Phylogenetic Properties of 50 Nuclear Loci in Medicago (Leguminosae) Generated Using Multiplexed Sequence Capture and Next-Generation Sequencing

摘要

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 evolutionaryhistory 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 speciesphylogeny of the genus and requires that more molecular data, preferably from low-copy nuclear genes, are obtainedacross different species. Here we report the development of 50 novel LCN markers in Medicago and assess the phylogeneticproperties of each marker. We used the genomic resources available for Medicago truncatula Gaertn., hybridisation-basedgene enrichment (sequence capture) techniques and Next-Generation Sequencing to generate sequences. This alternativeproves to be a cost-effective approach to amplicon sequencing in phylogenetic studies at the genus or tribe level andallows 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 ispresented for the first time. Aligned sequences of major species lineages of Medicago and its sister genus are made availableand can be used in further probe development for sequence-capture of the same markers.