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

  1. Bo Song
  2. Yue Song
  3. Yuan Fu
  4. Elizabeth Balyejusa Kizito
  5. Sandra Ndagire Kamenya
  6. Pamela Nahamya Kabod
  7. Huan Liu
  8. Samuel Muthemba
  9. Robert Kariba
  10. Joyce Njuguna
  11. Solomon Maina
  12. Francesca Stomeo
  13. Appolinaire Djikeng
  14. Prasad S Hendre
  15. Xiaoli Chen
  16. Wenbin Chen
  17. Xiuli Li
  18. Wenjing Sun
  19. Sibo Wang
  20. Shifeng Cheng
  21. Alice Muchugi
  22. Ramni Jamnadass
  23. Howard-Yana Shapiro
  24. Allen Van Deynze
  25. Huanming Yang
  26. Jian Wang
  27. Xun Xu
  28. Damaris Achieng Odeny
  29. Xin Liu

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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.

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  1. GigaScience

    Now published in GigaScience doi: 10.1093/gigascience/giz115

    Bo Song 1BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China2China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China3State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteYue Song 1BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China3State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China4BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteYuan Fu 1BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China2China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteElizabeth Balyejusa Kizito 5Uganda Christian University, Bishop Tucker Road, Box 4, Mukono, UgandaFind this author on Google ScholarFind this author on PubMedSearch for this author on this sitePamela Nahamya Kabod 5Uganda Christian University, Bishop Tucker Road, Box 4, Mukono, UgandaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteHuan Liu 1BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China2China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China3State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSandra Ndagire Kamenya 5Uganda Christian University, Bishop Tucker Road, Box 4, Mukono, UgandaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSamuel Muthemba 6African Orphan Crops Consortium, World Agroforestry Centre (ICRAF), Nairobi, KenyaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteRobert Kariba 6African Orphan Crops Consortium, World Agroforestry Centre (ICRAF), Nairobi, KenyaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteXiuli Li 1BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China2China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSibo Wang 1BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China3State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteShifeng Cheng 1BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China2China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAlice Muchugi 6African Orphan Crops Consortium, World Agroforestry Centre (ICRAF), Nairobi, KenyaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteRamni Jamnadass 6African Orphan Crops Consortium, World Agroforestry Centre (ICRAF), Nairobi, KenyaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteHoward-Yana Shapiro 6African Orphan Crops Consortium, World Agroforestry Centre (ICRAF), Nairobi, Kenya7University of California, 1 Shields Ave, Davis, USA9Mars, Incorporated, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAllen Van Deynze 7University of California, 1 Shields Ave, Davis, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteHuanming Yang 1BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China2China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJian Wang 1BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China2China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteXun Xu 1BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China2China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China3State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteDamaris Achieng Odeny 8ICRISAT-Nairobi, Nairobi, KenyaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: liuxin@genomics D.Odney@cigar.orgXin Liu 1BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China2China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China3State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: liuxin@genomics D.Odney@cigar.org

    A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz115 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.

    These peer reviews were as follows:

    Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101930 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101931 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101932

  2. Version published to 10.1093/gigascience/giz115
  3. Version published to 10.1101/532077v1 on bioRxiv