Draft genome sequence of Solanum aethiopicum provides insights into disease resistance, drought tolerance, and the evolution of the genome

Abstract

Background The African eggplant (Solanum aethiopicum) is a nutritious traditional vegetable used in many African countries, including Uganda and Nigeria. It is thought to have been domesticated in Africa from its wild relative, Solanum anguivi. S. aethiopicum has been routinely used as a source of disease resistance genes for several Solanaceae crops, including Solanum melongena. A lack of genomic resources has meant that breeding of S. aethiopicum has lagged behind other vegetable crops. Results We assembled a 1.02-Gb draft genome of S. aethiopicum, which contained predominantly repetitive sequences (78.9%). We annotated 37,681 gene models, including 34,906 protein-coding genes. Expansion of disease resistance genes was observed via 2 rounds of amplification of long terminal repeat retrotransposons, which may have occurred ∼1.25 and 3.5 million years ago, respectively. By resequencing 65 S. aethiopicum and S. anguivi genotypes, 18,614,838 single-nucleotide polymorphisms were identified, of which 34,171 were located within disease resistance genes. Analysis of domestication and demographic history revealed active selection for genes involved in drought tolerance in both “Gilo” and “Shum” groups. A pan-genome of S. aethiopicum was assembled, containing 51,351 protein-coding genes; 7,069 of these genes were missing from the reference genome. Conclusions The genome sequence of S. aethiopicum enhances our understanding of its biotic and abiotic resistance. The single-nucleotide polymorphisms identified are immediately available for use by breeders. The information provided here will accelerate selection and breeding of the African eggplant, as well as other crops within the Solanaceae family.

Root Growth Adaptation to Climate Change in Crops

“…In addition to wild relatives, crop landraces are a great source of genetic variability for their adaptation to specific ecosystems and climatic conditions (Cantalapiedra et al, 2017;Carvalho et al, 2017;Sani et al, 2018). On the other hand, latest studies with orphan crops have demonstrated that those crops are a powerful tool to improve their related global-traded crops due to its resistance against unfavorable conditions (Song et al, 2019;Tadele and Bartels, 2019).…”

Genetics and breeding for climate change in Orphan crops

“…melongenae (Rizza et al 2002;Toppino et al 2008) in brinjal eggplant was introduced from the African eggplant, while resistance to late blight (Phytophthora infestans) in potato (Solanum tuberosum) has been traditionally managed through the introgression of major genes from underutilized relatives (Ross 1986;Gebhardt and Valkonen 2001;Van Der Vossen et al 2003;Ghislain et al 2019). A recent whole genome analysis confirmed the abundance of disease resistance genes in the African eggplant (Song et al 2019), making it a great resource for future introgression and R gene cloning. The African rice (Oryza glaberrima Steud.…”

“…The use of molecular markers within the African eggplant has been mainly for germplasm or genome characterization (Sakata et al 1991 ; Sakata and Lester 1994 ; Gramazio et al 2016 ; Song et al 2019 ). There is currently no association or linkage mapping studies reported in the literature despite the recent availability of a reference genome (Song et al 2019 ).…”

“…Over the last five years alone, 30 orphan crops representing 13 families have had their genomes sequenced (Table 1 ). The selection criteria for genome sequencing included importance to local food security and nutritional value (Chang et al 2019; Hendre et al 2019 ; Jamnadass et al 2020 ), and tolerance to environmental stresses (Song et al 2019 ; Emmrich et al 2020 ). The sizes of genomes sequenced ranged from 0.217 Gb ( Moringa oleifera ) to about 1.5 Gb ( Eleusine coracana ) (Table 1 ), which is relatively small compared to the full range of plant genome size (Liu et al 2019 ).…”

Anaerococcus urinimassiliensis sp. nov., a new bacterium isolated from human urine

“…The assembly was performed using a pipeline containing several softwares (Velvet 28 , SPAdes 29 and SOAP Denovo 30 ) and trimmed (MiSeq and Trimmomatic 31 softwares) or untrimmed data (only MiSeq software). GapCloser software 32 was used to reduce assembly gaps. Scaffolds < 800 base pairs (bp) and scaffolds with a depth value lower than 25% of the mean depth were removed.…”