Nuclear and chloroplast sequence data for 130 samples from genera Medicago, Trigonella and Melilotus (Fabaceae)

We sequenced target-enriched genomic libraries of 71 species of genus Medicago (Fabaceae), as well as two species of genus Trigonella and six of genus Melilotus, in a total of 130 samples. Pair-end sequence reads were obtained with Illumina MiSeq (San Diego, California, USA) for 61 targeted low-copy nuclear genes, as well as for chloroplast genomes. The CLC Assembly Cell software (CLC Bio, Aarhus, Denmark) was used for trimming, quality filtering and mapping. Sequence data for the 61 low-sopy nuclear genes are presented in multifasta format, containing phased (alleles) and consensus sequences for each sample. Chloroplast sequence data are presented as individual fasta files for each sample. Two tables, containing information on sampling and on the 61 targeted nuclear genes, are also provided.