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

Authors :
C. Avanzato
Filippo Tatino
Alessandra Dal Molin
Domenico Carputo
Riccardo Aiese Cigliano
Alberto Ferrarini
Felice Contaldi
James M. Bradeen
Massimo Iorizzo
Walter Sanseverino
Luciano Xumerle
Massimo Delledonne
Valentina Grosso
Salvador Capella-Gutierrez
Maria Raffaella Ercolano
Toni Gabaldón
Luigi Frusciante
Riccardo Aversano
Aversano, Riccardo
Contaldi, Felice
Ercolano, Maria
Grosso, Valentina
Iorizzo, Massimo
Tatino, Filippo
Xumerle, Luciano
Dal Molin, Alessandra
Avanzato, Carla
Ferrarini, Alberto
Delledonne, Massimo
Sanseverino, Walter
Cigliano, Riccardo Aiese
Capella Gutierrez, Salvador
Gabaldón, Toni
Frusciante, Luigi
Bradeen, James M
Carputo, Domenico
Source :
The Plant Cell. 27:954-968
Publication Year :
2015
Publisher :
Oxford University Press (OUP), 2015.

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.

Details

ISSN :
1532298X and 10404651
Volume :
27
Database :
OpenAIRE
Journal :
The Plant Cell
Accession number :
edsair.doi.dedup.....1029addafd0496d78b089fcd16312db9
Full Text :
https://doi.org/10.1105/tpc.114.135954