title: A comprehensive draft genome sequence for lupin (Lupinus angustifolius), an emerging health food: insights into plant-microbe interactions and legume evolution.
abstract: Lupins are important grain legume crops that form a critical part of sustainable farming systems, reducing fertilizer use and providing disease breaks. It has a basal phylogenetic position relative to other crop and model legumes and a high speciation rate. Narrow-leafed lupin (NLL; Lupinus angustifolius L.) is gaining popularity as a health food, which is high in protein and dietary fibre but low in starch and gluten-free. We report the draft genome assembly (609 Mb) of NLL cultivar Tanjil, which has captured >98% of the gene content, sequences of additional lines and a dense genetic map. Lupins are unique among legumes and differ from most other land plants in that they do not form mycorrhizal associations. Remarkably, we find that NLL has lost all mycorrhiza-specific genes, but has retained genes commonly required for mycorrhization and nodulation. In addition, the genome also provided candidate genes for key disease resistance and domestication traits. We also find evidence of a whole-genome triplication at around 25 million years ago in the genistoid lineage leading to Lupinus. Our results will support detailed studies of legume evolution and accelerate lupin breeding programmes.
authors.affiliation: CSIRO Agriculture, Wembley, WA, Australia.|Department of Environment and Agriculture, CCDM Bioinformatics, Centre for Crop and Disease Management, Curtin University, Bentley, WA, Australia.|Curtin Institute for Computation, Curtin University, Bentley, WA, Australia.
authors.forename: James K
authors.initials: JK
authors.lastname: Hane
authors.affiliation: Department of Plant and Animal Genome Research, Beijing Genome Institute, Shenzhen, China.
authors.forename: Yao
authors.initials: Y
authors.lastname: Ming
authors.affiliation: CSIRO Agriculture, Wembley, WA, Australia.|UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia.
authors.forename: Lars G
authors.initials: LG
authors.lastname: Kamphuis
authors.affiliation: UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia.|School of Plant Biology, University of Western Australia, Crawley, WA, Australia.
authors.forename: Matthew N
authors.initials: MN
authors.lastname: Nelson
authors.affiliation: CSIRO Agriculture, Wembley, WA, Australia.
authors.forename: Gagan
authors.initials: G
authors.lastname: Garg
authors.affiliation: UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia.|School of Plant Biology, University of Western Australia, Crawley, WA, Australia.
authors.forename: Craig A
authors.initials: CA
authors.lastname: Atkins
authors.affiliation: School of Plant Biology, University of Western Australia, Crawley, WA, Australia.
authors.forename: Philipp E
authors.initials: PE
authors.lastname: Bayer
authors.affiliation: Boyce Thompson Institute for Plant Research, Ithaca, NY, USA.
authors.forename: Armando
authors.initials: A
authors.lastname: Bravo
authors.affiliation: Proteomics International, Nedlands, WA, Australia.
authors.forename: Scott
authors.initials: S
authors.lastname: Bringans
authors.affiliation: USDA-ARS Corn Insects and Crop Genetics Research Unit, Crop Genome Informatics Lab, Iowa State University, Ames, IA, USA.|Department of Agronomy, Iowa State University, Ames, IA, USA.
authors.forename: Steven
authors.initials: S
authors.lastname: Cannon
authors.affiliation: School of Plant Biology, University of Western Australia, Crawley, WA, Australia.|University of Queensland, Brisbane, Qld, Australia.
authors.forename: David
authors.initials: D
authors.lastname: Edwards
authors.affiliation: CSIRO Agriculture, Wembley, WA, Australia.
authors.forename: Rhonda
authors.initials: R
authors.lastname: Foley
authors.affiliation: CSIRO Agriculture, Wembley, WA, Australia.
authors.forename: Ling-Ling
authors.initials: LL
authors.lastname: Gao
authors.affiliation: Boyce Thompson Institute for Plant Research, Ithaca, NY, USA.
authors.forename: Maria J
authors.initials: MJ
authors.lastname: Harrison
authors.affiliation: Department of Agronomy, Iowa State University, Ames, IA, USA.
authors.forename: Wei
authors.initials: W
authors.lastname: Huang
authors.affiliation: School of Plant Biology, University of Western Australia, Crawley, WA, Australia.|University of Queensland, Brisbane, Qld, Australia.
authors.forename: Bhavna
authors.initials: B
authors.lastname: Hurgobin
authors.affiliation: Data61, CSIRO, Canberra, ACT, Australia.
authors.forename: Sean
authors.initials: S
authors.lastname: Li
authors.affiliation: John Innes Centre, Norwich Research Park, Norfolk, UK.
authors.forename: Cheng-Wu
authors.initials: CW
authors.lastname: Liu
authors.affiliation: Data61, CSIRO, Canberra, ACT, Australia.
authors.forename: Annette
authors.initials: A
authors.lastname: McGrath
authors.affiliation: Centre for Diabetes Research, University of Western Australia, Crawley, WA, Australia.
authors.forename: Grant
authors.initials: G
authors.lastname: Morahan
authors.affiliation: Data61, CSIRO, Canberra, ACT, Australia.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Murray
authors.affiliation: School of Biological Sciences, University of Tasmania, Hobart, TAS, Australia.
authors.forename: James
authors.initials: J
authors.lastname: Weller
authors.affiliation: Department of Plant and Animal Genome Research, Beijing Genome Institute, Shenzhen, China.
authors.forename: Jianbo
authors.initials: J
authors.lastname: Jian
authors.affiliation: CSIRO Agriculture, Wembley, WA, Australia.|UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia.
authors.forename: Karam B
authors.initials: KB
authors.lastname: Singh
mesh_terms: D060467:Disease Resistance / Q000235:genetics / Q000502:physiology; D018745:Genome, Plant / Q000235:genetics*; D031297:Lupinus / Q000235:genetics* / Q000382:microbiology*; D010940:Plant Proteins / Q000235:genetics* / Q000502:physiology; D011123:Polyploidy; D026801:Synteny / Q000235:genetics
chemical_list: D010940:Plant Proteins
keywords: Genistoids; Legume comparative genomics; flowering time genes; polyploidy; synteny; whole-genome assembly