Exploring the temporal dynamics of a disease suppressive rhizo-microbiome in eggplants.

The rhizosphere microbiome is important for plant health, yet their contributions to disease resistance and assembly dynamics remain unclear. This study employed rhizosphere microbiome transplantation (RMT) to delineate the impact of the rhizosphere microbiome and the immune response of eggplant (Solanum melongena) on resistance to bacterial wilt caused by Ralstonia solanacearum. We first identified disease-suppressive and disease-conducive rhizosphere microbiome in a susceptible tomato recipient. Using a non-destructive rhizobox and 16S rRNA amplicon sequencing, we monitored the dynamics of both microbiome types during the eggplant development. Most differences were observed at the early stage and then diminished over time. The suppressive microbiome maintained a higher proportion of initial community members throughout eggplant development and exhibited stronger deterministic processes in the early stage, underscoring the importance of plant selection in recruiting protective microbes for rhizosphere immunity. Our study sheds light on the development of microbiome-based strategies for plant disease management and resistance breeding.

Characteristics, Comparative Analysis, and Phylogenetic Relationships of Chloroplast Genomes of Cultivars and Wild Relatives of Eggplant (Solanum melongena).

The eggplant (Solanum melongena) is a popular vegetable around the world. However, the origin and evolution of eggplant has long been considered complex and unclear, which has become the barrier to improvements in eggplant breeding. Sequencing and comparative analyses of 13 complete chloroplast (cp) genomes of seven Solanum species were performed. Genome sizes were between 154,942 and 156,004 bp, the smallest genome was from S. torvum and the largest from S. macrocapon. Thirteen cp genomes showed highly conserved sequences and GC contents, particularly at the subgenus level. All genes in the 13 genomes were annotated. The cp genomes in this study comprised 130 genes (i.e., 80 protein-coding genes, 8 rRNA genes, and 42 tRNA genes), apart from S. sisymbriifolium, which had 129 (79 protein-coding genes, 8 rRNA genes, and 42 tRNA genes.). The rps16 was absent from the cp genome of S. sisymbriifolium, resulting in a nonsense mutation. Twelve hotspot regions of the cp genome were identified, which showed a series of sequence variations and differed significantly in the inverted repeat/single-copy boundary regions. Furthermore, phylogenetic analysis was conducted using 46 cp genomic sequences to determine interspecific genetic and phylogenetic relationships in Solanum species. All species formed two branches, one of which contained all cultivars of the subgenus Leptostemonum. The cp genome data and phylogenetic analysis provides molecular evidence revealing the origin and evolutionary relationships of S. melongena and its wild relatives. Our findings suggest precise intra- and interspecies relatedness within the subgenus Leptostemonum, which has positive implications for work on improvements in eggplant breeding, particularly in producing heterosis, expanding the source of species variation, and breeding new varieties.

Exploring rhizo-microbiome transplants as a tool for protective plant-microbiome manipulation.

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.

The first complete mitochondrial genome of eggplant (Solanum melongena).

Eggplant is an important vegetable crop because of its rich nutrition, but to date no mitochondrial genome has been reported. In this study, the complete mitochondrial genome of the eggplant was sequenced. The complete mitochondrial genome was 498,136bp, linear structure, containing 54 protein-coding genes, four rRNAs, and 32 tRNAs. The phylogenetic tree supported the hypothesis that the eggplant is most closely related to Solanum tuberosum and Solanum lycopersicum.

Inheritance of Solanum chloroplast genomic DNA in interspecific hybrids.

The chloroplast genomic information was obtained from three wild Solanum and four hybrids by chloroplast genome sequencing. The chloroplast genomes of the seven samples comprise of a circular structure and sizes from 155,581 to 155,612 bp and composed of 130 genes. The genome structures of the two hybrids were identical, while the other two hybrids showed 2 bp differences in the LSC when compared with their maternal parent. The total sites of SNP and InDel were 39-344 and 54-90, respectively. With the exception of one hybrid with two additional sites, the other hybrids were identical to their maternal.

A high-quality genome assembly of the eggplant provides insights into the molecular basis of disease resistance and chlorogenic acid synthesis.

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.

Comparative transcriptome analysis provides insights into the molecular mechanism underlying double fertilization between self-crossed Solanum melongena and that hybridized with Solanum aethiopicum.

Wild relatives represent a source of variation for many traits of interest for eggplant (Solanum melongena) breeding, as well as for broadening its genetic base. However, interspecific hybridization with wild relatives has been barely used in eggplant breeding programs, and reproductive barriers have resulted in reduced seed numbers in interspecific combinations. The mechanism underlying this phenomenon remains unclear. We hybridized females of cultivated eggplant 177 (Solanum melongena) with males of wild relatives 53 and Y11 (Solanum aethiopicum). Self-crossed 177 was the control. The seed number per control fruit was significantly higher than that of the hybrids. Paraffin sections showed no significant difference between control and 177×53 and 177×Y11. Double fertilization began 4 days post-pollination. Sperm cells were fused with egg cells 6 days post-pollination. To understand the differences in molecular mechanisms underlying this process, transcriptomes of ovaries at 0, 4, and 6 days after self-crossing and hybridization were analyzed. We screened 22,311 differentially expressed genes (DEGs) between the control and hybrids 4 and 6 days post-pollination. A total of 497 DEGs were shared among all pollination combinations. These DEGs were enriched in plant hormone transduction, cell senescence, metabolism, and biosynthesis pathways. DEG clustering analysis indicated distinct expression patterns between the control and hybrids but not between the hybrids. The DEGs in hybrids involved secondary metabolic process, phenylpropanoid metabolic process, and carboxypeptidase activity, while those in the control involved xyloglucan metabolic process, auxin-activated signaling pathway, cell wall polysaccharide metabolic process, and xyloglucosyl transferase activity. Additionally, 1683 transcription factors, including members of the AP2-ERF, MYB, bHLH, and B3 families may play important roles in self-crossing and hybridization. Our results provide insights into the regulatory mechanisms underlying variations between ovaries of self-crossed and hybrid eggplants and a basis for future studies on crossbreeding Solanum and genetic mechanisms underlying double fertilization.