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

Date
2017-04-12
Authors
Reyes-Chin-Wo, Sebastian
Wang, Zhiwen
Yang, Xinhua
Kozik, Alexander
Arikit, Siwaret
Song, Chi
Xia, Liangfeng
Froenicke, Lutz
Lavelle, Dean O.
Truco, Marı´a-Jose´
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).