title: Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce.
abstract: Lettuce (Lactuca sativa) is a major crop and a member of the large, highly successful Compositae family of flowering plants. Here we present a reference assembly for the species and family. This was generated using whole-genome shotgun Illumina reads plus in vitro proximity ligation data to create large superscaffolds; it was validated genetically and superscaffolds were oriented in genetic bins ordered along nine chromosomal pseudomolecules. We identify several genomic features that may have contributed to the success of the family, including genes encoding Cycloidea-like transcription factors, kinases, enzymes involved in rubber biosynthesis and disease resistance proteins that are expanded in the genome. We characterize 21 novel microRNAs, one of which may trigger phasiRNAs from numerous kinase transcripts. We provide evidence for a whole-genome triplication event specific but basal to the Compositae. We detect 26% of the genome in triplicated regions containing 30% of all genes that are enriched for regulatory sequences and depleted for genes involved in defence.
authors.affiliation: UC Davis Genome Center, Davis, California 95616, USA.
authors.forename: Sebastian
authors.identifier: 0000-0002-9635-609X
authors.initials: S
authors.lastname: Reyes-Chin-Wo
authors.affiliation: BGI Shenzhen, Shenzhen 518083, China.
authors.forename: Zhiwen
authors.initials: Z
authors.lastname: Wang
authors.affiliation: BGI Shenzhen, Shenzhen 518083, China.
authors.forename: Xinhua
authors.initials: X
authors.lastname: Yang
authors.affiliation: UC Davis Genome Center, Davis, California 95616, USA.
authors.forename: Alexander
authors.initials: A
authors.lastname: Kozik
authors.affiliation: Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA.
authors.forename: Siwaret
authors.initials: S
authors.lastname: Arikit
authors.affiliation: BGI Shenzhen, Shenzhen 518083, China.
authors.forename: Chi
authors.initials: C
authors.lastname: Song
authors.affiliation: BGI Shenzhen, Shenzhen 518083, China.
authors.forename: Liangfeng
authors.initials: L
authors.lastname: Xia
authors.affiliation: UC Davis Genome Center, Davis, California 95616, USA.
authors.forename: Lutz
authors.initials: L
authors.lastname: Froenicke
authors.affiliation: UC Davis Genome Center, Davis, California 95616, USA.
authors.forename: Dean O
authors.initials: DO
authors.lastname: Lavelle
authors.affiliation: UC Davis Genome Center, Davis, California 95616, USA.
authors.forename: María-José
authors.initials: MJ
authors.lastname: Truco
authors.affiliation: Donald Danforth Plant Science Center, 975 North Warson Road, St Louis, Missouri 63132, USA.
authors.forename: Rui
authors.initials: R
authors.lastname: Xia
authors.affiliation: BGI Shenzhen, Shenzhen 518083, China.
authors.forename: Shilin
authors.initials: S
authors.lastname: Zhu
authors.affiliation: BGI Shenzhen, Shenzhen 518083, China.
authors.forename: Chunyan
authors.initials: C
authors.lastname: Xu
authors.affiliation: UC Davis Genome Center, Davis, California 95616, USA.
authors.forename: Huaqin
authors.initials: H
authors.lastname: Xu
authors.affiliation: BGI Shenzhen, Shenzhen 518083, China.
authors.forename: Xun
authors.initials: X
authors.lastname: Xu
authors.affiliation: UC Davis Genome Center, Davis, California 95616, USA.
authors.forename: Kyle
authors.initials: K
authors.lastname: Cox
authors.affiliation: UC Davis Genome Center, Davis, California 95616, USA.|Department of Molecular &Cellular Biology, UC Davis, California 95616, USA.
authors.forename: Ian
authors.initials: I
authors.lastname: Korf
authors.affiliation: Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA.|Donald Danforth Plant Science Center, 975 North Warson Road, St Louis, Missouri 63132, USA.
authors.forename: Blake C
authors.identifier: 0000-0003-3436-6097
authors.initials: BC
authors.lastname: Meyers
authors.affiliation: UC Davis Genome Center, Davis, California 95616, USA.|Department of Molecular &Cellular Biology, UC Davis, California 95616, USA.|Department of Plant Sciences, UC Davis, California 95616, USA.|Department of Medical Microbiology &Immunology, UC Davis, California 95616, USA.
authors.forename: Richard W
authors.initials: RW
authors.lastname: Michelmore
mesh_terms: D019659:Asteraceae / Q000145:classification / Q000235:genetics; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D055106:Genome-Wide Association Study; D023281:Genomics / Q000379:methods*; D018545:Lactuca / Q000235:genetics*; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D057885:Triploidy; D000073336:Whole Genome Sequencing