WP2 Molecular Data
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WP 2 Molecular data

New molecular markers development from IRD team

As part of WP1 and WP2 activities at IRD, new molecular markers have been recently published in order to support the genetic and phylogenetic analyses conducted in the project. Namely, two low-copy nuclear genes, Agamous 1, a transcription factor involved in floral structure, and Phytochrome B, a gene involved in environmental response through far red light sensing, have been optimized for phylogenetic use in the palm family, with specific PCR primers designed, and their utility evaluated in the subtribe Bactridinae (Ludena et al., in press). A set of 100 new DNA chloroplast primer pairs has been designed and optimized in Monocotyledons through a joint effort of the PALMS project and two other projects on yams and African cereals at IRD (Scarcelli et al. 2011). These new markers are currently used in phylobetadiversity studies of South American palm communities (Eiserhardt, AAU), phylogeographic studies of the genus Ceroxylon (Sanin, UN) and phylogenetic/speciation studies of Astrocaryum (IRD).

Scarcelli N., Barnaud A., Eiserhardt W., Treier U., Seveno M., d’Anfray A., Vigouroux Y., Pintaud J.-C. 2011. A set of 100 DNA primer pairs to study population genetics and phylogeny in Monocotyledons. PLoS ONE 6(5): e19954. doi:10.1371/journal.pone.0019954.
245 sequences have been uploaded to GENBANK: From JF745763.1 GI: 343761085 to JF758190.1 GI: 340803628.

Ludeña B., Chabrillange N., Aberlenc-Bertossi F., Adam H., Tregear J.W., Pintaud J.C. (in press).Phylogenetic utility of the nuclear genes AGAMOUS 1 and PHYTOCHROME B in palms (Arecaceae): an example within Bactridinae. Annals of Botany, first published online August 9, 2011. doi:10.1093/aob/mcr191.
See PDF (early online)
56 sequences have been uploaded to GENBANK
List of sequences - Ludeña et al.

Link to GENBANK Nucleotide database


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