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

Sebastian Reyes-Chin-Wo, Zhiwen Wang, Xinhua Yang, Alexander Kozik, Siwaret Arikit, Chi Song, Liangfeng Xia, Lutz Froenicke, Dean O. Lavelle, María-José Truco, Rui Xia, Shilin Zhu, Chunyan Xu, Huaqin Xu, Xun Xu, Kyle Cox, Ian Korf, Blake C. Meyers and Richard W. Michelmore ()
Additional contact information
Sebastian Reyes-Chin-Wo: UC Davis Genome Center
Zhiwen Wang: BGI Shenzhen
Xinhua Yang: BGI Shenzhen
Alexander Kozik: UC Davis Genome Center
Siwaret Arikit: Delaware Biotechnology Institute, University of Delaware
Chi Song: BGI Shenzhen
Liangfeng Xia: BGI Shenzhen
Lutz Froenicke: UC Davis Genome Center
Dean O. Lavelle: UC Davis Genome Center
María-José Truco: UC Davis Genome Center
Rui Xia: Donald Danforth Plant Science Center
Shilin Zhu: BGI Shenzhen
Chunyan Xu: BGI Shenzhen
Huaqin Xu: UC Davis Genome Center
Xun Xu: BGI Shenzhen
Kyle Cox: UC Davis Genome Center
Ian Korf: UC Davis Genome Center
Blake C. Meyers: Delaware Biotechnology Institute, University of Delaware
Richard W. Michelmore: UC Davis Genome Center

Nature Communications, 2017, vol. 8, issue 1, 1-11

Abstract: 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.

Date: 2017
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Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:8:y:2017:i:1:d:10.1038_ncomms14953

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DOI: 10.1038/ncomms14953

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