title: The Solanum commersonii Genome Sequence Provides Insights into Adaptation to Stress Conditions and Genome Evolution of Wild Potato Relatives.
abstract: Here, we report the draft genome sequence of Solanum commersonii, which consists of ∼830 megabases with an N50 of 44,303 bp anchored to 12 chromosomes, using the potato (Solanum tuberosum) genome sequence as a reference. Compared with potato, S. commersonii shows a striking reduction in heterozygosity (1.5% versus 53 to 59%), and differences in genome sizes were mainly due to variations in intergenic sequence length. Gene annotation by ab initio prediction supported by RNA-seq data produced a catalog of 1703 predicted microRNAs, 18,882 long noncoding RNAs of which 20% are shown to target cold-responsive genes, and 39,290 protein-coding genes with a significant repertoire of nonredundant nucleotide binding site-encoding genes and 126 cold-related genes that are lacking in S. tuberosum. Phylogenetic analyses indicate that domesticated potato and S. commersonii lineages diverged ∼2.3 million years ago. Three duplication periods corresponding to genome enrichment for particular gene families related to response to salt stress, water transport, growth, and defense response were discovered. The draft genome sequence of S. commersonii substantially increases our understanding of the domesticated germplasm, facilitating translation of acquired knowledge into advances in crop stability in light of global climate and environmental changes.
authors: Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy.
authors: Riccardo
authors: http://orcid.org/0000-0002-4041-3702
authors: R
authors: Aversano
authors: Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy.
authors: Felice
authors: F
authors: Contaldi
authors: Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy.
authors: Maria Raffaella
authors: http://orcid.org/0000-0002-4475-6112
authors: MR
authors: Ercolano
authors: Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy.
authors: Valentina
authors: V
authors: Grosso
authors: Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy.
authors: Massimo
authors: M
authors: Iorizzo
authors: Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy.
authors: Filippo
authors: F
authors: Tatino
authors: Center of Functional Genomics, Department of Biotechnologies, University of Verona, 37134 Cà Vignal, Italy.
authors: Luciano
authors: L
authors: Xumerle
authors: Center of Functional Genomics, Department of Biotechnologies, University of Verona, 37134 Cà Vignal, Italy.
authors: Alessandra
authors: A
authors: Dal Molin
authors: Center of Functional Genomics, Department of Biotechnologies, University of Verona, 37134 Cà Vignal, Italy.
authors: Carla
authors: C
authors: Avanzato
authors: Center of Functional Genomics, Department of Biotechnologies, University of Verona, 37134 Cà Vignal, Italy.
authors: Alberto
authors: http://orcid.org/0000-0002-8452-3380
authors: A
authors: Ferrarini
authors: Center of Functional Genomics, Department of Biotechnologies, University of Verona, 37134 Cà Vignal, Italy.
authors: Massimo
authors: http://orcid.org/0000-0002-7100-4581
authors: M
authors: Delledonne
authors: Sequentia Biotech, Cerdanyola del Vallès, 08193 Barcelona, Spain.
authors: Walter
authors: W
authors: Sanseverino
authors: Sequentia Biotech, Cerdanyola del Vallès, 08193 Barcelona, Spain.
authors: Riccardo Aiese
authors: RA
authors: Cigliano
authors: Center for Genomic Regulation, 08003 Barcelona, Spain Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain.
authors: Salvador
authors: S
authors: Capella-Gutierrez
authors: Center for Genomic Regulation, 08003 Barcelona, Spain Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain.
authors: Toni
authors: http://orcid.org/0000-0003-0019-1735
authors: T
authors: Gabaldón
authors: Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy.
authors: Luigi
authors: L
authors: Frusciante
authors: Department of Plant Pathology and Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, Saint Paul, Minnesota 55108.
authors: James M
authors: JM
authors: Bradeen
authors: Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy carputo@unina.it.
authors: Domenico
authors: http://orcid.org/0000-0003-1735-9338
authors: D
authors: Carputo
mesh_terms: D000064:Acclimatization; D005075:Biological Evolution; D018745:Genome, Plant / Q000235:genetics*; D010802:Phylogeny; D032322:Solanum / Q000145:classification / Q000235:genetics*; D011198:Solanum tuberosum / Q000145:classification / Q000235:genetics*