The eggplant (Solanum melongena L.) is one of the most important Solanaceae crops, ranking third for total production and economic value in its genus. Herein, we report a high‐quality, chromosome‐scale eggplant reference genome sequence of 1155.8 Mb, with an N50 of 93.9 Mb, which was assembled by combining PacBio long reads and Hi‐C sequencing data. Repetitive sequences occupied 70.1% of the assembly length, and 35,018 high‐confidence protein‐coding genes were annotated based on multiple sources. Comparative analysis revealed 646 species‐specific families and 364 positive selection genes, conferring distinguishing traits on the eggplant. We performed genome‐wide comparative identification of disease resistance genes and discovered an expanded gene family of bacterial spot resistance in eggplant and pepper, but not in tomato and potato. The genes involved in chlorogenic acid synthesis were comprehensively characterized. Highly similar chromosomal distribution patterns of polyphenol oxidase genes were observed in the eggplant, tomato, and potato genomes. The eggplant reference genome sequence will not only facilitate evolutionary studies of the Solanaceae but also facilitate their breeding and improvement.

The development of strategies for effectively manipulating and engineering beneficial plant-associated microbiomes is a major challenge in microbial ecology. In this sense, the efficacy and potential implications of rhizosphere microbiome transplant (RMT) in plant disease management have only scarcely been explored in the literature. Here, we initially investigated potential differences in rhizosphere microbiomes of 12 Solanaceae eggplant varieties and accessed their level of resistance promoted against bacterial wilt disease caused by the pathogen Ralstonia solanacearum, in a 3-year field trial. We elected 6 resistant microbiomes and further tested the broad feasibility of using RMT from these donor varieties to a susceptible model Solanaceae tomato variety MicroTom. Overall, we found the rhizosphere microbiome of resistant varieties to enrich for distinct and specific bacterial taxa, of which some displayed significant associations with the disease suppression. Quantification of the RMT efficacy using source tracking analysis revealed more than 60% of the donor microbial communities to successfully colonize and establish in the rhizosphere of recipient plants. RTM from distinct resistant donors resulted in different levels of wilt disease suppression, reaching up to 47% of reduction in disease incidence. Last, we provide a culture-dependent validation of potential bacterial taxa associated with antagonistic interactions with the pathogen, thus contributing to a better understanding of the potential mechanism associated with the disease suppression. Our study shows RMT from appropriate resistant donors to be a promising tool to effectively modulate protective microbiomes and promote plant health. Together we advocate for future studies aiming at understanding the ecological processes and mechanisms mediating rates of coalescence between donor and recipient microbiomes in the plant rhizosphere.

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SummaryThe eggplant (Solanum melongena L.) is one of the most important Solanaceae crops, ranking third in the total production and economic value in the genus Solanum. Here, we report a high-quality, chromosome-scale eggplant reference genome sequence of 1,155.8 Mb, with N50 of 93.9 Mb, which was assembled by combining PacBio long reads and Hi-C sequencing data. Repetitive sequences occupied 70.1% of the assembly length, and 35,018 high-confidence protein-coding genes were annotated based on multiple evidence. Comparative analysis revealed 646 species-specific families and 364 positive selection genes, conferring distinguishing traits to the eggplant. We performed genome-wide identification of disease resistance genes and discovered an expanded gene family of bacterial spot resistance in the eggplant and pepper but not in tomato and potato. The genes involved in chlorogenic acid synthesis were comprehensively characterized. Highly similar chromosomal distribution patterns of polyphenol oxidase genes were observed in the eggplant, tomato, and potato genomes. The eggplant reference genome sequence will not only facilitate evolutionary studies in the Solanaceae but also facilitate their breeding and improvement.

Distant hybridization constitutes an important process in plant evolution. Outbreeding of Solanum plants can produce hybrid progeny with heterobeltiosis in terms of growth, development, and resistance. In this study, the genomic characteristics and genetic variation of reciprocal cross F1 hybrids of strains 177 (Solanum melongena L.) and Y11 (Solanum aethiopicum L.) were quantified to analyze the relationship between heterosis and genomic characteristics. While no significant phenotypic differences existed between the F1 hybrids, their phenotypes were closer to those of the Y11 parent. Using whole-genome resequencing, large numbers of single-nucleotide polymorphisms, insertion or deletions, structural variations, and copy number variation (CNV) were found. The variation rate of the Y11 parent was the highest, while those of the F1 hybrids were similar to each other but closer to Y11. These results reflect the fact that the genome of the heterozygous progenies was stable at the chromosome level; nevertheless, a lot of variation sites were produced, which may underlie the increased phenotypic diversities compared to that found in the cultivated parent plants. Mining and functional annotation of variant genes with different variant types revealed that the highest number of variant genes were caused by CNVs. Moreover, the variant genes were significantly enriched in pathways associated with glucose metabolism, protein synthesis, and phytohormone signaling, indicating that CNVs may be responsible for the heterosis observed in the progeny of outbred crosses. These data can provide a reference for future heterosis research, molecular marker development, genetic engineering, high-density linkage map construction, and genome-wide association analysis.