Exploring the genomic diversity and breeding applications of the Solanum sessiliflorum transcriptome via phylogenetic analysis

Abstract

Compelling evidence supports the potential application of wild crop relatives in Solanum breeding. Efforts have been made to generate genomic data from wild Solanum plants to assess the insertion of advantageous traits into crop species. South America hosts a broad range of plants that have not been widely evaluated at the molecular level. Solanum sessiliflorum is a wild species that shows tolerance to Ralstonia solanacearum and nematode infections. The Illumina platform was used to construct the transcriptome of S. sessiliflorum. The data were analyzed using bioinformatics tools for both phylogenetic comparison and bioprospecting of disease-related genes. Our leaf transcriptome assembly of S. sessiliflorum enables phylogenetic comparisons and stress-tolerant gene bioprospecting. De novo assembly generated 114,184 unigenes. A comparison of the S. sessiliflorum unigene dataset with other Solanum nucleotide genomic resources revealed greater similarity with Solanum tuberosum than with Solanum melongena. Additionally, S. sessiliflorum within the Leptostemonum group, along with S. melongena, possesses features related to Solanum clade evolution. Bioprospection of disease response targets identified 122 potential candidate unigenes retrieved from the S. sessiliflorum dataset. The abundant expression of fragments of disease-related and hormonal defense genes appears to constitute a housekeeping mechanism to avoid pathogen attacks on leaves. In total, 1091 unigenes were classified as transcription factors (TFs), with a large number of TFs associated with biotic resilience. These results highlight the potential for exploring the genomic diversity of S. sessiliflorum, which will be useful for applications in breeding programs.