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Nat Commun. 2017 Apr 12;8:14953. doi: 10.1038/ncomms14953.

Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce.

Author information

1
UC Davis Genome Center, Davis, California 95616, USA.
2
BGI Shenzhen, Shenzhen 518083, China.
3
Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA.
4
Donald Danforth Plant Science Center, 975 North Warson Road, St Louis, Missouri 63132, USA.
5
Department of Molecular &Cellular Biology, UC Davis, California 95616, USA.
6
Department of Plant Sciences, UC Davis, California 95616, USA.
7
Department of Medical Microbiology &Immunology, UC Davis, California 95616, USA.

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.

PMID:
28401891
PMCID:
PMC5394340
DOI:
10.1038/ncomms14953
[Indexed for MEDLINE]
Free PMC Article

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