Alignments used for the phylogenetic analysis of sweet cucumber (Solanum muricatum, Solanaceae)

Sweet cucumber (Solanum muricatum) sect. Basarthrum, is a neglected native crop to the Andean region. It is naturally distributed very close to potatoes (Solanum sect. Petota) and tomatoes (Solanum sect. Lycopersicon), two groups with great economic importance. We obtained the first complete chloroplast (cp) genome of sweet cucumber and compared with seven Solanacea species. Pair-end clean reads were obtained by PE 150 library and the Illumina HiSeq 2500 platform. The complete cp genome of S. muricatum had a 155,681 bp with typical quadripartite structure, containing a large single copy (LSC) region (86,182 bp) and a small single-copy (SSC) region (18,360 bp), separated by two inverted repeat (IR) regions (25,568 bp). The annotation of chloroplast genome predicted 88 protein-coding genes (CDS), 8 ribosomal RNA (rRNA) genes, 37 transfer RNA (tRNA) genes, and one pseudogene. A total of 48 perfect microsatellites were identified, divided in mononucleotide repeats (32), followed by tetranuc...