A chromosome-anchored eggplant genome sequence reveals key events in Solanaceae evolution

Abstract

With approximately 450 species, spiny Solanum species constitute the largest monophyletic group in the Solanaceae family, but a high-quality genome assembly from this group is presently missing. We obtained a chromosome-anchored genome assembly of eggplant (Solanum melongena), containing 34,916 genes, confirming that the diploid gene number in the Solanaceae is around 35,000. Comparative genomic studies with tomato (S. lycopersicum), potato (S. tuberosum) and pepper (Capsicum annuum) highlighted the rapid evolution of miRNA:mRNA regulatory pairs and R-type defense genes in the Solanaceae, and provided a genomic basis for the lack of steroidal glycoalkaloid compounds in the Capsicum genus. Using parsimony methods, we reconstructed the putative chromosomal complements of the key founders of the main Solanaceae clades and the rearrangements that led to the karyotypes of extant species and their ancestors. From 10% to 15% of the genes present in the four genomes were syntenic paralogs (ohnologs) generated by the pre-γ, γ and T paleopolyploidy events, and were enriched in transcription factors. Our data suggest that the basic gene network controlling fruit ripening is conserved in different Solanaceae clades, and that climacteric fruit ripening involves a differential regulation of relatively few components of this network, including CNR and ethylene biosynthetic genes.

Figure 1

Topography of the eggplant genome. Track (A) Eggplant chromosomes with the genetic map (black bars represent the position of genetic markers used for anchoring scaffolds to pseudomolecules; Track (B) gene density; Track (C) RNA-seq expression data density; Track (D) overall repeat density; Track (E) DNA transposon density; Track (F) LTR-Gypsy transposon density; Track (G) LTR-Copia transposon density; Track (H) Intragenome syntenic regions originated from paleopolyploid events (for the parameters used to define syntenic thresholds, see Supplementary Information 2.7). Densities for tracks (B,D,E,F,G) are presented in 1-Mb intervals; for track (C) in 100-Kb intervals).

Figure 2

Solanaceae genome dynamics. (A) Dating of insertions for complete LTR retrotransposons in the various Solanaceae genomes. (B) Syntenic relationships between the chromosomes eggplant (E), tomato (T) and pepper (P). For the parameters used to define synthenic thresholds, see Supplementary Information 2.7. (C) Reconstruction of chromosome dynamics during Solanaceae evolution. Each chromosome of the hypothetical Solanaceae common ancestor is assigned a different colour. The reconstructed karyotypes of evolutionary intermediates are shown on the left, the actual karyotypes of extant species on the right. Chromosomal segments derived from each ancestral chromosome are painted with the corresponding colour, and the arrows indicate the orientation with respect to the ancestral chromosome segment. The minimum number of translocations and inversions occurring between two karyotypes are reported.

Figure 3

miR156 overexpression affects tomato and eggplant development in similar ways. MiR156 – mediated regulation of vegetative growth in tomato (upper panel) and eggplant (lower panel). Wild type plants (left) and plants overexpressing Arabidopsis miR156a (right) under the CaMV 35S promoter.

Figure 4

Evolution of fruit ripening control in the Solanaceae. (A) Expression (log₂ FPKM) of ripening transcription factor regulators CNR, NOR, RIN, TAGL1, FUL1/2, AP2a and ARF2A in different tissue types (root, leaf and flower) plus different stages of fruit ripening (stage 1, stage 2 and stage 3) of eggplant (upper panel), tomato (middle panel) and pepper (lower panel). (B) Co-expression (R-value ≥ 0.8) of ripening -related genes with the RIN ripening regulator; ellipses, diamonds and rectangles indicate, respectively, transcription factor-, receptor-, and enzyme-encoding genes; purple, red and green shading indicate, respectively, co-expression with RIN in eggplant, tomato and pepper. Detailed co-expression values are shown in Supplementary Table S31. (C) Wild-type tomato fruit at two stages of ripening (upper left two panels); wild-type eggplant fruit at two stages of ripening (upper right two panels); and over-expression of the TOMATO AGAMOUS-LIKE 1 (TAGL1) gene in tomato fruit at two ripening stages (lower left two panels) and in eggplant fruit at two ripening stages (lower right two panels).

Figure 5

Control of fruit biochemical composition. (A) Schematic pathways for flavonoid (left) and carotenoid (right) biosynthesis in eggplant fruits. Genes and compounds overexpressed at each stage are shown in large bold character. Regulatory genes are indicated in blue. (B) Schematic cuticle biosynthesis pathway. Shortened gene names are indicated in blue. Genes showing fruit cuticle-enriched expression in both eggplant and tomato are indicated in red.

Figure 6

Gene family evolution in the Solanaceae. (A) Phylogenetic tree of CNL (in blue) and TNL (in green) NB-LRR genes. The distinctive evolutionary dynamics of ten NB-LRR groups in eggplant (purple), potato (yellow), tomato (red) and pepper (green) genomes are displayed. The number of NB-LRR genes included in each group is indicated on the vertical axis. The plant pathogens (fungi, virus, bacteria or nematodes) to which known genes in the clade confer resistance are indicated by pictures. Gro1.4 and Hero confer resistance to Globodera rostochiensis. Gpa2 and Mi1.2 confer resistance to Globodera pallida and Meloidogyne incognita, respectively. Rx and Rx2 confer resistance to Potato Virus X. N, Ry1, Tm2 and Sw5 confer resistance to Tobacco Mosaic Virus, Potato Virus Y, Tomato Mosaic Virus and Tomato Spotted Wilt Virus, respectively. Bs2 and Bs4 confer resistance to Xanthomonas campestris and Prf to Pseudomonas syringae. Rpi-blb1, Rpi-blb2, R1, R2 and R3 confer resistance to Phytophthora infestans and I2 to Fusarium oxysporum. (B) Independent expansion of Mi1.2/Rpi-blb2 homologous genes in eggplant, pepper, potato and tomato. The human APAF1 (Apoptotic Protease Activating Factor 1), is a human cytoplasmic protein showing similar structure to nucleotide binding site–leucine rich repeat proteins of plants, and was used to re-root the tree of plant NLR phylogenetic analysis^,. (C) The steroidal glycoalkaloid metabolic gene cluster in four Solanaceous genomes. In tomato, six genes (GAME1, GAME2, GAME6, GAME11, GAME17, GAME18) are located on CH7 and two (GAME4 and GAME12) on CH12. In potato, four-SGA associated genes (SGT3, GAME6, GAME11 and SGT1/GAME1) are found in CH7 and two in CH12 (GAME4 and GAME12). In eggplant, four putative SGA genes namely, GAME1/SGT1, SGT3, GAME6 and GAME11 are also physically linked to each other on CH7 and two, GAME4 and GAME12 on CH12. In pepper, five genes (GAME1, GAME6, GAME11, GAME17 and GAME18) were found to be present on CH7. GAME4 and GAME12 homologous sequences were not detected in the pepper genome.