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.

Construction of a SNP-Based Genetic Map Using SLAF-Seq and QTL Analysis of Morphological Traits in Eggplant

“…Sequences with over 95% similarity were considered as one SLAF locus. The clean reads were mapped to the eggplant reference genome (Barchi et al, 2019), and the GATK software kit was used to detect SNPs between two parents and F 2 offspring. For the detailed process, see GATK's official website, https://www.broadinstitute.org/gatk/ guide/best-practices.php (McKenna et al, 2010).…”

“…Detailed sequence information and alignment positions for all markers are presented in Table 3 and Supplementary Table S3. The SNPs of each QTL were mapped to the eggplant genome (Barchi et al, 2019) to anchor the physical locations, and the distribution of these QTL loci on chromosomes determined with two terminal markers are shown in Supplementary Figure S1. One QTL for MSH, designated msh5.1, was detected on LG5 and could explain 6.8% of the observed phenotypic variation.…”

Genome sequence and analysis of the eggplant (Solanum melongenaL.)

“…Benchmarking Universal Single-Copy Ortholog (BUSCO) evaluations of the genome sequence revealed 96.2% completeness. Compared with the previously published eggplant genomes (SME_r2.5.1 and Eggplant_V3) [13, 28], which both mainly employed the Illumina short-read sequencing technology, resulting in more fragmented assemblies (contig N50 lengths: 14.3 and 16.7 kb, respectively) and larger gap sizes (Ns: 4.75% and 28.23%, respectively), our genome assembly achieved a great improvement in both quality and integrity (Table 1 and Table S2).…”

“…The world production of eggplants was approximately 52.3 million tons in 2017, with China being the main producer. Previous studies of the eggplant focused on the evolution [9-12], genetic linkage map [13, 14], molecular marker development [15, 16], resistance [17, 18], fruit quality [19, 20], and high-throughput genotyping [2, 21].…”

“…Therefore, a high-quality reference genome is urgently needed for eggplant research. Two published eggplant references (SME_r2.5.1 and Eggplant_V3) [13, 28] were obtained by mainly employing the Illumina short-read sequencing technology, thus exhibiting assembly fragmentation and significant gap sizes.…”