In silico mining of microsatellites in coding sequences of the date palm (ARECACEAE) genome, characterization, and transferability

Frederique Aberlenc-Bertossi, Karina Castillo, Christine Tranchant-Dubreuil, Emira Cherif, Marco Ballardini, Sabira Abdoulkader, Muriel Gros-Balthazard, Nathalie Chabrillange, Sylvain Santoni, Antonio Mercuri, Jean Christophe Pintaud

    Research output: Contribution to journalArticle

    Abstract

    Premise of the study: To complement existing sets of primarily dinucleotide microsatellite loci from noncoding sequences of date palm, we developed primers for tri-And hexanucleotide microsatellite loci identifi ed within genes. Due to their conserved genomic locations, the primers should be useful in other palm taxa, and their utility was tested in seven other Phoenix species and in Chamaerops , Livistona , and Hyphaene . Methods and Results: Tandem repeat motifs of 3-6 bp were searched using a simple sequence repeat (SSR)-pipeline package in coding portions of the date palm draft genome sequence. Fifteen loci produced highly consistent amplifi cation, intraspecifi c polymorphisms, and stepwise mutation patterns. Conclusions: These microsatellite loci showed suffi cient levels of variability and transferability to make them useful for population genetic, selection signature, and interspecifi c gene fl ow studies in Phoenix and other Coryphoideae genera.

    Original languageEnglish (US)
    Article number1300058
    JournalApplications in Plant Sciences
    Volume2
    Issue number1
    DOIs
    StatePublished - Jan 1 2014

    Fingerprint

    Phoenix dactylifera
    Phoenix (Arecaceae)
    genome
    microsatellite repeats
    loci
    gene
    population genetics
    Hyphaene
    mutation
    genomics
    polymorphism
    Livistona
    cation
    tandem repeat sequences
    cations
    complement
    genes
    genetic polymorphism
    method

    Keywords

    • Arecaceae
    • Coryphoideae
    • Microsatellite/SSR mining
    • Phoenix dactylifera
    • Transferability.

    ASJC Scopus subject areas

    • Ecology, Evolution, Behavior and Systematics
    • Plant Science

    Cite this

    Aberlenc-Bertossi, F., Castillo, K., Tranchant-Dubreuil, C., Cherif, E., Ballardini, M., Abdoulkader, S., ... Pintaud, J. C. (2014). In silico mining of microsatellites in coding sequences of the date palm (ARECACEAE) genome, characterization, and transferability. Applications in Plant Sciences, 2(1), [1300058]. https://doi.org/10.3732/apps.1300058

    In silico mining of microsatellites in coding sequences of the date palm (ARECACEAE) genome, characterization, and transferability. / Aberlenc-Bertossi, Frederique; Castillo, Karina; Tranchant-Dubreuil, Christine; Cherif, Emira; Ballardini, Marco; Abdoulkader, Sabira; Gros-Balthazard, Muriel; Chabrillange, Nathalie; Santoni, Sylvain; Mercuri, Antonio; Pintaud, Jean Christophe.

    In: Applications in Plant Sciences, Vol. 2, No. 1, 1300058, 01.01.2014.

    Research output: Contribution to journalArticle

    Aberlenc-Bertossi, F, Castillo, K, Tranchant-Dubreuil, C, Cherif, E, Ballardini, M, Abdoulkader, S, Gros-Balthazard, M, Chabrillange, N, Santoni, S, Mercuri, A & Pintaud, JC 2014, 'In silico mining of microsatellites in coding sequences of the date palm (ARECACEAE) genome, characterization, and transferability', Applications in Plant Sciences, vol. 2, no. 1, 1300058. https://doi.org/10.3732/apps.1300058
    Aberlenc-Bertossi, Frederique ; Castillo, Karina ; Tranchant-Dubreuil, Christine ; Cherif, Emira ; Ballardini, Marco ; Abdoulkader, Sabira ; Gros-Balthazard, Muriel ; Chabrillange, Nathalie ; Santoni, Sylvain ; Mercuri, Antonio ; Pintaud, Jean Christophe. / In silico mining of microsatellites in coding sequences of the date palm (ARECACEAE) genome, characterization, and transferability. In: Applications in Plant Sciences. 2014 ; Vol. 2, No. 1.
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    AU - Cherif, Emira

    AU - Ballardini, Marco

    AU - Abdoulkader, Sabira

    AU - Gros-Balthazard, Muriel

    AU - Chabrillange, Nathalie

    AU - Santoni, Sylvain

    AU - Mercuri, Antonio

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