Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce
| Author(s) | Reyes-Chin-Wo, Sebastian | |
| Author(s) | Wang, Zhiwen | |
| Author(s) | Yang, Xinhua | |
| Author(s) | Kozik, Alexander | |
| Author(s) | Arikit, Siwaret | |
| Author(s) | Song, Chi | |
| Author(s) | Xia, Liangfeng | |
| Author(s) | Froenicke, Lutz | |
| Author(s) | Lavelle, Dean O. | |
| Author(s) | Truco, Marı´a-Jose´ | |
| Author(s) | Xia, Rui | |
| Author(s) | Zhu, Shilin | |
| Author(s) | Xu, Chunyan | |
| Author(s) | Xu, Huaqin | |
| Author(s) | Xu, Xun | |
| Author(s) | Cox, Kyle | |
| Author(s) | Korf, Ian | |
| Author(s) | Meyers, Blake C. | |
| Author(s) | Michelmore, Richard W. | |
| Ordered Author | Sebastian Reyes-Chin-Wo, Zhiwen Wang, Xinhua Yang, Alexander Kozik, Siwaret Arikit, Chi Song, Liangfeng Xia, Lutz Froenicke, Dean O. Lavelle, Marı´a-Jose´ Truco, Rui Xia, Shilin Zhu, Chunyan Xu, Huaqin Xu, Xun Xu, Kyle Cox, Ian Korf, Blake C. Meyers & Richard W. Michelmore | |
| UD Author | Arikit, Siwaret | en_US |
| UD Author | Meyers, Blake C | en_US |
| Date Accessioned | 2018-06-07T15:08:11Z | |
| Date Available | 2018-06-07T15:08:11Z | |
| Copyright Date | Copyright © The Author(s) 2017 | en_US |
| Publication Date | 2017-04-12 | |
| Description | Publisher's PDF | en_US |
| 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. | en_US |
| Department | University of Delaware. Delaware Biotechnology Institute. | en_US |
| 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). | en_US |
| DOI | 10.1038/ncomms14953 | en_US |
| ISSN | 2041-1723 | en_US |
| URL | http://udspace.udel.edu/handle/19716/23553 | |
| Language | en_US | en_US |
| Publisher | Nature Publishing Group | en_US |
| dc.rights | This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/r The Authors 2017 | en_US |
| dc.source | Nature Communications | en_US |
| dc.source.uri | https://www.nature.com/ncomms/ | en_US |
| Title | Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce | en_US |
| Type | Article | en_US |
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