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 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 S.
muricatum is a sister species to members of sections Petota + Lycopersicum
+ Etuberosum. This study reports for the first time the genome
organization, gene content, and structural features of the chloroplast
genome of S. muricatum. Also, this study 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.