title: Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity.
abstract: Cassava (Manihot esculenta) provides calories and nutrition for more than half a billion people. It was domesticated by native Amazonian peoples through cultivation of the wild progenitor M. esculenta ssp. flabellifolia and is now grown in tropical regions worldwide. Here we provide a high-quality genome assembly for cassava with improved contiguity, linkage, and completeness; almost 97% of genes are anchored to chromosomes. We find that paleotetraploidy in cassava is shared with the related rubber tree Hevea, providing a resource for comparative studies. We also sequence a global collection of 58 Manihot accessions, including cultivated and wild cassava accessions and related species such as Ceará or India rubber (M. glaziovii), and genotype 268 African cassava varieties. We find widespread interspecific admixture, and detect the genetic signature of past cassava breeding programs. As a clonally propagated crop, cassava is especially vulnerable to pathogens and abiotic stresses. This genomic resource will inform future genome-enabled breeding efforts to improve this staple crop.
authors.affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, California, USA.
authors.forename: Jessen V
authors.initials: JV
authors.lastname: Bredeson
authors.affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, California, USA.
authors.forename: Jessica B
authors.identifier: 0000-0002-3886-2146
authors.initials: JB
authors.lastname: Lyons
authors.affiliation: United States Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, California, USA.
authors.forename: Simon E
authors.initials: SE
authors.lastname: Prochnik
authors.affiliation: United States Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, California, USA.
authors.forename: G Albert
authors.initials: GA
authors.lastname: Wu
authors.affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, California, USA.
authors.forename: Cindy M
authors.initials: CM
authors.lastname: Ha
authors.affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, California, USA.
authors.forename: Eric
authors.initials: E
authors.lastname: Edsinger-Gonzales
authors.affiliation: United States Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, California, USA.|HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA.
authors.forename: Jane
authors.initials: J
authors.lastname: Grimwood
authors.affiliation: United States Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, California, USA.|HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Schmutz
authors.affiliation: International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria.
authors.forename: Ismail Y
authors.initials: IY
authors.lastname: Rabbi
authors.affiliation: National Root Crops Research Institute (NRCRI), Umudike, Nigeria.
authors.forename: Chiedozie
authors.initials: C
authors.lastname: Egesi
authors.affiliation: Department of Agriculture, Ministry of Primary Industries, Koronivia Research Station, Fiji.
authors.forename: Poasa
authors.initials: P
authors.lastname: Nauluvula
authors.affiliation: Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Port-Vila, Vanuatu.
authors.forename: Vincent
authors.initials: V
authors.lastname: Lebot
authors.affiliation: Mikocheni Agricultural Research Institute (MARI), Dar es Salaam, Tanzania.
authors.forename: Joseph
authors.initials: J
authors.lastname: Ndunguru
authors.affiliation: Naliendele Agricultural Research Institute (NARI), Mtwara, Tanzania.
authors.forename: Geoffrey
authors.initials: G
authors.lastname: Mkamilo
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, Missouri, USA.
authors.forename: Rebecca S
authors.initials: RS
authors.lastname: Bart
authors.affiliation: Section of Soil and Crop Sciences, School of Integrative Plant Science, Cornell University, Ithaca, New York, USA.
authors.forename: Tim L
authors.initials: TL
authors.lastname: Setter
authors.affiliation: School of Biological Sciences, Monash University, Melbourne, Victoria, Australia.
authors.forename: Roslyn M
authors.identifier: 0000-0003-4756-0411
authors.initials: RM
authors.lastname: Gleadow
authors.affiliation: International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria.
authors.forename: Peter
authors.initials: P
authors.lastname: Kulakow
authors.affiliation: International Institute of Tropical Agriculture (IITA), Nairobi, Kenya.
authors.forename: Morag E
authors.initials: ME
authors.lastname: Ferguson
authors.affiliation: Dow AgroSciences, Indianapolis, Indiana, USA.
authors.forename: Steve
authors.identifier: 0000-0002-3016-6795
authors.initials: S
authors.lastname: Rounsley
authors.affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, California, USA.|United States Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, California, USA.|Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan.
authors.forename: Daniel S
authors.initials: DS
authors.lastname: Rokhsar
mesh_terms: D002874:Chromosome Mapping / Q000379:methods; D017124:Conserved Sequence / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics*; D014644:Genetic Variation; D018745:Genome, Plant / Q000235:genetics; D006824:Hybridization, Genetic / Q000235:genetics*; D002365:Manihot / Q000145:classification* / Q000235:genetics*; D000069600:Plant Breeding / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D013045:Species Specificity
chemical_list: D018744:DNA, Plant