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Phylogenetic properties of 50 nuclear loci in Medicago (Leguminosae) generated using multiplexed sequence capture and next-generation sequencing

Journal article
Authors Filipe de Sousa
Yann Bertrand
Stephan Nylinder
Bengt Oxelman
Jonna S. Eriksson
Bernard E. Pfeil
Published in PLoS ONE
Volume 9
Issue 10
ISSN 1932-6203
Publication year 2014
Published at Department of Biological and Environmental Sciences
Language en
Links doi.org/10.1371/journal.pone.010970...
Keywords sequence capture, low-copy nuclear genes, substitution rates, phylogenetics, Medicago, legume family
Subject categories Bioinformatics (Computational Biology), Botany, Genetics, Biological Systematics

Abstract

Next-generation sequencing technology has increased the capacity to generate molecular data for plant biological research, including phylogenetics, and can potentially contribute to resolving complex phylogenetic problems. The evolutionary history of Medicago L. (Leguminosae: Trifoliae) remains unresolved due to incongruence between published phylogenies. Identification of the processes causing this genealogical incongruence is essential for the inference of a correct species phylogeny of the genus and requires that more molecular data, preferably from low-copy nuclear genes, are obtained across different species. Here we report the development of 50 novel LCN markers in Medicago and assess the phylogenetic properties of each marker. We used the genomic resources available for Medicago truncatula Gaertn., hybridisation-based gene enrichment (sequence capture) techniques and Next-Generation Sequencing to generate sequences. This alternative proves to be a cost-effective approach to amplicon sequencing in phylogenetic studies at the genus or tribe level and allows for an increase in number and size of targeted loci. Substitution rate estimates for each of the 50 loci are provided, and an overview of the variation in substitution rates among a large number of low-copy nuclear genes in plants is presented for the first time. Aligned sequences of major species lineages of Medicago and its sister genus are made available and can be used in further probe development for sequence-capture of the same markers.

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