,
  abstract     = {Single-nucleotide polymorphisms (SNPs) represent natural DNA sequence variation. They can be used for various applications including the construction of high-density genetic maps, analysis of genetic variability, genome-wide association studies, and mapbased cloning. Here we report on transcriptome sequencing in the two forage grasses, meadow fescue (Festuca pratensis Huds.) and Italian ryegrass (Lolium multiflorum Lam.), and identification of various classes of SNPs. Using the Orthology Guided Assembly (OGA) strategy, we assembled and annotated a total of 18,952 and 19,036 transcripts for Italian ryegrass and meadow fescue, respectively. In addition, we used transcriptome sequence data of perennial ryegrass (L. perenne L.) from a previous study to identify 16,613 transcripts shared across all three species. Large numbers of intraspecific SNPs were identified in all three species: 248,000 in meadow fescue, 715,000 in Italian ryegrass, and 529,000 in perennial ryegrass. Moreover, we identified almost 25,000 interspecific SNPs located in 5343 genes that can distinguish meadow fescue from Italian ryegrass and 15,000 SNPs located in 3976 genes that discriminate meadow fescue from both Lolium species. All identified SNPs were positioned in silico on the seven linkage groups (LGs) of L. perenne using the GenomeZipper approach. With the identification and positioning of interspecific SNPs, our study provides a valuable resource for the grass research and breeding community and will enable detailed characterization of genomic composition and gene expression analysis in prospective Festuca  Lolium hybrids.},
  author       = {Stočes, Štěpán and Ruttink, Tom and Bartoš, Jan and Studer, Bruno and Yates, Steven and Zwierzykowski, Zbigniew and Abrouk, Michael and Roldàn-Ruiz, Isabel and Książczyk, Tomasz and Rey, Elodie and Doležel, Jaroslav and Kopecký, David},
  issn         = {1940-3372},
  journal      = {PLANT GENOME},
  keywords     = {FESTUCA-PRATENSIS HUDS.,DNA-SEQUENCING DATA,LOLIUM-PERENNE L.,RNA-SEQ DATA,GENOME,CULTIVARS,FESTULOLIUM,MULTIFLORUM,HYBRID,RECOMBINATION},
  language     = {eng},
  number       = {3},
  pages        = {14},
  title        = {Orthology guided transcriptome assembly of Italian ryegrass and meadow fescue for single-nucleotide polymorphism discovery},
  url          = {http://dx.doi.org/10.3835/plantgenome2016.02.0017},
  volume       = {9},
  year         = {2016},
}

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