1
|
Li X, Yang J, Zhang Q, Zhang L, Cheng F, Xu W. Phosphorus-Use-Efficiency Gene Identification in Fabaceae and RSL2 Expansion in Lupinus albus Is Associated with Low-Phosphorus Adaptation. Genes (Basel) 2024; 15:1049. [PMID: 39202409 PMCID: PMC11353381 DOI: 10.3390/genes15081049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Revised: 08/01/2024] [Accepted: 08/07/2024] [Indexed: 09/03/2024] Open
Abstract
Phosphorus is critical for plant growth but often becomes less accessible due to its precipitation with cations in soil. Fabaceae, a diverse plant family, exhibits robust adaptability and includes species like Lupinus albus, known for its efficient phosphorus utilization via cluster roots. Here, we systematically identified phosphorus-utilization-efficiency (PUE) gene families across 35 Fabaceae species, highlighting significant gene amplification in PUE pathways in Fabaceae. Different PUE pathways exhibited variable amplification, evolution, and retention patterns among various Fabaceae crops. Additionally, the number of homologous genes of the root hair development gene RSL2 in L. albus was far more than that in other Fabaceae species. Multiple copies of the RSL2 gene were amplified and retained in L. albus after whole genome triplication. The gene structure and motifs specifically retained in L. albus were different from homologous genes in other plants. Combining transcriptome analysis under low-phosphorus treatment, it was found that most of the homologous genes of RSL2 in L. albus showed high expression in the cluster roots, suggesting that the RSL2 gene family plays an important role in the adaptation process of L. albus to low-phosphorus environments and the formation of cluster roots.
Collapse
Affiliation(s)
- Xing Li
- Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Provincial Key Laboratory of Plant Functional Biology and College of Resources and Environment, College of JunCao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.L.); (J.Y.); (Q.Z.)
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China;
| | - Jinyong Yang
- Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Provincial Key Laboratory of Plant Functional Biology and College of Resources and Environment, College of JunCao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.L.); (J.Y.); (Q.Z.)
| | - Qian Zhang
- Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Provincial Key Laboratory of Plant Functional Biology and College of Resources and Environment, College of JunCao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.L.); (J.Y.); (Q.Z.)
| | - Lingkui Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China;
| | - Feng Cheng
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China;
| | - Weifeng Xu
- Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Provincial Key Laboratory of Plant Functional Biology and College of Resources and Environment, College of JunCao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.L.); (J.Y.); (Q.Z.)
| |
Collapse
|
2
|
Zeng S, Wang Z, Shi D, Yu F, Liu T, Peng T, Bi G, Yan J, Wang Y. The high-quality genome of Grona styracifolia uncovers the genomic mechanism of high levels of schaftoside, a promising drug candidate for treatment of COVID-19. HORTICULTURE RESEARCH 2024; 11:uhae089. [PMID: 38799125 PMCID: PMC11119794 DOI: 10.1093/hr/uhae089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 03/20/2024] [Indexed: 05/29/2024]
Abstract
Recent study has evidenced that traditional Chinese medicinal (TCM) plant-derived schaftoside shows promise as a potential drug candidate for COVID-19 treatment. However, the biosynthetic pathway of schaftoside in TCM plants remains unknown. In this study, the genome of the TCM herb Grona styracifolia (Osbeck) H.Ohashi & K.Ohashi (GSO), which is rich in schaftoside, was sequenced, and a high-quality assembly of GSO genome was obtained. Our findings revealed that GSO did not undergo recent whole genome duplication (WGD) but shared an ancestral papilionoid polyploidy event, leading to the gene expansion of chalcone synthase (CHS) and isoflavone 2'-hydroxylase (HIDH). Furthermore, GSO-specific tandem gene duplication resulted in the gene expansion of C-glucosyltransferase (CGT). Integrative analysis of the metabolome and transcriptome identified 13 CGTs and eight HIDHs involved in the biosynthetic pathway of schaftoside. Functional studies indicated that CGTs and HIDHs identified here are bona fide responsible for the biosynthesis of schaftoside in GSO, as confirmed through hairy root transgenic system and in vitro enzyme activity assay. Taken together, the ancestral papilionoid polyploidy event expanding CHSs and HIDHs, along with the GSO-specific tandem duplication of CGT, contributes, partially if not completely, to the robust biosynthesis of schaftoside in GSO. These findings provide insights into the genomic mechanisms underlying the abundant biosynthesis of schaftoside in GSO, highlighting the potential of GSO as a source of bioactive compounds for pharmaceutical development.
Collapse
Affiliation(s)
- Shaohua Zeng
- Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China National Botanical Garden, State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiqiang Wang
- Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China National Botanical Garden, State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dingding Shi
- Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China National Botanical Garden, State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fangqin Yu
- Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China National Botanical Garden, State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China
| | - Ting Liu
- Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China National Botanical Garden, State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China
| | - Ting Peng
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China
| | - Guiqi Bi
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Jianbin Yan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Ying Wang
- Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China National Botanical Garden, State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
3
|
Nouwen N, Pervent M, El M’Chirgui F, Tellier F, Rios M, Horta Araújo N, Klopp C, Gressent F, Arrighi JF. OROSOMUCOID PROTEIN 1 regulation of sphingolipid synthesis is required for nodulation in Aeschynomene evenia. PLANT PHYSIOLOGY 2024; 194:1611-1630. [PMID: 38039119 PMCID: PMC10904325 DOI: 10.1093/plphys/kiad642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/31/2023] [Accepted: 10/31/2023] [Indexed: 12/03/2023]
Abstract
Legumes establish symbiotic interactions with nitrogen-fixing rhizobia that are accommodated in root-derived organs known as nodules. Rhizobial recognition triggers a plant symbiotic signaling pathway that activates 2 coordinated processes: infection and nodule organogenesis. How these processes are orchestrated in legume species utilizing intercellular infection and lateral root base nodulation remains elusive. Here, we show that Aeschynomene evenia OROSOMUCOID PROTEIN 1 (AeORM1), a key regulator of sphingolipid biosynthesis, is required for nodule formation. Using A. evenia orm1 mutants, we demonstrate that alterations in AeORM1 function trigger numerous early aborted nodules, defense-like reactions, and shorter lateral roots. Accordingly, AeORM1 is expressed during lateral root initiation and elongation, including at lateral root bases where nodule primordium form in the presence of symbiotic bradyrhizobia. Sphingolipidomics revealed that mutations in AeORM1 lead to sphingolipid overaccumulation in roots relative to the wild type, particularly for very long-chain fatty acid-containing ceramides. Taken together, our findings reveal that AeORM1-regulated sphingolipid homeostasis is essential for rhizobial infection and nodule organogenesis, as well as for lateral root development in A. evenia.
Collapse
Affiliation(s)
- Nico Nouwen
- Plant Health Institute of Montpellier (PHIM), IRD, UMR Univ Montpellier/IRD/SupAgro/INRAE/CIRAD, TA-A82/J Campus de Baillarguet, 34398 Montpellier, France
| | - Marjorie Pervent
- Plant Health Institute of Montpellier (PHIM), INRAE, UMR Univ Montpellier/IRD/SupAgro/INRAE/CIRAD, TA-A82/J Campus de Baillarguet, 34398 Montpellier, France
| | - Franck El M’Chirgui
- Plant Health Institute of Montpellier (PHIM), IRD, UMR Univ Montpellier/IRD/SupAgro/INRAE/CIRAD, TA-A82/J Campus de Baillarguet, 34398 Montpellier, France
| | - Frédérique Tellier
- Institut Jean-Pierre Bourgin (IJPB), INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | - Maëlle Rios
- Plant Health Institute of Montpellier (PHIM), IRD, UMR Univ Montpellier/IRD/SupAgro/INRAE/CIRAD, TA-A82/J Campus de Baillarguet, 34398 Montpellier, France
| | - Natasha Horta Araújo
- Plant Health Institute of Montpellier (PHIM), IRD, UMR Univ Montpellier/IRD/SupAgro/INRAE/CIRAD, TA-A82/J Campus de Baillarguet, 34398 Montpellier, France
| | - Christophe Klopp
- Plateforme Bioinformatique Genotoul, BioinfoMics, UR875 Biométrie et Intelligence Artificielle, INRAE, 31326 Castanet-Tolosan, France
| | - Frédéric Gressent
- Plant Health Institute of Montpellier (PHIM), INRAE, UMR Univ Montpellier/IRD/SupAgro/INRAE/CIRAD, TA-A82/J Campus de Baillarguet, 34398 Montpellier, France
| | - Jean-François Arrighi
- Plant Health Institute of Montpellier (PHIM), IRD, UMR Univ Montpellier/IRD/SupAgro/INRAE/CIRAD, TA-A82/J Campus de Baillarguet, 34398 Montpellier, France
| |
Collapse
|
4
|
Zhang Y, Fu Y, Xian W, Li X, Feng Y, Bu F, Shi Y, Chen S, van Velzen R, Battenberg K, Berry AM, Salgado MG, Liu H, Yi T, Fournier P, Alloisio N, Pujic P, Boubakri H, Schranz ME, Delaux PM, Wong GKS, Hocher V, Svistoonoff S, Gherbi H, Wang E, Kohlen W, Wall LG, Parniske M, Pawlowski K, Normand P, Doyle JJ, Cheng S. Comparative phylogenomics and phylotranscriptomics provide insights into the genetic complexity of nitrogen-fixing root-nodule symbiosis. PLANT COMMUNICATIONS 2024; 5:100671. [PMID: 37553834 PMCID: PMC10811378 DOI: 10.1016/j.xplc.2023.100671] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/10/2023] [Accepted: 08/03/2023] [Indexed: 08/10/2023]
Abstract
Plant root-nodule symbiosis (RNS) with mutualistic nitrogen-fixing bacteria is restricted to a single clade of angiosperms, the Nitrogen-Fixing Nodulation Clade (NFNC), and is best understood in the legume family. Nodulating species share many commonalities, explained either by divergence from a common ancestor over 100 million years ago or by convergence following independent origins over that same time period. Regardless, comparative analyses of diverse nodulation syndromes can provide insights into constraints on nodulation-what must be acquired or cannot be lost for a functional symbiosis-and the latitude for variation in the symbiosis. However, much remains to be learned about nodulation, especially outside of legumes. Here, we employed a large-scale phylogenomic analysis across 88 species, complemented by 151 RNA-seq libraries, to elucidate the evolution of RNS. Our phylogenomic analyses further emphasize the uniqueness of the transcription factor NIN as a master regulator of nodulation and identify key mutations that affect its function across the NFNC. Comparative transcriptomic assessment revealed nodule-specific upregulated genes across diverse nodulating plants, while also identifying nodule-specific and nitrogen-response genes. Approximately 70% of symbiosis-related genes are highly conserved in the four representative species, whereas defense-related and host-range restriction genes tend to be lineage specific. Our study also identified over 900 000 conserved non-coding elements (CNEs), over 300 000 of which are unique to sampled NFNC species. NFNC-specific CNEs are enriched with the active H3K9ac mark and are correlated with accessible chromatin regions, thus representing a pool of candidate regulatory elements for genes involved in RNS. Collectively, our results provide novel insights into the evolution of nodulation and lay a foundation for engineering of RNS traits in agriculturally important crops.
Collapse
Affiliation(s)
- Yu Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yuan Fu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenfei Xian
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Xiuli Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yong Feng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Fengjiao Bu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yan Shi
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Shiyu Chen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Robin van Velzen
- Biosystematics Group, Department of Plant Sciences, Wageningen University, 6708PB Wageningen, the Netherlands
| | - Kai Battenberg
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Alison M Berry
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Marco G Salgado
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden
| | - Hui Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road, Kunming 650201, China
| | - Tingshuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road, Kunming 650201, China
| | - Pascale Fournier
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France
| | - Nicole Alloisio
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France
| | - Petar Pujic
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France
| | - Hasna Boubakri
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France
| | - M Eric Schranz
- Biosystematics Group, Department of Plant Sciences, Wageningen University, 6708PB Wageningen, the Netherlands
| | - Pierre-Marc Delaux
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, 24 chemin de Borde Rouge, Auzeville, BP42617, 31326 Castanet Tolosan, France
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Valerie Hocher
- French National Research Institute for Sustainable Development (IRD), UMR LSTM (IRD/CIRAD/INRAe/Montpellier University/Supagro)- Campus International Baillarguet, TA A-82/J, 34398 Montpellier Cedex 5, France
| | - Sergio Svistoonoff
- French National Research Institute for Sustainable Development (IRD), UMR LSTM (IRD/CIRAD/INRAe/Montpellier University/Supagro)- Campus International Baillarguet, TA A-82/J, 34398 Montpellier Cedex 5, France
| | - Hassen Gherbi
- French National Research Institute for Sustainable Development (IRD), UMR LSTM (IRD/CIRAD/INRAe/Montpellier University/Supagro)- Campus International Baillarguet, TA A-82/J, 34398 Montpellier Cedex 5, France
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, SIBS, Chinese Academy of Sciences, Shanghai, China
| | - Wouter Kohlen
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708PB Wageningen, the Netherlands
| | - Luis G Wall
- Laboratory of Biochemistry, Microbiology and Soil Biological Interactions, Department of Science and Technology, National University of Quilmes, CONICET, Bernal, Argentina
| | - Martin Parniske
- Faculty of Biology, Genetics, LMU Munich, Großhaderner Strasse 2-4, 82152 Martinsried, Germany
| | - Katharina Pawlowski
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden
| | - Philippe Normand
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France
| | - Jeffrey J Doyle
- School of Integrative Plant Science, Sections of Plant Biology and Plant Breeding & Genetics, Cornell University, Ithaca, NY 14853, USA.
| | - Shifeng Cheng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.
| |
Collapse
|
5
|
Chen Y, Fang T, Su H, Duan S, Ma R, Wang P, Wu L, Sun W, Hu Q, Zhao M, Sun L, Dong X. A reference-grade genome assembly for Astragalus mongholicus and insights into the biosynthesis and high accumulation of triterpenoids and flavonoids in its roots. PLANT COMMUNICATIONS 2023; 4:100469. [PMID: 36307985 PMCID: PMC10030368 DOI: 10.1016/j.xplc.2022.100469] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 09/18/2022] [Accepted: 10/23/2022] [Indexed: 05/04/2023]
Abstract
Astragalus membranaceus var. mongholicus (AMM), a member of the Leguminosae, is one of the most important medicinal plants worldwide. The dried roots of AMM have a wide range of pharmacological effects and are a traditional Chinese medicine. Here, we report the first chromosome-level reference genome of AMM, comprising nine pseudochromosomes with a total size of 1.47 Gb and 27 868 protein-encoding genes. Comparative genomic analysis reveals that AMM has not experienced an independent whole-genome duplication (WGD) event after the WGD event shared by the Papilionoideae species. Analysis of long terminal repeat retrotransposons suggests a recent burst of these elements at approximately 0.13 million years ago, which may explain the large size of the AMM genome. Multiple gene families involved in the biosynthesis of triterpenoids and flavonoids were expanded, and our data indicate that tandem duplication has been the main driver for expansion of these families. Among the expanded families, the phenylalanine ammonia-lyase gene family was primarily expressed in the roots of AMM, suggesting their roles in the biosynthesis of phenylpropanoid compounds. The functional versatility of 2,3-oxidosqualene cyclase genes in cluster III may play a critical role in the diversification of triterpenoids in AMM. Our findings provide novel insights into triterpenoid and flavonoid biosynthesis and can facilitate future research on the genetics and medical applications of AMM.
Collapse
Affiliation(s)
- Yi Chen
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Ting Fang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - He Su
- The Second Clinical Medical College of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou 510120, China
| | - Sifei Duan
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Ruirui Ma
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Ping Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Lin Wu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Wenbin Sun
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Qichen Hu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Meixia Zhao
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Lianjun Sun
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China.
| | - Xuehui Dong
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China.
| |
Collapse
|
6
|
Vlk D, Trněný O, Řepková J. Genes Associated with Biological Nitrogen Fixation Efficiency Identified Using RNA Sequencing in Red Clover ( Trifolium pratense L.). LIFE (BASEL, SWITZERLAND) 2022; 12:life12121975. [PMID: 36556339 PMCID: PMC9785344 DOI: 10.3390/life12121975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/22/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022]
Abstract
Commonly studied in the context of legume-rhizobia symbiosis, biological nitrogen fixation (BNF) is a key component of the nitrogen cycle in nature. Despite its potential in plant breeding and many years of research, information is still lacking as to the regulation of hundreds of genes connected with plant-bacteria interaction, nodulation, and nitrogen fixation. Here, we compared root nodule transcriptomes of red clover (Trifolium pratense L.) genotypes with contrasting nitrogen fixation efficiency, and we found 491 differentially expressed genes (DEGs) between plants with high and low BNF efficiency. The annotation of genes expressed in nodules revealed more than 800 genes not yet experimentally confirmed. Among genes mediating nodule development, four nod-ule-specific cysteine-rich (NCR) peptides were confirmed in the nodule transcriptome. Gene duplication analyses revealed that genes originating from tandem and dispersed duplication are significantly over-represented among DEGs. Weighted correlation network analysis (WGCNA) organized expression profiles of the transcripts into 16 modules linked to the analyzed traits, such as nitrogen fixation efficiency or sample-specific modules. Overall, the results obtained broaden our knowledge about transcriptomic landscapes of red clover's root nodules and shift the phenotypic description of BNF efficiency on the level of gene expression in situ.
Collapse
Affiliation(s)
- David Vlk
- Department of Experimental Biology, Faculty of Sciences, Masaryk University, 611 37 Brno, Czech Republic
| | - Oldřich Trněný
- Agricultural Research, Ltd., Zahradní 1, 664 41 Troubsko, Czech Republic
| | - Jana Řepková
- Department of Experimental Biology, Faculty of Sciences, Masaryk University, 611 37 Brno, Czech Republic
- Correspondence: ; Tel.: +420-549-49-6895
| |
Collapse
|
7
|
Kim JM, Lyu JI, Kim DG, Hung NN, Seo JS, Ahn JW, Lim YJ, Eom SH, Ha BK, Kwon SJ. Genome wide association study to detect genetic regions related to isoflavone content in a mutant soybean population derived from radiation breeding. FRONTIERS IN PLANT SCIENCE 2022; 13:968466. [PMID: 36061785 PMCID: PMC9433930 DOI: 10.3389/fpls.2022.968466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
Isoflavones are major secondary metabolites that are exclusively produced by legumes, including soybean. Soy isoflavones play important roles in human health as well as in the plant defense system. The isoflavone content is influenced by minor-effect quantitative trait loci, which interact with polygenetic and environmental factors. It has been difficult to clarify the regulation of isoflavone biosynthesis because of its complex heritability and the influence of external factors. Here, using a genotype-by-sequencing-based genome-wide association mapping study, 189 mutant soybean genotypes (the mutant diversity pool, MDP) were genotyped on the basis of 25,646 high-quality single nucleotide polymorphisms (SNPs) with minor allele frequency of >0.01 except for missing data. All the accessions were phenotyped by determining the contents of 12 isoflavones in the soybean seeds in two consecutive years (2020 and 2021). Then, quantitative trait nucleotides (QTNs) related to isoflavone contents were identified and validated using multi-locus GWAS models. A total of 112 and 46 QTNs related to isoflavone contents were detected by multiple MLM-based models in 2020 and 2021, respectively. Of these, 12 and 5 QTNs were related to more than two types of isoflavones in 2020 and 2021, respectively. Forty-four QTNs were detected within the 441-Kb physical interval surrounding Gm05:38940662. Of them, four QTNs (Gm05:38936166, Gm05:38936167, Gm05:38940662, and Gm05:38940717) were located at Glyma.05g206900 and Glyma.05g207000, which encode glutathione S-transferase THETA 1 (GmGSTT1), as determined from previous quantitative trait loci annotations and the literature. We detected substantial differences in the transcript levels of GmGSTT1 and two other core genes (IFS1 and IFS2) in the isoflavone biosynthetic pathway between the original cultivar and its mutant. The results of this study provide new information about the factors affecting isoflavone contents in soybean seeds and will be useful for breeding soybean lines with high and stable concentrations of isoflavones.
Collapse
Affiliation(s)
- Jung Min Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, South Korea
- Division of Plant Biotechnology, Chonnam National University, Gwangju, South Korea
| | - Jae Il Lyu
- Department of Horticulture, College of Industrial Sciences, Kongju National University, Yesan, South Korea
| | - Dong-Gun Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, South Korea
| | - Nguyen Ngoc Hung
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, South Korea
- Division of Plant Biotechnology, Chonnam National University, Gwangju, South Korea
| | - Ji Su Seo
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, South Korea
- Division of Plant Biotechnology, Chonnam National University, Gwangju, South Korea
| | - Joon-Woo Ahn
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, South Korea
| | - You Jin Lim
- Department of Horticultural Biotechnology, Institute of Life Sciences & Resources, Kyung Hee University, Yongin, South Korea
| | - Seok Hyun Eom
- Department of Horticultural Biotechnology, Institute of Life Sciences & Resources, Kyung Hee University, Yongin, South Korea
| | - Bo-Keun Ha
- Division of Plant Biotechnology, Chonnam National University, Gwangju, South Korea
| | - Soon-Jae Kwon
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, South Korea
| |
Collapse
|
8
|
Chang D, Gao S, Zhou G, Deng S, Jia J, Wang E, Cao W. The chromosome-level genome assembly of Astragalus sinicus and comparative genomic analyses provide new resources and insights for understanding legume-rhizobial interactions. PLANT COMMUNICATIONS 2022; 3:100263. [PMID: 35529952 PMCID: PMC9073321 DOI: 10.1016/j.xplc.2021.100263] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 11/02/2021] [Accepted: 11/05/2021] [Indexed: 05/20/2023]
Abstract
The legume species Astragalus sinicus (Chinese milk vetch [CMV]) has been widely cultivated for centuries in southern China as one of the most important green manures/cover crops for improving rice productivity and preventing soil degeneration. In this study, we generated the first chromosome-scale reference genome of CMV by combining PacBio and Illumina sequencing with high-throughput chromatin conformation capture (Hi-C) technology. The CMV genome was 595.52 Mb in length, with a contig N50 size of 1.50 Mb. Long terminal repeats (LTRs) had been amplified and contributed to genome size expansion in CMV. CMV has undergone two whole-genome duplication (WGD) events, and the genes retained after the WGD shared by Papilionoideae species shaped the rhizobial symbiosis and the hormonal regulation of nodulation. The chalcone synthase (CHS) gene family was expanded and was expressed primarily in the roots of CMV. Intriguingly, we found that resistance genes were more highly expressed in roots than in nodules of legume species, suggesting that their expression may be increased to bolster plant immunity in roots to cope with pathogen infection in legumes. Our work sheds light on the genetic basis of nodulation and symbiosis in CMV and provides a benchmark for accelerating genetic research and molecular breeding in the future.
Collapse
Affiliation(s)
- Danna Chang
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Songjuan Gao
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Guopeng Zhou
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shuhan Deng
- Glbizzia Biological Science and Technology, Co, Ltd, Beijing, China
| | - Jizeng Jia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Corresponding author
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- Corresponding author
| | - Weidong Cao
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Corresponding author
| |
Collapse
|
9
|
Ji H, Xiao R, Lyu X, Chen J, Zhang X, Wang Z, Deng Z, Wang Y, Wang H, Li R, Chai Q, Hao Y, Xu Q, Liao J, Wang Q, Liu Y, Tang R, Liu B, Li X. Differential light-dependent regulation of soybean nodulation by papilionoid-specific HY5 homologs. Curr Biol 2022; 32:783-795.e5. [PMID: 35081330 DOI: 10.1016/j.cub.2021.12.041] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 11/15/2021] [Accepted: 12/16/2021] [Indexed: 11/30/2022]
Abstract
Legumes have evolved photosynthesis and symbiotic nitrogen fixation for the acquisition of energy and nitrogen nutrients. During the transition from heterotrophic to autotrophic growth, blue light primarily triggers photosynthesis and low soil nitrogen induces symbiotic nodulation. Whether and how darkness and blue light influence root symbiotic nodulation during this transition is unknown. Here, we show that short-term darkness promotes nodulation and that blue light inhibits nodulation through two soybean TGACG-motif-binding factors (STF1 and STF2), which are Papilionoideae-specific transcription factors and divergent orthologs of Arabidopsis ELONGATED HYPOCOTYL 5 (HY5). STF1 and STF2 negatively regulate soybean nodulation by repressing the transcription of nodule inception a (GmNINa), which is a central regulator of nodulation, in response to darkness and blue light. STF1 and STF2 are not capable of moving from the shoots to roots, and they act both locally and systemically to mediate darkness- and blue-light-regulated nodulation. We further show that cryptochromes GmCRY1s are required for nodulation in the dark and partially contribute to the blue light inhibition of nodulation. In addition, root GmCRY1s mediate blue-light-induced transcription of STF1 and STF2, and intriguingly, GmCRY1b can interact with STF1 and STF2 to stabilize the protein stability of STF1 and STF2. Our results establish that the blue light receptor GmCRY1s-STF1/2 module plays a pivotal role in integrating darkness/blue light and nodulation signals. Furthermore, our findings reveal a molecular basis by which photosensory pathways modulate nodulation and autotrophic growth through an intricate interplay facilitating seedling establishment in response to low nitrogen and light signals.
Collapse
Affiliation(s)
- Hongtao Ji
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Renhao Xiao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiangguang Lyu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jiahuan Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuehai Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhijuan Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhiping Deng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China
| | - Yongliang Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hui Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ran Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qingqing Chai
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yongfang Hao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qi Xu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Junwen Liao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qian Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yu Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ruizhen Tang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Bin Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Xia Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| |
Collapse
|
10
|
Yuan S, Zhou S, Feng Y, Zhang C, Huang Y, Shan Z, Chen S, Guo W, Yang H, Yang Z, Qiu D, Chen H, Zhou X. Identification of the Important Genes of Bradyrhizobium diazoefficiens 113-2 Involved in Soybean Nodule Development and Senescence. Front Microbiol 2021; 12:754837. [PMID: 34858367 PMCID: PMC8632152 DOI: 10.3389/fmicb.2021.754837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 10/04/2021] [Indexed: 11/20/2022] Open
Abstract
Legume nodule development and senescence directly affect nitrogen fixation efficiency and involve a programmed series of molecular events. These molecular events are carried out synchronously by legumes and rhizobia. The characteristics and molecular mechanisms of nitrogen fixation at soybean important developmental stages play critical roles in soybean cultivation and fertilizer application. Although the gene expression of soybean were analyzed in nodules at five important soybean developmental stages, information on the expression of rhizobial genes in these nodule samples is limited. In the present study, we investigated the expression of Bradyrhizobium diazoefficiens 113-2 genes in the nodule samples from five developmental stages of soybean (Branching stage, flowering stage, fruiting stage, pod stage and harvest stage). Similar gene expression patterns of B. diazoefficiens 113-2 were existed during optimal symbiotic functioning, while different expression patterns were found among early nodule development, nitrogen fixation progress and nodule senescence. Besides, we identified 164 important different expression genes (DEGs) associated with nodule development and senescence. These DEGs included those encoding nod, nif, fix proteins and T3SS secretion system-related proteins, as well as proteins involved in nitrogen metabolism, ABC transporters and two-component system pathways. Gene Ontology, KEGG pathway and homology analysis of the identified DEGs revealed that most of these DEGs are uncharacterized genes associated with nodule development and senescence, and they are not core genes among the rhizobia genomes. Our results provide new clues for the understanding of the genetic determinants of soil rhizobia in nodule development and senescence, and supply theoretical basis for the creation of high efficiency soybean cultivation technology.
Collapse
Affiliation(s)
- Songli Yuan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of PRC, Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, China
| | - Shunxin Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of PRC, Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, China
| | - Yong Feng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Chanjuan Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of PRC, Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, China
| | - Yi Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of PRC, Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, China
| | - Zhihui Shan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of PRC, Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, China
| | - Shuilian Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of PRC, Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, China
| | - Wei Guo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of PRC, Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, China
| | - Hongli Yang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of PRC, Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, China
| | - Zhonglu Yang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of PRC, Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, China
| | - Dezhen Qiu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of PRC, Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, China
| | - Haifeng Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of PRC, Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, China
| | - Xinan Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of PRC, Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, China
| |
Collapse
|
11
|
Zhao Y, Zhang R, Jiang KW, Qi J, Hu Y, Guo J, Zhu R, Zhang T, Egan AN, Yi TS, Huang CH, Ma H. Nuclear phylotranscriptomics and phylogenomics support numerous polyploidization events and hypotheses for the evolution of rhizobial nitrogen-fixing symbiosis in Fabaceae. MOLECULAR PLANT 2021; 14:748-773. [PMID: 33631421 DOI: 10.1016/j.molp.2021.02.006] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 07/31/2020] [Accepted: 02/19/2021] [Indexed: 05/20/2023]
Abstract
Fabaceae are the third largest angiosperm family, with 765 genera and ∼19 500 species. They are important both economically and ecologically, and global Fabaceae crops are intensively studied in part for their nitrogen-fixing ability. However, resolution of the intrasubfamilial Fabaceae phylogeny and divergence times has remained elusive, precluding a reconstruction of the evolutionary history of symbiotic nitrogen fixation in Fabaceae. Here, we report a highly resolved phylogeny using >1500 nuclear genes from newly sequenced transcriptomes and genomes of 391 species, along with other datasets, for a total of 463 legumes spanning all 6 subfamilies and 333 of 765 genera. The subfamilies are maximally supported as monophyletic. The clade comprising subfamilies Cercidoideae and Detarioideae is sister to the remaining legumes, and Duparquetioideae and Dialioideae are successive sisters to the clade of Papilionoideae and Caesalpinioideae. Molecular clock estimation revealed an early radiation of subfamilies near the K/Pg boundary, marked by mass extinction, and subsequent divergence of most tribe-level clades within ∼15 million years. Phylogenomic analyses of thousands of gene families support 28 proposed putative whole-genome duplication/whole-genome triplication events across Fabaceae, including those at the ancestors of Fabaceae and five of the subfamilies, and further analyses supported the Fabaceae ancestral polyploidy. The evolution of rhizobial nitrogen-fixing nodulation in Fabaceae was probed by ancestral character reconstruction and phylogenetic analyses of related gene families and the results support the hypotheses of one or two switch(es) to rhizobial nodulation followed by multiple losses. Collectively, these results provide a foundation for further morphological and functional evolutionary analyses across Fabaceae.
Collapse
Affiliation(s)
- Yiyong Zhao
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of 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
| | - Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road, Kunming 650201, China
| | - Kai-Wen Jiang
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming 650224, PR China; Ningbo Botanical Garden Herbarium, Ningbo 315201, PR China
| | - Ji Qi
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of 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
| | - Jing Guo
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | - Renbin Zhu
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, PR China
| | - Taikui Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | - Ashley N Egan
- Department of Biology, Utah Valley University, Orem, UT 84058, USA
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road, Kunming 650201, China.
| | - Chien-Hsun Huang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China.
| | - Hong Ma
- Department of Biology, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA.
| |
Collapse
|
12
|
Yuan S, Ke D, Li R, Li X, Wang L, Chen H, Zhang C, Huang Y, Chen L, Hao Q, Yang H, Cao D, Chen S, Guo W, Shan Z, Yang Z, Zhang X, Qiu D, Guan Y, Zhou X. Genome-wide survey of soybean papain-like cysteine proteases and their expression analysis in root nodule symbiosis. BMC PLANT BIOLOGY 2020; 20:517. [PMID: 33183238 PMCID: PMC7659060 DOI: 10.1186/s12870-020-02725-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 10/26/2020] [Indexed: 05/23/2023]
Abstract
BACKGROUND Plant papain-like cysteine proteases (PLCPs) are a large class of proteolytic enzymes and play important roles in root nodule symbiosis (RNS), while the whole-genome studies of PLCP family genes in legume are quite limited, and the roles of Glycine max PLCPs (GmPLCPs) in nodulation, nodule development and senescence are not fully understood. RESULTS In the present study, we identified 97 GmPLCPs and performed a genome-wide survey to explore the expansion of soybean PLCP family genes and their relationships to RNS. Nineteen paralogous pairs of genomic segments, consisting of 77 GmPLCPs, formed by whole-genome duplication (WGD) events were identified, showing a high degree of complexity in duplication. Phylogenetic analysis among different species showed that the lineage differentiation of GmPLCPs occurred after family expansion, and large tandem repeat segment were specifically in soybean. The expression patterns of GmPLCPs in symbiosis-related tissues and nodules identified RNS-related GmPLCPs and provided insights into their putative symbiotic functions in soybean. The symbiotic function analyses showed that a RNS-related GmPLCP gene (Glyma.04G190700) really participate in nodulation and nodule development. CONCLUSIONS Our findings improved our understanding of the functional diversity of legume PLCP family genes, and provided insights into the putative roles of the legume PLCPs in nodulation, nodule development and senescence.
Collapse
Affiliation(s)
- Songli Yuan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Danxia Ke
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Life Sciences & Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, China
| | - Rong Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiangyong Li
- College of Life Sciences & Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, China
| | - Lei Wang
- College of Life Sciences & Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, China
| | - Haifeng Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Chanjuan Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yi Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Limiao Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Qingnan Hao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Hongli Yang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Dong Cao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Shuilian Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Wei Guo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Zhihui Shan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Zhonglu Yang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiaojuan Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Dezhen Qiu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yuefeng Guan
- FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Xinan Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China.
| |
Collapse
|
13
|
Wu Z, Liu H, Huang W, Yi L, Qin E, Yang T, Wang J, Qin R. Genome-Wide Identification, Characterization, and Regulation of RWP-RK Gene Family in the Nitrogen-Fixing Clade. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1178. [PMID: 32932820 PMCID: PMC7569760 DOI: 10.3390/plants9091178] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/09/2020] [Accepted: 09/09/2020] [Indexed: 12/12/2022]
Abstract
RWP-RK is a plant-specific family of transcription factors, involved in nitrate response, gametogenesis, and nodulation. However, genome-wide characterization, phylogeny, and the regulation of RWP-RK genes in the nodulating and non-nodulating plant species of nitrogen-fixing clade (NFC) are widely unknown. Therefore, we identified a total of 292 RWP-RKs, including 278 RWP-RKs from 25 NFC species and 14 RWP-RKs from the outgroup, Arabidopsis thaliana. We classified the 292 RWP-RKs in two subfamilies: the NIN-like proteins (NLPs) and the RWP-RK domain proteins (RKDs). The transcriptome and phylogenetic analysis of RWP-RKs suggested that, compared to RKD genes, the NLP genes were just upregulated in nitrate response and nodulation. Moreover, nodule-specific NLP genes of some nodulating NFC species may have a common ancestor (OG0002084) with AtNLP genes in A. thaliana. Further, co-expression networks of A.thaliana under N-starvation and N-supplementation conditions revealed that there is a higher correlation between expression of AtNLP genes and symbiotic genes during N-starvation. In P. vulgaris, we confirmed that N-starvation stimulated nodulation by regulating expression of PvNLP2, closely related to AtNLP6 and AtNLP7 with another common origin (OG0004041). Taken together, we concluded that different origins of the NLP genes involved in both N-starvation response and specific expression of nodulation would contribute to the evolution of nodulation in NFC plant species. Our results shed light on the phylogenetic relationships of NLP genes and their differential regulation in nitrate response of A. thaliana and nodulation of NFC.
Collapse
Affiliation(s)
- Zhihua Wu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China & Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, Wuhan 430074, China; (Z.W.); (H.L.); (W.H.); (L.Y.); (E.Q.); (T.Y.)
| | - Hong Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China & Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, Wuhan 430074, China; (Z.W.); (H.L.); (W.H.); (L.Y.); (E.Q.); (T.Y.)
| | - Wen Huang
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China & Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, Wuhan 430074, China; (Z.W.); (H.L.); (W.H.); (L.Y.); (E.Q.); (T.Y.)
| | - Lisha Yi
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China & Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, Wuhan 430074, China; (Z.W.); (H.L.); (W.H.); (L.Y.); (E.Q.); (T.Y.)
| | - Erdai Qin
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China & Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, Wuhan 430074, China; (Z.W.); (H.L.); (W.H.); (L.Y.); (E.Q.); (T.Y.)
| | - Tiange Yang
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China & Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, Wuhan 430074, China; (Z.W.); (H.L.); (W.H.); (L.Y.); (E.Q.); (T.Y.)
| | - Jing Wang
- Institute of Food and Nutrition Development, Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Rui Qin
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China & Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, Wuhan 430074, China; (Z.W.); (H.L.); (W.H.); (L.Y.); (E.Q.); (T.Y.)
| |
Collapse
|
14
|
Forrester NJ, Rebolleda-Gómez M, Sachs JL, Ashman TL. Polyploid plants obtain greater fitness benefits from a nutrient acquisition mutualism. THE NEW PHYTOLOGIST 2020; 227:944-954. [PMID: 32248526 DOI: 10.1111/nph.16574] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 03/20/2020] [Indexed: 06/11/2023]
Abstract
Polyploidy is a key driver of ecological and evolutionary processes in plants, yet little is known about its effects on biotic interactions. This gap in knowledge is especially profound for nutrient acquisition mutualisms, despite the fact that they regulate global nutrient cycles and structure ecosystems. Generalism in mutualistic interactions depends on the range of potential partners (niche breadth), the benefits obtained and ability to maintain benefits across a variety of partners (fitness plasticity). Here, we determine how each of these is influenced by polyploidy in the legume-rhizobium mutualism. We inoculated a broad geographic sample of natural diploid and autotetraploid alfalfa (Medicago sativa) lineages with a diverse panel of Sinorhizobium bacterial symbionts. To analyze the extent and mechanism of generalism, we measured host growth benefits and functional traits. Autotetraploid plants obtained greater fitness enhancement from mutualistic interactions and were better able to maintain this across diverse rhizobial partners (i.e. low plasticity in fitness) relative to diploids. These benefits were not attributed to increases in niche breadth, but instead reflect increased rewards from investment in the mutualism. Polyploid plants displayed greater generalization in bacterial mutualisms relative to diploids, illustrating another axis of advantage for polyploids over diploids.
Collapse
Affiliation(s)
- Nicole J Forrester
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Ave., Pittsburgh, PA, 15260, USA
| | - Maria Rebolleda-Gómez
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Ave., Pittsburgh, PA, 15260, USA
| | - Joel L Sachs
- Department of Evolution, Ecology, and Organismal Biology, University of California, 3401 Watkins Drive, Riverside, CA, 92521, USA
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Ave., Pittsburgh, PA, 15260, USA
| |
Collapse
|
15
|
Forrester NJ, Ashman TL. Autopolyploidy alters nodule-level interactions in the legume-rhizobium mutualism. AMERICAN JOURNAL OF BOTANY 2020; 107:179-185. [PMID: 31721161 DOI: 10.1002/ajb2.1375] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 06/17/2019] [Indexed: 05/22/2023]
Abstract
PREMISE Polyploidy is a major genetic driver of ecological and evolutionary processes in plants, yet its effects on plant interactions with mutualistic microbes remain unresolved. The legume-rhizobium symbiosis regulates global nutrient cycles and plays a role in the diversification of legume species. In this mutualism, rhizobia bacteria fix nitrogen in exchange for carbon provided by legume hosts. This exchange occurs inside root nodules, which house bacterial cells and represent the interface of legume-rhizobium interactions. Although polyploidy may directly impact the legume-rhizobium mutualism, no studies have explored how it alters the internal structure of nodules. METHODS We created synthetic autotetraploids using Medicago sativa subsp. caerulea. Neotetraploid plants and their diploid progenitors were singly inoculated with two strains of rhizobia, Sinorhizobium meliloti and S. medicae. Confocal microscopy was used to quantify internal traits of nodules produced by diploid and neotetraploid plants. RESULTS Autotetraploid plants produced larger nodules with larger nitrogen fixation zones than diploids for both strains of rhizobia, although the significance of these differences was limited by power. Neotetraploid M. sativa subsp. caerulea plants also produced symbiosomes that were significantly larger, nearly twice the size, than those present in diploids. CONCLUSIONS This study sheds light on how polyploidy directly affects a plant-bacterium mutualism and uncovers novel mechanisms. Changes in plant-microbe interactions that directly result from polyploidy likely contribute to the increased ability of polyploid legumes to establish in diverse environments.
Collapse
Affiliation(s)
- Nicole J Forrester
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA, 15260, USA
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA, 15260, USA
| |
Collapse
|
16
|
Wu Z, Wang M, Yang S, Chen S, Chen X, Liu C, Wang S, Wang H, Zhang B, Liu H, Qin R, Wang X. A global coexpression network of soybean genes gives insights into the evolution of nodulation in nonlegumes and legumes. THE NEW PHYTOLOGIST 2019; 223:2104-2119. [PMID: 30977533 DOI: 10.1111/nph.15845] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 04/02/2019] [Indexed: 06/09/2023]
Abstract
A coexpression network is a powerful tool for revealing genes' relationship with many biological processes. Mass transcriptomic and genomic data from different plant species provide the foundation for understanding the evolution of nodulation across the Viridiplantae at a systematic level. We used weighted coexpression network analysis (WGCNA) to mine a nodule-related module (NRM) in Glycine max. Comparative genomic analysis of 78 green plant species revealed that NRM genes are recruited from different evolutionary nodes along with gene duplication events. A set of core coexpressed genes within legumes may play vital roles in regulating nodule environments essential for nitrogen fixation, including oxygen concentrations, sulfur transport, and iron homeostasis (such as GmCHY). The regulation of these genes occurred mainly at the transcription level, although some of them, such as sulfate transporters, may also undergo positive selection at protein level. We revealed that ancient orthologs and duplication events before the origin of legumes were preadapted for symbiosis. Conserved coregulated genes found within legumes paved the way for nodule formation and nitrogen fixation. These findings provide significant insights into the evolution of nodulation and indicate promising candidates for identifying other key components of legume nodulation and nitrogen fixation.
Collapse
Affiliation(s)
- Zhihua Wu
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, South-Central University for Nationalities, Wuhan, Hubei Province, 430074, China
| | - Meirong Wang
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Siyu Yang
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Shengcai Chen
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Xu Chen
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Chang Liu
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Shixiang Wang
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Haijiao Wang
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Bao Zhang
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Hong Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, South-Central University for Nationalities, Wuhan, Hubei Province, 430074, China
| | - Rui Qin
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, South-Central University for Nationalities, Wuhan, Hubei Province, 430074, China
| | - Xuelu Wang
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| |
Collapse
|
17
|
Zhang L, Liu JY, Gu H, Du Y, Zuo JF, Zhang Z, Zhang M, Li P, Dunwell JM, Cao Y, Zhang Z, Zhang YM. Bradyrhizobium diazoefficiens USDA 110- Glycine max Interactome Provides Candidate Proteins Associated with Symbiosis. J Proteome Res 2018; 17:3061-3074. [PMID: 30091610 DOI: 10.1021/acs.jproteome.8b00209] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although the legume-rhizobium symbiosis is a most-important biological process, there is a limited knowledge about the protein interaction network between host and symbiont. Using interolog- and domain-based approaches, we constructed an interspecies protein interactome containing 5115 protein-protein interactions between 2291 Glycine max and 290 Bradyrhizobium diazoefficiens USDA 110 proteins. The interactome was further validated by the expression pattern analysis in nodules, gene ontology term semantic similarity, co-expression analysis, and luciferase complementation image assay. In the G. max-B. diazoefficiens interactome, bacterial proteins are mainly ion channel and transporters of carbohydrates and cations, while G. max proteins are mainly involved in the processes of metabolism, signal transduction, and transport. We also identified the top 10 highly interacting proteins (hubs) for each species. Kyoto Encyclopedia of Genes and Genomes pathway analysis for each hub showed that a pair of 14-3-3 proteins (SGF14g and SGF14k) and 5 heat shock proteins in G. max are possibly involved in symbiosis, and 10 hubs in B. diazoefficiens may be important symbiotic effectors. Subnetwork analysis showed that 18 symbiosis-related soluble N-ethylmaleimide sensitive factor attachment protein receptor proteins may play roles in regulating bacterial ion channels, and SGF14g and SGF14k possibly regulate the rhizobium dicarboxylate transport protein DctA. The predicted interactome provide a valuable basis for understanding the molecular mechanism of nodulation in soybean.
Collapse
Affiliation(s)
- Li Zhang
- Crop Information Center , College of Plant Science and Technology, Huazhong Agricultural University , Wuhan 430070 , China
- School of Public Health , Xinxiang Medical University , Xinxiang 453003 , China
| | - Jin-Yang Liu
- College of Agriculture, Nanjing Agricultural University , Nanjing 210095 , China
| | - Huan Gu
- College of Agriculture, Nanjing Agricultural University , Nanjing 210095 , China
| | - Yanfang Du
- Crop Information Center , College of Plant Science and Technology, Huazhong Agricultural University , Wuhan 430070 , China
| | - Jian-Fang Zuo
- Crop Information Center , College of Plant Science and Technology, Huazhong Agricultural University , Wuhan 430070 , China
| | - Zhibin Zhang
- Crop Information Center , College of Plant Science and Technology, Huazhong Agricultural University , Wuhan 430070 , China
| | - Menglin Zhang
- Crop Information Center , College of Plant Science and Technology, Huazhong Agricultural University , Wuhan 430070 , China
| | - Pan Li
- School of Public Health , Xinxiang Medical University , Xinxiang 453003 , China
| | - Jim M Dunwell
- School of Agriculture, Policy and Development , University of Reading , Reading RG6 6AR , United Kingdom
| | - Yangrong Cao
- College of Life Science and Technology , Huazhong Agricultural University , Wuhan 430070 , China
| | - Zuxin Zhang
- Crop Information Center , College of Plant Science and Technology, Huazhong Agricultural University , Wuhan 430070 , China
| | - Yuan-Ming Zhang
- Crop Information Center , College of Plant Science and Technology, Huazhong Agricultural University , Wuhan 430070 , China
| |
Collapse
|
18
|
Forrester NJ, Ashman TL. The direct effects of plant polyploidy on the legume-rhizobia mutualism. ANNALS OF BOTANY 2018; 121:209-220. [PMID: 29182713 PMCID: PMC5808787 DOI: 10.1093/aob/mcx121] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 09/08/2017] [Indexed: 05/09/2023]
Abstract
BACKGROUND Polyploidy is known to significantly alter plant genomes, phenotypes and interactions with the abiotic environment, yet the impacts of polyploidy on plant-biotic interactions are less well known. A particularly important plant-biotic interaction is the legume-rhizobia mutualism, in which rhizobia fix atmospheric nitrogen in exchange for carbon provided by legume hosts. This mutualism regulates nutrient cycles in natural ecosystems and provides nitrogen to agricultural environments. Despite the ecological, evolutionary and agricultural importance of plant polyploidy and the legume-rhizobia mutualism, it is not yet fully understood whether plant polyploidy directly alters mutualism traits or the consequences on plant growth. SCOPE The aim was to propose a conceptual framework to understand how polyploidy might directly enhance the quantity and quality of rhizobial symbionts hosted by legume plants, resulting in increased host access to fixed nitrogen (N). Mechanistic hypotheses have been devised to examine how polyploidy can directly alter traits that impact the quantity (e.g. nodule number, nodule size, terminal bacteroid differentiation) and quality of symbionts (e.g. nodule environment, partner choice, host sanctions). To evaluate these hypotheses, an exhaustive review of studies testing the effects of plant polyploidy on the mutualism was conducted. In doing so, overall trends were synthesized, highlighting the limited understanding of the mechanisms that underlie variation in results achieved thus far, revealing striking gaps in knowledge and uncovering areas ripe for future research. CONCLUSIONS Plant polyploidy can immediately alter nodule size, N fixation rate and the identity of rhizobial symbionts hosted by polyploid legumes, but many of the mechanistic hypotheses proposed here, such as bacteroid number and enhancements of the nodule environment, remain unexplored. Although current evidence supports a role of plant polyploidy in enhancing key aspects of the legume-rhizobia mutualism, the underlying mechanisms and effects on host benefit from the mutualism remain unresolved.
Collapse
Affiliation(s)
- Nicole J Forrester
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
- For correspondence. E-mail
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| |
Collapse
|
19
|
Powell AF, Doyle JJ. Non-Additive Transcriptomic Responses to Inoculation with Rhizobia in a Young Allopolyploid Compared with Its Diploid Progenitors. Genes (Basel) 2017; 8:E357. [PMID: 29189710 PMCID: PMC5748675 DOI: 10.3390/genes8120357] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 11/24/2017] [Accepted: 11/27/2017] [Indexed: 12/29/2022] Open
Abstract
Root nodule symbioses (nodulation) and whole genome duplication (WGD, polyploidy) are both important phenomena in the legume family (Leguminosae). Recently, it has been proposed that polyploidy may have played a critical role in the origin or refinement of nodulation. However, while nodulation and polyploidy have been studied independently, there have been no direct studies of mechanisms affecting the interactions between these phenomena in symbiotic, nodule-forming species. Here, we examined the transcriptome-level responses to inoculation in the young allopolyploid Glycine dolichocarpa (T2) and its diploid progenitor species to identify underlying processes leading to the enhanced nodulation responses previously identified in T2. We assessed the differential expression of genes and, using weighted gene co-expression network analysis (WGCNA), identified modules associated with nodulation and compared their expression between species. These transcriptomic analyses revealed patterns of non-additive expression in T2, with evidence of transcriptional responses to inoculation that were distinct from one or both progenitors. These differential responses elucidate mechanisms underlying the nodulation-related differences observed between T2 and the diploid progenitors. Our results indicate that T2 has reduced stress-related transcription, coupled with enhanced transcription of modules and genes implicated in hormonal signaling, both of which are important for nodulation.
Collapse
Affiliation(s)
- Adrian F Powell
- Section of Plant Biology, School of Integrated Plant Sciences, Cornell University, Ithaca, NY 14853, USA.
- Boyce Thompson Institute, Ithaca, NY 14853, USA.
| | - Jeff J Doyle
- Section of Plant Breeding and Genetics, School of Integrated Plant Sciences, Cornell University, Ithaca, NY 14853, USA.
| |
Collapse
|
20
|
Taylor A, Qiu YL. Evolutionary History of Subtilases in Land Plants and Their Involvement in Symbiotic Interactions. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:489-501. [PMID: 28353400 DOI: 10.1094/mpmi-10-16-0218-r] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Subtilases, a family of proteases involved in a variety of developmental processes in land plants, are also involved in both mutualistic symbiosis and host-pathogen interactions in different angiosperm lineages. We examined the evolutionary history of subtilase genes across land plants through a phylogenetic analysis integrating amino acid sequence data from full genomes, transcriptomes, and characterized subtilases of 341 species of diverse green algae and land plants along with subtilases from 12 species of other eukaryotes, archaea, and bacteria. Our analysis reconstructs the subtilase gene phylogeny and identifies 11 new gene lineages, six of which have no previously characterized members. Two large, previously unnamed, subtilase gene lineages that diverged before the origin of angiosperms accounted for the majority of subtilases shown to be associated with symbiotic interactions. These lineages expanded through both whole-genome and tandem duplication, with differential neofunctionalization and subfunctionalization creating paralogs associated with different symbioses, including nodulation with nitrogen-fixing bacteria, arbuscular mycorrhizae, and pathogenesis in different plant clades. This study demonstrates for the first time that a key gene family involved in plant-microbe interactions proliferated in size and functional diversity before the explosive radiation of angiosperms.
Collapse
Affiliation(s)
- Alexander Taylor
- University of Michigan, Department of Ecology and Evolutionary Biology, Ann Arbor, MI, U.S.A
| | - Yin-Long Qiu
- University of Michigan, Department of Ecology and Evolutionary Biology, Ann Arbor, MI, U.S.A
| |
Collapse
|
21
|
Yano K, Aoki S, Liu M, Umehara Y, Suganuma N, Iwasaki W, Sato S, Soyano T, Kouchi H, Kawaguchi M. Function and evolution of a Lotus japonicus AP2/ERF family transcription factor that is required for development of infection threads. DNA Res 2017; 24:193-203. [PMID: 28028038 PMCID: PMC5397602 DOI: 10.1093/dnares/dsw052] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 10/25/2016] [Indexed: 01/05/2023] Open
Abstract
Legume-rhizobium symbiosis is achieved by two major events evolutionarily acquired: root hair infection and organogenesis. Infection thread (IT) development is a distinct element for rhizobial infection. Through ITs, rhizobia are efficiently transported from infection foci on root hairs to dividing meristematic cortical cells. To unveil this process, we performed genetic screening using Lotus japonicus MG-20 and isolated symbiotic mutant lines affecting nodulation, root hair morphology, and IT development. Map-based cloning identified an AP2/ERF transcription factor gene orthologous to Medicago truncatula ERN1. LjERN1 was activated in response to rhizobial infection and depended on CYCLOPS and NSP2. Legumes conserve an ERN1 homolog, ERN2, that functions redundantly with ERN1 in M. truncatula. Phylogenetic analysis showed that the lineages of ERN1 and ERN2 genes originated from a gene duplication event in the common ancestor of legume plants. However, genomic analysis suggested the lack of ERN2 gene in the L. japonicus genome, consistent with Ljern1 mutants exhibited a root hair phenotype that is observed in ern1/ern2 double mutants in M. truncatula. Molecular evolutionary analysis suggested that the nonsynonymous/synonymous rate ratios of legume ERN1 genes was almost identical to that of non-legume plants, whereas the ERN2 genes experienced a relaxed selective constraint.
Collapse
Affiliation(s)
- Koji Yano
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
- Division of Symbiotic Systems, National Institute for Basic Biology, National Institute for Natural Sciences, Okazaki 444-8585, Japan
| | - Seishiro Aoki
- Department of General Systems Studies, Graduate School of Arts and Sciences, the University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Meng Liu
- Division of Symbiotic Systems, National Institute for Basic Biology, National Institute for Natural Sciences, Okazaki 444-8585, Japan
- Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Okazaki 444-8585, Japan and
| | - Yosuke Umehara
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Norio Suganuma
- Department of Life Science, Aichi University of Education, Kariya, Aichi 448–8542, Japan
| | - Wataru Iwasaki
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Shusei Sato
- Kazusa DNA Research Institute, Kisarazu, Chiba 292–0812, Japan
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8577, Japan
| | - Takashi Soyano
- Division of Symbiotic Systems, National Institute for Basic Biology, National Institute for Natural Sciences, Okazaki 444-8585, Japan
- Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Okazaki 444-8585, Japan and
| | - Hiroshi Kouchi
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Masayoshi Kawaguchi
- Division of Symbiotic Systems, National Institute for Basic Biology, National Institute for Natural Sciences, Okazaki 444-8585, Japan
- Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Okazaki 444-8585, Japan and
| |
Collapse
|
22
|
Roberts WR, Roalson EH. Comparative transcriptome analyses of flower development in four species of Achimenes (Gesneriaceae). BMC Genomics 2017; 18:240. [PMID: 28320315 PMCID: PMC5359931 DOI: 10.1186/s12864-017-3623-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 03/11/2017] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Flowers have an amazingly diverse display of colors and shapes, and these characteristics often vary significantly among closely related species. The evolution of diverse floral form can be thought of as an adaptive response to pollination and reproduction, but it can also be seen through the lens of morphological and developmental constraints. To explore these interactions, we use RNA-seq across species and development to investigate gene expression and sequence evolution as they relate to the evolution of the diverse flowers in a group of Neotropical plants native to Mexico-magic flowers (Achimenes, Gesneriaceae). RESULTS The assembled transcriptomes contain between 29,000 and 42,000 genes expressed during development. We combine sequence orthology and coexpression clustering with analyses of protein evolution to identify candidate genes for roles in floral form evolution. Over 25% of transcripts captured were distinctive to Achimenes and overrepresented by genes involved in transcription factor activity. Using a model-based clustering approach we find dynamic, temporal patterns of gene expression among species. Selection tests provide evidence of positive selection in several genes with roles in pigment production, flowering time, and morphology. Combining these approaches to explore genes related to flower color and flower shape, we find distinct patterns that correspond to transitions of floral form among Achimenes species. CONCLUSIONS The floral transcriptomes developed from four species of Achimenes provide insight into the mechanisms involved in the evolution of diverse floral form among closely related species with different pollinators. We identified several candidate genes that will serve as an important and useful resource for future research. High conservation of sequence structure, patterns of gene coexpression, and detection of positive selection acting on few genes suggests that large phenotypic differences in floral form may be caused by genetic differences in a small set of genes. Our characterized floral transcriptomes provided here should facilitate further analyses into the genomics of flower development and the mechanisms underlying the evolution of diverse flowers in Achimenes and other Neotropical Gesneriaceae.
Collapse
Affiliation(s)
- Wade R. Roberts
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA 99164-1030 USA
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4236 USA
| | - Eric H. Roalson
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA 99164-1030 USA
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4236 USA
| |
Collapse
|
23
|
Powell AF, Doyle JJ. Enhanced rhizobial symbiotic capacity in an allopolyploid species of Glycine (Leguminosae). AMERICAN JOURNAL OF BOTANY 2016; 103:1771-1782. [PMID: 27562208 DOI: 10.3732/ajb.1600060] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 06/15/2016] [Indexed: 06/06/2023]
Abstract
PREMISE OF THE STUDY Previous studies have shown that polyploidy can alter biotic interactions, and it has been suggested that these effects may contribute to the increased ability for colonization of new habitats shown by many allopolyploids. Little is known, however, about the effects of allopolyploidy, which combines hybridity and genome doubling, on symbiotic interactions with rhizobial bacteria. METHODS We examined interactions of the allopolyploid Glycine dolichocarpa (designated T2) with novel rhizobial partners, such as might occur in a context of colonization, and compared these with the responses of its diploid progenitors, G. tomentella (D3) and G. syndetika (D4). We assessed root hair response, nodule formation, nodule mass, nodule number, and plant biomass. KEY RESULTS The allopolyploid (T2) showed a greater root hair deformation response when exposed to rhizobia, compared with either diploid. T2 had a greater probability of forming nodules with NGR234 compared with diploid D4, and greater total nodule mass per nodulated plant compared with diploid D3. T2 also had greater plant biomass responses to nitrogen and when exposed to NGR234. CONCLUSIONS The allopolyploid is characterized by transgressive responses to rhizobia for some variables, while also combining certain parental diploid responses such that its capacity for interactions with rhizobia appears to be greater than for either diploid progenitor. This overall enhanced nodulation capacity and the ability to make greater gains from exposure to both rhizobia and additional nitrogen indicate a greater potential of the allopolyploid to benefit from these factors both generally and in a context of colonization.
Collapse
Affiliation(s)
- Adrian F Powell
- Cornell University, Section of Plant Biology, 412 Mann Library, Cornell University, Ithaca, New York 14853 USA
| | - Jeff J Doyle
- Cornell University, Section of Plant Biology, 412 Mann Library, Cornell University, Ithaca, New York 14853 USA
- Cornell University, Section of Plant Breeding and Genetics, 240 Emerson Hall, Cornell University, Ithaca, New York 14853 USA
| |
Collapse
|
24
|
Xu X, Feng Y, Fang S, Xu J, Wang X, Guo W. Genome-wide characterization of the β-1,3-glucanase gene family in Gossypium by comparative analysis. Sci Rep 2016; 6:29044. [PMID: 27353015 PMCID: PMC4926093 DOI: 10.1038/srep29044] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 06/10/2016] [Indexed: 01/10/2023] Open
Abstract
The β-1,3-glucanase gene family is involved in a wide range of plant developmental processes as well as pathogen defense mechanisms. Comprehensive analyses of β-1,3-glucanase genes (GLUs) have not been reported in cotton. Here, we identified 67, 68, 130 and 158 GLUs in four sequenced cotton species, G. raimondii (D5), G. arboreum (A2), G. hirsutum acc. TM-1 (AD1), and G. barbadense acc. 3-79 (AD2), respectively. Cotton GLUs can be classified into the eight subfamilies (A-H), and their protein domain architecture and intron/exon structure are relatively conserved within each subfamily. Sixty-seven GLUs in G. raimondii were anchored onto 13 chromosomes, with 27 genes involved in segmental duplications, and 13 in tandem duplications. Expression patterns showed highly developmental and spatial regulation of GLUs in TM-1. In particular, the expression of individual member of GLUs in subfamily E was limited to roots, leaves, floral organs or fibers. Members of subfamily E also showed more protein evolution and subgenome expression bias compared with members of other subfamilies. We clarified that GLU42 and GLU43 in subfamily E were preferentially expressed in root and leaf tissues and significantly upregulated after Verticillium dahliae inoculation. Silencing of GLU42 and GLU43 significantly increased the susceptibility of cotton to V. dahliae.
Collapse
Affiliation(s)
- Xiaoyang Xu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R&D Engineering Research Center, MOE, Nanjing Agricultural University, Nanjing 210095, China
| | - Yue Feng
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R&D Engineering Research Center, MOE, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuai Fang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R&D Engineering Research Center, MOE, Nanjing Agricultural University, Nanjing 210095, China
| | - Jun Xu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R&D Engineering Research Center, MOE, Nanjing Agricultural University, Nanjing 210095, China
| | - Xinyu Wang
- College of Life Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Wangzhen Guo
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R&D Engineering Research Center, MOE, Nanjing Agricultural University, Nanjing 210095, China
| |
Collapse
|
25
|
Shi FX, Li MR, Li YL, Jiang P, Zhang C, Pan YZ, Liu B, Xiao HX, Li LF. The impacts of polyploidy, geographic and ecological isolations on the diversification of Panax (Araliaceae). BMC PLANT BIOLOGY 2015; 15:297. [PMID: 26690782 PMCID: PMC4687065 DOI: 10.1186/s12870-015-0669-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 11/23/2015] [Indexed: 05/12/2023]
Abstract
BACKGROUND Panax L. is a medicinally important genus within family Araliaceae, where almost all species are of cultural significance for traditional Chinese medicine. Previous studies suggested two independent origins of the East Asia and North America disjunct distribution of this genus and multiple rounds of whole genome duplications (WGDs) might have occurred during the evolutionary process. RESULTS We employed multiple chloroplast and nuclear markers to investigate the evolution and diversification of Panax. Our phylogenetic analyses confirmed previous observations of the independent origins of disjunct distribution and both ancient and recent WGDs have occurred within Panax. The estimations of divergence time implied that the ancient WGD might have occurred before the establishment of Panax. Thereafter, at least two independent recent WGD events have occurred within Panax, one of which has led to the formation of three geographically isolated tetraploid species P. ginseng, P. japonicus and P. quinquefolius. Population genetic analyses showed that the diploid species P. notoginseng harbored significantly lower nucleotide diversity than those of the two tetraploid species P. ginseng and P. quinquefolius and the three species showed distinct nucleotide variation patterns at exon regions. CONCLUSION Our findings based on the phylogenetic and population genetic analyses, coupled with the species distribution patterns of Panax, suggested that the two rounds of WGD along with the geographic and ecological isolations might have together contributed to the evolution and diversification of this genus.
Collapse
Affiliation(s)
- Feng-Xue Shi
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
| | - Ming-Rui Li
- Institute of Grassland Science, Northeast Normal University, Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, 130024, China.
| | - Ya-Ling Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
| | - Peng Jiang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
| | - Cui Zhang
- Institute of Grassland Science, Northeast Normal University, Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, 130024, China.
| | - Yue-Zhi Pan
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
| | - Hong-Xing Xiao
- Institute of Grassland Science, Northeast Normal University, Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, 130024, China.
| | - Lin-Feng Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
| |
Collapse
|
26
|
Qiu L, Lin JS, Xu J, Sato S, Parniske M, Wang TL, Downie JA, Xie F. SCARN a Novel Class of SCAR Protein That Is Required for Root-Hair Infection during Legume Nodulation. PLoS Genet 2015; 11:e1005623. [PMID: 26517270 PMCID: PMC4627827 DOI: 10.1371/journal.pgen.1005623] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 09/30/2015] [Indexed: 12/22/2022] Open
Abstract
Rhizobial infection of legume root hairs requires a rearrangement of the actin cytoskeleton to enable the establishment of plant-made infection structures called infection threads. In the SCAR/WAVE (Suppressor of cAMP receptor defect/WASP family verpolin homologous protein) actin regulatory complex, the conserved N-terminal domains of SCAR proteins interact with other components of the SCAR/WAVE complex. The conserved C-terminal domains of SCAR proteins bind to and activate the actin-related protein 2/3 (ARP2/3) complex, which can bind to actin filaments catalyzing new actin filament formation by nucleating actin branching. We have identified, SCARN (SCAR-Nodulation), a gene required for root hair infection of Lotus japonicus by Mesorhizobium loti. Although the SCARN protein is related to Arabidopsis thaliana SCAR2 and SCAR4, it belongs to a distinct legume-sub clade. We identified other SCARN-like proteins in legumes and phylogeny analyses suggested that SCARN may have arisen from a gene duplication and acquired specialized functions in root nodule symbiosis. Mutation of SCARN reduced formation of infection-threads and their extension into the root cortex and slightly reduced root-hair length. Surprisingly two of the scarn mutants showed constitutive branching of root hairs in uninoculated plants. However we observed no effect of scarn mutations on trichome development or on the early actin cytoskeletal accumulation that is normally seen in root hair tips shortly after M. loti inoculation, distinguishing them from other symbiosis mutations affecting actin nucleation. The C-terminal domain of SCARN binds to ARPC3 and ectopic expression of the N-terminal SCAR-homology domain (but not the full length protein) inhibited nodulation. In addition, we found that SCARN expression is enhanced by M. loti in epidermal cells and that this is directly regulated by the NODULE INCEPTION (NIN) transcription factor. Characterization of Lotus japonicus mutants defective for nodule infection by rhizobia led to the identification of a gene we named SCARN. Two of the five alleles caused formation of branched root-hairs in uninoculated seedlings, suggesting SCARN plays a role in the microtubule and actin-regulated polar growth of root hairs. SCARN is one of three L. japonicus proteins containing the conserved N and C terminal domains predicted to be required for rearrangement of the actin cytoskeleton. SCARN expression is induced in response to rhizobial nodulation factors by the NIN (NODULE INCEPTION) transcription factor and appears to be adapted to promoting rhizobial infection, possibly arising from a gene duplication event. SCARN binds to ARPC3, one of the predicted components in the actin-related protein complex involved in the activation of actin nucleation.
Collapse
Affiliation(s)
- Liping Qiu
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jie-shun Lin
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ji Xu
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Shusei Sato
- Kazusa DNA Research Institute, Kisarazu, Japan
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Martin Parniske
- University of Munich LMU, Faculty of Biology, Martinsried, Germany
| | | | | | - Fang Xie
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- * E-mail:
| |
Collapse
|
27
|
Werner GDA, Cornwell WK, Cornelissen JHC, Kiers ET. Evolutionary signals of symbiotic persistence in the legume-rhizobia mutualism. Proc Natl Acad Sci U S A 2015; 112:10262-9. [PMID: 26041807 PMCID: PMC4547229 DOI: 10.1073/pnas.1424030112] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Understanding the origins and evolutionary trajectories of symbiotic partnerships remains a major challenge. Why are some symbioses lost over evolutionary time whereas others become crucial for survival? Here, we use a quantitative trait reconstruction method to characterize different evolutionary stages in the ancient symbiosis between legumes (Fabaceae) and nitrogen-fixing bacteria, asking how labile is symbiosis across different host clades. We find that more than half of the 1,195 extant nodulating legumes analyzed have a high likelihood (>95%) of being in a state of high symbiotic persistence, meaning that they show a continued capacity to form the symbiosis over evolutionary time, even though the partnership has remained facultative and is not obligate. To explore patterns associated with the likelihood of loss and retention of the N2-fixing symbiosis, we tested for correlations between symbiotic persistence and legume distribution, climate, soil and trait data. We found a strong latitudinal effect and demonstrated that low mean annual temperatures are associated with high symbiotic persistence in legumes. Although no significant correlations between soil variables and symbiotic persistence were found, nitrogen and phosphorus leaf contents were positively correlated with legumes in a state of high symbiotic persistence. This pattern suggests that highly demanding nutrient lifestyles are associated with more stable partnerships, potentially because they "lock" the hosts into symbiotic dependency. Quantitative reconstruction methods are emerging as a powerful comparative tool to study broad patterns of symbiont loss and retention across diverse partnerships.
Collapse
Affiliation(s)
- Gijsbert D A Werner
- Department of Ecological Science, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - William K Cornwell
- Ecology and Evolution Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Johannes H C Cornelissen
- Department of Ecological Science, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - E Toby Kiers
- Department of Ecological Science, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands;
| |
Collapse
|
28
|
Zhou L, Wang SB, Jian J, Geng QC, Wen J, Song Q, Wu Z, Li GJ, Liu YQ, Dunwell JM, Zhang J, Feng JY, Niu Y, Zhang L, Ren WL, Zhang YM. Identification of domestication-related loci associated with flowering time and seed size in soybean with the RAD-seq genotyping method. Sci Rep 2015; 5:9350. [PMID: 25797785 PMCID: PMC4369735 DOI: 10.1038/srep09350] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 03/02/2015] [Indexed: 12/02/2022] Open
Abstract
Flowering time and seed size are traits related to domestication. However, identification of domestication-related loci/genes of controlling the traits in soybean is rarely reported. In this study, we identified a total of 48 domestication-related loci based on RAD-seq genotyping of a natural population comprising 286 accessions. Among these, four on chromosome 12 and additional two on chromosomes 11 and 15 were associated with flowering time, and four on chromosomes 11 and 16 were associated with seed size. Of the five genes associated with flowering time and the three genes associated with seed size, three genes Glyma11g18720, Glyma11g15480 and Glyma15g35080 were homologous to Arabidopsis genes, additional five genes were found for the first time to be associated with these two traits. Glyma11g18720 and Glyma05g28130 were co-expressed with five genes homologous to flowering time genes in Arabidopsis, and Glyma11g15480 was co-expressed with 24 genes homologous to seed development genes in Arabidopsis. This study indicates that integration of population divergence analysis, genome-wide association study and expression analysis is an efficient approach to identify candidate domestication-related genes.
Collapse
Affiliation(s)
- Ling Zhou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Shi-Bo Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | | | - Qing-Chun Geng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Jia Wen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland 20705, USA
| | | | - Guang-Jun Li
- College of Life Science, Linyi University, Linyi 276005, China
| | - Yu-Qin Liu
- Crop Research Institute, Linyi Academy of Agricultural Sciences, Linyi 276012, China
| | - Jim M. Dunwell
- School of Agriculture, Policy and Development, University of Reading, Reading RG6 6AR, United Kingdom
| | - Jin Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Jian-Ying Feng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuan Niu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Li Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Wen-Long Ren
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuan-Ming Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
- Statistical Genomics Lab, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| |
Collapse
|
29
|
Vanneste K, Maere S, Van de Peer Y. Tangled up in two: a burst of genome duplications at the end of the Cretaceous and the consequences for plant evolution. Philos Trans R Soc Lond B Biol Sci 2015; 369:rstb.2013.0353. [PMID: 24958926 PMCID: PMC4071526 DOI: 10.1098/rstb.2013.0353] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Genome sequencing has demonstrated that besides frequent small-scale duplications, large-scale duplication events such as whole genome duplications (WGDs) are found on many branches of the evolutionary tree of life. Especially in the plant lineage, there is evidence for recurrent WGDs, and the ancestor of all angiosperms was in fact most likely a polyploid species. The number of WGDs found in sequenced plant genomes allows us to investigate questions about the roles of WGDs that were hitherto impossible to address. An intriguing observation is that many plant WGDs seem associated with periods of increased environmental stress and/or fluctuations, a trend that is evident for both present-day polyploids and palaeopolyploids formed around the Cretaceous–Palaeogene (K–Pg) extinction at 66 Ma. Here, we revisit the WGDs in plants that mark the K–Pg boundary, and discuss some specific examples of biological innovations and/or diversifications that may be linked to these WGDs. We review evidence for the processes that could have contributed to increased polyploid establishment at the K–Pg boundary, and discuss the implications on subsequent plant evolution in the Cenozoic.
Collapse
Affiliation(s)
- Kevin Vanneste
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Steven Maere
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium Genomics Research Institute (GRI), University of Pretoria, 0028 Pretoria, South Africa
| |
Collapse
|
30
|
Cannon SB, McKain MR, Harkess A, Nelson MN, Dash S, Deyholos MK, Peng Y, Joyce B, Stewart CN, Rolf M, Kutchan T, Tan X, Chen C, Zhang Y, Carpenter E, Wong GKS, Doyle JJ, Leebens-Mack J. Multiple polyploidy events in the early radiation of nodulating and nonnodulating legumes. Mol Biol Evol 2014; 32:193-210. [PMID: 25349287 DOI: 10.1093/molbev/msu296] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Unresolved questions about evolution of the large and diverse legume family include the timing of polyploidy (whole-genome duplication; WGDs) relative to the origin of the major lineages within the Fabaceae and to the origin of symbiotic nitrogen fixation. Previous work has established that a WGD affects most lineages in the Papilionoideae and occurred sometime after the divergence of the papilionoid and mimosoid clades, but the exact timing has been unknown. The history of WGD has also not been established for legume lineages outside the Papilionoideae. We investigated the presence and timing of WGDs in the legumes by querying thousands of phylogenetic trees constructed from transcriptome and genome data from 20 diverse legumes and 17 outgroup species. The timing of duplications in the gene trees indicates that the papilionoid WGD occurred in the common ancestor of all papilionoids. The earliest diverging lineages of the Papilionoideae include both nodulating taxa, such as the genistoids (e.g., lupin), dalbergioids (e.g., peanut), phaseoloids (e.g., beans), and galegoids (=Hologalegina, e.g., clovers), and clades with nonnodulating taxa including Xanthocercis and Cladrastis (evaluated in this study). We also found evidence for several independent WGDs near the base of other major legume lineages, including the Mimosoideae-Cassiinae-Caesalpinieae (MCC), Detarieae, and Cercideae clades. Nodulation is found in the MCC and papilionoid clades, both of which experienced ancestral WGDs. However, there are numerous nonnodulating lineages in both clades, making it unclear whether the phylogenetic distribution of nodulation is due to independent gains or a single origin followed by multiple losses.
Collapse
Affiliation(s)
- Steven B Cannon
- USDA-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, IA
| | - Michael R McKain
- Department of Plant Biology, University of Georgia Donald Danforth Plant Sciences Center, St Louis, MO
| | - Alex Harkess
- Department of Plant Biology, University of Georgia
| | - Matthew N Nelson
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia The School of Plant Biology, The University of Western Australia, Crawley, WA, Australia
| | - Sudhansu Dash
- Virtual Reality Application Center, Iowa State University
| | - Michael K Deyholos
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Yanhui Peng
- Department of Plant Sciences, The University of Tennessee
| | - Blake Joyce
- Department of Plant Sciences, The University of Tennessee
| | | | - Megan Rolf
- Donald Danforth Plant Sciences Center, St Louis, MO
| | - Toni Kutchan
- Donald Danforth Plant Sciences Center, St Louis, MO
| | - Xuemei Tan
- BGI-Shenzhen, Bei Shan Industrial Zone, Shenzhen, China
| | - Cui Chen
- BGI-Shenzhen, Bei Shan Industrial Zone, Shenzhen, China
| | - Yong Zhang
- BGI-Shenzhen, Bei Shan Industrial Zone, Shenzhen, China
| | - Eric Carpenter
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada BGI-Shenzhen, Bei Shan Industrial Zone, Shenzhen, China Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Jeff J Doyle
- L. H. Bailey Hortorium, Department of Plant Biology, Cornell University
| | | |
Collapse
|
31
|
Sherman-Broyles S, Bombarely A, Powell AF, Doyle JL, Egan AN, Coate JE, Doyle JJ. The wild side of a major crop: soybean's perennial cousins from Down Under. AMERICAN JOURNAL OF BOTANY 2014; 101:1651-65. [PMID: 25326613 DOI: 10.3732/ajb.1400121] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The accumulation of over 30 years of basic research on the biology, genetic variation, and evolution of the wild perennial relatives of soybean (Glycine max) provides a foundation to improve cultivated soybean. The cultivated soybean and its wild progenitor, G. soja, have a center of origin in eastern Asia and are the only two species in the annual subgenus Soja. Systematic and evolutionary studies of the ca. 30 perennial species of subgenus Glycine, native to Australia, have benefited from the availability of the G. max genomic sequence. The perennial species harbor many traits of interest to soybean breeders, among them resistance to major soybean pathogens such as cyst nematode and leaf rust. New species in the Australian subgenus continue to be described, due to the collection of new material and to insights gleaned through systematic studies of accessions in germplasm collections. Ongoing studies in perennial species focus on genomic regions that contain genes for key traits relevant to soybean breeding. These comparisons also include the homoeologous regions that are the result of polyploidy in the common ancestor of all Glycine species. Subgenus Glycine includes a complex of recently formed allopolyploids that are the focus of studies aimed at elucidating genomic, transcriptomic, physiological, taxonomic, morphological, developmental, and ecological processes related to polyploid evolution. Here we review what has been learned over the past 30 years and outline ongoing work on photosynthesis, nitrogen fixation, and floral biology, much of it drawing on new technologies and resources.
Collapse
Affiliation(s)
| | | | - Adrian F Powell
- Cornell University, 412 Mann Library Building, Ithaca, New York 14853 USA
| | - Jane L Doyle
- Cornell University, 412 Mann Library Building, Ithaca, New York 14853 USA
| | - Ashley N Egan
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington D.C. 20013-7012 USA
| | - Jeremy E Coate
- Reed College, Department of Biology, 3203 SE Woodstock Blvd., Portland, Oregon 97202 USA
| | - Jeff J Doyle
- Cornell University, 412 Mann Library Building, Ithaca, New York 14853 USA
| |
Collapse
|
32
|
A single evolutionary innovation drives the deep evolution of symbiotic N2-fixation in angiosperms. Nat Commun 2014; 5:4087. [PMID: 24912610 PMCID: PMC4059933 DOI: 10.1038/ncomms5087] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 05/09/2014] [Indexed: 01/16/2023] Open
Abstract
Symbiotic associations occur in every habitat on earth, but we know very little about their evolutionary histories. Current models of trait evolution cannot adequately reconstruct the deep history of symbiotic innovation, because they assume homogenous evolutionary processes across millions of years. Here we use a recently developed, heterogeneous and quantitative phylogenetic framework to study the origin of the symbiosis between angiosperms and nitrogen-fixing (N2) bacterial symbionts housed in nodules. We compile the largest database of global nodulating plant species and reconstruct the symbiosis’ evolution. We identify a single, cryptic evolutionary innovation driving symbiotic N2-fixation evolution, followed by multiple gains and losses of the symbiosis, and the subsequent emergence of ‘stable fixers’ (clades extremely unlikely to lose the symbiosis). Originating over 100 MYA, this innovation suggests deep homology in symbiotic N2-fixation. Identifying cryptic innovations on the tree of life is key to understanding the evolution of complex traits, including symbiotic partnerships. Symbiotic associations are widespread, yet their evolutionary histories remain poorly understood. Here, Werner et. al. show a single evolutionary innovation driving symbiotic nitrogen fixation, followed by multiple gains and losses of the symbiosis and the emergence of groups with stable nitrogen fixers.
Collapse
|