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    Gene expression atlas of fruit ripening and transcriptome assembly from RNA-seq data in octoploid strawberry (Fragaria × ananassa)

    • Autor
      Sánchez-Sevilla, José F; Vallarino Castro, José G.; Osorio-Algar, SoniaAutoridad Universidad de Málaga; Bombarely, Aureliano; Posé-Padilla, DavidAutoridad Universidad de Málaga; Merchante-Berg, Catharina; Botella-Mesa, Miguel ÁngelAutoridad Universidad de Málaga; Amaya Saavedra, Iraida; Valpuesta-Fernández, VictorianoAutoridad Universidad de Málaga
    • Fecha
      2017-10-23
    • Editorial/Editor
      Springer Nature
    • Palabras clave
      Fresas - Variedades
    • Resumen
      RNA-seq has been used to perform global expression analysis of the achene and the receptacle at four stages of fruit ripening, and of the roots and leaves of strawberry (Fragaria × ananassa). About 967 million reads and 191 Gb of sequence were produced, using Illumina sequencing. Mapping the reads in the related genome of the wild diploid Fragaria vesca revealed differences between the achene and receptacle development program, and reinforced the role played by ethylene in the ripening receptacle. For the strawberry transcriptome assembly, a de novo strategy was followed, generating separate assemblies for each of the ten tissues and stages sampled. The Trinity program was used for these assemblies, resulting in over 1.4 M isoforms. Filtering by a threshold of 0.3 FPKM, and doing Blastx (E-value < 1 e-30) against the UniProt database of plants reduced the number to 472,476 isoforms. Their assembly with the MIRA program (90% homology) resulted in 26,087 contigs. From these, 91.34 percent showed high homology to Fragaria vesca genes and 87.30 percent Fragaria iinumae (BlastN E-value < 1 e-100). Mapping back the reads on the MIRA contigs identified polymorphisms at nucleotide level, using FREEBAYES, as well as estimate their relative abundance in each sample.
    • URI
      https://hdl.handle.net/10630/23560
    • DOI
      https://dx.doi.org/10.1038/s41598-017-14239-6
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    Sci Rep 2017 Sánchez-Sevilla.pdf (2.293Mb)
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    REPOSITORIO INSTITUCIONAL UNIVERSIDAD DE MÁLAGA
    REPOSITORIO INSTITUCIONAL UNIVERSIDAD DE MÁLAGA
     

     

    REPOSITORIO INSTITUCIONAL UNIVERSIDAD DE MÁLAGA
    REPOSITORIO INSTITUCIONAL UNIVERSIDAD DE MÁLAGA