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

<p><span><span>Sweet cucumber <em>(Solanum muricatum) </em>sect. <em>Basarthrum, </em>is a neglected native crop to the Andean region. It is naturally distributed very close to potatoes (<em>Solanum </em>sect. <em>Petota</em>) and tomatoes (<em>Solanum</em> sect. <em>Lycopersicon</em>), 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 <em>S. muricatum</em> 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 tetranucleotide (6) and dinucleotides (5). SSRs with trinucleotides repeats (3), pentanucleotide (1) and hexanucleotide (1) repeats motifs in these genomes were identified in lower quantity. Most of these repeats were distributed in the noncoding regions. Whole chloroplast genome comparison with the other seven Solanaceae species revealed that the small single copy and large single copy regions showed more divergence than inverted regions. Finally, phylogenetic analyses resolved that <em>S. muricatum</em> is a sister species to members of sections <em>Petota</em> + <em>Lycopersicum</em> + <em>Etuberosum</em>. This study reports for the first time the genome organization, gene content, and structural features of the chloroplast genome of <em>S. muricatum</em>. Also, this study </span><span>may provide the basis for evaluating genetic diversity within the Solanaceae species, and will be useful to examine the evolutionary processes in sweet cucumber landraces.</span></span></p>