Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce
Date
2017-04-12
Journal Title
Journal ISSN
Volume Title
Publisher
Nature Publishing Group
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.
Description
Publisher's PDF
Keywords
Citation
Reyes-Chin-Wo, S. et al. Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce. Nat. Commun. 8, 14953 doi: 10.1038/ncomms14953 (2017).