Phylogenetic properties of 50 nuclear loci in Medicago (Leguminosae) generated using multiplexed sequence capture and Next-Generation Sequencing

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 approach 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. An estimate of the substitution rate for each of the 50 loci is 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 these 50 markers. These nuclear markers have potential phylogenetic utility for the inference of species relationships in Medicago and in other plant genera, particularly within the legume family.