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 F Korf, Blake C. Meyers, Richard W Michelmore

Research output: Contribution to journalArticle

74 Citations (Scopus)

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.

Original languageEnglish (US)
Article number14953
JournalNature Communications
Volume8
DOIs
StatePublished - Apr 12 2017

Fingerprint

Lettuce
genome
Ligation
proximity
assembly
Genes
Genome
genes
Asteraceae
Phosphotransferases
biosynthesis
Disease Resistance
crops
Rubber
Firearms
Regulator Genes
MicroRNAs
rubber
enzymes
coding

ASJC Scopus subject areas

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)

Cite this

Reyes-Chin-Wo, S., Wang, Z., Yang, X., Kozik, A., Arikit, S., Song, C., ... Michelmore, R. W. (2017). Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce. Nature Communications, 8, [14953]. https://doi.org/10.1038/ncomms14953

Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce. / Reyes-Chin-Wo, Sebastian; Wang, Zhiwen; Yang, Xinhua; Kozik, Alexander; Arikit, Siwaret; Song, Chi; Xia, Liangfeng; Froenicke, Lutz; Lavelle, Dean O.; Truco, María José; Xia, Rui; Zhu, Shilin; Xu, Chunyan; Xu, Huaqin; Xu, Xun; Cox, Kyle; Korf, Ian F; Meyers, Blake C.; Michelmore, Richard W.

In: Nature Communications, Vol. 8, 14953, 12.04.2017.

Research output: Contribution to journalArticle

Reyes-Chin-Wo, S, Wang, Z, Yang, X, Kozik, A, Arikit, S, Song, C, Xia, L, Froenicke, L, Lavelle, DO, Truco, MJ, Xia, R, Zhu, S, Xu, C, Xu, H, Xu, X, Cox, K, Korf, IF, Meyers, BC & Michelmore, RW 2017, 'Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce', Nature Communications, vol. 8, 14953. https://doi.org/10.1038/ncomms14953
Reyes-Chin-Wo, Sebastian ; Wang, Zhiwen ; Yang, Xinhua ; Kozik, Alexander ; Arikit, Siwaret ; Song, Chi ; Xia, Liangfeng ; Froenicke, Lutz ; Lavelle, Dean O. ; Truco, María José ; Xia, Rui ; Zhu, Shilin ; Xu, Chunyan ; Xu, Huaqin ; Xu, Xun ; Cox, Kyle ; Korf, Ian F ; Meyers, Blake C. ; Michelmore, Richard W. / Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce. In: Nature Communications. 2017 ; Vol. 8.
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