101
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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: 199] [Impact Index Per Article: 49.8] [Reference Citation Analysis] [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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102
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Alonso MÁ, Vicente A, Crespo MB. Diversification of Biscutella ser. Biscutella (Brassicaceae) followed post-Miocene geologic and climatic changes in the Mediterranean basin. Mol Phylogenet Evol 2020; 142:106644. [DOI: 10.1016/j.ympev.2019.106644] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 10/01/2019] [Accepted: 10/07/2019] [Indexed: 10/25/2022]
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103
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Xue JY, Wang Y, Chen M, Dong S, Shao ZQ, Liu Y. Maternal Inheritance of U's Triangle and Evolutionary Process of Brassica Mitochondrial Genomes. FRONTIERS IN PLANT SCIENCE 2020; 11:805. [PMID: 32595682 PMCID: PMC7303332 DOI: 10.3389/fpls.2020.00805] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 05/19/2020] [Indexed: 05/21/2023]
Abstract
The sequences and genomic structures of plant mitochondrial (mt) genomes provide unique material for phylogenetic studies. The nature of uniparental inheritance renders an advantage when utilizing mt genomes for determining the parental sources of hybridized taxa. In this study, a concatenated matrix of mt genes was used to infer the phylogenetic relationships of six cultivated Brassica taxa and explore the maternal origins of three allotetraploids. The well-resolved sister relationships between two pairs of diploid and allotetraploid taxa suggest that Brassica carinata (car) possessed a maternal origin from Brassica nigra, while Brassica juncea (jun) was maternally derived from Brassica rapa (cam). Another allotetraploid taxon, Brassica napus (cv. Wester) may have been maternally derived from the common ancestor of B. rapa and Brassica oleracea (ole), and/or have undergone (an) extra hybridization event(s) along its evolutionary history. The characteristics of Brassica mt genomic structures also supported the phylogenetic results. Sinapis arvensis was nested inside the Brassica species, sister to the B. nigra-B. carinata lineage, and possessed an mt genome structure that mostly resembled B. nigra. Collectively, the evidence supported a systematic revision that placed S. arvensis within Brassica. Finally, ancestral mt genomes at each evolutionary node of Brassica were reconstructed, and the detailed and dynamic evolution of Brassica mt genomes was successfully reproduced. The mt genome of B. nigra structurally resembled that of the Brassica ancestor the most, with only one reversion of a block, and the Brassica oleracea underwent the most drastic changes. These findings suggested that repeat-mediated recombinations were largely responsible for the observed structural variations in the evolutionary history of Brassica mt genomes.
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Affiliation(s)
- Jia-Yu Xue
- Center for Plant Diversity and Systematics, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yue Wang
- Center for Plant Diversity and Systematics, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Min Chen
- Center for Plant Diversity and Systematics, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Shanshan Dong
- Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
| | - Zhu-Qing Shao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
- *Correspondence: Zhu-Qing Shao,
| | - Yang Liu
- Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
- Yang Liu,
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104
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Shen TT, Ran JH, Wang XQ. Phylogenomics disentangles the evolutionary history of spruces (Picea) in the Qinghai-Tibetan Plateau: Implications for the design of population genetic studies and species delimitation of conifers. Mol Phylogenet Evol 2019; 141:106612. [DOI: 10.1016/j.ympev.2019.106612] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 09/09/2019] [Accepted: 09/09/2019] [Indexed: 12/13/2022]
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105
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Shao CC, Shen TT, Jin WT, Mao HJ, Ran JH, Wang XQ. Phylotranscriptomics resolves interspecific relationships and indicates multiple historical out-of-North America dispersals through the Bering Land Bridge for the genus Picea (Pinaceae). Mol Phylogenet Evol 2019; 141:106610. [DOI: 10.1016/j.ympev.2019.106610] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 08/30/2019] [Accepted: 09/05/2019] [Indexed: 01/21/2023]
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106
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Desta ZA, Kolano B, Shamim Z, Armstrong SJ, Rewers M, Sliwinska E, Kushwaha SK, Parkin IAP, Ortiz R, de Koning DJ. Field cress genome mapping: Integrating linkage and comparative maps with cytogenetic analysis for rDNA carrying chromosomes. Sci Rep 2019; 9:17028. [PMID: 31745130 PMCID: PMC6863836 DOI: 10.1038/s41598-019-53320-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 10/30/2019] [Indexed: 11/09/2022] Open
Abstract
Field cress (Lepidium campestre L.), despite its potential as a sustainable alternative oilseed plant, has been underutilized, and no prior attempts to characterize the genome at the genetic or molecular cytogenetic level have been conducted. Genetic maps are the foundation for anchoring and orienting annotated genome assemblies and positional cloning of candidate genes. Our principal goal was to construct a genetic map using integrated approaches of genetic, comparative and cytogenetic map analyses. In total, 503 F2 interspecific hybrid individuals were genotyped using 7,624 single nucleotide polymorphism markers. Comparative analysis demonstrated that ~57% of the sequenced loci in L. campestre were congruent with Arabidopsis thaliana (L.) genome and suggested a novel karyotype, which predates the ancestral crucifer karyotype. Aceto-orcein chromosome staining and fluorescence in situ hybridization (FISH) analyses confirmed that L. campestre, L. heterophyllum Benth. and their hybrids had a chromosome number of 2n = 2x = 16. Flow cytometric analysis revealed that both species possess 2C roughly 0.4 picogram DNA. Integrating linkage and comparative maps with cytogenetic map analyses assigned two linkage groups to their particular chromosomes. Future work could incorporate FISH utilizing A. thaliana mapped BAC clones to allow the chromosomes of field cress to be identified reliably.
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Affiliation(s)
- Zeratsion Abera Desta
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Sundesvagen 10, Box 101, SE-23053, Alnarp, Sweden.
| | - Bozena Kolano
- Department of Plant Anatomy and Cytology, University of Silesia, Jagiellonska 28, 40-032, Katowice, Poland
| | - Zeeshan Shamim
- Mirpur University of Science and Technology (MUST), Mirpur AJK, Pakistan
- School of Biosciences, University of Birmingham, Birmingham, B 15 2TT, United Kingdom
| | - Susan J Armstrong
- School of Biosciences, University of Birmingham, Birmingham, B 15 2TT, United Kingdom
| | - Monika Rewers
- Laboratory of Molecular Biology and Cytometry, Department of Agricultural Biotechnology, UTP University of Science and Technology, Kaliskiego Ave. 7, 85-789, Bydgoszcz, Poland
| | - Elwira Sliwinska
- Laboratory of Molecular Biology and Cytometry, Department of Agricultural Biotechnology, UTP University of Science and Technology, Kaliskiego Ave. 7, 85-789, Bydgoszcz, Poland
| | - Sandeep Kumar Kushwaha
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Sundesvagen 10, Box 101, SE-23053, Alnarp, Sweden
| | - Isobel A P Parkin
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N0X2, Canada
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Sundesvagen 10, Box 101, SE-23053, Alnarp, Sweden
| | - Dirk-Jan de Koning
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, SE 75007, Uppsala, Sweden
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107
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Dong Y, Gupta S, Sievers R, Wargent JJ, Wheeler D, Putterill J, Macknight R, Gechev T, Mueller-Roeber B, Dijkwel PP. Genome draft of the Arabidopsis relative Pachycladon cheesemanii reveals novel strategies to tolerate New Zealand's high ultraviolet B radiation environment. BMC Genomics 2019; 20:838. [PMID: 31718535 PMCID: PMC6849220 DOI: 10.1186/s12864-019-6084-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 09/06/2019] [Indexed: 11/10/2022] Open
Abstract
Background Pachycladon cheesemanii is a close relative of Arabidopsis thaliana and is an allotetraploid perennial herb which is widespread in the South Island of New Zealand. It grows at altitudes of up to 1000 m where it is subject to relatively high levels of ultraviolet (UV)-B radiation. To gain first insights into how Pachycladon copes with UV-B stress, we sequenced its genome and compared the UV-B tolerance of two Pachycladon accessions with those of two A. thaliana accessions from different altitudes. Results A high-quality draft genome of P. cheesemanii was assembled with a high percentage of conserved single-copy plant orthologs. Synteny analysis with genomes from other species of the Brassicaceae family found a close phylogenetic relationship of P. cheesemanii with Boechera stricta from Brassicaceae lineage I. While UV-B radiation caused a greater growth reduction in the A. thaliana accessions than in the P. cheesemanii accessions, growth was not reduced in one P. cheesemanii accession. The homologues of A. thaliana UV-B radiation response genes were duplicated in P. cheesemanii, and an expression analysis of those genes indicated that the tolerance mechanism in P. cheesemanii appears to differ from that in A. thaliana. Conclusion Although the P. cheesemanii genome shows close similarity with that of A. thaliana, it appears to have evolved novel strategies allowing the plant to tolerate relatively high UV-B radiation.
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Affiliation(s)
- Yanni Dong
- School of Fundamental Sciences, Massey University, Tennent Drive, Palmerston North, 4410, New Zealand
| | - Saurabh Gupta
- Department Molecular Biology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, Haus 20, 14476, Potsdam, Germany
| | - Rixta Sievers
- School of Agriculture & Environment, Massey University, Palmerston North, 4442, New Zealand
| | - Jason J Wargent
- School of Agriculture & Environment, Massey University, Palmerston North, 4442, New Zealand
| | - David Wheeler
- School of Fundamental Sciences, Massey University, Tennent Drive, Palmerston North, 4410, New Zealand
| | - Joanna Putterill
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Richard Macknight
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Tsanko Gechev
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 24 Tsar Assen str, 4000, Plovdiv, Bulgaria.,Center of Plant Systems Biology and Biotechnology (CPSBB), 139 Ruski Blvd, 4000, Plovdiv, Bulgaria
| | - Bernd Mueller-Roeber
- Department Molecular Biology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, Haus 20, 14476, Potsdam, Germany.,Center of Plant Systems Biology and Biotechnology (CPSBB), 139 Ruski Blvd, 4000, Plovdiv, Bulgaria.,Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Paul P Dijkwel
- School of Fundamental Sciences, Massey University, Tennent Drive, Palmerston North, 4410, New Zealand.
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108
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A fossil-calibrated phylogeny reveals the biogeographic history of the Cladrastis clade, an amphi-Pacific early-branching group in papilionoid legumes. Mol Phylogenet Evol 2019; 143:106673. [PMID: 31707137 DOI: 10.1016/j.ympev.2019.106673] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/05/2019] [Accepted: 11/05/2019] [Indexed: 11/24/2022]
Abstract
The early-branching Cladrastis clade of papilionoid legumes (Leguminosae, Papilionoideae) has an intriguing amphi-Pacific disjunct distribution in eastern Asia and temperate-tropical Americas. Here we used nuclear and three plastid regions to reconstruct the phylogenetic relationships and divergence times in the Cladrastis clade, as well as the evolution of morphological characters that might have been key in its biogeographic history. The ancestral character state estimation revealed that the most recent common ancestor of the Cladrastis clade was deciduous trees possessing compressed, winged fruits. The Cladrastis clade was inferred to have originated in the mid-latitude thermophilic forests of North America in the early Eocene, followed by the split between ancestors of wing-fruited Platyosprion and the non-wing-fruited group, and later the divergence of Cladrastis s.s. from the non-wing-fruited group in middle Eocene. Platyosprion and Cladrastis s.s. display an "out-of-North-America" biogeographic pattern and might have migrated to Asia via the Bering land bridge (BLB) or the North Atlantic land bridges (NALB) during middle to late Eocene. Our results, coupled with the relatively well documented fossil record for the clade, suggest that Platyosprion experienced an extinction event in North America caused by climatic cooling around the Eocene-Oligocene transition, which drove a major vegetation shift in western North America, in turn serving as a barrier for the vicariance of Pickeringia and Styphnolobium. The evolution of shrubby habit and sclerophyllous leaves in the former might be adaption to the chaparral vegetation in southwestern North America; the latter gained the trait of moniliform, succulent fruit. Styphnolobium further dispersed southward to tropical North America in the Oligocene, and eastward to Asia through BLB during middle Miocene. Subsequent sundering of BLB facilitated the vicariance of St. affine and St. japonicum.
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109
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Genome Improvement and Genetic Map Construction for Aethionema arabicum, the First Divergent Branch in the Brassicaceae Family. G3-GENES GENOMES GENETICS 2019; 9:3521-3530. [PMID: 31554715 PMCID: PMC6829135 DOI: 10.1534/g3.119.400657] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The genus Aethionema is a sister-group to the core-group of the Brassicaceae family that includes Arabidopsis thaliana and the Brassica crops. Thus, Aethionema is phylogenetically well-placed for the investigation and understanding of genome and trait evolution across the family. We aimed to improve the quality of the reference genome draft version of the annual species Aethionema arabicum. Second, we constructed the first Ae. arabicum genetic map. The improved reference genome and genetic map enabled the development of each other. We started with the initially published genome (version 2.5). PacBio and MinION sequencing together with genetic map v2.5 were incorporated to produce the new reference genome v3.0. The improved genome contains 203 MB of sequence, with approximately 94% of the assembly made up of called (non-gap) bases, assembled into 2,883 scaffolds (with only 6% of the genome made up of non-called bases (Ns)). The N50 (10.3 MB) represents an 80-fold increase over the initial genome release. We generated a Recombinant Inbred Line (RIL) population that was derived from two ecotypes: Cyprus and Turkey (the reference genotype. Using a Genotyping by Sequencing (GBS) approach, we generated a high-density genetic map with 749 (v2.5) and then 632 SNPs (v3.0) was generated. The genetic map and reference genome were integrated, thus greatly improving the scaffolding of the reference genome into 11 linkage groups. We show that long-read sequencing data and genetics are complementary, resulting in an improved genome assembly in Ae. arabicum. They will facilitate comparative genetic mapping work for the Brassicaceae family and are also valuable resources to investigate wide range of life history traits in Aethionema.
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Li M, Stragliati L, Bellini E, Ricci A, Saba A, Sanità di Toppi L, Varotto C. Evolution and functional differentiation of recently diverged phytochelatin synthase genes from Arundo donax L. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:5391-5405. [PMID: 31145784 PMCID: PMC6793451 DOI: 10.1093/jxb/erz266] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 05/24/2019] [Indexed: 05/15/2023]
Abstract
Phytochelatin synthases (PCSs) play pivotal roles in the detoxification of heavy metals and metalloids in plants; however, little information on the evolution of recently duplicated PCS genes in plant species is available. Here we characterize the evolution and functional differentiation of three PCS genes from the giant reed (Arundo donax L.), a biomass/bioenergy crop with remarkable resistance to cadmium and other heavy metals. Phylogenetic reconstruction with PCS genes from fully sequenced monocotyledonous genomes indicated that the three A. donax PCSs, namely AdPCS1-3, form a monophyletic clade. The AdPCS1-3 genes were expressed at low levels in many A. donax organs and displayed different levels of cadmium-responsive expression in roots. Overexpression of AdPCS1-3 in Arabidopsis thaliana and yeast reproduced the phenotype of functional PCS genes. Mass spectrometry analyses confirmed that AdPCS1-3 are all functional enzymes, but with significant differences in the amount of the phytochelatins synthesized. Moreover, heterogeneous evolutionary rates characterized the AdPCS1-3 genes, indicative of relaxed natural selection. These results highlight the elevated functional differentiation of A. donax PCS genes from both a transcriptional and an enzymatic point of view, providing evidence of the high evolvability of PCS genes and of plant responsiveness to heavy metal stress.
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Affiliation(s)
- Mingai Li
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige (TN) , Italy
| | - Luca Stragliati
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università degli studi di Parma, Parco Area delle Scienze, Parma, Italy
| | - Erika Bellini
- Dipartimento di Biologia, Università di Pisa, Pisa, Italy
| | - Ada Ricci
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università degli studi di Parma, Parco Area delle Scienze, Parma, Italy
| | - Alessandro Saba
- Dipartimento di Patologia Chirurgica, Medica, Molecolare e dell’Area Critica, Università di Pisa, Pisa, Italy
| | | | - Claudio Varotto
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige (TN) , Italy
- Correspondence: or
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Trichoderma harzianum favours the access of arbuscular mycorrhizal fungi to non-host Brassicaceae roots and increases plant productivity. Sci Rep 2019; 9:11650. [PMID: 31406170 PMCID: PMC6690897 DOI: 10.1038/s41598-019-48269-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 08/01/2019] [Indexed: 12/20/2022] Open
Abstract
The family Brassicaceae includes plants that are non-host for arbuscular mycorrhizal fungi (AMF) such as the model plant Arabidopsis thaliana (arabidopsis) and the economically important crop plant Brassica napus (rapeseed). It is well known that Trichoderma species have the ability to colonize the rhizosphere of Brassicaceae plants, promoting growth and development as well as stimulating systemic defenses. The aim of the present work is to ascertain that Brassicaceae plants increase productivity when AMF and Trichoderma are combinedly applied, and how such an effect can be ruled. This simultaneous application of a Trichoderma harzianum biocontrol strain and an AMF formulation produces a significant increase in the colonization by Trichoderma and the presence of AMF in arabidopsis and rapeseed roots, such colonization accompanied by improved productivity in both Brassicaceae species. Expression profiling of defense-related marker genes suggests that the phytohormone salicylic acid plays a key role in the modulation of the root colonization process when both fungi are jointly applied.
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Li MM, Wang DY, Zhang L, Kang MH, Lu ZQ, Zhu RB, Mao XX, Xi ZX, Tao M. Intergeneric Relationships within the Family Salicaceae s.l. based on Plastid Phylogenomics. Int J Mol Sci 2019; 20:ijms20153788. [PMID: 31382526 PMCID: PMC6696080 DOI: 10.3390/ijms20153788] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 07/26/2019] [Accepted: 07/31/2019] [Indexed: 12/16/2022] Open
Abstract
Many Salicaceae s.l. plants are recognized for their important role in the production of products such as wood, oils, and medicines, and as a model organism in life studies. However, the difference in plastid sequence, phylogenetic relationships, and lineage diversification of the family Salicaceae s.l. remain poorly understood. In this study, we compare 24 species representing 18 genera of the family. Simple sequence repeats (SSRs) are considered effective molecular markers for plant species identification and population genetics. Among them, a total of 1798 SSRs were identified, among which mononucleotide repeat was the most common with 1455 accounts representing 80.92% of the total. Most of the SSRs are located in the non-coding region. We also identified five other types of repeats, including 1750 tandems, 434 forward, 407 palindromic, 86 reverse, and 30 complementary repeats. The species in Salicaceae s.l. have a conserved plastid genome. Each plastome presented a typical quadripartite structure and varied in size due to the expansion and contraction of the inverted repeat (IR) boundary, lacking major structural variations, but we identified six divergence hotspot regions. We obtained phylogenetic relationships of 18 genera in Salicaceae s.l. and the 24 species formed a highly supported lineage. Casearia was identified as the basal clade. The divergence time between Salicaceae s.l. and the outgroup was estimated as ~93 Mya; Salix, and Populus diverged around 34 Mya, consistent with the previously reported time. Our research will contribute to a better understanding of the phylogenetic relationships among the members of the Salicaceae s.l.
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Affiliation(s)
- Meng-Meng Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - De-Yan Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Lei Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Ming-Hui Kang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Zhi-Qiang Lu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China
| | - Ren-Bin Zhu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China
| | - Xing-Xing Mao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Zhen-Xiang Xi
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Ma Tao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China.
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Hloušková P, Mandáková T, Pouch M, Trávníček P, Lysak MA. The large genome size variation in the Hesperis clade was shaped by the prevalent proliferation of DNA repeats and rarer genome downsizing. ANNALS OF BOTANY 2019; 124:103-120. [PMID: 31220201 PMCID: PMC6676390 DOI: 10.1093/aob/mcz036] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 02/28/2019] [Indexed: 05/13/2023]
Abstract
BACKGROUND AND AIMS Most crucifer species (Brassicaceae) have small nuclear genomes (mean 1C-value 617 Mb). The species with the largest genomes occur within the monophyletic Hesperis clade (Mandáková et al., Plant Physiology174: 2062-2071; also known as Clade E or Lineage III). Whereas most chromosome numbers in the clade are 6 or 7, monoploid genome sizes vary 16-fold (256-4264 Mb). To get an insight into genome size evolution in the Hesperis clade (~350 species in ~48 genera), we aimed to identify, quantify and localize in situ the repeats from which these genomes are built. We analysed nuclear repeatomes in seven species, covering the phylogenetic and genome size breadth of the clade, by low-pass whole-genome sequencing. METHODS Genome size was estimated by flow cytometry. Genomic DNA was sequenced on an Illumina sequencer and DNA repeats were identified and quantified using RepeatExplorer; the most abundant repeats were localized on chromosomes by fluorescence in situ hybridization. To evaluate the feasibility of bacterial artificial chromosome (BAC)-based comparative chromosome painting in Hesperis-clade species, BACs of arabidopsis were used as painting probes. KEY RESULTS Most biennial and perennial species of the Hesperis clade possess unusually large nuclear genomes due to the proliferation of long terminal repeat retrotransposons. The prevalent genome expansion was rarely, but repeatedly, counteracted by purging of transposable elements in ephemeral and annual species. CONCLUSIONS The most common ancestor of the Hesperis clade has experienced genome upsizing due to transposable element amplification. Further genome size increases, dominating diversification of all Hesperis-clade tribes, contrast with the overall stability of chromosome numbers. In some subclades and species genome downsizing occurred, presumably as an adaptive transition to an annual life cycle. The amplification versus purging of transposable elements and tandem repeats impacted the chromosomal architecture of the Hesperis-clade species.
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Affiliation(s)
- Petra Hloušková
- CEITEC - Central European Institute of Technology, and Faculty of Science, Masaryk University, Kamenice, Brno, Czech Republic
| | - Terezie Mandáková
- CEITEC - Central European Institute of Technology, and Faculty of Science, Masaryk University, Kamenice, Brno, Czech Republic
| | - Milan Pouch
- CEITEC - Central European Institute of Technology, and Faculty of Science, Masaryk University, Kamenice, Brno, Czech Republic
| | - Pavel Trávníček
- Institute of Botany, Czech Academy of Sciences, Zámek 1, 252 43 Průhonice, Czech Republic
| | - Martin A Lysak
- CEITEC - Central European Institute of Technology, and Faculty of Science, Masaryk University, Kamenice, Brno, Czech Republic
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Kiefer C, Willing EM, Jiao WB, Sun H, Piednoël M, Hümann U, Hartwig B, Koch MA, Schneeberger K. Interspecies association mapping links reduced CG to TG substitution rates to the loss of gene-body methylation. NATURE PLANTS 2019; 5:846-855. [PMID: 31358959 DOI: 10.1038/s41477-019-0486-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 06/25/2019] [Indexed: 05/18/2023]
Abstract
Comparative genomics can unravel the genetic basis of species differences; however, successful reports on quantitative traits are still scarce. Here we present genome assemblies of 31 so-far unassembled Brassicaceae plant species and combine them with 16 previously published assemblies to establish the Brassicaceae Diversity Panel. Using a new interspecies association strategy for quantitative traits, we found a so-far unknown association between the unexpectedly high variation in CG to TG substitution rates in genes and the absence of CHROMOMETHYLASE3 (CMT3) orthologues. Low substitution rates were associated with the loss of CMT3, while species with conserved CMT3 orthologues showed high substitution rates. Species without CMT3 also lacked gene-body methylation (gbM), suggesting an evolutionary trade-off between the unknown function of gbM and low substitution rates in Brassicaceae, possibly due to low mutability of non-methylated cytosines.
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Affiliation(s)
- Christiane Kiefer
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Eva-Maria Willing
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- NEO New Oncology, Cologne, Germany
| | - Wen-Biao Jiao
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Hequan Sun
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Mathieu Piednoël
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Ulrike Hümann
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Benjamin Hartwig
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- NEO New Oncology, Cologne, Germany
| | - Marcus A Koch
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Korbinian Schneeberger
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
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115
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Wang B, Mojica JP, Perera N, Lee CR, Lovell JT, Sharma A, Adam C, Lipzen A, Barry K, Rokhsar DS, Schmutz J, Mitchell-Olds T. Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta. Genome Biol 2019; 20:126. [PMID: 31227026 PMCID: PMC6587263 DOI: 10.1186/s13059-019-1729-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 06/04/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Genomic variation is widespread, and both neutral and selective processes can generate similar patterns in the genome. These processes are not mutually exclusive, so it is difficult to infer the evolutionary mechanisms that govern population and species divergence. Boechera stricta is a perennial relative of Arabidopsis thaliana native to largely undisturbed habitats with two geographic and ecologically divergent subspecies. Here, we delineate the evolutionary processes driving the genetic diversity and population differentiation in this species. RESULTS Using whole-genome re-sequencing data from 517 B. stricta accessions, we identify four genetic groups that diverged around 30-180 thousand years ago, with long-term small effective population sizes and recent population expansion after the Last Glacial Maximum. We find three genomic regions with elevated nucleotide diversity, totaling about 10% of the genome. These three regions of elevated nucleotide diversity show excess of intermediate-frequency alleles, higher absolute divergence (dXY), and lower relative divergence (FST) than genomic background, and significant enrichment in immune-related genes, reflecting long-term balancing selection. Scattered across the genome, we also find regions with both high FST and dXY among the groups, termed FST-islands. Population genetic signatures indicate that FST-islands with elevated divergence, which have experienced directional selection, are derived from divergent sorting of ancient polymorphisms. CONCLUSIONS Our results suggest that long-term balancing selection on disease resistance genes may have maintained ancestral haplotypes across different geographical lineages, and unequal sorting of balanced polymorphisms may have generated genomic regions with elevated divergence. This study highlights the importance of ancestral balanced polymorphisms as crucial components of genome-wide variation.
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Affiliation(s)
- Baosheng Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- Department of Biology, Duke University, Box 90338, Durham, NC, 27708, USA.
| | - Julius P Mojica
- Department of Biology, Duke University, Box 90338, Durham, NC, 27708, USA
| | - Nadeesha Perera
- Department of Biology, Duke University, Box 90338, Durham, NC, 27708, USA
| | - Cheng-Ruei Lee
- Institute of Ecology and Evolutionary Biology and Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan, ROC
| | - John T Lovell
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Aditi Sharma
- Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Catherine Adam
- Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Anna Lipzen
- Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Daniel S Rokhsar
- Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
- Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
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Hoffmeier A, Gramzow L, Bhide AS, Kottenhagen N, Greifenstein A, Schubert O, Mummenhoff K, Becker A, Theißen G. A Dead Gene Walking: Convergent Degeneration of a Clade of MADS-Box Genes in Crucifers. Mol Biol Evol 2019; 35:2618-2638. [PMID: 30053121 DOI: 10.1093/molbev/msy142] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Genes are "born," and eventually they "die." These processes shape the phenotypic evolution of organisms and are hence of great biological interest. If genes die in plants, they generally do so quite rapidly. Here, we describe the fate of GOA-like genes that evolve in a dramatically different manner. GOA-like genes belong to the subfamily of Bsister genes of MIKC-type MADS-box genes. Typical MIKC-type genes encode conserved transcription factors controlling plant development. We show that ABS-like genes, a clade of Bsister genes, are indeed highly conserved in crucifers (Brassicaceae) maintaining the ancestral function of Bsister genes in ovule and seed development. In contrast, their closest paralogs, the GOA-like genes, have been undergoing convergent gene death in Brassicaceae. Intriguingly, erosion of GOA-like genes occurred after millions of years of coexistence with ABS-like genes. We thus describe Delayed Convergent Asymmetric Degeneration, a so far neglected but possibly frequent pattern of duplicate gene evolution that does not fit classical scenarios. Delayed Convergent Asymmetric Degeneration of GOA-like genes may have been initiated by a reduction in the expression of an ancestral GOA-like gene in the stem group of Brassicaceae and driven by dosage subfunctionalization. Our findings have profound implications for gene annotations in genomics, interpreting patterns of gene evolution and using genes in phylogeny reconstructions of species.
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Affiliation(s)
- Andrea Hoffmeier
- Genetics, Matthias Schleiden Institute, Friedrich-Schiller-University Jena, Jena, Germany
| | - Lydia Gramzow
- Genetics, Matthias Schleiden Institute, Friedrich-Schiller-University Jena, Jena, Germany
| | - Amey S Bhide
- Plant Developmental Biology Group, Institute of Botany, Justus-Liebig-University Giessen, Giessen, Germany
| | - Nina Kottenhagen
- Genetics, Matthias Schleiden Institute, Friedrich-Schiller-University Jena, Jena, Germany
| | - Andreas Greifenstein
- Genetics, Matthias Schleiden Institute, Friedrich-Schiller-University Jena, Jena, Germany
| | - Olesia Schubert
- Plant Developmental Biology Group, Institute of Botany, Justus-Liebig-University Giessen, Giessen, Germany
| | - Klaus Mummenhoff
- Department of Biology/Botany, University of Osnabrück, Osnabrück, Germany
| | - Annette Becker
- Plant Developmental Biology Group, Institute of Botany, Justus-Liebig-University Giessen, Giessen, Germany
| | - Günter Theißen
- Genetics, Matthias Schleiden Institute, Friedrich-Schiller-University Jena, Jena, Germany
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Méndez-Vigo B, Ausín I, Zhu W, Mollá-Morales A, Balasubramanian S, Alonso-Blanco C. Genetic Interactions and Molecular Evolution of the Duplicated Genes ICARUS2 and ICARUS1 Help Arabidopsis Plants Adapt to Different Ambient Temperatures. THE PLANT CELL 2019; 31:1222-1237. [PMID: 30992321 PMCID: PMC6588312 DOI: 10.1105/tpc.18.00938] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 03/29/2019] [Accepted: 04/12/2019] [Indexed: 05/30/2023]
Abstract
Understanding how plants adapt to ambient temperatures has become a major challenge prompted by global climate change. This has led to the identification of several genes regulating the thermal plasticity of plant growth and flowering time. However, the mechanisms accounting for the natural variation and evolution of such developmental plasticity remain mostly unknown. In this study, we determined that natural variation at ICARUS2 (ICA2), which interacts genetically with its homolog ICA1, alters growth and flowering time plasticity in relation to temperature in Arabidopsis (Arabidopsis thaliana). Transgenic analyses demonstrated multiple functional effects for ICA2 and supported the notion that structural polymorphisms in ICA2 likely underlie its natural variation. Two major ICA2 haplogroups carrying distinct functionally active alleles showed high frequency, strong geographic structure, and significant associations with climatic variables related to annual and daily fluctuations in temperature. Genome analyses across the plant phylogeny indicated that the prevalent plant ICA genes encoding two tRNAHis guanylyl transferase 1 units evolved ∼120 million years ago during the early divergence of mono- and dicotyledonous clades. In addition, ICA1/ICA2 duplication occurred specifically in the Camelineae tribe (Brassicaceae). Thus, ICA2 appears to be ubiquitous across plant evolution and likely contributes to climate adaptation through modifications of thermal developmental plasticity in Arabidopsis.
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Affiliation(s)
- Belén Méndez-Vigo
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049, Madrid, Spain
| | - Israel Ausín
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049, Madrid, Spain
| | - Wangsheng Zhu
- School of Biological Sciences, Monash University, Victoria 3800, Australia
| | - Almudena Mollá-Morales
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049, Madrid, Spain
| | | | - Carlos Alonso-Blanco
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049, Madrid, Spain
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Zhang Z, Li Y, Luo Z, Kong S, Zhao Y, Zhang C, Zhang W, Yuan H, Cheng L. Expansion and Functional Divergence of Inositol Polyphosphate 5-Phosphatases in Angiosperms. Genes (Basel) 2019; 10:genes10050393. [PMID: 31121965 PMCID: PMC6562803 DOI: 10.3390/genes10050393] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/15/2019] [Accepted: 05/17/2019] [Indexed: 11/16/2022] Open
Abstract
Inositol polyphosphate 5-phosphatase (5PTase), a key enzyme that hydrolyzes the 5` position of the inositol ring, has essential functions in growth, development, and stress responses in plants, yeasts, and animals. However, the evolutionary history and patterns of 5PTases have not been examined systematically. Here, we report a comprehensive molecular evolutionary analysis of the 5PTase gene family and define four groups. These four groups are different from former classifications, which were based on in vitro substrate specificity. Most orthologous groups appear to be conserved as single or low-copy genes in all lineages in Groups II-IV, whereas 5PTase genes in Group I underwent several duplication events in angiosperm, resulting in multiple gene copies. Whole-genome duplication (WGD) was the main mechanism for 5PTase duplications in angiosperm. Plant 5PTases have more members than that of animals, and most plant 5PTase genes appear to have evolved under strong purifying selection. The paralogs have diverged in substrate specificity and expression pattern, showing evidence of selection pressure. Meanwhile, the increase in 5PTases and divergences in sequence, expression, and substrate might have contributed to the divergent functions of 5PTase genes, allowing the angiosperms to successfully adapt to a great number of ecological niches.
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Affiliation(s)
- Zaibao Zhang
- Henan Key Laboratory of Tea Plant Biology, Xinyang Normal University, Xinyang 464000, Henan, China.
- College of Life Science, Xinyang Normal University, Xinyang 464000, Henan, China.
| | - Yuting Li
- College of Life Science, Xinyang Normal University, Xinyang 464000, Henan, China.
| | - Zhaoyi Luo
- College of Life Science, Xinyang Normal University, Xinyang 464000, Henan, China.
| | - Shuwei Kong
- College of Life Science, Xinyang Normal University, Xinyang 464000, Henan, China.
| | - Yilin Zhao
- College of Life Science, Xinyang Normal University, Xinyang 464000, Henan, China.
| | - Chi Zhang
- College of Life Science, Xinyang Normal University, Xinyang 464000, Henan, China.
| | - Wei Zhang
- College of Life Science, Xinyang Normal University, Xinyang 464000, Henan, China.
| | - Hongyu Yuan
- Henan Key Laboratory of Tea Plant Biology, Xinyang Normal University, Xinyang 464000, Henan, China.
- College of Life Science, Xinyang Normal University, Xinyang 464000, Henan, China.
| | - Lin Cheng
- College of Life Science, Xinyang Normal University, Xinyang 464000, Henan, China.
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Nikolov LA. Brassicaceae flowers: diversity amid uniformity. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2623-2635. [PMID: 30824938 DOI: 10.1093/jxb/erz079] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 02/12/2019] [Accepted: 02/25/2019] [Indexed: 06/09/2023]
Abstract
The mustard family Brassicaceae, which includes the model plant Arabidopsis thaliana, exhibits morphological stasis and significant uniformity of floral plan. Nonetheless, there is untapped diversity in almost every aspect of floral morphology in the family that lends itself to comparative study, including organ number, shape, form, and color. Studies on the genetic basis of morphological diversity, enabled by extensive genetic tools and genomic resources and the close phylogenetic distance among mustards, have revealed a mosaic of conservation and divergence in numerous floral traits. Here I review the morphological diversity of the flowers of Brassicaceae and discuss studies addressing the underlying genetic and developmental mechanisms shaping floral diversity. To put flowers in the context of the floral display, I describe diversity in inflorescence morphology and the variation that exists in the structures preceding the floral organs. Reconstructing the floral morphospace in Brassicaceae coupled with next-generation sequencing data and unbiased approaches to interrogate gene function in species throughout the mustard phylogeny offers promising ways to understand how developmental mechanisms originate and diversify.
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Affiliation(s)
- Lachezar A Nikolov
- Department of Molecular, Cell and Developmental Biology, Molecular Biology Institute, University of California, Los Angeles, CA, USA
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Li HT, Yi TS, Gao LM, Ma PF, Zhang T, Yang JB, Gitzendanner MA, Fritsch PW, Cai J, Luo Y, Wang H, van der Bank M, Zhang SD, Wang QF, Wang J, Zhang ZR, Fu CN, Yang J, Hollingsworth PM, Chase MW, Soltis DE, Soltis PS, Li DZ. Origin of angiosperms and the puzzle of the Jurassic gap. NATURE PLANTS 2019; 5:461-470. [PMID: 31061536 DOI: 10.1038/s41477-019-0421-0] [Citation(s) in RCA: 348] [Impact Index Per Article: 69.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Accepted: 04/02/2019] [Indexed: 05/19/2023]
Abstract
Angiosperms are by far the most species-rich clade of land plants, but their origin and early evolutionary history remain poorly understood. We reconstructed angiosperm phylogeny based on 80 genes from 2,881 plastid genomes representing 85% of extant families and all orders. With a well-resolved plastid tree and 62 fossil calibrations, we dated the origin of the crown angiosperms to the Upper Triassic, with major angiosperm radiations occurring in the Jurassic and Lower Cretaceous. This estimated crown age is substantially earlier than that of unequivocal angiosperm fossils, and the difference is here termed the 'Jurassic angiosperm gap'. Our time-calibrated plastid phylogenomic tree provides a highly relevant framework for future comparative studies of flowering plant evolution.
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Affiliation(s)
- Hong-Tao Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Peng-Fei Ma
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Ting Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Matthew A Gitzendanner
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | | | - Jie Cai
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Yang Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Hong Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Michelle van der Bank
- Department of Botany & Plant Biotechnology, University of Johannesburg, Johannesburg, South Africa
| | - Shu-Dong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Qing-Feng Wang
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Jian Wang
- Queensland Herbarium, Department of Environment and Science, Brisbane Botanic Gardens, Toowong, Queensland, Australia
| | - Zhi-Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Chao-Nan Fu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Jing Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | | | - Mark W Chase
- Royal Botanic Gardens, Kew, UK
- Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, Australia
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
- Genetics Institute, University of Florida, Gainesville, FL, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA.
- Genetics Institute, University of Florida, Gainesville, FL, USA.
- Biodiversity Institute, University of Florida, Gainesville, FL, USA.
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.
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Nikolov LA, Shushkov P, Nevado B, Gan X, Al-Shehbaz IA, Filatov D, Bailey CD, Tsiantis M. Resolving the backbone of the Brassicaceae phylogeny for investigating trait diversity. THE NEW PHYTOLOGIST 2019; 222:1638-1651. [PMID: 30735246 DOI: 10.1111/nph.15732] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 01/10/2019] [Indexed: 05/03/2023]
Abstract
The Brassicaceae family comprises c. 4000 species including economically important crops and the model plant Arabidopsis thaliana. Despite their importance, the relationships among major lineages in the family remain unresolved, hampering comparative research. Here, we inferred a Brassicaceae phylogeny using newly generated targeted enrichment sequence data of 1827 exons (> 940 000 bases) representing 63 species, as well as sequenced genome data of 16 species, together representing 50 of the 52 currently recognized Brassicaceae tribes. A third of the samples were derived from herbarium material, facilitating broad taxonomic coverage of the family. Six major clades formed successive sister groups to the rest of Brassicaceae. We also recovered strong support for novel relationships among tribes, and resolved the position of 16 taxa previously not assigned to a tribe. The broad utility of these phylogenetic results is illustrated through a comparative investigation of genome-wide expression signatures that distinguish simple from complex leaves in Brassicaceae. Our study provides an easily extendable dataset for further advances in Brassicaceae systematics and a timely higher-level phylogenetic framework for a wide range of comparative studies of multiple traits in an intensively investigated group of plants.
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Affiliation(s)
- Lachezar A Nikolov
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
| | - Philip Shushkov
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Bruno Nevado
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Xiangchao Gan
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
| | - Ihsan A Al-Shehbaz
- Missouri Botanical Garden, 4344 Shaw Boulevard, St Louis, MO, 63110, USA
| | - Dmitry Filatov
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - C Donovan Bailey
- Department of Biology, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Miltos Tsiantis
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
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Brukhin V, Osadtchiy JV, Florez-Rueda AM, Smetanin D, Bakin E, Nobre MS, Grossniklaus U. The Boechera Genus as a Resource for Apomixis Research. FRONTIERS IN PLANT SCIENCE 2019; 10:392. [PMID: 31001306 PMCID: PMC6454215 DOI: 10.3389/fpls.2019.00392] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 03/14/2019] [Indexed: 05/03/2023]
Abstract
The genera Boechera (A. Löve et D. Löve) and Arabidopsis, the latter containing the model plant Arabidopsis thaliana, belong to the same clade within the Brassicaceae family. Boechera is the only among the more than 370 genera in the Brassicaceae where apomixis is well documented. Apomixis refers to the asexual reproduction through seed, and a better understanding of the underlying mechanisms has great potential for applications in agriculture. The Boechera genus currently includes 110 species (of which 38 are reported to be triploid and thus apomictic), which are distributed mostly in the North America. The apomictic lineages of Boechera occur at both the diploid and triploid level and show signs of a hybridogenic origin, resulting in a modification of their chromosome structure, as reflected by alloploidy, aneuploidy, substitutions of homeologous chromosomes, and the presence of aberrant chromosomes. In this review, we discuss the advantages of the Boechera genus to study apomixis, consider its modes of reproduction as well as the inheritance and possible mechanisms controlling apomixis. We also consider population genetic aspects and a possible role of hybridization at the origin of apomixis in Boechera. The molecular tools available to study Boechera, such as transformation techniques, laser capture microdissection, analysis of transcriptomes etc. are also discussed. We survey available genome assemblies of Boechera spp. and point out the challenges to assemble the highly heterozygous genomes of apomictic species. Due to these challenges, we argue for the application of an alternative reference-free method for the comparative analysis of such genomes, provide an overview of genomic sequencing data in the genus Boechera suitable for such analysis, and provide examples of its application.
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Affiliation(s)
- Vladimir Brukhin
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, Saint Petersburg, Russia
- Department of Plant Embryology and Reproductive Biology, Komarov Botanical Institute RAS, Saint Petersburg, Russia
| | - Jaroslaw V. Osadtchiy
- Department of Plant Embryology and Reproductive Biology, Komarov Botanical Institute RAS, Saint Petersburg, Russia
| | - Ana Marcela Florez-Rueda
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Dmitry Smetanin
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Evgeny Bakin
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, Saint Petersburg, Russia
- Bioinformatics Institute, Saint Petersburg, Russia
| | - Margarida Sofia Nobre
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
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Genome of Crucihimalaya himalaica, a close relative of Arabidopsis, shows ecological adaptation to high altitude. Proc Natl Acad Sci U S A 2019; 116:7137-7146. [PMID: 30894495 PMCID: PMC6452661 DOI: 10.1073/pnas.1817580116] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Crucihimalaya himalaica, a close relative of Arabidopsis and Capsella, grows on the Qinghai-Tibet Plateau (QTP) about 4,000 m above sea level and represents an attractive model system for studying speciation and ecological adaptation in extreme environments. We assembled a draft genome sequence of 234.72 Mb encoding 27,019 genes and investigated its origin and adaptive evolutionary mechanisms. Phylogenomic analyses based on 4,586 single-copy genes revealed that C. himalaica is most closely related to Capsella (estimated divergence 8.8 to 12.2 Mya), whereas both species form a sister clade to Arabidopsis thaliana and Arabidopsis lyrata, from which they diverged between 12.7 and 17.2 Mya. LTR retrotransposons in C. himalaica proliferated shortly after the dramatic uplift and climatic change of the Himalayas from the Late Pliocene to Pleistocene. Compared with closely related species, C. himalaica showed significant contraction and pseudogenization in gene families associated with disease resistance and also significant expansion in gene families associated with ubiquitin-mediated proteolysis and DNA repair. We identified hundreds of genes involved in DNA repair, ubiquitin-mediated proteolysis, and reproductive processes with signs of positive selection. Gene families showing dramatic changes in size and genes showing signs of positive selection are likely candidates for C. himalaica's adaptation to intense radiation, low temperature, and pathogen-depauperate environments in the QTP. Loss of function at the S-locus, the reason for the transition to self-fertilization of C. himalaica, might have enabled its QTP occupation. Overall, the genome sequence of C. himalaica provides insights into the mechanisms of plant adaptation to extreme environments.
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Wang L, Ma H, Lin J. Angiosperm-Wide and Family-Level Analyses of AP2/ ERF Genes Reveal Differential Retention and Sequence Divergence After Whole-Genome Duplication. FRONTIERS IN PLANT SCIENCE 2019; 10:196. [PMID: 30863419 PMCID: PMC6399210 DOI: 10.3389/fpls.2019.00196] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 02/05/2019] [Indexed: 05/21/2023]
Abstract
Plants are immobile and often face stressful environmental conditions, prompting the evolution of genes regulating environmental responses. Such evolution is achieved largely through gene duplication and subsequent divergence. One of the most important gene families involved in regulating plant environmental responses and development is the AP2/ERF superfamily; however, the evolutionary history of these genes is unclear across angiosperms and in major angiosperm families adapted to various ecological niches. Specifically, the impact on gene copy number of whole-genome duplication events occurring around the time of the origins of several plant families is unknown. Here, we present the first angiosperm-wide comparative study of AP2/ERF genes, identifying 75 Angiosperm OrthoGroups (AOGs), each derived from an ancestral angiosperm gene copy. Among these AOGs, 21 retain duplicates with increased copy number in many angiosperm lineages, while the remaining 54 AOGs tend to maintain low copy number. Further analyses of multiple species in the Brassicaceae family indicated that family-specific duplicates experienced differential selective pressures in coding regions, with some paralogs showing signs of positive selection. Further, cis regulatory elements also exhibit extensive divergence between duplicates in Arabidopsis. Moreover, comparison of expression levels suggested that AP2/ERF genes with frequently retained duplicates are enriched for broad expression patterns, offering increased opportunities for functional diversification via changes in expression patterns, and providing a mechanism for repeated duplicate retention in some AOGs. Our results represent the most comprehensive evolutionary history of the AP2/ERF gene family, and support the hypothesis that AP2/ERF genes with broader expression patterns are more likely to be retained as duplicates than those with narrower expression profiles, which could lead to a higher chance of duplicate gene subfunctionalization. The greater tendency of some AOGs to retain duplicates, allowing expression and functional divergence, may facilitate the evolution of complex signaling networks in response to new environmental conditions.
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Affiliation(s)
- Linbo Wang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, School of Life Sciences, Fudan University, Shanghai, China
| | - Hong Ma
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, School of Life Sciences, Fudan University, Shanghai, China
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States
| | - Juan Lin
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, School of Life Sciences, Fudan University, Shanghai, China
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Phylogenomics recovers monophyly and early Tertiary diversification of Dipteronia (Sapindaceae). Mol Phylogenet Evol 2019; 130:9-17. [DOI: 10.1016/j.ympev.2018.09.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/16/2018] [Accepted: 09/19/2018] [Indexed: 11/23/2022]
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Massatti R, Prendeville HR, Larson S, Richardson BA, Waldron B, Kilkenny FF. Population history provides foundational knowledge for utilizing and developing native plant restoration materials. Evol Appl 2018; 11:2025-2039. [PMID: 30459846 PMCID: PMC6231468 DOI: 10.1111/eva.12704] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 08/21/2018] [Accepted: 08/26/2018] [Indexed: 01/14/2023] Open
Abstract
A species' population structure and history are critical pieces of information that can help guide the use of available native plant materials in restoration treatments and decide what new native plant materials should be developed to meet future restoration needs. In the western United States, Pseudoroegneria spicata (bluebunch wheatgrass; Poaceae) is an important component of grassland and shrubland plant communities and commonly used for restoration due to its drought resistance and competitiveness with exotic weeds. We used next-generation sequencing data to investigate the processes that shaped P. spicata's geographic pattern of genetic variation across the Intermountain West. Pseudoroegneria spicata's genetic diversity is partitioned into populations that likely differentiated since the Last Glacial Maximum. Adjacent populations display varying magnitudes of historical gene flow, with migration rates ranging from multiple migrants per generation to multiple generations per migrant. When considering the commercial germplasm sources available for restoration, genetic identities remain representative of the wildland localities from which germplasm sources were originally developed, and they maintain high levels of heterozygosity and nucleotide diversity. However, the commercial germplasm sources represent a small fraction of the overall genetic diversity of P. spicata in the Intermountain West. Given the low migration rates and long divergence times between some pairs of P. spicata populations, using commercial germplasm sources could facilitate undesirable restoration outcomes when used in certain geographic areas, even if the environment in which the commercial materials thrive is similar to that of the restoration site. As such, population structure and history can be used to provide guidance on what geographic areas may need additional native plant materials so that restoration efforts support species and community resilience and improve outcomes.
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Affiliation(s)
- Rob Massatti
- Southwest Biological Science CenterU.S. Geological SurveyFlagstaffArizona
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Hajiboland R, Bahrami-Rad S, Akhani H, Poschenrieder C. Salt tolerance mechanisms in three Irano-Turanian Brassicaceae halophytes relatives of Arabidopsis thaliana. JOURNAL OF PLANT RESEARCH 2018; 131:1029-1046. [PMID: 29967980 DOI: 10.1007/s10265-018-1053-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 06/15/2018] [Indexed: 06/08/2023]
Abstract
Salt tolerance mechanisms were studied in three Irano-Turanian halophytic species from the Brassicaceae (Lepidium latifolium, L. perfoliatum and Schrenkiella parvula) and compared with the glycophyte Arabidopsis thaliana. According to seed germination under salt stress, L. perfoliatum was the most tolerant species, while L. latifolium and S. parvula were rather susceptible. Contrastingly, based on biomass production L. perfoliatum was more salt sensitive than the other two species. In S. parvula biomass was increased up to 2.8-fold by 100 mM NaCl; no significant growth reduction was observed even when exposed to 400 mM NaCl. Stable activities of antioxidative defense enzymes, nil or negligible accumulation of superoxide anion and hydrogen peroxide, as well as stable membrane integrity in the three halophytes revealed that no oxidative stress occurred in these tolerant species under salt stress. Proline levels increased in response to salt treatment. However, it contributed only by 0.3‒2.0% to the total osmolyte concentration in the three halophytes (at 400 mM NaCl) and even less (0.04%) in the glycophyte, A. thaliana (at 100 mM NaCl). Soluble sugars in all three halophytes and free amino acids pool in S. parvula decreased under salt treatment in contrast to the glycophyte, A. thaliana. The contribution of organic osmolytes to the total osmolyte pool increased by salt treatment in the roots, while decreased in halophyte and glycophyte, A. thaliana leaves. Interestingly, this reduction was compensated by a higher relative contribution of K in the leaves of the halophytes, but of Na in A. thaliana. Taken together, biomass data and biochemical indicators show that S. parvula is more salt tolerant than the two Lepidium species. Our data indicate that L. latifolium, as a perennial halophyte with a large biomass, is highly suitable for both restoration of saline habitats and saline agriculture.
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Affiliation(s)
- Roghieh Hajiboland
- Department of Plant Science, University of Tabriz, Tabriz, 51666-16471, Iran.
| | - Sara Bahrami-Rad
- Department of Plant Science, University of Tabriz, Tabriz, 51666-16471, Iran
| | - Hossein Akhani
- Halophytes and C4 Plants Research Laboratory, Department of Plant Science, School of Biology, University of Tehran, P.O. Box 14155-6455, Tehran, Iran
| | - Charlotte Poschenrieder
- Plant Physiology Laboratory, Bioscience Faculty, Universidad Autónoma de Barcelona, 08193, Bellaterra, Spain
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Mandáková T, Guo X, Özüdoğru B, Mummenhoff K, Lysak MA. Hybridization-facilitated genome merger and repeated chromosome fusion after 8 million years. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:748-760. [PMID: 30101476 DOI: 10.1111/tpj.14065] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 08/01/2018] [Accepted: 08/06/2018] [Indexed: 05/22/2023]
Abstract
The small genus Ricotia (nine species, Brassicaceae) is confined to the eastern Mediterranean. By comparative chromosome painting and a dated multi-gene chloroplast phylogeny, we reconstructed the origin and subsequent evolution of Ricotia. The ancestral Ricotia genome originated through hybridization between two older genomes with n = 7 and n = 8 chromosomes, respectively, on the Turkish mainland during the Early Miocene (c. 17.8 million years ago, Ma). Since then, the allotetraploid (n = 15) genome has been altered by two independent descending dysploidies (DD) to n = 14 in Ricotia aucheri and the Tenuifolia clade (2 spp.). By the Late Miocene (c. 10 Ma), the latter clade started to evolve in the most diverse Ricotia core clade (6 spp.), the process preceded by a DD event to n = 13. It is noteworthy that this dysploidy was mediated by a unique chromosomal rearrangement, merging together the same two chromosomes as were merged during the origin of a fusion chromosome within the paternal n = 7 genome c. 20 Ma. This shows that within a time period of c. 8 Myr genome evolution can repeat itself and that structurally very similar chromosomes may originate repeatedly from the same ancestral chromosomes by different pathways (end-to-end translocation versus nested chromosome insertion).
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Affiliation(s)
- Terezie Mandáková
- CEITEC - Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic
| | - Xinyi Guo
- CEITEC - Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic
| | - Barış Özüdoğru
- Department of Biology, Faculty of Science, Hacettepe University, 06800, Beytepe, Ankara, Turkey
| | - Klaus Mummenhoff
- Department of Biology/Botany, University of Osnabrück, Barbarastraße 11, 49076, Osnabrück, Germany
| | - Martin A Lysak
- CEITEC - Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic
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Yang CK, Huang BH, Ho SW, Huang MY, Wang JC, Gao J, Liao PC. Molecular genetic and biochemical evidence for adaptive evolution of leaf abaxial epicuticular wax crystals in the genus Lithocarpus (Fagaceae). BMC PLANT BIOLOGY 2018; 18:196. [PMID: 30223774 PMCID: PMC6142356 DOI: 10.1186/s12870-018-1420-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 09/07/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Leaf epicuticular wax is an important functional trait for physiological regulation and pathogen defense. This study tests how selective pressure may have forced the trait of leaf abaxial epicuticular wax crystals (LAEWC) and whether the presence/absence of LAEWC is associated with other ecophysiological traits. Scanning Electron Microscopy was conducted to check for LAEWC in different Lithocarpus species. Four wax biosynthesis related genes, including two wax backbone genes ECERIFERUM 1 (CER1) and CER3, one regulatory gene CER7 and one transport gene CER5, were cloned and sequenced. Ecophysiological measurements of secondary metabolites, photosynthesis, water usage efficiency, and nutrition indices were also determined. Evolutionary hypotheses of leaf wax character transition associated with the evolution of those ecophysiological traits as well as species evolution were tested by maximum likelihood. RESULTS Eight of 14 studied Lithocarpus species have obvious LAEWC appearing with various types of trichomes. Measurements of ecophysiological traits show no direct correlations with the presence/absence of LAEWC. However, the content of phenolic acids is significantly associated with the gene evolution of the wax biosynthetic backbone gene CER1, which was detected to be positively selected when LAEWC was gained during the late-Miocene-to-Pliocene period. CONCLUSIONS Changes of landmass and vegetation type accelerated the diversification of tropical and subtropical forest trees and certain herbivores during the late Miocene. As phenolic acids were long thought to be associated with defense against herbivories, co-occurrence of LAEWC and phenolic acids may suggest that LAEWC might be an adaptive defensive mechanism in Lithocarpus.
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Affiliation(s)
- Chih-Kai Yang
- School of Life Science, National Taiwan Normal University, Postal address: No. 88, Tingchow Rd. Sect. 4, Taipei, 11677 Taiwan
- The Experimental Forest, College of Bio-Resources and Agriculture, National Taiwan University, Taipei, Nantou 55750 Taiwan
| | - Bing-Hong Huang
- School of Life Science, National Taiwan Normal University, Postal address: No. 88, Tingchow Rd. Sect. 4, Taipei, 11677 Taiwan
| | - Shao-Wei Ho
- School of Life Science, National Taiwan Normal University, Postal address: No. 88, Tingchow Rd. Sect. 4, Taipei, 11677 Taiwan
| | - Meng-Yuan Huang
- Department of Horticulture and Biotechnology, Chinese Culture University, Taipei, 11119 Taiwan
| | - Jenn-Che Wang
- School of Life Science, National Taiwan Normal University, Postal address: No. 88, Tingchow Rd. Sect. 4, Taipei, 11677 Taiwan
| | - Jian Gao
- Faculty of Resources and Environment, Baotou Teachers’ College, Inner Mongolia University of Science and Technology, Inner Mongolia, 014010 China
| | - Pei-Chun Liao
- School of Life Science, National Taiwan Normal University, Postal address: No. 88, Tingchow Rd. Sect. 4, Taipei, 11677 Taiwan
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de Santana Lopes A, Gomes Pacheco T, do Nascimento Vieira L, Guerra MP, Nodari RO, Maltempi de Souza E, de Oliveira Pedrosa F, Rogalski M. The Crambe abyssinica plastome: Brassicaceae phylogenomic analysis, evolution of RNA editing sites, hotspot and microsatellite characterization of the tribe Brassiceae. Gene 2018; 671:36-49. [DOI: 10.1016/j.gene.2018.05.088] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 05/20/2018] [Accepted: 05/22/2018] [Indexed: 12/18/2022]
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Shekhar S, Roch S, Mirarab S. Species Tree Estimation Using ASTRAL: How Many Genes Are Enough? IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 15:1738-1747. [PMID: 28976320 DOI: 10.1109/tcbb.2017.2757930] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Species tree reconstruction from genomic data is increasingly performed using methods that account for sources of gene tree discordance such as incomplete lineage sorting. One popular method for reconstructing species trees from unrooted gene tree topologies is ASTRAL. In this paper, we derive theoretical sample complexity results for the number of genes required by ASTRAL to guarantee reconstruction of the correct species tree with high probability. We also validate those theoretical bounds in a simulation study. Our results indicate that ASTRAL requires gene trees to reconstruct the species tree correctly with high probability where is the number of species and is the length of the shortest branch in the species tree. Our simulations, some under the anomaly zone, show trends consistent with the theoretical bounds and also provide some practical insights on the conditions where ASTRAL works well.
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Letsch H, Gottsberger B, Metzl C, Astrin J, Friedman ALL, McKenna DD, Fiedler K. Climate and host-plant associations shaped the evolution of ceutorhynch weevils throughout the Cenozoic. Evolution 2018; 72:1815-1828. [PMID: 30040114 PMCID: PMC6175111 DOI: 10.1111/evo.13520] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 04/26/2018] [Accepted: 05/30/2018] [Indexed: 12/19/2022]
Abstract
Using molecular phylogenetic data and methods we inferred divergence times and diversification patterns for the weevil subfamily Ceutorhynchinae in the context of host‐plant associations and global climate over evolutionary time. We detected four major diversification shifts that correlate with both host shifts and major climate events. Ceutorhynchinae experienced an increase in diversification rate at ∼53 Ma, during the Early Eocene Climate Optimum, coincident with a host shift to Lamiaceae. A second major diversification phase occurred at the end of the Eocene (∼34 Ma). This contrasts with the overall deterioration in climate equability at the Eocene‐Oligocene boundary, but tracks the diversification of important host plant clades in temperate (higher) latitudes, leading to increased diversification rates in the weevil clades infesting temperate hosts. A third major phase of diversification is correlated with the rising temperatures of the Late Oligocene Warming Event (∼26.5 Ma); diversification rates then declined shortly after the Middle Miocene Climate Transition (∼14.9 Ma). Our results indicate that biotic and abiotic factors together explain the evolution of Ceutorhynchinae better than each of these drivers viewed in isolation.
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Affiliation(s)
- Harald Letsch
- Department für Botanik und Biodiversitätsforschung, Universität Wien, Rennweg 14, 1030, Vienna, Austria
| | - Brigitte Gottsberger
- Department für Botanik und Biodiversitätsforschung, Universität Wien, Rennweg 14, 1030, Vienna, Austria
| | - Christian Metzl
- Department für Botanik und Biodiversitätsforschung, Universität Wien, Rennweg 14, 1030, Vienna, Austria
| | - Jonas Astrin
- Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53113, Bonn, Germany
| | | | - Duane D McKenna
- Department of Biological Sciences, University of Memphis, Memphis, Tennessee, 38152
| | - Konrad Fiedler
- Department für Botanik und Biodiversitätsforschung, Universität Wien, Rennweg 14, 1030, Vienna, Austria
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133
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Claudel P, Chesnais Q, Fouché Q, Krieger C, Halter D, Bogaert F, Meyer S, Boissinot S, Hugueney P, Ziegler-Graff V, Ameline A, Brault V. The Aphid-Transmitted Turnip yellows virus Differentially Affects Volatiles Emission and Subsequent Vector Behavior in Two Brassicaceae Plants. Int J Mol Sci 2018; 19:E2316. [PMID: 30087282 PMCID: PMC6121887 DOI: 10.3390/ijms19082316] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/27/2018] [Accepted: 08/03/2018] [Indexed: 12/04/2022] Open
Abstract
Aphids are important pests which cause direct damage by feeding or indirect prejudice by transmitting plant viruses. Viruses are known to induce modifications of plant cues in ways that can alter vector behavior and virus transmission. In this work, we addressed whether the modifications induced by the aphid-transmitted Turnip yellows virus (TuYV) in the model plant Arabidopsis thaliana also apply to the cultivated plant Camelina sativa, both belonging to the Brassicaceae family. In most experiments, we observed a significant increase in the relative emission of volatiles from TuYV-infected plants. Moreover, due to plant size, the global amounts of volatiles emitted by C. sativa were higher than those released by A. thaliana. In addition, the volatiles released by TuYV-infected C. sativa attracted the TuYV vector Myzus persicae more efficiently than those emitted by non-infected plants. In contrast, no such preference was observed for A. thaliana. We propose that high amounts of volatiles rather than specific metabolites are responsible for aphid attraction to infected C. sativa. This study points out that the data obtained from the model pathosystem A. thaliana/TuYV cannot be straightforwardly extrapolated to a related plant species infected with the same virus.
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Affiliation(s)
- Patricia Claudel
- SVQV, Université de Strasbourg, INRA, 28 rue de Herrlisheim, 68000 Colmar, France.
| | - Quentin Chesnais
- UMR CNRS 7058 EDYSAN, Université de Picardie Jules Verne, 80039 Amiens, France.
- Department of Entomology, University of California, Entomology Building, 900 University Ave., Riverside, CA 92521, USA.
| | - Quentin Fouché
- UMR CNRS 7058 EDYSAN, Université de Picardie Jules Verne, 80039 Amiens, France.
- CHU Lille, EA 7367-UTML-Unité de Taphonomie Médico-Légale, Université de Lille, 59000 Lille, France.
| | - Célia Krieger
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 67000 Strasbourg, France.
| | - David Halter
- SVQV, Université de Strasbourg, INRA, 28 rue de Herrlisheim, 68000 Colmar, France.
| | - Florent Bogaert
- SVQV, Université de Strasbourg, INRA, 28 rue de Herrlisheim, 68000 Colmar, France.
| | - Sophie Meyer
- SVQV, Université de Strasbourg, INRA, 28 rue de Herrlisheim, 68000 Colmar, France.
| | - Sylvaine Boissinot
- SVQV, Université de Strasbourg, INRA, 28 rue de Herrlisheim, 68000 Colmar, France.
| | - Philippe Hugueney
- SVQV, Université de Strasbourg, INRA, 28 rue de Herrlisheim, 68000 Colmar, France.
| | - Véronique Ziegler-Graff
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 67000 Strasbourg, France.
| | - Arnaud Ameline
- UMR CNRS 7058 EDYSAN, Université de Picardie Jules Verne, 80039 Amiens, France.
| | - Véronique Brault
- SVQV, Université de Strasbourg, INRA, 28 rue de Herrlisheim, 68000 Colmar, France.
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134
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Yu X, Yang D, Guo C, Gao L. Plant phylogenomics based on genome-partitioning strategies: Progress and prospects. PLANT DIVERSITY 2018; 40:158-164. [PMID: 30740560 PMCID: PMC6137260 DOI: 10.1016/j.pld.2018.06.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 06/26/2018] [Accepted: 06/27/2018] [Indexed: 05/26/2023]
Abstract
The rapid expansion of next-generation sequencing (NGS) has generated a powerful array of approaches to address fundamental questions in biology. Several genome-partitioning strategies to sequence selected subsets of the genome have emerged in the fields of phylogenomics and evolutionary genomics. In this review, we summarize the applications, advantages and limitations of four NGS-based genome-partitioning approaches in plant phylogenomics: genome skimming, transcriptome sequencing (RNA-seq), restriction site associated DNA sequencing (RAD-Seq), and targeted capture (Hyb-seq). Of these four genome-partitioning approaches, targeted capture (especially Hyb-seq) shows the greatest promise for plant phylogenetics over the next few years. This review will aid researchers in their selection of appropriate genome-partitioning approaches to address questions of evolutionary scale, where we anticipate continued development and expansion of whole-genome sequencing strategies in the fields of plant phylogenomics and evolutionary biology research.
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Affiliation(s)
- Xiangqin Yu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Dan Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Cen Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Lianming Gao
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
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135
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Sayyari E, Whitfield JB, Mirarab S. Fragmentary Gene Sequences Negatively Impact Gene Tree and Species Tree Reconstruction. Mol Biol Evol 2018; 34:3279-3291. [PMID: 29029241 DOI: 10.1093/molbev/msx261] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Species tree reconstruction from genome-wide data is increasingly being attempted, in most cases using a two-step approach of first estimating individual gene trees and then summarizing them to obtain a species tree. The accuracy of this approach, which promises to account for gene tree discordance, depends on the quality of the inferred gene trees. At the same time, phylogenomic and phylotranscriptomic analyses typically use involved bioinformatics pipelines for data preparation. Errors and shortcomings resulting from these preprocessing steps may impact the species tree analyses at the other end of the pipeline. In this article, we first show that the presence of fragmentary data for some species in a gene alignment, as often seen on real data, can result in substantial deterioration of gene trees, and as a result, the species tree. We then investigate a simple filtering strategy where individual fragmentary sequences are removed from individual genes but the rest of the gene is retained. Both in simulations and by reanalyzing a large insect phylotranscriptomic data set, we show the effectiveness of this simple filtering strategy.
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Affiliation(s)
- Erfan Sayyari
- Department of Electrical and Computer Engineering, University of California at San Diego, La Jolla, CA
| | | | - Siavash Mirarab
- Department of Electrical and Computer Engineering, University of California at San Diego, La Jolla, CA
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136
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Kirioukhova O, Shah JN, Larsen DS, Tayyab M, Mueller NE, Govind G, Baroux C, Federer M, Gheyselinck J, Barrell PJ, Ma H, Sprunck S, Huettel B, Wallace H, Grossniklaus U, Johnston AJ. Aberrant imprinting may underlie evolution of parthenogenesis. Sci Rep 2018; 8:10626. [PMID: 30006526 PMCID: PMC6045609 DOI: 10.1038/s41598-018-27863-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 05/11/2018] [Indexed: 01/10/2023] Open
Abstract
Genomic imprinting confers parent-of-origin-specific gene expression, thus non-equivalent and complementary function of parental genomes. As a consequence, genomic imprinting poses an epigenetic barrier to parthenogenesis in sexual organisms. We report aberrant imprinting in Boechera, a genus in which apomicts evolved from sexuals multiple times. Maternal activation of a MADS-box gene, a homolog of which is imprinted and paternally expressed in the sexual relative Arabidopsis, is accompanied by locus-specific DNA methylation changes in apomicts where parental imprinting seems to be relaxed.
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Affiliation(s)
- Olga Kirioukhova
- University of Heidelberg, Centre for Organismal Studies, Laboratory of Germline Genetics & Evo-Devo, Heidelberg, Germany.,Jacobs University, Life Sciences & Chemistry, Laboratory of Germline Genetics & Evo-Devo, Bremen, Germany
| | - Jubin N Shah
- University of Heidelberg, Centre for Organismal Studies, Laboratory of Germline Genetics & Evo-Devo, Heidelberg, Germany
| | - Danaé S Larsen
- University of Heidelberg, Centre for Organismal Studies, Laboratory of Germline Genetics & Evo-Devo, Heidelberg, Germany
| | - Muhammad Tayyab
- University of Heidelberg, Centre for Organismal Studies, Laboratory of Germline Genetics & Evo-Devo, Heidelberg, Germany
| | - Nora E Mueller
- University of Heidelberg, Centre for Organismal Studies, Laboratory of Germline Genetics & Evo-Devo, Heidelberg, Germany
| | - Geetha Govind
- University of Heidelberg, Centre for Organismal Studies, Laboratory of Germline Genetics & Evo-Devo, Heidelberg, Germany.,University of Agricultural Sciences, College of Agriculture Sciences, Department of crop physiology, Hassan, India
| | - Célia Baroux
- University of Zurich, Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, Zurich, Switzerland
| | - Michael Federer
- University of Zurich, Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, Zurich, Switzerland
| | - Jacqueline Gheyselinck
- University of Zurich, Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, Zurich, Switzerland
| | - Philippa J Barrell
- University of Zurich, Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, Zurich, Switzerland.,New Zealand Institute for Plant and Food Research, Christchurch, New Zealand
| | - Hong Ma
- University of Zurich, Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, Zurich, Switzerland.,The Pennsylvania State University, the Huck Institute of Life Sciences, Department of Biology, The University Park, Pennsylvania, USA.,Fudan University, State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Stefanie Sprunck
- University of Regensburg, Cell Biology and Plant Biochemistry, Regensburg, Germany
| | - Bruno Huettel
- Max-Planck-Institute for Plant Breeding, Cologne, Germany
| | - Helen Wallace
- University of the Sunshine Coast, Faculty of Science, Health, Education and Engineering, Genecology Research Centre, Maroochydore, Australia
| | - Ueli Grossniklaus
- University of Zurich, Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, Zurich, Switzerland.
| | - Amal J Johnston
- University of Heidelberg, Centre for Organismal Studies, Laboratory of Germline Genetics & Evo-Devo, Heidelberg, Germany. .,Jacobs University, Life Sciences & Chemistry, Laboratory of Germline Genetics & Evo-Devo, Bremen, Germany. .,University of Zurich, Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, Zurich, Switzerland. .,ETH Zurich, Department of Biology and Zurich-Basel Plant Science Center, Zurich, Switzerland.
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137
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Kirioukhova O, Shah JN, Larsen DS, Tayyab M, Mueller NE, Govind G, Baroux C, Federer M, Gheyselinck J, Barrell PJ, Ma H, Sprunck S, Huettel B, Wallace H, Grossniklaus U, Johnston AJ. Aberrant imprinting may underlie evolution of parthenogenesis. Sci Rep 2018. [PMID: 30006526 DOI: 10.1038/s41598-018-27863-27867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023] Open
Abstract
Genomic imprinting confers parent-of-origin-specific gene expression, thus non-equivalent and complementary function of parental genomes. As a consequence, genomic imprinting poses an epigenetic barrier to parthenogenesis in sexual organisms. We report aberrant imprinting in Boechera, a genus in which apomicts evolved from sexuals multiple times. Maternal activation of a MADS-box gene, a homolog of which is imprinted and paternally expressed in the sexual relative Arabidopsis, is accompanied by locus-specific DNA methylation changes in apomicts where parental imprinting seems to be relaxed.
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Affiliation(s)
- Olga Kirioukhova
- University of Heidelberg, Centre for Organismal Studies, Laboratory of Germline Genetics & Evo-Devo, Heidelberg, Germany
- Jacobs University, Life Sciences & Chemistry, Laboratory of Germline Genetics & Evo-Devo, Bremen, Germany
| | - Jubin N Shah
- University of Heidelberg, Centre for Organismal Studies, Laboratory of Germline Genetics & Evo-Devo, Heidelberg, Germany
| | - Danaé S Larsen
- University of Heidelberg, Centre for Organismal Studies, Laboratory of Germline Genetics & Evo-Devo, Heidelberg, Germany
| | - Muhammad Tayyab
- University of Heidelberg, Centre for Organismal Studies, Laboratory of Germline Genetics & Evo-Devo, Heidelberg, Germany
| | - Nora E Mueller
- University of Heidelberg, Centre for Organismal Studies, Laboratory of Germline Genetics & Evo-Devo, Heidelberg, Germany
| | - Geetha Govind
- University of Heidelberg, Centre for Organismal Studies, Laboratory of Germline Genetics & Evo-Devo, Heidelberg, Germany
- University of Agricultural Sciences, College of Agriculture Sciences, Department of crop physiology, Hassan, India
| | - Célia Baroux
- University of Zurich, Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, Zurich, Switzerland
| | - Michael Federer
- University of Zurich, Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, Zurich, Switzerland
| | - Jacqueline Gheyselinck
- University of Zurich, Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, Zurich, Switzerland
| | - Philippa J Barrell
- University of Zurich, Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, Zurich, Switzerland
- New Zealand Institute for Plant and Food Research, Christchurch, New Zealand
| | - Hong Ma
- University of Zurich, Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, Zurich, Switzerland
- The Pennsylvania State University, the Huck Institute of Life Sciences, Department of Biology, The University Park, Pennsylvania, USA
- Fudan University, State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Stefanie Sprunck
- University of Regensburg, Cell Biology and Plant Biochemistry, Regensburg, Germany
| | - Bruno Huettel
- Max-Planck-Institute for Plant Breeding, Cologne, Germany
| | - Helen Wallace
- University of the Sunshine Coast, Faculty of Science, Health, Education and Engineering, Genecology Research Centre, Maroochydore, Australia
| | - Ueli Grossniklaus
- University of Zurich, Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, Zurich, Switzerland.
| | - Amal J Johnston
- University of Heidelberg, Centre for Organismal Studies, Laboratory of Germline Genetics & Evo-Devo, Heidelberg, Germany.
- Jacobs University, Life Sciences & Chemistry, Laboratory of Germline Genetics & Evo-Devo, Bremen, Germany.
- University of Zurich, Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, Zurich, Switzerland.
- ETH Zurich, Department of Biology and Zurich-Basel Plant Science Center, Zurich, Switzerland.
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138
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Xu J, Chu Y, Liao B, Xiao S, Yin Q, Bai R, Su H, Dong L, Li X, Qian J, Zhang J, Zhang Y, Zhang X, Wu M, Zhang J, Li G, Zhang L, Chang Z, Zhang Y, Jia Z, Liu Z, Afreh D, Nahurira R, Zhang L, Cheng R, Zhu Y, Zhu G, Rao W, Zhou C, Qiao L, Huang Z, Cheng YC, Chen S. Panax ginseng genome examination for ginsenoside biosynthesis. Gigascience 2018; 6:1-15. [PMID: 29048480 PMCID: PMC5710592 DOI: 10.1093/gigascience/gix093] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 09/22/2017] [Indexed: 11/14/2022] Open
Abstract
Ginseng, which contains ginsenosides as bioactive compounds, has been regarded as an important traditional medicine for several millennia. However, the genetic background of ginseng remains poorly understood, partly because of the plant's large and complex genome composition. We report the entire genome sequence of Panax ginseng using next-generation sequencing. The 3.5-Gb nucleotide sequence contains more than 60% repeats and encodes 42 006 predicted genes. Twenty-two transcriptome datasets and mass spectrometry images of ginseng roots were adopted to precisely quantify the functional genes. Thirty-one genes were identified to be involved in the mevalonic acid pathway. Eight of these genes were annotated as 3-hydroxy-3-methylglutaryl-CoA reductases, which displayed diverse structures and expression characteristics. A total of 225 UDP-glycosyltransferases (UGTs) were identified, and these UGTs accounted for one of the largest gene families of ginseng. Tandem repeats contributed to the duplication and divergence of UGTs. Molecular modeling of UGTs in the 71st, 74th, and 94th families revealed a regiospecific conserved motif located at the N-terminus. Molecular docking predicted that this motif captures ginsenoside precursors. The ginseng genome represents a valuable resource for understanding and improving the breeding, cultivation, and synthesis biology of this key herb.
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Affiliation(s)
- Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Yang Chu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Baosheng Liao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Shuiming Xiao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Qinggang Yin
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Rui Bai
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - He Su
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.,Guangdong Provincial Hospital of Chinese Medicine, Guangzhou 510006, China
| | - Linlin Dong
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Xiwen Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Jun Qian
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Jingjing Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Yujun Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Xiaoyan Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Mingli Wu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Jie Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Guozheng Li
- National Data Center of Traditional Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Lei Zhang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Zhenzhan Chang
- Department of Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yuebin Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zhengwei Jia
- Waters Corporation Shanghai Science & Technology Co Ltd, Shanghai 201206, China
| | - Zhixiang Liu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Daniel Afreh
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/Key Laboratory of Crop Physiology and Ecology, Ministry of Agriculture, Beijing 100081, China
| | - Ruth Nahurira
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/Key Laboratory of Crop Physiology and Ecology, Ministry of Agriculture, Beijing 100081, China
| | - Lianjuan Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Ruiyang Cheng
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Yingjie Zhu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Guangwei Zhu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Wei Rao
- Waters Corporation Shanghai Science & Technology Co Ltd, Shanghai 201206, China
| | - Chao Zhou
- Waters Corporation Shanghai Science & Technology Co Ltd, Shanghai 201206, China
| | - Lirui Qiao
- Waters Corporation Shanghai Science & Technology Co Ltd, Shanghai 201206, China
| | - Zhihai Huang
- Guangdong Provincial Hospital of Chinese Medicine, Guangzhou 510006, China
| | - Yung-Chi Cheng
- Department of Pharmacology, School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Shilin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
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139
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Qi X, Kuo LY, Guo C, Li H, Li Z, Qi J, Wang L, Hu Y, Xiang J, Zhang C, Guo J, Huang CH, Ma H. A well-resolved fern nuclear phylogeny reveals the evolution history of numerous transcription factor families. Mol Phylogenet Evol 2018; 127:961-977. [PMID: 29981932 DOI: 10.1016/j.ympev.2018.06.043] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 06/27/2018] [Accepted: 06/27/2018] [Indexed: 10/28/2022]
Abstract
Ferns account for 80% of nonflowering vascular plant species and are the sister lineage of seed plants. Recent molecular phylogenetics have greatly advanced understanding of fern tree of life, but relationships among some major lineages remain unclear. To better resolve the phylogenetic relationships of ferns, we generated transcriptomes from 125 ferns and two lycophytes, with three additional public datasets, to represent all 11 orders and 85% of families of ferns. Our nuclear phylogeny provides strong supports for the monophyly of all four subclasses and nearly all orders and families, and for relationships among these lineages. The only exception is Gleicheniales, which was highly supported as being paraphyletic with Dipteridaceae sister to a clade with Gleicheniaceae + Hymenophyllales. In addition, new and strongly supported phylogenetic relationships are found for suborders and families in Polypodiales. We provide the first dated fern phylogenomic tree using many nuclear genes from a large majority of families, with an estimate for separation of the ancestors of ferns and seed plants in early Devonian at ∼400 Mya and subsequent gradual divergences of fern orders from ∼380 to 200 Mya. Moreover, the newly obtained fern phylogeny provides a framework for gene family analyses, which indicate that the vast majority of transcription factor families found in seed plants were already present in the common ancestor of extant vascular plants. In addition, fern transcription factor genes show similar duplication patterns to those in seed plants, with some showing stable copy number and others displaying independent expansions in both ferns and seed plants. This study provides a robust phylogenetic and gene family evolution framework, as well as rich molecular resources for understanding the morphological and functional evolution in ferns.
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Affiliation(s)
- Xinping Qi
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | | | - Chunce Guo
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | - Hao Li
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | - Zhongyang Li
- College of Life and Environmental Sciences, Gannan Normal University, Ganzhou, Jiangxi 341000, China
| | - Ji Qi
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | - Linbo Wang
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | - Yi Hu
- Department of Biology, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jianying Xiang
- College of Biodiversity Conservation and Utilization, Southwest Forestry University, 300 Bailong Road, Kunming 650224, China
| | - Caifei Zhang
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | - Jing Guo
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | - Chien-Hsun Huang
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China.
| | - Hong Ma
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China; Department of Biology, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA.
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140
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Chen H, Al-Shehbaz IA, Yue J, Sun H. New insights into the taxonomy of tribe Euclidieae (Brassicaceae), evidence from nrITS sequence data. PHYTOKEYS 2018; 100:125-139. [PMID: 29962892 PMCID: PMC6023952 DOI: 10.3897/phytokeys.100.24756] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 05/01/2018] [Indexed: 05/16/2023]
Abstract
As currently delimitated, the species-rich mustard tribe Euclidieae DC. (Brassicaceae) comprises 28 genera and 152 species distributed primarily in Asia. To date, no tribe-wide comprehensive phylogenetic analysis has been conducted. In this study, sequence data from the nuclear ribosomal internal transcribed spacer (nrITS) region of 82 species in all 28 genera of Euclidieae were used to test its monophyly and infer inter- and intra-generic relationships within. Phylogenetic analyses revealed that Rhammatophyllum and Sisymbriopsis are embedded within Solms-laubachia s.l., and Solms-laubachia lanuginosa (Eurycarpus lanuginosus) fell outside the tribe. Therefore, Solms-laubachia s.l. as currently recognized is not monophyletic and its generic delimitation needed further study. Besides, our results suggest that the genera Lepidostemon, Neotorularia, and Tetracme are polyphyletic.
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Affiliation(s)
- Hongliang Chen
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ihsan A. Al-Shehbaz
- Missouri Botanical Garden, P.O. Box 299, St. Louis, Missouri 63166-0299, USA
| | - Jipei Yue
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, Yunnan 650201, China
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, Yunnan 650201, China
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141
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Gustafsson C, Willforss J, Lopes-Pinto F, Ortiz R, Geleta M. Identification of genes regulating traits targeted for domestication of field cress (Lepidium campestre) as a biennial and perennial oilseed crop. BMC Genet 2018; 19:36. [PMID: 29843613 PMCID: PMC5975587 DOI: 10.1186/s12863-018-0624-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 05/18/2018] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND The changing climate and the desire to use renewable oil sources necessitate the development of new oilseed crops. Field cress (Lepidium campestre) is a species in the Brassicaceae family that has been targeted for domestication not only as an oilseed crop that produces seeds with a desirable industrial oil quality but also as a cover/catch crop that provides valuable ecosystem services. Lepidium is closely related to Arabidopsis and display significant proportions of syntenic regions in their genomes. Arabidopsis genes are among the most characterized genes in the plant kingdom and, hence, comparative genomics of Lepidium-Arabidopsis would facilitate the identification of Lepidium candidate genes regulating various desirable traits. RESULTS Homologues of 30 genes known to regulate vernalization, flowering time, pod shattering, oil content and quality in Arabidopsis were identified and partially characterized in Lepidium. Alignments of sequences representing field cress and two of its closely related perennial relatives: L. heterophyllum and L. hirtum revealed 243 polymorphic sites across the partial sequences of the 30 genes, of which 95 were within the predicted coding regions and 40 led to a change in amino acids of the target proteins. Within field cress, 34 polymorphic sites including nine non-synonymous substitutions were identified. The phylogenetic analysis of the data revealed that field cress is more closely related to L. heterophyllum than to L. hirtum. CONCLUSIONS There is significant variation within and among Lepidium species within partial sequences of the 30 genes known to regulate traits targeted in the present study. The variation within these genes are potentially useful to speed-up the process of domesticating field cress as future oil crop. The phylogenetic relationship between the Lepidium species revealed in this study does not only shed some light on Lepidium genome evolution but also provides important information to develop efficient schemes for interspecific hybridization between different Lepidium species as part of the domestication efforts.
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Affiliation(s)
- Cecilia Gustafsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 101, SE-23053, Alnarp, Sweden
| | - Jakob Willforss
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Box 102, SE-23053, Alnarp, Sweden
| | - Fernando Lopes-Pinto
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, SE-750 07, Uppsala, Sweden
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 101, SE-23053, Alnarp, Sweden
| | - Mulatu Geleta
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 101, SE-23053, Alnarp, Sweden.
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142
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Arsovski AA, Zemke JE, Haagen BD, Kim SH, Nemhauser JL. Phytochrome B regulates resource allocation in Brassica rapa. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69. [PMID: 29514292 PMCID: PMC5961229 DOI: 10.1093/jxb/ery080] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Crop biomass and yield are tightly linked to how the light signaling network translates information about the environment into allocation of resources, including photosynthates. Once activated, the phytochrome (phy) class of photoreceptors signal and re-deploy carbon resources to alter growth, plant architecture, and reproductive timing. Most of the previous characterization of the light-modulated growth program has been performed in the reference plant Arabidopsis thaliana. Here, we use Brassica rapa as a crop model to test for conservation of the phytochrome-carbon network. In response to elevated levels of CO2, B. rapa seedlings showed increases in hypocotyl length, shoot and root fresh weight, and the number of lateral roots. All of these responses were dependent on nitrogen and polar auxin transport. In addition, we identified putative B. rapa orthologs of PhyB and isolated two nonsense alleles. BrphyB mutants had significantly decreased or absent CO2-stimulated growth responses. Mutant seedlings also showed misregulation of auxin-dependent genes and genes involved in chloroplast development. Adult mutant plants had reduced chlorophyll levels, photosynthetic rate, stomatal index, and seed yield. These findings support a recently proposed holistic role for phytochromes in regulating resource allocation, biomass production, and metabolic state in the developing plant.
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Affiliation(s)
| | - Joseph E Zemke
- Department of Biology, University of Washington, Seattle, WA, USA
| | | | - Soo-Hyung Kim
- School of Environmental and Forest Sciences, University of Washington, Seattle, WA, USA
| | - Jennifer L Nemhauser
- Department of Biology, University of Washington, Seattle, WA, USA
- Correspondence:
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143
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Gaynor ML, Ng J, Laport RG. Phylogenetic Structure of Plant Communities: Are Polyploids Distantly Related to Co-occurring Diploids? Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00052] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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144
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Šamec D, Urlić B, Salopek-Sondi B. Kale ( Brassica oleracea var. acephala) as a superfood: Review of the scientific evidence behind the statement. Crit Rev Food Sci Nutr 2018; 59:2411-2422. [PMID: 29557674 DOI: 10.1080/10408398.2018.1454400] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Kale (Brassica oleracea var. acephala) is a cruciferous vegetable, characterized by leaves along the stem, which, in recent years, have gained a great popularity as a ´superfood´. Consequently, in a popular culture it is listed in many ´lists of the healthiest vegetables´. Without the doubt, a scientific evidences support the fact that cruciferous vegetables included in human diet can positively affect health and well-being, but remains unclear why kale is declared superior in comparison with other cruciferous. It is questionable if this statement about kale is triggered by scientific evidence or by some other factors. Our review aims to bring an overview of kale's botanical characteristics, agronomic requirements, contemporary and traditional use, macronutrient and phytochemical content and biological activity, in order to point out the reasons for tremendous kale popularity.
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Affiliation(s)
- Dunja Šamec
- a Ruđer Bošković Institute, Department for Molecular Biology , Zagreb , Croatia
| | - Branimir Urlić
- b Institute for Adriatic Crops and Karst Reclamation , Split , Croatia
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145
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Singh S, Das S, Geeta R. A segmental duplication in the common ancestor of Brassicaceae is responsible for the origin of the paralogs KCS6-KCS5, which are not shared with other angiosperms. Mol Phylogenet Evol 2018; 126:331-345. [PMID: 29698723 DOI: 10.1016/j.ympev.2018.04.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 04/11/2018] [Accepted: 04/11/2018] [Indexed: 12/14/2022]
Abstract
Novel morphological structures allowed adaptation to dry conditions in early land plants. The cuticle, one such novelty, plays diverse roles in tolerance to abiotic and biotic stresses and plant development. Cuticular waxes represent a major constituent of the cuticle and are comprised of an assortment of chemicals that include, among others, very long chain fatty acids (VLCFAs). Members of the β-ketoacyl coenzyme A synthases (KCS) gene family code for enzymes that are essential for fatty acid biosynthesis. The gene KCS6 (CUT1) is known to be a key player in the production of VLCFA precursors essential for the synthesis of cuticular waxes in the model plant Arabidopsis thaliana (Brassicaceae). Despite its functional importance, relatively little is known about the evolutionary history of KCS6 or its paralog KCS5 in Brassicaceae or beyond. This lacuna becomes important when we extrapolate understanding of mechanisms gained from the model plant to its containing clades Brassicaceae, flowering plants, or beyond. The Brassicaceae, with several sequenced genomes and a known history of paleoploidy, mesopolyploidy and neopolyploidy, offer a system in which to study the evolution and diversification of the KCS6-KCS5 paralogy. Our phylogenetic analyses across green plants, combined with comparative genomic, microsynteny and evolutionary rates analyses across nine genomes of Brassicaceae, reveal that (1) the KCS6-KCS5 paralogy arose as the result of a large segmental duplication in the ancestral Brassicaceae, (2) the KCS6-KCS5 lineage is represented by a single copy in other flowering plant lineages, (3) the duplicated segments undergo different degrees of retention and loss, and (4) most of the genes in the KCS6 and KCS5 gene blocks (including KCS6 and KCS5 themselves) are under purifying selection. The last also true for most members of the KCS gene family in Brassicaceae, except for KCS8, KCS9 and KCS17, which are under positive selection and may be undergoing functional evolution, meriting further investigation. Overall, our results clearly establish that the ancestral KCS6/5 gene duplicated in the Brassicaceae lineage. It is possible that any specialized functions of KCS5 found in Brassicaceae are either part of a set of KCS6/5 gene functions in the rest of the flowering plants, or unique to Brassicaceae.
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Affiliation(s)
- Swati Singh
- Department of Botany, University of Delhi, Delhi 110007, India
| | - Sandip Das
- Department of Botany, University of Delhi, Delhi 110007, India
| | - R Geeta
- Department of Botany, University of Delhi, Delhi 110007, India.
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146
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Kawanabe T, Nukii H, Furihata HY, Yoshida T, Kawabe A. The complete chloroplast genome of Sisymbrium irio. Mitochondrial DNA B Resour 2018; 3:488-489. [PMID: 33474214 PMCID: PMC7799896 DOI: 10.1080/23802359.2018.1464412] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The complete chloroplast genome of Sisymbrium irio was determined. The length of the complete chloroplast genome is 154,001 bp. The whole chloroplast genome consists of 83,891 bp long single copy (LSC) and 17,630 bp small single copy (SSC) regions, separated by a pair of 26,240 bp inverted repeat (IR) regions. The S. irio chloroplast genome encodes 112 annotated known unique genes including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. The phylogenetic position of S. irio is sister to Brassiceae and Thlaspideae.
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Affiliation(s)
| | - Hiroaki Nukii
- Faculty of Life Science, Kyoto Sangyo University, Kyoto, Japan
| | | | | | - Akira Kawabe
- Faculty of Life Science, Kyoto Sangyo University, Kyoto, Japan
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147
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Emery M, Willis MMS, Hao Y, Barry K, Oakgrove K, Peng Y, Schmutz J, Lyons E, Pires JC, Edger PP, Conant GC. Preferential retention of genes from one parental genome after polyploidy illustrates the nature and scope of the genomic conflicts induced by hybridization. PLoS Genet 2018; 14:e1007267. [PMID: 29590103 PMCID: PMC5891031 DOI: 10.1371/journal.pgen.1007267] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 04/09/2018] [Accepted: 02/21/2018] [Indexed: 11/18/2022] Open
Abstract
Polyploidy is increasingly seen as a driver of both evolutionary innovation and ecological success. One source of polyploid organisms' successes may be their origins in the merging and mixing of genomes from two different species (e.g., allopolyploidy). Using POInT (the Polyploid Orthology Inference Tool), we model the resolution of three allopolyploidy events, one from the bakers' yeast (Saccharomyces cerevisiae), one from the thale cress (Arabidopsis thaliana) and one from grasses including Sorghum bicolor. Analyzing a total of 21 genomes, we assign to every gene a probability for having come from each parental subgenome (i.e., derived from the diploid progenitor species), yielding orthologous segments across all genomes. Our model detects statistically robust evidence for the existence of biased fractionation in all three lineages, whereby genes from one of the two subgenomes were more likely to be lost than those from the other subgenome. We further find that a driver of this pattern of biased losses is the co-retention of genes from the same parental genome that share functional interactions. The pattern of biased fractionation after the Arabidopsis and grass allopolyploid events was surprisingly constant in time, with the same parental genome favored throughout the lineages' history. In strong contrast, the yeast allopolyploid event shows evidence of biased fractionation only immediately after the event, with balanced gene losses more recently. The rapid loss of functionally associated genes from a single subgenome is difficult to reconcile with the action of genetic drift and suggests that selection may favor the removal of specific duplicates. Coupled to the evidence for continuing, functionally-associated biased fractionation after the A. thaliana At-α event, we suggest that, after allopolyploidy, there are functional conflicts between interacting genes encoded in different subgenomes that are ultimately resolved through preferential duplicate loss.
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Affiliation(s)
- Marianne Emery
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri, United States of America
| | - M. Madeline S. Willis
- Department of Biochemistry, University of Missouri-Columbia, Columbia, Missouri, United States of America
| | - Yue Hao
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Khouanchy Oakgrove
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Yi Peng
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Jeremy Schmutz
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Eric Lyons
- School of Plant Sciences, University of Arizona, Tucson, Arizona, United States of America
| | - J. Chris Pires
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri, United States of America
- Informatics Institute, University of Missouri-Columbia, Columbia, Missouri, United States of America
- Bond Life Sciences Center, University of Missouri-Columbia, Columbia, Missouri, United States of America
| | - Patrick P. Edger
- Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America
- Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, Michigan, United States of America
| | - Gavin C. Conant
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, United States of America
- Division of Animal Sciences, University of Missouri-Columbia, Columbia, Missouri, United States of America
- Program in Genetics, North Carolina State University, Raleigh, North Carolina, United States of America
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
- * E-mail:
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148
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Ren R, Wang H, Guo C, Zhang N, Zeng L, Chen Y, Ma H, Qi J. Widespread Whole Genome Duplications Contribute to Genome Complexity and Species Diversity in Angiosperms. MOLECULAR PLANT 2018; 11:414-428. [PMID: 29317285 DOI: 10.1016/j.molp.2018.01.002] [Citation(s) in RCA: 185] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 12/13/2017] [Accepted: 01/02/2018] [Indexed: 05/18/2023]
Abstract
Gene duplications provide evolutionary potentials for generating novel functions, while polyploidization or whole genome duplication (WGD) doubles the chromosomes initially and results in hundreds to thousands of retained duplicates. WGDs are strongly supported by evidence commonly found in many species-rich lineages of eukaryotes, and thus are considered as a major driving force in species diversification. We performed comparative genomic and phylogenomic analyses of 59 public genomes/transcriptomes and 46 newly sequenced transcriptomes covering major lineages of angiosperms to detect large-scale gene duplication events by surveying tens of thousands of gene family trees. These analyses confirmed most of the previously reported WGDs and provided strong evidence for novel ones in many lineages. The detected WGDs supported a model of exponential gene loss during evolution with an estimated half-life of approximately 21.6 million years, and were correlated with both the emergence of lineages with high degrees of diversification and periods of global climate changes. The new datasets and analyses detected many novel WGDs widely spread during angiosperm evolution, uncovered preferential retention of gene functions in essential cellular metabolisms, and provided clues for the roles of WGD in promoting angiosperm radiation and enhancing their adaptation to environmental changes.
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Affiliation(s)
- Ren Ren
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering and Institute of Biodiversity Science, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Haifeng Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Chunce Guo
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering and Institute of Biodiversity Science, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Ning Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering and Institute of Biodiversity Science, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China; Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, USA
| | - Liping Zeng
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering and Institute of Biodiversity Science, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yamao Chen
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering and Institute of Biodiversity Science, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Hong Ma
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering and Institute of Biodiversity Science, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China; Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
| | - Ji Qi
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering and Institute of Biodiversity Science, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China.
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149
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Edger PP, Hall JC, Harkess A, Tang M, Coombs J, Mohammadin S, Schranz ME, Xiong Z, Leebens-Mack J, Meyers BC, Sytsma KJ, Koch MA, Al-Shehbaz IA, Pires JC. Brassicales phylogeny inferred from 72 plastid genes: A reanalysis of the phylogenetic localization of two paleopolyploid events and origin of novel chemical defenses. AMERICAN JOURNAL OF BOTANY 2018; 105:463-469. [PMID: 29574686 DOI: 10.1002/ajb2.1040] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 11/06/2017] [Indexed: 05/10/2023]
Abstract
PREMISE OF THE STUDY Previous phylogenetic studies employing molecular markers have yielded various insights into the evolutionary history across Brassicales, but many relationships between families remain poorly supported or unresolved. A recent phylotranscriptomic approach utilizing 1155 nuclear markers obtained robust estimates for relationships among 14 of 17 families. Here we report a complete family-level phylogeny estimated using the plastid genome. METHODS We conducted phylogenetic analyses on a concatenated data set comprising 44,926 bp from 72 plastid genes for species distributed across all 17 families. Our analysis includes three additional families, Tovariaceae, Salvadoraceae, and Setchellanthaceae, that were omitted in the previous phylotranscriptomic study. KEY RESULTS Our phylogenetic analyses obtained fully resolved and strongly supported estimates for all nodes across Brassicales. Importantly, these findings are congruent with the topology reported in the phylotranscriptomic study. This consistency suggests that future studies could utilize plastid genomes as markers for resolving relationships within some notoriously difficult clades across Brassicales. We used this new phylogenetic framework to verify the placement of the At-α event near the origin of Brassicaceae, with median date estimates of 31.8 to 42.8 million years ago and restrict the At-β event to one of two nodes with median date estimates between 85 to 92.2 million years ago. These events ultimately gave rise to novel chemical defenses and are associated with subsequent shifts in net diversification rates. CONCLUSIONS We anticipate that these findings will aid future comparative evolutionary studies across Brassicales, including selecting candidates for whole-genome sequencing projects.
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Affiliation(s)
- Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, Michigan, 48864, USA
- Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI, 48864, USA
| | - Jocelyn C Hall
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
| | - Alex Harkess
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO, 63132, USA
| | - Michelle Tang
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Jill Coombs
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Setareh Mohammadin
- Biosystematics, Plant Science Group, Wageningen University and Research, Wageningen, Netherlands
| | - M Eric Schranz
- Biosystematics, Plant Science Group, Wageningen University and Research, Wageningen, Netherlands
| | - Zhiyong Xiong
- Potato Engineering & Technology Research Center, Inner Mongolia University, Hohhot, China
| | - James Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Blake C Meyers
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO, 63132, USA
| | - Kenneth J Sytsma
- Department of Botany, University of Wisconsin, Madison, WI, 53706, USA
| | - Marcus A Koch
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | | | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
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150
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Leins P, Fligge K, Erbar C. Silique valves as sails in anemochory of Lunaria (Brassicaceae). PLANT BIOLOGY (STUTTGART, GERMANY) 2018; 20:238-243. [PMID: 29105935 DOI: 10.1111/plb.12659] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 10/30/2017] [Indexed: 05/25/2023]
Abstract
The generally held opinion that seeds of Lunaria remain at the replum after detachment of the two valves and then wind causes a shaking or rattling of the replum with its diaphragm, thus launching the seeds, is challenged. In a sparse forest in the Swabian Alb, the first author noticed flying valves of Lunaria rediviva to which the narrow-winged flat seeds are attached. Investigations with SEM and histology have shown that the valves secrete a glue only at those sites where the seeds rest on the valves before valve tissues die. Further analysis has shown (using the periodic acid-Schiff reaction) that the glue consists of polysaccharides. After detachment and dispersal of the valves, the adhesive strength continuously decreases. This is the first report for a sticky valve exudate in the Brassicaceae. Because of the adhesion of Lunaria seeds to their valves for some time, the 1st order diaspore is a mericarp, in a broad sense, and can be interpreted as an adaptation to long-distance dispersal by stronger winds. In this context, the 'flying carpets' of Lunaria are more effective and transport more than one seed. Molecular studies assigned Lunaria to the tribe Biscutelleae, which now contains the angustiseptate genera Biscutella and Megadenia as well as the latiseptate genera Lunaria and Ricotia. The valves in Ricotia can easily be detached (studied in herbarium material and a living plant), but, in contrast to Lunaria, the ripe seeds remain at the replum and its diaphragm, respectively.
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Affiliation(s)
- P Leins
- Centre for Organismal Studies Heidelberg, Biodiversity and Plant Systematics, Heidelberg University, Heidelberg, Germany
| | - K Fligge
- Centre for Organismal Studies Heidelberg, Biodiversity and Plant Systematics, Heidelberg University, Heidelberg, Germany
| | - C Erbar
- Centre for Organismal Studies Heidelberg, Biodiversity and Plant Systematics, Heidelberg University, Heidelberg, Germany
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