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Sensalari C, Maere S, Lohaus R. ksrates: positioning whole-genome duplications relative to speciation events in KS distributions. Bioinformatics 2022; 38:530-532. [PMID: 34406368 DOI: 10.1093/bioinformatics/btab602] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/07/2021] [Accepted: 08/17/2021] [Indexed: 02/03/2023] Open
Abstract
SUMMARY We present ksrates, a user-friendly command-line tool to position ancient whole-genome duplication events with respect to speciation events in a phylogeny by comparing paralog and ortholog KS distributions derived from genomic or transcriptomic sequences, while adjusting for substitution rate differences among the lineages involved. AVAILABILITY AND IMPLEMENTATION ksrates is implemented in Python 3 and as a Nextflow pipeline. The source code, Singularity and Docker containers, documentation and tutorial are available via https://github.com/VIB-PSB/ksrates. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Cecilia Sensalari
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium.,VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Steven Maere
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium.,VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Rolf Lohaus
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium.,VIB Center for Plant Systems Biology, Ghent 9052, Belgium
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2
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Zhang GQ, Liu KW, Li Z, Lohaus R, Hsiao YY, Niu SC, Wang JY, Lin YC, Xu Q, Chen LJ, Yoshida K, Fujiwara S, Wang ZW, Zhang YQ, Mitsuda N, Wang M, Liu GH, Pecoraro L, Huang HX, Xiao XJ, Lin M, Wu XY, Wu WL, Chen YY, Chang SB, Sakamoto S, Ohme-Takagi M, Yagi M, Zeng SJ, Shen CY, Yeh CM, Luo YB, Tsai WC, Van de Peer Y, Liu ZJ. Author Correction: The Apostasia genome and the evolution of orchids. Nature 2020; 583:E30. [PMID: 32681116 PMCID: PMC7608229 DOI: 10.1038/s41586-020-2524-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Guo-Qiang Zhang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China
| | - Ke-Wei Liu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Gent, Belgium.,VIB Center for Plant Systems Biology, 9052, Gent, Belgium
| | - Rolf Lohaus
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Gent, Belgium.,VIB Center for Plant Systems Biology, 9052, Gent, Belgium
| | - Yu-Yun Hsiao
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701, Taiwan.,Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan
| | - Shan-Ce Niu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China.,State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jie-Yu Wang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China.,College of Forestry, South China Agricultural University, Guangzhou, 510640, China
| | - Yao-Cheng Lin
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Gent, Belgium.,VIB Center for Plant Systems Biology, 9052, Gent, Belgium.,Biotechnology Center in Southern Taiwan, Agricultural Biotechnology Research Center, Academia Sinica, 741, Tainan, Taiwan
| | - Qing Xu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China
| | - Li-Jun Chen
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China
| | - Kouki Yoshida
- Technology Center, Taisei Corporation, Nase-cho 344-1, Totsuka-ku, Yokohama, Kanagawa, 245-0051, Japan
| | - Sumire Fujiwara
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8562, Japan
| | - Zhi-Wen Wang
- PubBio-Tech Services Corporation, Wuhan, 430070, China
| | - Yong-Qiang Zhang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8562, Japan
| | - Meina Wang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China
| | - Guo-Hui Liu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China
| | - Lorenzo Pecoraro
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China
| | - Hui-Xia Huang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China
| | - Xin-Ju Xiao
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China
| | - Min Lin
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China
| | - Xin-Yi Wu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China
| | - Wan-Lin Wu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China.,Orchid Research and Development Center, National Cheng Kung University, Tainan, 701, Taiwan
| | - You-Yi Chen
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701, Taiwan.,Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan
| | - Song-Bin Chang
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701, Taiwan.,Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan
| | - Shingo Sakamoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8562, Japan
| | - Masaru Ohme-Takagi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8562, Japan.,Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Masafumi Yagi
- NARO Institute of Floricultural Science (NIFS), 2-1 Fujimoto, Tsukuba, Ibaraki, 305-8519, Japan
| | - Si-Jin Zeng
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China.,College of Forestry, South China Agricultural University, Guangzhou, 510640, China
| | - Ching-Yu Shen
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, 701, Taiwan
| | - Chuan-Ming Yeh
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Yi-Bo Luo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Wen-Chieh Tsai
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701, Taiwan.,Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan.,Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, 701, Taiwan
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Gent, Belgium.,VIB Center for Plant Systems Biology, 9052, Gent, Belgium.,Department of Genetics, Genomics Research Institute, Pretoria, 0028, South Africa
| | - Zhong-Jian Liu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China. .,College of Forestry, South China Agricultural University, Guangzhou, 510640, China. .,College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,The Center for Biotechnology and BioMedicine, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China.
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3
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Zhang L, Chen F, Zhang X, Li Z, Zhao Y, Lohaus R, Chang X, Dong W, Ho SYW, Liu X, Song A, Chen J, Guo W, Wang Z, Zhuang Y, Wang H, Chen X, Hu J, Liu Y, Qin Y, Wang K, Dong S, Liu Y, Zhang S, Yu X, Wu Q, Wang L, Yan X, Jiao Y, Kong H, Zhou X, Yu C, Chen Y, Li F, Wang J, Chen W, Chen X, Jia Q, Zhang C, Jiang Y, Zhang W, Liu G, Fu J, Chen F, Ma H, Van de Peer Y, Tang H. The water lily genome and the early evolution of flowering plants. Nature 2020; 577:79-84. [PMID: 31853069 PMCID: PMC7015852 DOI: 10.1038/s41586-019-1852-5] [Citation(s) in RCA: 184] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 10/31/2019] [Indexed: 12/16/2022]
Abstract
Water lilies belong to the angiosperm order Nymphaeales. Amborellales, Nymphaeales and Austrobaileyales together form the so-called ANA-grade of angiosperms, which are extant representatives of lineages that diverged the earliest from the lineage leading to the extant mesangiosperms1-3. Here we report the 409-megabase genome sequence of the blue-petal water lily (Nymphaea colorata). Our phylogenomic analyses support Amborellales and Nymphaeales as successive sister lineages to all other extant angiosperms. The N. colorata genome and 19 other water lily transcriptomes reveal a Nymphaealean whole-genome duplication event, which is shared by Nymphaeaceae and possibly Cabombaceae. Among the genes retained from this whole-genome duplication are homologues of genes that regulate flowering transition and flower development. The broad expression of homologues of floral ABCE genes in N. colorata might support a similarly broadly active ancestral ABCE model of floral organ determination in early angiosperms. Water lilies have evolved attractive floral scents and colours, which are features shared with mesangiosperms, and we identified their putative biosynthetic genes in N. colorata. The chemical compounds and biosynthetic genes behind floral scents suggest that they have evolved in parallel to those in mesangiosperms. Because of its unique phylogenetic position, the N. colorata genome sheds light on the early evolution of angiosperms.
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Affiliation(s)
- Liangsheng Zhang
- 0000 0004 1760 2876grid.256111.0Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Fei Chen
- 0000 0004 1760 2876grid.256111.0Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China ,0000 0000 9750 7019grid.27871.3bCollege of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xingtan Zhang
- 0000 0004 1760 2876grid.256111.0Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhen Li
- 0000 0001 2069 7798grid.5342.0Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium ,0000000104788040grid.11486.3aVIB Center for Plant Systems Biology, Ghent, Belgium
| | - Yiyong Zhao
- 0000 0001 0125 2443grid.8547.eState Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China ,0000 0001 2097 4281grid.29857.31Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA USA
| | - Rolf Lohaus
- 0000 0001 2069 7798grid.5342.0Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium ,0000000104788040grid.11486.3aVIB Center for Plant Systems Biology, Ghent, Belgium
| | - Xiaojun Chang
- 0000 0004 1760 2876grid.256111.0Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China ,Fairy Lake Botanical Garden, Shenzhen and Chinese Academy of Sciences, Shenzhen, China
| | - Wei Dong
- 0000 0004 1760 2876grid.256111.0Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Simon Y. W. Ho
- 0000 0004 1936 834Xgrid.1013.3School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales Australia
| | - Xing Liu
- 0000 0004 1760 2876grid.256111.0Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Aixia Song
- 0000 0004 1760 2876grid.256111.0Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Junhao Chen
- 0000 0000 9152 7385grid.443483.cState Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Wenlei Guo
- 0000 0000 9152 7385grid.443483.cState Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Zhengjia Wang
- 0000 0000 9152 7385grid.443483.cState Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Yingyu Zhuang
- 0000 0004 1760 2876grid.256111.0Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Haifeng Wang
- 0000 0004 1760 2876grid.256111.0Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xuequn Chen
- 0000 0004 1760 2876grid.256111.0Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Juan Hu
- 0000 0004 1760 2876grid.256111.0Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanhui Liu
- 0000 0004 1760 2876grid.256111.0Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuan Qin
- 0000 0004 1760 2876grid.256111.0Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kai Wang
- 0000 0004 1760 2876grid.256111.0Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shanshan Dong
- Fairy Lake Botanical Garden, Shenzhen and Chinese Academy of Sciences, Shenzhen, China
| | - Yang Liu
- Fairy Lake Botanical Garden, Shenzhen and Chinese Academy of Sciences, Shenzhen, China ,0000 0001 2034 1839grid.21155.32BGI-Shenzhen, Shenzhen, China
| | - Shouzhou Zhang
- Fairy Lake Botanical Garden, Shenzhen and Chinese Academy of Sciences, Shenzhen, China
| | - Xianxian Yu
- 0000 0000 8989 0732grid.412992.5School of Urban-Rural Planning and Landscape Architecture, Xuchang University, Xuchang, China
| | - Qian Wu
- 0000000119573309grid.9227.eKey Laboratory of Plant Resources/Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China ,0000 0004 1797 8419grid.410726.6University of the Chinese Academy of Sciences, Beijing, China
| | - Liangsheng Wang
- 0000000119573309grid.9227.eKey Laboratory of Plant Resources/Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China ,0000 0004 1797 8419grid.410726.6University of the Chinese Academy of Sciences, Beijing, China
| | - Xueqing Yan
- 0000 0004 1797 8419grid.410726.6University of the Chinese Academy of Sciences, Beijing, China ,0000000119573309grid.9227.eState Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yuannian Jiao
- 0000 0004 1797 8419grid.410726.6University of the Chinese Academy of Sciences, Beijing, China ,0000000119573309grid.9227.eState Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Hongzhi Kong
- 0000 0004 1797 8419grid.410726.6University of the Chinese Academy of Sciences, Beijing, China ,0000000119573309grid.9227.eState Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiaofan Zhou
- 0000 0000 9546 5767grid.20561.30Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Cuiwei Yu
- Hangzhou Tianjing Aquatic Botanical Garden, Zhejiang Humanities Landscape Co. Ltd., Hangzhou, China
| | - Yuchu Chen
- Hangzhou Tianjing Aquatic Botanical Garden, Zhejiang Humanities Landscape Co. Ltd., Hangzhou, China
| | - Fan Li
- 0000 0004 1799 1111grid.410732.3National Engineering Research Center for Ornamental Horticulture, Key Laboratory for Flower Breeding of Yunnan Province, Floriculture Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Jihua Wang
- 0000 0004 1799 1111grid.410732.3National Engineering Research Center for Ornamental Horticulture, Key Laboratory for Flower Breeding of Yunnan Province, Floriculture Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Wei Chen
- 0000 0001 0376 205Xgrid.411304.3Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xinlu Chen
- 0000 0001 2315 1184grid.411461.7Department of Plant Sciences, University of Tennessee, Knoxville, TN USA
| | - Qidong Jia
- 0000 0001 2315 1184grid.411461.7Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN USA
| | - Chi Zhang
- 0000 0001 2315 1184grid.411461.7Department of Plant Sciences, University of Tennessee, Knoxville, TN USA
| | - Yifan Jiang
- 0000 0000 9750 7019grid.27871.3bCollege of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Wanbo Zhang
- 0000 0000 9750 7019grid.27871.3bCollege of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Guanhua Liu
- 0000 0001 0526 1937grid.410727.7Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Jianyu Fu
- 0000 0001 0526 1937grid.410727.7Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Feng Chen
- 0000 0000 9750 7019grid.27871.3bCollege of Horticulture, Nanjing Agricultural University, Nanjing, China ,0000 0001 2315 1184grid.411461.7Department of Plant Sciences, University of Tennessee, Knoxville, TN USA ,0000 0001 2315 1184grid.411461.7Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN USA
| | - Hong Ma
- 0000 0001 2097 4281grid.29857.31Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA USA
| | - Yves Van de Peer
- 0000 0001 2069 7798grid.5342.0Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium ,0000000104788040grid.11486.3aVIB Center for Plant Systems Biology, Ghent, Belgium ,0000 0001 2107 2298grid.49697.35Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Haibao Tang
- 0000 0004 1760 2876grid.256111.0Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
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4
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Linsmith G, Rombauts S, Montanari S, Deng CH, Celton JM, Guérif P, Liu C, Lohaus R, Zurn JD, Cestaro A, Bassil NV, Bakker LV, Schijlen E, Gardiner SE, Lespinasse Y, Durel CE, Velasco R, Neale DB, Chagné D, Van de Peer Y, Troggio M, Bianco L. Pseudo-chromosome-length genome assembly of a double haploid "Bartlett" pear (Pyrus communis L.). Gigascience 2019; 8:giz138. [PMID: 31816089 PMCID: PMC6901071 DOI: 10.1093/gigascience/giz138] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/18/2019] [Accepted: 10/30/2019] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND We report an improved assembly and scaffolding of the European pear (Pyrus communis L.) genome (referred to as BartlettDHv2.0), obtained using a combination of Pacific Biosciences RSII long-read sequencing, Bionano optical mapping, chromatin interaction capture (Hi-C), and genetic mapping. The sample selected for sequencing is a double haploid derived from the same "Bartlett" reference pear that was previously sequenced. Sequencing of di-haploid plants makes assembly more tractable in highly heterozygous species such as P. communis. FINDINGS A total of 496.9 Mb corresponding to 97% of the estimated genome size were assembled into 494 scaffolds. Hi-C data and a high-density genetic map allowed us to anchor and orient 87% of the sequence on the 17 pear chromosomes. Approximately 50% (247 Mb) of the genome consists of repetitive sequences. Gene annotation confirmed the presence of 37,445 protein-coding genes, which is 13% fewer than previously predicted. CONCLUSIONS We showed that the use of a doubled-haploid plant is an effective solution to the problems presented by high levels of heterozygosity and duplication for the generation of high-quality genome assemblies. We present a high-quality chromosome-scale assembly of the European pear Pyrus communis and demostrate its high degree of synteny with the genomes of Malus x Domestica and Pyrus x bretschneideri.
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Affiliation(s)
- Gareth Linsmith
- Center for Plant Systems Biology, VIB, Technologiepark 71, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Gent, Belgium
- Fondazione Edmund Mach, via E. Mach 1, 38010, San Michele all'Adige (TN), Italy
| | - Stephane Rombauts
- Center for Plant Systems Biology, VIB, Technologiepark 71, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Gent, Belgium
| | - Sara Montanari
- University of California Davis, Department of Plant Sciences, One Shields Ave, Davis, CA 95616, USA
| | - Cecilia H Deng
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre,120 Mt Albert Road, Sandringham, Auckland, 1025, New Zealand
| | - Jean-Marc Celton
- IRHS, INRA, Agrocampus-Ouest, Université d'Angers, SFR 4207 Quasav, 42 rue Georges Morel, F-49071 Beaucouzé, France
| | - Philippe Guérif
- IRHS, INRA, Agrocampus-Ouest, Université d'Angers, SFR 4207 Quasav, 42 rue Georges Morel, F-49071 Beaucouzé, France
| | - Chang Liu
- ZMBP, Allgemeine Genetik, Universität Tübingen, Auf der Morgenstelle 32, D-72076 Tübingen, Germany
| | - Rolf Lohaus
- Center for Plant Systems Biology, VIB, Technologiepark 71, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Gent, Belgium
| | - Jason D Zurn
- USDA-ARS National Clonal Germplasm Repository, 33447 Peoria Road, Corvallis, OR 97333, USA
| | - Alessandro Cestaro
- Fondazione Edmund Mach, via E. Mach 1, 38010, San Michele all'Adige (TN), Italy
| | - Nahla V Bassil
- USDA-ARS National Clonal Germplasm Repository, 33447 Peoria Road, Corvallis, OR 97333, USA
| | - Linda V Bakker
- Wageningen UR – Bioscience P.O. Box 16, 6700AA, Wageningen, The Netherlands
| | - Elio Schijlen
- Wageningen UR – Bioscience P.O. Box 16, 6700AA, Wageningen, The Netherlands
| | - Susan E Gardiner
- The New Zealand Institute for Plant & Food Research Limited (PFR), Palmerston North Research Centre, Palmerston North, New Zealand
| | - Yves Lespinasse
- IRHS, INRA, Agrocampus-Ouest, Université d'Angers, SFR 4207 Quasav, 42 rue Georges Morel, F-49071 Beaucouzé, France
| | - Charles-Eric Durel
- IRHS, INRA, Agrocampus-Ouest, Université d'Angers, SFR 4207 Quasav, 42 rue Georges Morel, F-49071 Beaucouzé, France
| | - Riccardo Velasco
- CREA Research Centre for Viticulture and Enology, Via XXVIII Aprile 26, 31015 Conegliano (TV), Italy
| | - David B Neale
- University of California Davis, Department of Plant Sciences, One Shields Ave, Davis, CA 95616, USA
| | - David Chagné
- The New Zealand Institute for Plant & Food Research Limited (PFR), Palmerston North Research Centre, Palmerston North, New Zealand
| | - Yves Van de Peer
- Center for Plant Systems Biology, VIB, Technologiepark 71, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Gent, Belgium
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Roper street, Pretoria 0028, South Africa
| | - Michela Troggio
- Fondazione Edmund Mach, via E. Mach 1, 38010, San Michele all'Adige (TN), Italy
| | - Luca Bianco
- Fondazione Edmund Mach, via E. Mach 1, 38010, San Michele all'Adige (TN), Italy
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5
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Zwaenepoel A, Li Z, Lohaus R, Van de Peer Y. Finding Evidence for Whole Genome Duplications: A Reappraisal. Mol Plant 2019; 12:133-136. [PMID: 30599206 DOI: 10.1016/j.molp.2018.12.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 11/13/2018] [Accepted: 12/21/2018] [Indexed: 06/09/2023]
Affiliation(s)
- Arthur Zwaenepoel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Rolf Lohaus
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium; Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
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6
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Wan T, Liu ZM, Li LF, Leitch AR, Leitch IJ, Lohaus R, Liu ZJ, Xin HP, Gong YB, Liu Y, Wang WC, Chen LY, Yang Y, Kelly LJ, Yang J, Huang JL, Li Z, Liu P, Zhang L, Liu HM, Wang H, Deng SH, Liu M, Li J, Ma L, Liu Y, Lei Y, Xu W, Wu LQ, Liu F, Ma Q, Yu XR, Jiang Z, Zhang GQ, Li SH, Li RQ, Zhang SZ, Wang QF, Van de Peer Y, Zhang JB, Wang XM. A genome for gnetophytes and early evolution of seed plants. Nat Plants 2018; 4:82-89. [PMID: 29379155 DOI: 10.1038/s41477-017-0097-2] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 12/27/2017] [Indexed: 05/07/2023]
Abstract
Gnetophytes are an enigmatic gymnosperm lineage comprising three genera, Gnetum, Welwitschia and Ephedra, which are morphologically distinct from all other seed plants. Their distinctiveness has triggered much debate as to their origin, evolution and phylogenetic placement among seed plants. To increase our understanding of the evolution of gnetophytes, and their relation to other seed plants, we report here a high-quality draft genome sequence for Gnetum montanum, the first for any gnetophyte. By using a novel genome assembly strategy to deal with high levels of heterozygosity, we assembled >4 Gb of sequence encoding 27,491 protein-coding genes. Comparative analysis of the G. montanum genome with other gymnosperm genomes unveiled some remarkable and distinctive genomic features, such as a diverse assemblage of retrotransposons with evidence for elevated frequencies of elimination rather than accumulation, considerable differences in intron architecture, including both length distribution and proportions of (retro) transposon elements, and distinctive patterns of proliferation of functional protein domains. Furthermore, a few gene families showed Gnetum-specific copy number expansions (for example, cellulose synthase) or contractions (for example, Late Embryogenesis Abundant protein), which could be connected with Gnetum's distinctive morphological innovations associated with their adaptation to warm, mesic environments. Overall, the G. montanum genome enables a better resolution of ancestral genomic features within seed plants, and the identification of genomic characters that distinguish Gnetum from other gymnosperms.
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Affiliation(s)
- Tao Wan
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
- Sino-Africa Joint Research Centre, Chinese Academy of Science, Wuhan, China
| | - Zhi-Ming Liu
- Novogene Bioinformatics Institute, Beijing, China
| | - Ling-Fei Li
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | | | - Rolf Lohaus
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Centre for Plant Systems Biology, VIB, Ghent, Belgium
| | - Zhong-Jian Liu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Centre of China and Orchid Conservation and Research Centre, Shenzhen, China
| | - Hai-Ping Xin
- Sino-Africa Joint Research Centre, Chinese Academy of Science, Wuhan, China
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Yan-Bing Gong
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yang Liu
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Wen-Cai Wang
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Ling-Yun Chen
- Sino-Africa Joint Research Centre, Chinese Academy of Science, Wuhan, China
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Yong Yang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Laura J Kelly
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Ji Yang
- Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Jin-Ling Huang
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China
- Department of Biology, East Carolina University, Greenville, NC, USA
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Centre for Plant Systems Biology, VIB, Ghent, Belgium
| | - Ping Liu
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Li Zhang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Hong-Mei Liu
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Hui Wang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Shu-Han Deng
- Novogene Bioinformatics Institute, Beijing, China
| | - Meng Liu
- Novogene Bioinformatics Institute, Beijing, China
| | - Ji Li
- Novogene Bioinformatics Institute, Beijing, China
| | - Lu Ma
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Yan Liu
- Novogene Bioinformatics Institute, Beijing, China
| | - Yang Lei
- Novogene Bioinformatics Institute, Beijing, China
| | - Wei Xu
- Novogene Bioinformatics Institute, Beijing, China
| | - Ling-Qing Wu
- Novogene Bioinformatics Institute, Beijing, China
| | - Fan Liu
- Sino-Africa Joint Research Centre, Chinese Academy of Science, Wuhan, China
| | - Qian Ma
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xin-Ran Yu
- Novogene Bioinformatics Institute, Beijing, China
| | - Zhi Jiang
- Novogene Bioinformatics Institute, Beijing, China
| | - Guo-Qiang Zhang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Centre of China and Orchid Conservation and Research Centre, Shenzhen, China
| | - Shao-Hua Li
- Beijing Key Laboratory of Grape Sciences and Enology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Rui-Qiang Li
- Novogene Bioinformatics Institute, Beijing, China
| | - Shou-Zhou Zhang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Qing-Feng Wang
- Sino-Africa Joint Research Centre, Chinese Academy of Science, Wuhan, China.
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- Centre for Plant Systems Biology, VIB, Ghent, Belgium.
- Genomics Research Institute, University of Pretoria, Pretoria, South Africa.
| | - Jin-Bo Zhang
- Novogene Bioinformatics Institute, Beijing, China.
| | - Xiao-Ming Wang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China.
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7
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Unver T, Wu Z, Sterck L, Turktas M, Lohaus R, Li Z, Yang M, He L, Deng T, Escalante FJ, Llorens C, Roig FJ, Parmaksiz I, Dundar E, Xie F, Zhang B, Ipek A, Uranbey S, Erayman M, Ilhan E, Badad O, Ghazal H, Lightfoot DA, Kasarla P, Colantonio V, Tombuloglu H, Hernandez P, Mete N, Cetin O, Van Montagu M, Yang H, Gao Q, Dorado G, Van de Peer Y. Genome of wild olive and the evolution of oil biosynthesis. Proc Natl Acad Sci U S A 2017; 114:E9413-E9422. [PMID: 29078332 PMCID: PMC5676908 DOI: 10.1073/pnas.1708621114] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Here we present the genome sequence and annotation of the wild olive tree (Olea europaea var. sylvestris), called oleaster, which is considered an ancestor of cultivated olive trees. More than 50,000 protein-coding genes were predicted, a majority of which could be anchored to 23 pseudochromosomes obtained through a newly constructed genetic map. The oleaster genome contains signatures of two Oleaceae lineage-specific paleopolyploidy events, dated at ∼28 and ∼59 Mya. These events contributed to the expansion and neofunctionalization of genes and gene families that play important roles in oil biosynthesis. The functional divergence of oil biosynthesis pathway genes, such as FAD2, SACPD, EAR, and ACPTE, following duplication, has been responsible for the differential accumulation of oleic and linoleic acids produced in olive compared with sesame, a closely related oil crop. Duplicated oleaster FAD2 genes are regulated by an siRNA derived from a transposable element-rich region, leading to suppressed levels of FAD2 gene expression. Additionally, neofunctionalization of members of the SACPD gene family has led to increased expression of SACPD2, 3, 5, and 7, consequently resulting in an increased desaturation of steric acid. Taken together, decreased FAD2 expression and increased SACPD expression likely explain the accumulation of exceptionally high levels of oleic acid in olive. The oleaster genome thus provides important insights into the evolution of oil biosynthesis and will be a valuable resource for oil crop genomics.
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Affiliation(s)
- Turgay Unver
- İzmir International Biomedicine and Genome Institute, Dokuz Eylül University, 35340 İzmir, Turkey;
| | | | - Lieven Sterck
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Mine Turktas
- Department of Biology, Faculty of Science, Cankiri Karatekin University, 18100 Cankiri, Turkey
| | - Rolf Lohaus
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Ming Yang
- BGI Shenzhen, 518038 Shenzhen, China
| | - Lijuan He
- BGI Shenzhen, 518038 Shenzhen, China
| | | | | | | | | | - Iskender Parmaksiz
- Department of Molecular Biology and Genetics, Faculty of Science, Gaziosmanpasa University, 60250 Tokat, Turkey
| | - Ekrem Dundar
- Department of Molecular Biology and Genetics, Faculty of Science, Balikesir University, 10145 Balikesir, Turkey
| | - Fuliang Xie
- Department of Biology, East Carolina University, Greenville, NC 27858
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858
| | - Arif Ipek
- Department of Biology, Faculty of Science, Cankiri Karatekin University, 18100 Cankiri, Turkey
| | - Serkan Uranbey
- Department of Field Crops, Faculty of Agriculture, Ankara University, 06120 Ankara, Turkey
| | - Mustafa Erayman
- Department of Biology, Faculty of Arts and Science, Mustafa Kemal University, 31060 Hatay, Turkey
| | - Emre Ilhan
- Department of Biology, Faculty of Arts and Science, Mustafa Kemal University, 31060 Hatay, Turkey
| | - Oussama Badad
- Laboratory of Plant Physiology, University Mohamed V, 10102 Rabat, Morocco
| | - Hassan Ghazal
- Polydisciplinary Faculty of Nador, University Mohamed Premier, 62700 Nador, Morocco
| | - David A Lightfoot
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901
| | - Pavan Kasarla
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901
| | - Vincent Colantonio
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901
| | - Huseyin Tombuloglu
- Institute for Research and Medical Consultation, University of Dammam, 34212 Dammam, Saudi Arabia
| | - Pilar Hernandez
- Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas, 14004 Córdoba, Spain
| | - Nurengin Mete
- Olive Research Institute of Bornova, 35100 Izmir, Turkey
| | - Oznur Cetin
- Olive Research Institute of Bornova, 35100 Izmir, Turkey
| | - Marc Van Montagu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | | | - Qiang Gao
- BGI Shenzhen, 518038 Shenzhen, China
| | - Gabriel Dorado
- Departamento Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Genetics, Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa
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8
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Zhang GQ, Liu KW, Li Z, Lohaus R, Hsiao YY, Niu SC, Wang JY, Lin YC, Xu Q, Chen LJ, Yoshida K, Fujiwara S, Wang ZW, Zhang YQ, Mitsuda N, Wang M, Liu GH, Pecoraro L, Huang HX, Xiao XJ, Lin M, Wu XY, Wu WL, Chen YY, Chang SB, Sakamoto S, Ohme-Takagi M, Yagi M, Zeng SJ, Shen CY, Yeh CM, Luo YB, Tsai WC, Van de Peer Y, Liu ZJ. The Apostasia genome and the evolution of orchids. Nature 2017; 549:379-383. [PMID: 28902843 PMCID: PMC7416622 DOI: 10.1038/nature23897] [Citation(s) in RCA: 212] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 08/07/2017] [Indexed: 12/15/2022]
Abstract
WebComparing the whole genome sequence of Apostasia shenzhenica with transcriptome and genome data from five orchid subfamilies permits the reconstruction of an ancestral gene toolkit, providing insight into orchid origins, evolution and diversification. Around 10 per cent of flowering plant species are orchids, with a broad diversity in both morphology and lifestyle. Apostasia is one of the earliest-diverging genera of Orchidaceae. To study the evolution and diversity of Orchidaceae, Zhong-Jian Liu, Yves Van de Peer and colleagues sequenced the genome of Apostasia shenzhenica, a self-pollinating species found in southeast China. The authors also report improved genomes for two species of Epidendroideae, Phalaenopsis equestris and Dendrobium catenatum, as well as transcriptome analysis of representatives of subfamilies of Orchidaceae. Their analyses provide insights into orchid origins, genome evolution, adaptation and diversification. Constituting approximately 10% of flowering plant species, orchids (Orchidaceae) display unique flower morphologies, possess an extraordinary diversity in lifestyle, and have successfully colonized almost every habitat on Earth1,2,3. Here we report the draft genome sequence of Apostasia shenzhenica4, a representative of one of two genera that form a sister lineage to the rest of the Orchidaceae, providing a reference for inferring the genome content and structure of the most recent common ancestor of all extant orchids and improving our understanding of their origins and evolution. In addition, we present transcriptome data for representatives of Vanilloideae, Cypripedioideae and Orchidoideae, and novel third-generation genome data for two species of Epidendroideae, covering all five orchid subfamilies. A. shenzhenica shows clear evidence of a whole-genome duplication, which is shared by all orchids and occurred shortly before their divergence. Comparisons between A. shenzhenica and other orchids and angiosperms also permitted the reconstruction of an ancestral orchid gene toolkit. We identify new gene families, gene family expansions and contractions, and changes within MADS-box gene classes, which control a diverse suite of developmental processes, during orchid evolution. This study sheds new light on the genetic mechanisms underpinning key orchid innovations, including the development of the labellum and gynostemium, pollinia, and seeds without endosperm, as well as the evolution of epiphytism; reveals relationships between the Orchidaceae subfamilies; and helps clarify the evolutionary history of orchids within the angiosperms.
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Affiliation(s)
- Guo-Qiang Zhang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Ke-Wei Liu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium.,VIB Center for Plant Systems Biology, 9052 Gent, Belgium
| | - Rolf Lohaus
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium.,VIB Center for Plant Systems Biology, 9052 Gent, Belgium
| | - Yu-Yun Hsiao
- Orchid Research and Development Center, National Cheng Kung University, Tainan 701, Taiwan.,Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Shan-Ce Niu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China.,State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jie-Yu Wang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China.,College of Forestry, South China Agricultural University, Guangzhou 510640, China
| | - Yao-Cheng Lin
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium.,VIB Center for Plant Systems Biology, 9052 Gent, Belgium
| | - Qing Xu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Li-Jun Chen
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Kouki Yoshida
- Technology Center, Taisei Corporation, Nase-cho 344-1, Totsuka-ku, Yokohama, Kanagawa 245-0051, Japan
| | - Sumire Fujiwara
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8562, Japan
| | - Zhi-Wen Wang
- PubBio-Tech Services Corporation, Wuhan 430070, China
| | - Yong-Qiang Zhang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8562, Japan
| | - Meina Wang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Guo-Hui Liu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Lorenzo Pecoraro
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Hui-Xia Huang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Xin-Ju Xiao
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Min Lin
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Xin-Yi Wu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Wan-Lin Wu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China.,Orchid Research and Development Center, National Cheng Kung University, Tainan 701, Taiwan
| | - You-Yi Chen
- Orchid Research and Development Center, National Cheng Kung University, Tainan 701, Taiwan.,Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Song-Bin Chang
- Orchid Research and Development Center, National Cheng Kung University, Tainan 701, Taiwan.,Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Shingo Sakamoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8562, Japan
| | - Masaru Ohme-Takagi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8562, Japan.,Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Masafumi Yagi
- NARO Institute of Floricultural Science (NIFS), 2-1 Fujimoto, Tsukuba, Ibaraki 305-8519, Japan
| | - Si-Jin Zeng
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China.,College of Forestry, South China Agricultural University, Guangzhou 510640, China
| | - Ching-Yu Shen
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Chuan-Ming Yeh
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Yi-Bo Luo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Wen-Chieh Tsai
- Orchid Research and Development Center, National Cheng Kung University, Tainan 701, Taiwan.,Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan.,Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium.,VIB Center for Plant Systems Biology, 9052 Gent, Belgium.,Department of Genetics, Genomics Research Institute, Pretoria 0028, South Africa
| | - Zhong-Jian Liu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China.,College of Forestry, South China Agricultural University, Guangzhou 510640, China.,College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China.,The Center for Biotechnology and BioMedicine, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China
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9
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Roodt D, Lohaus R, Sterck L, Swanepoel RL, Van de Peer Y, Mizrachi E. Evidence for an ancient whole genome duplication in the cycad lineage. PLoS One 2017; 12:e0184454. [PMID: 28886111 PMCID: PMC5590961 DOI: 10.1371/journal.pone.0184454] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 08/24/2017] [Indexed: 11/26/2022] Open
Abstract
Contrary to the many whole genome duplication events recorded for angiosperms (flowering plants), whole genome duplications in gymnosperms (non-flowering seed plants) seem to be much rarer. Although ancient whole genome duplications have been reported for most gymnosperm lineages as well, some are still contested and need to be confirmed. For instance, data for ginkgo, but particularly cycads have remained inconclusive so far, likely due to the quality of the data available and flaws in the analysis. We extracted and sequenced RNA from both the cycad Encephalartos natalensis and Ginkgo biloba. This was followed by transcriptome assembly, after which these data were used to build paralog age distributions. Based on these distributions, we identified remnants of an ancient whole genome duplication in both cycads and ginkgo. The most parsimonious explanation would be that this whole genome duplication event was shared between both species and had occurred prior to their divergence, about 300 million years ago.
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Affiliation(s)
- Danielle Roodt
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Private bag X20, Pretoria, South Africa
- Centre for Bioinformatics and Computational Biology, Genomics Research Institute, University of Pretoria, Private bag X20, Pretoria, South Africa
| | - Rolf Lohaus
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- VIB Center for Plant Systems Biology, Gent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Lieven Sterck
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- VIB Center for Plant Systems Biology, Gent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Riaan L. Swanepoel
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Private bag X20, Pretoria, South Africa
- Centre for Bioinformatics and Computational Biology, Genomics Research Institute, University of Pretoria, Private bag X20, Pretoria, South Africa
| | - Yves Van de Peer
- Centre for Bioinformatics and Computational Biology, Genomics Research Institute, University of Pretoria, Private bag X20, Pretoria, South Africa
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- VIB Center for Plant Systems Biology, Gent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Eshchar Mizrachi
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Private bag X20, Pretoria, South Africa
- Centre for Bioinformatics and Computational Biology, Genomics Research Institute, University of Pretoria, Private bag X20, Pretoria, South Africa
- * E-mail:
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10
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Ruprecht C, Lohaus R, Vanneste K, Mutwil M, Nikoloski Z, Van de Peer Y, Persson S. Revisiting ancestral polyploidy in plants. Sci Adv 2017; 3:e1603195. [PMID: 28695205 PMCID: PMC5498109 DOI: 10.1126/sciadv.1603195] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 05/26/2017] [Indexed: 05/18/2023]
Abstract
Whole-genome duplications (WGDs) or polyploidy events have been studied extensively in plants. In a now widely cited paper, Jiao et al. presented evidence for two ancient, ancestral plant WGDs predating the origin of flowering and seed plants, respectively. This finding was based primarily on a bimodal age distribution of gene duplication events obtained from molecular dating of almost 800 phylogenetic gene trees. We reanalyzed the phylogenomic data of Jiao et al. and found that the strong bimodality of the age distribution may be the result of technical and methodological issues and may hence not be a "true" signal of two WGD events. By using a state-of-the-art molecular dating algorithm, we demonstrate that the reported bimodal age distribution is not robust and should be interpreted with caution. Thus, there exists little evidence for two ancient WGDs in plants from phylogenomic dating.
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Affiliation(s)
- Colin Ruprecht
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam, Germany
- Corresponding author. (C.R.); (R.L.)
| | - Rolf Lohaus
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 927, 9052 Ghent, Belgium
- Bioinformatics Institute Ghent, Technologiepark 927, 9052 Ghent, Belgium
- Corresponding author. (C.R.); (R.L.)
| | - Kevin Vanneste
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 927, 9052 Ghent, Belgium
| | - Marek Mutwil
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam, Germany
| | - Zoran Nikoloski
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam, Germany
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 927, 9052 Ghent, Belgium
- Bioinformatics Institute Ghent, Technologiepark 927, 9052 Ghent, Belgium
- Department of Genetics, Genomics Research Institute, University of Pretoria, Pretoria, South Africa
| | - Staffan Persson
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam, Germany
- School of Biosciences, University of Melbourne, Parkville, Victoria 3010, Australia
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11
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Lohaus R, Van de Peer Y. Of dups and dinos: evolution at the K/Pg boundary. Curr Opin Plant Biol 2016; 30:62-9. [PMID: 26894611 DOI: 10.1016/j.pbi.2016.01.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 01/18/2016] [Accepted: 01/24/2016] [Indexed: 05/21/2023]
Abstract
Fifteen years into sequencing entire plant genomes, more than 30 paleopolyploidy events could be mapped on the tree of flowering plants (and many more when also transcriptome data sets are considered). While some genome duplications are very old and have occurred early in the evolution of dicots and monocots, or even before, others are more recent and seem to have occurred independently in many different plant lineages. Strikingly, a majority of these duplications date somewhere between 55 and 75 million years ago (mya), and thus likely correlate with the K/Pg boundary. If true, this would suggest that plants that had their genome duplicated at that time, had an increased chance to survive the most recent mass extinction event, at 66mya, which wiped out a majority of plant and animal life, including all non-avian dinosaurs. Here, we review several processes, both neutral and adaptive, that might explain the establishment of polyploid plants, following the K/Pg mass extinction.
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Affiliation(s)
- Rolf Lohaus
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; Department of Plant Systems Biology, VIB, Ghent, Belgium; Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; Department of Plant Systems Biology, VIB, Ghent, Belgium; Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium; Genomics Research Institute, University of Pretoria, Pretoria, South Africa.
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12
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Abstract
Theoretical investigations of the advantages of sex have tended to treat the genetic architecture of organisms as static and have not considered that genetic architecture might coevolve with reproductive mode. As a result, some potential advantages of sex may have been missed. Using a gene network model, we recently showed that recombination imposes selection for robustness to mutation and that negative epistasis can evolve as a by-product of this selection. These results motivated a detailed exploration of the mutational deterministic hypothesis, a hypothesis in which the advantage of sex depends critically on epistasis. We found that sexual populations do evolve higher mean fitness and lower genetic load than asexual populations at equilibrium, and, under moderate stabilizing selection and large population size, these equilibrium sexual populations resist invasion by asexuals. However, we found no evidence that these long- and short-term advantages to sex were explained by the negative epistasis that evolved in our experiments. The long-term advantage of sex was that sexual populations evolved a lower deleterious mutation rate, but this property was not sufficient to account for the ability of sexual populations to resist invasion by asexuals. The ability to resist asexual invasion was acquired simultaneously with an increase in recombinational robustness that minimized the cost of sex. These observations provide the first direct evidence that sexual reproduction does indeed select for conditions that favor its own maintenance. Furthermore, our results highlight the importance of considering a dynamic view of the genetic architecture to understand the evolution of sex and recombination.
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Affiliation(s)
- Rolf Lohaus
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204-5001, USA
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13
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Affiliation(s)
- Ricardo B R Azevedo
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204-5001, USA.
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14
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Abstract
The evolution of life on earth has been characterized by generalized long-term increases in phenotypic complexity. Although natural selection is a plausible cause for these trends, one alternative hypothesis--generative bias--has been proposed repeatedly based on theoretical considerations. Here, we introduce a computational model of a developmental system and use it to test the hypothesis that long-term increasing trends in phenotypic complexity are caused by a generative bias towards greater complexity. We use our model to generate random organisms with different levels of phenotypic complexity and analyse the distributions of mutational effects on complexity. We show that highly complex organisms are easy to generate but there are trade-offs between different measures of complexity. We also find that only the simplest possible phenotypes show a generative bias towards higher complexity, whereas phenotypes with high complexity display a generative bias towards lower complexity. These results suggest that generative biases alone are not sufficient to explain long-term evolutionary increases in phenotypic complexity. Rather, our finding of a generative bias towards average complexity argues for a critical role of selective biases in driving increases in phenotypic complexity and in maintaining high complexity once it has evolved.
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Affiliation(s)
- Rolf Lohaus
- Department of Biology and Biochemistry, University of HoustonHouston, Texas 77204-5001, USA
| | - Nicholas L Geard
- ARC Centre for Complex Systems, School of Information Technology and Electrical Engineering, The University of QueenslandBrisbane 4072, Australia
| | - Janet Wiles
- ARC Centre for Complex Systems, School of Information Technology and Electrical Engineering, The University of QueenslandBrisbane 4072, Australia
| | - Ricardo B.R Azevedo
- Department of Biology and Biochemistry, University of HoustonHouston, Texas 77204-5001, USA
- Author for correspondence ()
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15
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Azevedo RBR, Lohaus R, Srinivasan S, Dang KK, Burch CL. Sexual reproduction selects for robustness and negative epistasis in artificial gene networks. Nature 2006; 440:87-90. [PMID: 16511495 DOI: 10.1038/nature04488] [Citation(s) in RCA: 161] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2005] [Accepted: 11/22/2005] [Indexed: 11/09/2022]
Abstract
The mutational deterministic hypothesis for the origin and maintenance of sexual reproduction posits that sex enhances the ability of natural selection to purge deleterious mutations after recombination brings them together into single genomes. This explanation requires negative epistasis, a type of genetic interaction where mutations are more harmful in combination than expected from their separate effects. The conceptual appeal of the mutational deterministic hypothesis has been offset by our inability to identify the mechanistic and evolutionary bases of negative epistasis. Here we show that negative epistasis can evolve as a consequence of sexual reproduction itself. Using an artificial gene network model, we find that recombination between gene networks imposes selection for genetic robustness, and that negative epistasis evolves as a by-product of this selection. Our results suggest that sexual reproduction selects for conditions that favour its own maintenance, a case of evolution forging its own path.
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Affiliation(s)
- Ricardo B R Azevedo
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5001, USA.
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16
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Azevedo RBR, Lohaus R, Braun V, Gumbel M, Umamaheshwar M, Agapow PM, Houthoofd W, Platzer U, Borgonie G, Meinzer HP, Leroi AM. The simplicity of metazoan cell lineages. Nature 2005; 433:152-6. [PMID: 15650738 DOI: 10.1038/nature03178] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2004] [Accepted: 11/09/2004] [Indexed: 11/09/2022]
Abstract
Developmental processes are thought to be highly complex, but there have been few attempts to measure and compare such complexity across different groups of organisms. Here we introduce a measure of biological complexity based on the similarity between developmental and computer programs. We define the algorithmic complexity of a cell lineage as the length of the shortest description of the lineage based on its constituent sublineages. We then use this measure to estimate the complexity of the embryonic lineages of four metazoan species from two different phyla. We find that these cell lineages are significantly simpler than would be expected by chance. Furthermore, evolutionary simulations show that the complexity of the embryonic lineages surveyed is near that of the simplest lineages evolvable, assuming strong developmental constraints on the spatial positions of cells and stabilizing selection on cell number. We propose that selection for decreased complexity has played a major role in moulding metazoan cell lineages.
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Affiliation(s)
- Ricardo B R Azevedo
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5001, USA.
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Weyhenmeyer R, Dingler E, Lohaus R, Mayer D, Teicher H, Wybitul K, Wangemann G, Steim H. [Bioequivalence of phenylbutazone preparations following a single intramuscular administration]. Arzneimittelforschung 1984; 34:721-3. [PMID: 6541493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
Bioequivalence was estimated in 6 resp. 7 male volunteers for two combination drugs of phenylbutazone (Neuro-Elmedal, Sigma Elmedal) after intramuscular administration using a monopreparation as a standard. Plasma levels of phenylbutazone were assayed by high pressure liquid chromatography. With respect to rate and extent both combination drugs were identical to the mono drug.
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Kukovetz WR, Brunner F, Beubler E, Weyhenmeyer R, Lohaus R, Grob M, Mayer D. Single dose pharmacokinetics of fendiline in humans. Eur J Drug Metab Pharmacokinet 1982; 7:105-10. [PMID: 7117293 DOI: 10.1007/bf03188726] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Fendiline was administered intravenously (3 mg) and orally (50 mg and 75 mg) in a cross-over study to six healthy volunteers. The plasma levels of unchanged fendiline and of total radioactivity were measured. Fendiline was absorbed well and its concentration declined biexponentially with mean terminal half-lives of 20-35 h. Since the drug is extensively metabolized, only 12% of total radioactivity in plasma corresponded to fendiline in the case of intravenous administration as compared to less than 2% after oral administration. 56-65% of the administered dose are excreted via the urine and 18-25% with the feces within five days.
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