The Solanum commersonii Genome Sequence Provides Insights into Adaptation to Stress Conditions and Genome Evolution of Wild Potato Relatives

作者：Riccardo Aversano, Felice Contaldi, Maria Raffaella Ercolano, Valentina Grosso, Massimo Iorizzo, Filippo Tatino, Luciano Xumerle, Alessandra Dal Molin, C. Avanzato, Alberto Ferrarini, Massimo Delledonne, Walter Sanseverino, Riccardo Aiese Cigliano, Salvador Capella-Gutiérrez, Toni Gabaldón, Luigi Frusciante, James M. Bradeen, Domenico Carputo · 发表于：The Plant Cell · 年份：2015 · DOI：10.1105/tpc.114.135954 · 被引用次数：202 · 研究领域：Plant Disease Resistance and Genetics、Genomics and Phylogenetic Studies、Plant Pathogens and Resistance

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.