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. 2014 Jan 7;2(1):apps.1300058.
doi: 10.3732/apps.1300058. eCollection 2014 Jan.

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

Frédérique Aberlenc-Bertossi  1 , Karina Castillo  1 , Christine Tranchant-Dubreuil  1 , Emira Chérif  2 , Marco Ballardini  3 , Sabira Abdoulkader  4 , Muriel Gros-Balthazard  5 , Nathalie Chabrillange  1 , Sylvain Santoni  6 , Antonio Mercuri  3 , Jean-Christophe Pintaud  1
Affiliations

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

Frédérique Aberlenc-Bertossi et al. Appl Plant Sci. .

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 identified 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 amplification, intraspecific polymorphisms, and stepwise mutation patterns. •

Conclusions: These microsatellite loci showed sufficient levels of variability and transferability to make them useful for population genetic, selection signature, and interspecific gene flow studies in Phoenix and other Coryphoideae genera.

Keywords: Arecaceae; Coryphoideae; Phoenix dactylifera; microsatellite/SSR mining; transferability.

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References

    1. Al-Dous E. K., George B., Al-Mahmoud M. E., Al-Jaber M. Y., Wang H., Salameh Y. M., Al-Azwani E. K., et al. 2011. De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera). Nature Biotechnology 29: 521–527 - PubMed
    1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. 1990. Basic local alignment search tool. Journal of Molecular Biology 215: 403–410 - PubMed
    1. Arabnezhad H., Bahar M., Mohammadi H. R., Latifian M. 2012. Development, characterization and use of microsatellite markers for germplasm analysis in date palm (Phoenix dactylifera L.). Scientia Horticulturae 134: 150–156
    1. Belkhir K., Borsa P., Chikhi L., Raufaste N., Bonhomme F. 2004. GENETIX 4.05, logiciel sous WindowsTM pour la génétique des populations. Laboratoire Génome, Populations, Interactions, Université de Montpellier II, Montpellier, France
    1. Benson G. 1999. Tandem repeats finder: A program to analyze DNA sequences. Nucleic Acids Research 27: 573–580 - PMC - PubMed

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