The first complete chloroplast genome of Peruvian “chila” identified as Solanum lasiocarpum: comparative plastomics and phylogenomic insights

Rodriguez-Grados P.M.; Hernández-Amasifuen A.D.; Vargas R.; Arbizu C.I. · Genetic Resources and Crop Evolution (2026) · DOI: 10.1007/s10722-026-02891-9

Resumen

Chloroplasts are very important resources for research on plant evolution and phylogenetic inference. This is motivated by their highly conserved structure and also by the low rate of recombination, which prevents many mutations from being found in this organelle. In this research study, we successfully performed the assembly and annotation of the first chloroplast of a Peruvian cultivar locally known as "Chila," in addition to carrying out a genetic comparison with other Solanaceae species belonging to the Solanum Leptostemonum clade. We also performed comparative chloroplast genome and phylogenomic analyses among species belonging to the Solanum Leptostemonum clade. We successfully assembled the chloroplast genome, thanks to a hybrid assembly method, which combined short reads sequenced by Illumina with long reads generated by ONT. According to our study, this assembled chloroplast genome has a length of 155,671 bp, in addition to presenting a structure composed of an large single-copy (LSC) region of 86,380 bp, an SSC region of 18,559 bp, and two inverted repeat (IR) regions of 25,366 bp each, which is the normal quadripartite structure of chloroplast. Also, the organelle showed a total of 120 unique genes in this organelle, including 85 coding DNA sequences (CDS), 4 rRNA genes, and 31 tRNA genes, in addition to presenting a GC content of 37.72%. We performed the comparison with 17 chloroplast genomes of species belonging to the Solanum Leptostemonum clade, which revealed highly conserved genome organization, gene content, and GC composition, with only minor variation mainly associated with the dynamics of the IR boundaries. The results of the codon usage analysis showed that it had a high preference for codons ending in A or U; in addition, the results of the simple sequence repeat (SSR) analyses showed the abundance of A/T-rich motifs in all the species studied. The nucleotide diversity analysis identified matK, ndhF, and rps15 as highly variable loci with potential applications for the development of new molecular markers for Solanaceae, which are valuable for species diversity research, phylogenetic investigations, and population genetics. Phylogeny analyses support the monophyly of S. lasiocarpum and identified that the Amazonian chloroplast sample (PX971186) is in the clade within the S. lasiocarpum accessions from Asia, demonstrating a high level of chloroplast conservation in geographically distinct populations. © The Author(s), under exclusive licence to Springer Nature B.V. 2026.

Instituciones: Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas