Sequencing and Analyzing the Transcriptomes of a Thousand Species Across the Tree of Life for Green Plants

Annual Review of Plant Biology - Tập 71 Số 1 - Trang 741-765 - 2020
Gane Ka‐Shu Wong1,2, Pamela S. Soltis3,4, Jim Leebens‐Mack5, Norman J. Wickett6, Michael S. Barker7, Yves Van de Peer8,9, Sean W. Graham10, Michael Melkonian11
1BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
2Department of Biological Sciences and Department of Medicine, University of Alberta, Edmonton, Alberta T6G 2E9, Canada;
3Department of Biology, University of Florida, Gainesville, Florida 32611, USA
4Florida Museum of Natural History, Gainesville, Florida 32611, USA
5Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
6Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Glencoe, Illinois 60022, USA
7Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721 USA
8Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
9Department of Plant Biotechnology and Bioinformatics, VIB Center for Plant Systems Biology, Ghent University, 9052 Ghent, Belgium
10Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
11Faculty of Biology, University of Duisburg-Essen, D-45141 Essen, Germany

Tóm tắt

The 1,000 Plants (1KP) initiative was the first large-scale effort to collect next-generation sequencing (NGS) data across a phylogenetically representative sampling of species for a major clade of life, in this case the Viridiplantae, or green plants. As an international multidisciplinary consortium, we focused on plant evolution and its practical implications. Among the major outcomes were the inference of a reference species tree for green plants by phylotranscriptomic analysis of low-copy genes, a survey of paleopolyploidy (whole-genome duplications) across the Viridiplantae, the inferred evolutionary histories for many gene families and biological processes, the discovery of novel light-sensitive proteins for optogenetic studies in mammalian neuroscience, and elucidation of the genetic network for a complex trait (C4photosynthesis). Altogether, 1KP demonstrated how value can be extracted from a phylodiverse sequencing data set, providing a template for future projects that aim to generate even more data, including complete de novo genomes, across the tree of life.

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Annual Review of Plant Biology

Tập 71 Số 1

741-765

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