De novo genome assembly of Solanum sitiens reveals structural variation associated with drought and salinity tolerance

Motivation: Solanum sitiens is a self-incompatible wild relative of tomato, characterized by salt and drought-resistance traits, with the potential to contribute through breeding programmes to crop improvement in cultivated tomato. This species has a distinct morphology, classification and ecotype compared to other stress resistant wild tomato relatives such as S.pennellii and S.chilense. Therefore, the availability of a reference genome for S.sitiens will facilitate the genetic and molecular understanding of salt and drought resistance. Results: A high-quality de novo genome and transcriptome assembly for S.sitiens (Accession LA1974) has been developed. A hybrid assembly strategy was followed using Illumina short reads (similar to 159 x coverage) and PacBio long reads (similar to 44 x coverage), generating a total of similar to 262 Gbp of DNA sequence. A reference genome of 1245 Mbp, arranged in 1483 scaffolds with an N50 of 1.826 Mbp was generated. Genome completeness was estimated at 95% using the Benchmarking Universal Single-Copy Orthologs (BUSCO) and the K-mer Analysis Tool (KAT). In addition, similar to 63 Gbp of RNA-Seq were generated to support the prediction of 31 164 genes from the assembly, and to perform a de novo transcriptome. Lastly, we identified three large inversions compared to S.lycopersicum, containing several drought-resistance-related genes, such as beta-amylase 1 and YUCCA7.

Automated summary

Solanum sitiens, a self-incompatible wild relative of tomato, has salt and drought-resistance traits and its high-quality de novo genome and transcriptome assembly have been successfully developed. Compared to other stress resistant wild tomato relatives, it has distinct morphology, classification, and ecotype, with identified genes related to drought resistance.