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

Bo Song,Elizabeth Balyejusa Kizito,Francesca Stomeo,Solomon Maina,Xun Xu,Huan Liu,Xiaoli Chen,Ramni Jamnadass,Alice Muchugi,Appolinaire Djikeng,Pamela Nahamya Kabod,Xiuli Li,Jian Wang,Robert Kariba,Samuel Muthemba,Sibo Wang,Wenjing Sun,Huanming Yang,Joyce Njuguna,Shifeng Cheng,Sandra Ndagire Kamenya,Xin Liu,Wenbin Chen,Yue Song,Howard Shapiro ,Damaris A Odeny ,Prasad S Hendre ,Yuan Fang ,Allen Van Deynze

doi:10.1093/gigascience/giz115

Abstract

BackgroundThe 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.ResultsWe 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.ConclusionsThe 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.

Highlights

The African eggplant (Solanum aethiopicum) is a nutritious traditional vegetable used in many African countries, including Uganda and Nigeria
No Gene Ontology (GO) term enrichment was seen in genes that were disrupted by long terminal repeat (LTR)-Rs
This suggests that gene disruption by Long terminal repeat retrotransposon (LTR-R) may be a random event in terms of gene function

Summary

Background

The African eggplant, Solanum aethiopicum (NCBI:txid205524), is an indigenous non-tuberiferous Solanaceae crop that is mainly grown in tropical Africa [1], especially in Central and West Africa. The mean length of coding sequences, exons, and introns was 1,104, 265, and 613 bp, respectively (Table 1, Supplementary Table 5, Supplementary Fig. 2) As expected, these gene features were similar to those of other released genomes, including Arabidopsis thaliana [23] and other Solanaceae crops including S. lycopersicum, S. tuberosum, C. annuum, and N. sylvestris [16, 18, 19, 24] (Supplementary Table 5). The time of LTR-Rs amplification is vertically coincident between different species, they occurred separately in each genome since the ancestor of S. aethiopicum diverged from that of hot pepper and tomato ∼20 and 4 MYA, respectively (Fig. 1A). These results imply that environmental stimulators shared between these species during their evolution could have triggered the amplifications observed. Compared with the amplification time of Ty3/Gypsy and Ty1/Copia LTR-Rs in differ-

Draft genome sequence of Solanum aethiopicum

Discussion

Methods

Findings

Availability of supporting data and materials