De Novo Genome Assembly of Two Tomato Ancestors, Solanum Pimpinellifolium and Solanum Lycopersicum Var. Cerasiforme, by Long-read Sequencing

Overview

Journal DNA Res

Publisher Oxford University Press

Specialties Genetics
Molecular Biology

Date 2021 Jan 21

PMID 33475141

Citations 19

Authors

Hitomi Takei

Kenta Shirasawa

Kosuke Kuwabara

Atsushi Toyoda

Yuma Matsuzawa

Shinji Iioka

Tohru Ariizumi

Affiliations

Soon will be listed here.

Abstract

The ancestral tomato species are known to possess genes that are valuable for improving traits in breeding. Here, we aimed to construct high-quality de novo genome assemblies of Solanum pimpinellifolium 'LA1670' and S. lycopersicum var. cerasiforme 'LA1673', originating from Peru. The Pacific Biosciences (PacBio) long-read sequences with 110× and 104× coverages were assembled and polished to generate 244 and 202 contigs spanning 808.8 Mbp for 'LA1670' and 804.5 Mbp for 'LA1673', respectively. After chromosome-level scaffolding with reference guiding, 14 scaffold sequences corresponding to 12 tomato chromosomes and 2 unassigned sequences were constructed. High-quality genome assemblies were confirmed using the Benchmarking Universal Single-Copy Orthologs and long terminal repeat assembly index. The protein-coding sequences were then predicted, and their transcriptomes were confirmed. The de novo assembled genomes of S. pimpinellifolium and S. lycopersicum var. cerasiforme were predicted to have 71,945 and 75,230 protein-coding genes, including 29,629 and 29,185 non-redundant genes, respectively, as supported by the transcriptome analysis results. The chromosome-level genome assemblies coupled with transcriptome data sets of the two accessions would be valuable for gaining insights into tomato domestication and understanding genome-scale breeding.

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References

Fernie A, Aharoni A . Pan-Genomic Illumination of Tomato Identifies Novel Gene-Trait Interactions. Trends Plant Sci. 2019; 24(10):882-884. DOI: 10.1016/j.tplants.2019.08.001. View

Shirasawa K, Hirakawa H, Fukino N, Kitashiba H, Isobe S . Genome sequence and analysis of a Japanese radish (Raphanus sativus) cultivar named 'Sakurajima Daikon' possessing giant root. DNA Res. 2020; 27(2). PMC: 7334891. DOI: 10.1093/dnares/dsaa010. View

Lin Y, Liu C, Chen K . Assessment of Genetic Differentiation and Linkage Disequilibrium in Using Genome-Wide High-Density SNP Markers. G3 (Bethesda). 2019; 9(5):1497-1505. PMC: 6505160. DOI: 10.1534/g3.118.200862. View

Yan Z, Perez-de-Castro A, Diez M, Hutton S, Visser R, Wolters A . Resistance to Tomato Yellow Leaf Curl Virus in Tomato Germplasm. Front Plant Sci. 2018; 9:1198. PMC: 6110163. DOI: 10.3389/fpls.2018.01198. View

Gao L, Gonda I, Sun H, Ma Q, Bao K, Tieman D . The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor. Nat Genet. 2019; 51(6):1044-1051. DOI: 10.1038/s41588-019-0410-2. View

Johansen K, Morton M, Malbeteau Y, Aragon B, Al-Mashharawi S, Ziliani M . Unmanned Aerial Vehicle-Based Phenotyping Using Morphometric and Spectral Analysis Can Quantify Responses of Wild Tomato Plants to Salinity Stress. Front Plant Sci. 2019; 10:370. PMC: 6449481. DOI: 10.3389/fpls.2019.00370. View

. The tomato genome sequence provides insights into fleshy fruit evolution. Nature. 2012; 485(7400):635-41. PMC: 3378239. DOI: 10.1038/nature11119. View

Mata-Nicolas E, Montero-Pau J, Gimeno-Paez E, Garcia-Carpintero V, Ziarsolo P, Menda N . Exploiting the diversity of tomato: the development of a phenotypically and genetically detailed germplasm collection. Hortic Res. 2020; 7:66. PMC: 7192925. DOI: 10.1038/s41438-020-0291-7. View

Anderson L, Covey P, Larsen L, Bedinger P, Stack S . Structural differences in chromosomes distinguish species in the tomato clade. Cytogenet Genome Res. 2010; 129(1-3):24-34. DOI: 10.1159/000313850. View

10.

Ou S, Chen J, Jiang N . Assessing genome assembly quality using the LTR Assembly Index (LAI). Nucleic Acids Res. 2018; 46(21):e126. PMC: 6265445. DOI: 10.1093/nar/gky730. View

11.

Salehi B, Sharifi-Rad R, Sharopov F, Namiesnik J, Roointan A, Kamle M . Beneficial effects and potential risks of tomato consumption for human health: An overview. Nutrition. 2019; 62:201-208. DOI: 10.1016/j.nut.2019.01.012. View

12.

Goff S, Klee H . Plant volatile compounds: sensory cues for health and nutritional value?. Science. 2006; 311(5762):815-9. DOI: 10.1126/science.1112614. View

13.

Razali R, Bougouffa S, Morton M, Lightfoot D, Alam I, Essack M . The Genome Sequence of the Wild Tomato Provides Insights Into Salinity Tolerance. Front Plant Sci. 2018; 9:1402. PMC: 6186997. DOI: 10.3389/fpls.2018.01402. View

14.

Moyle L . Ecological and evolutionary genomics in the wild tomatoes (Solanum sect. Lycopersicon). Evolution. 2008; 62(12):2995-3013. DOI: 10.1111/j.1558-5646.2008.00487.x. View

15.

Wang X, Gao L, Jiao C, Stravoravdis S, Hosmani P, Saha S . Genome of Solanum pimpinellifolium provides insights into structural variants during tomato breeding. Nat Commun. 2020; 11(1):5817. PMC: 7670462. DOI: 10.1038/s41467-020-19682-0. View

16.

Zhu G, Wang S, Huang Z, Zhang S, Liao Q, Zhang C . Rewiring of the Fruit Metabolome in Tomato Breeding. Cell. 2018; 172(1-2):249-261.e12. DOI: 10.1016/j.cell.2017.12.019. View

17.

Alonge M, Wang X, Benoit M, Soyk S, Pereira L, Zhang L . Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato. Cell. 2020; 182(1):145-161.e23. PMC: 7354227. DOI: 10.1016/j.cell.2020.05.021. View

18.

Ranc N, Munos S, Santoni S, Causse M . A clarified position for Solanum lycopersicum var. cerasiforme in the evolutionary history of tomatoes (solanaceae). BMC Plant Biol. 2008; 8:130. PMC: 2657798. DOI: 10.1186/1471-2229-8-130. View

19.

Blanca J, Canizares J, Cordero L, Pascual L, Diez M, Nuez F . Variation revealed by SNP genotyping and morphology provides insight into the origin of the tomato. PLoS One. 2012; 7(10):e48198. PMC: 3485194. DOI: 10.1371/journal.pone.0048198. View