A dedicated target capture approach reveals variable genetic markers across micro- and macro-evolutionary time scales in palms

Harpe, Marylaure de La; Hess, Jaqueline; Loiseau, Oriane; Salamin, Nicolas; Lexer, Christian; Paris, Margot

doi:10.1111/1755-0998.12945

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A dedicated target capture approach reveals variable genetic markers across micro- and macro-evolutionary time scales in palms

Harpe, Marylaure de La Department of Botany and Biodiversity Research, University of Vienna, Austria
Hess, Jaqueline Department of Botany and Biodiversity Research, University of Vienna, Austria
Loiseau, Oriane Department of Computational Biology, University of Lausanne, Switzerland - Swiss Institute of Bioinformatics, Lausanne, Switzerland
Salamin, Nicolas Department of Computational Biology, University of Lausanne, Switzerland - Swiss Institute of Bioinformatics, Lausanne, Switzerland
Lexer, Christian Department of Botany and Biodiversity Research, University of Vienna, Austria
Paris, Margot Department of Biology, Unit Ecology and Evolution, University of Fribourg, Switzerland

2019

Published in:

Molecular Ecology Resources. - 2019, vol. 19, no. 1, p. 221-234

English Understanding the genetics of biological diversification across micro‐ and macro‐ evolutionary time scales is a vibrant field of research for molecular ecologists as rapid advances in sequencing technologies promise to overcome former limitations. In palms, an emblematic, economically and ecologically important plant family with high diversity in the tropics, studies of diversification at the population and species levels are still hampered by a lack of genomic markers suitable for the genotyping of large numbers of recently diverged taxa. To fill this gap, we used a whole genome sequencing approach to develop target sequencing for molecular markers in 4,184 genome regions, including 4,051 genes and 133 non‐genic putatively neutral regions. These markers were chosen to cover a wide range of evolutionary rates allowing future studies at the family, genus, species and population levels. Special emphasis was given to the avoidance of copy number variation during marker selection. In addition, a set of 149 well‐known sequence regions previously used as phylogenetic markers by the palm biological research community were included in the target regions, to open the possibility to combine and jointly analyse already available data sets with genomic data to be produced with this new toolkit. The bait set was effective for species belonging to all three palm sub‐families tested (Arecoideae, Ceroxyloideae and Coryphoideae), with high mapping rates, specificity and efficiency. The number of high‐quality single nucleotide polymorphisms (SNPs) detected at both the sub‐family and population levels facilitates efficient analyses of genomic diversity across micro‐ and macro‐evolutionary time scales.

Faculty

Faculté des sciences et de médecine

Department

Département de Biologie

Language