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The de Novo Reference Genome and Transcriptome Assemblies of the Wild Tomato Species Solanum chilense Highlights Birth and Death of NLR Genes Between Tomato Species.
Stam, Remco; Nosenko, Tetyana; Hörger, Anja C; Stephan, Wolfgang; Seidel, Michael; Kuhn, José M M; Haberer, Georg; Tellier, Aurelien.
Afiliação
  • Stam R; Phytopathology, Technical University Munich, Germany, stam@wzw.tum.de.
  • Nosenko T; Population Genetics, Technical University Munich, Germany.
  • Hörger AC; Plant Genome and Systems Biology, Helmholtz Center of Munich, Germany.
  • Stephan W; Environmental Simulations, Helmholtz Center of Munich, Germany.
  • Seidel M; Department of Biosciences, University of Salzburg, Austria.
  • Kuhn JMM; Evolutionary Biology, LMU Munich and Natural History Museum Berlin, Germany, and.
  • Haberer G; Plant Genome and Systems Biology, Helmholtz Center of Munich, Germany.
  • Tellier A; Evolutionary Biology and Ecology, Albert-Ludwig University of Freiburg, Germany.
G3 (Bethesda) ; 9(12): 3933-3941, 2019 12 03.
Article em En | MEDLINE | ID: mdl-31604826
Wild tomato species, like Solanum chilense, are important germplasm resources for enhanced biotic and abiotic stress resistance in tomato breeding. S. chilense also serves as a model to study adaptation of plants to drought and the evolution of seed banks. The absence of a well-annotated reference genome in this compulsory outcrossing, very diverse species limits in-depth studies on the genes involved.We generated ∼134 Gb of DNA and 157 Gb of RNA sequence data for S chilense, which yielded a draft genome with an estimated length of 914 Mb, encoding 25,885 high-confidence predicted gene models, which show homology to known protein-coding genes of other tomato species. Approximately 71% of these gene models are supported by RNA-seq data derived from leaf tissue samples. Benchmarking with Universal Single-Copy Orthologs (BUSCO) analysis of predicted gene models retrieved 93.3% of BUSCO genes. To further verify the genome annotation completeness and accuracy, we manually inspected the NLR resistance gene family and assessed its assembly quality. We find subfamilies of NLRs unique to S. chilense Synteny analysis suggests significant degree of the gene order conservation between the S. chilense, S. lycopersicum and S. pennellii genomesWe generated the first genome and transcriptome sequence assemblies for the wild tomato species Solanum chilense and demonstrated their value in comparative genomics analyses. These data are an important resource for studies on adaptation to biotic and abiotic stress in Solanaceae, on evolution of self-incompatibility and for tomato breeding.
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Genes de Plantas / Solanum / Transcriptoma Tipo de estudo: Prognostic_studies País/Região como assunto: America do sul / Chile Idioma: En Revista: G3 (Bethesda) Ano de publicação: 2019 Tipo de documento: Article País de publicação: Reino Unido
Texto completo
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Genes de Plantas / Solanum / Transcriptoma Tipo de estudo: Prognostic_studies País/Região como assunto: America do sul / Chile Idioma: En Revista: G3 (Bethesda) Ano de publicação: 2019 Tipo de documento: Article País de publicação: Reino Unido