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Orthology Guided Transcriptome Assembly of Italian Ryegrass and Meadow Fescue for Single-Nucleotide Polymorphism Discovery

Identifikátory výsledku

  • Kód výsledku v IS VaVaI

    <a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61389030%3A_____%2F16%3A00473313" target="_blank" >RIV/61389030:_____/16:00473313 - isvavai.cz</a>

  • Výsledek na webu

    <a href="http://dx.doi.org/10.3835/plantgenome2016.02.0017" target="_blank" >http://dx.doi.org/10.3835/plantgenome2016.02.0017</a>

  • DOI - Digital Object Identifier

    <a href="http://dx.doi.org/10.3835/plantgenome2016.02.0017" target="_blank" >10.3835/plantgenome2016.02.0017</a>

Alternativní jazyky

  • Jazyk výsledku

    angličtina

  • Název v původním jazyce

    Orthology Guided Transcriptome Assembly of Italian Ryegrass and Meadow Fescue for Single-Nucleotide Polymorphism Discovery

  • Popis výsledku v původním jazyce

    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 map-based 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.

  • Název v anglickém jazyce

    Orthology Guided Transcriptome Assembly of Italian Ryegrass and Meadow Fescue for Single-Nucleotide Polymorphism Discovery

  • Popis výsledku anglicky

    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 map-based 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.

Klasifikace

  • Druh

    J<sub>x</sub> - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)

  • CEP obor

    EB - Genetika a molekulární biologie

  • OECD FORD obor

Návaznosti výsledku

  • Projekt

    <a href="/cs/project/LO1204" target="_blank" >LO1204: Udržitelný rozvoj výzkumu v Centru regionu Haná</a><br>

  • Návaznosti

    I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Ostatní

  • Rok uplatnění

    2016

  • Kód důvěrnosti údajů

    S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Údaje specifické pro druh výsledku

  • Název periodika

    Plant Genome

  • ISSN

    1940-3372

  • e-ISSN

  • Svazek periodika

    9

  • Číslo periodika v rámci svazku

    3

  • Stát vydavatele periodika

    US - Spojené státy americké

  • Počet stran výsledku

    14

  • Strana od-do

  • Kód UT WoS článku

    000393120000011

  • EID výsledku v databázi Scopus