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Meziadi C, Alvarez-Diaz JC, Thareau V, Gratias A, Marande W, Soler-Garzon A, Miklas PN, Pflieger S, Geffroy V. Fine-mapping and evolutionary history of R-BPMV, a dominant resistance gene to Bean pod mottle virus in Phaseolus vulgaris L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 137:8. [PMID: 38092992 DOI: 10.1007/s00122-023-04513-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023]
Abstract
KEY MESSAGE R-BPMV is located within a recently expanded TNL cluster in the Phaseolus genus with suppressed recombination and known for resistance to multiple pathogens including potyviruses controlled by the I gene. Bean pod mottle virus (BPMV) is a comovirus that infects common bean and legumes in general. BPMV is distributed throughout the world and is a major threat on soybean, a closely related species of common bean. In common bean, BAT93 was reported to carry the R-BPMV resistance gene conferring resistance to BPMV and linked with the I resistance gene. To fine map R-BPMV, 182 recombinant inbred lines (RILs) derived from the cross BAT93 × JaloEEP558 were genotyped with polymerase chain reaction (PCR)-based markers developed using genome assemblies from G19833 and BAT93, as well as BAT93 BAC clone sequences. Analysis of RILs carrying key recombination events positioned R-BPMV to a target region containing at least 16 TIR-NB-LRR (TNL) sequences in BAT93. Because the I cluster presents a suppression of recombination and a large number of repeated sequences, none of the 16 TNLs could be excluded as R-BPMV candidate gene. The evolutionary history of the TNLs for the I cluster were reconstructed using microsynteny and phylogenetic analyses within the legume family. A single I TNL was present in Medicago truncatula and lost in soybean, mirroring the absence of complete BPMV resistance in soybean. Amplification of TNLs in the I cluster predates the divergence of the Phaseolus species, in agreement with the emergence of R-BPMV before the separation of the common bean wild centers of diversity. This analysis provides PCR-based markers useful in marker-assisted selection (MAS) and laid the foundation for cloning of R-BPMV resistance gene in order to transfer the resistance into soybean.
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Affiliation(s)
- Chouaïb Meziadi
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, 91190, Gif Sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Cité, CNRS, INRAE, 91190, Gif Sur Yvette, Rue Noetzlin, 91405, Orsay, France
| | - Juan-Camilo Alvarez-Diaz
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, 91190, Gif Sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Cité, CNRS, INRAE, 91190, Gif Sur Yvette, Rue Noetzlin, 91405, Orsay, France
| | - Vincent Thareau
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, 91190, Gif Sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Cité, CNRS, INRAE, 91190, Gif Sur Yvette, Rue Noetzlin, 91405, Orsay, France
| | - Ariane Gratias
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, 91190, Gif Sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Cité, CNRS, INRAE, 91190, Gif Sur Yvette, Rue Noetzlin, 91405, Orsay, France
| | | | - Alvaro Soler-Garzon
- Irrigated Agriculture Research and Extension Center, Washington State Univ, Prosser, WA, USA
| | - Phillip N Miklas
- Grain Legume Genetics and Physiology Research Unit, USDA ARS, Prosser, WA, USA
| | - Stéphanie Pflieger
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, 91190, Gif Sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Cité, CNRS, INRAE, 91190, Gif Sur Yvette, Rue Noetzlin, 91405, Orsay, France
| | - Valérie Geffroy
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, 91190, Gif Sur Yvette, France.
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Cité, CNRS, INRAE, 91190, Gif Sur Yvette, Rue Noetzlin, 91405, Orsay, France.
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Chen S, Wang T, Shu J, Xiang Q, Yang T, Zhang X, Yan Y. Plastid Phylogenomics and Plastomic Diversity of the Extant Lycophytes. Genes (Basel) 2022; 13:genes13071280. [PMID: 35886063 PMCID: PMC9316050 DOI: 10.3390/genes13071280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/12/2022] [Accepted: 07/13/2022] [Indexed: 02/01/2023] Open
Abstract
Although extant lycophytes represent the most ancient surviving lineage of early vascular plants, their plastomic diversity has long been neglected. The ancient evolutionary history and distinct genetic diversity patterns of the three lycophyte families, each with its own characteristics, provide an ideal opportunity to investigate the interfamilial relationships of lycophytes and their associated patterns of evolution. To compensate for the lack of data on Lycopodiaceae, we sequenced and assembled 14 new plastid genomes (plastomes). Combined with other lycophyte plastomes available online, we reconstructed the phylogenetic relationships of the extant lycophytes based on 93 plastomes. We analyzed, traced, and compared the plastomic diversity and divergence of the three lycophyte families (Isoëtaceae, Lycopodiaceae, and Selaginellaceae) in terms of plastomic diversity by comparing their plastome sizes, GC contents, substitution rates, structural rearrangements, divergence times, ancestral states, RNA editings, and gene losses. Comparative analysis of plastid phylogenomics and plastomic diversity of three lycophyte families will set a foundation for further studies in biology and evolution in lycophytes and therefore in vascular plants.
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Affiliation(s)
- Sisi Chen
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen 518114, China; (S.C.); (T.W.); (J.S.); (T.Y.)
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing 100093, China;
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ting Wang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen 518114, China; (S.C.); (T.W.); (J.S.); (T.Y.)
- College of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, China
| | - Jiangping Shu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen 518114, China; (S.C.); (T.W.); (J.S.); (T.Y.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Qiaoping Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing 100093, China;
| | - Tuo Yang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen 518114, China; (S.C.); (T.W.); (J.S.); (T.Y.)
| | - Xianchun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing 100093, China;
- Correspondence: (X.Z.); (Y.Y.)
| | - Yuehong Yan
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen 518114, China; (S.C.); (T.W.); (J.S.); (T.Y.)
- Correspondence: (X.Z.); (Y.Y.)
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Tang Y, Zhao Y, Li C, Yang G, Peng J, Xu Z. New insights into the evolutionary characteristic between the New World and Old World Lupinus species using complete chloroplast genomes. ALL LIFE 2021. [DOI: 10.1080/26895293.2021.1926341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Affiliation(s)
- Yiwang Tang
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, People’s Republic of China
| | - Yunlin Zhao
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, People’s Republic of China
| | - Chaoyang Li
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, People’s Republic of China
| | - Guiyan Yang
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, People’s Republic of China
- College of Forestry, Northwest A & F University, Yangling, People’s Republic of China
| | - Jiao Peng
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, People’s Republic of China
| | - Zhenggang Xu
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, People’s Republic of China
- College of Forestry, Northwest A & F University, Yangling, People’s Republic of China
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Circadian Rhythms in Legumes: What Do We Know and What Else Should We Explore? Int J Mol Sci 2021; 22:ijms22094588. [PMID: 33925559 PMCID: PMC8123782 DOI: 10.3390/ijms22094588] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/16/2021] [Accepted: 04/21/2021] [Indexed: 12/15/2022] Open
Abstract
The natural timing devices of organisms, commonly known as biological clocks, are composed of specific complex folding molecules that interact to regulate the circadian rhythms. Circadian rhythms, the changes or processes that follow a 24-h light–dark cycle, while endogenously programmed, are also influenced by environmental factors, especially in sessile organisms such as plants, which can impact ecosystems and crop productivity. Current knowledge of plant clocks emanates primarily from research on Arabidopsis, which identified the main components of the circadian gene regulation network. Nonetheless, there remain critical knowledge gaps related to the molecular components of circadian rhythms in important crop groups, including the nitrogen-fixing legumes. Additionally, little is known about the synergies and trade-offs between environmental factors and circadian rhythm regulation, especially how these interactions fine-tune the physiological adaptations of the current and future crops in a rapidly changing world. This review highlights what is known so far about the circadian rhythms in legumes, which include major as well as potential future pulse crops that are packed with nutrients, particularly protein. Based on existing literature, this review also identifies the knowledge gaps that should be addressed to build a sustainable food future with the reputed “poor man’s meat”.
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Developments and Prospects in Imperative Underexploited Vegetable Legumes Breeding: A Review. Int J Mol Sci 2020; 21:ijms21249615. [PMID: 33348635 PMCID: PMC7766301 DOI: 10.3390/ijms21249615] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/15/2020] [Accepted: 11/23/2020] [Indexed: 02/07/2023] Open
Abstract
Vegetable legumes are an essential source of carbohydrates, vitamins, and minerals, along with health-promoting bioactive chemicals. The demand for the use of either fresh or processed vegetable legumes is continually expanding on account of the growing consumer awareness about their well-balanced diet. Therefore, sustaining optimum yields of vegetable legumes is extremely important. Here we seek to present d etails of prospects of underexploited vegetable legumes for food availability, accessibility, and improved livelihood utilization. So far research attention was mainly focused on pulse legumes' performance as compared to vegetable legumes. Wild and cultivated vegetable legumes vary morphologically across diverse habitats. This could make them less known, underutilized, and underexploited, and make them a promising potential nutritional source in developing nations where malnutrition still exists. Research efforts are required to promote underexploited vegetable legumes, for improving their use to feed the ever-increasing population in the future. In view of all the above points, here we have discussed underexploited vegetable legumes with tremendous potential; namely, vegetable pigeon pea (Cajanus cajan), cluster bean (Cyamopsis tetragonoloba), winged bean (Psophocarpus tetragonolobus), dolichos bean (Lablab purpureus), and cowpea (Vigna unguiculata), thereby covering the progress related to various aspects such as pre-breeding, molecular markers, quantitative trait locus (QTLs), genomics, and genetic engineering. Overall, this review has summarized the information related to advancements in the breeding of vegetable legumes which will ultimately help in ensuring food and nutritional security in developing nations.
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Elessawy FM, Bazghaleh N, Vandenberg A, Purves RW. Polyphenol profile comparisons of seed coats of five pulse crops using a semi-quantitative liquid chromatography-mass spectrometric method. PHYTOCHEMICAL ANALYSIS : PCA 2020; 31:458-471. [PMID: 31869515 DOI: 10.1002/pca.2909] [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: 08/08/2019] [Revised: 10/22/2019] [Accepted: 11/22/2019] [Indexed: 06/10/2023]
Abstract
INTRODUCTION Pulse crops are nutritious and therefore widely grown. Pulse seed coats are typically discarded, despite their high content of polyphenols that are known for their antioxidant properties and health benefits. A better understanding of polyphenol diversity and biochemical pathways will ultimately provide insight into how polyphenols are linked to health benefits, which will help to better utilise these seed coats. OBJECTIVES To explore polyphenol profiles among seed coats of diverse genotypes of five pulse crops using a targeted liquid chromatography mass spectrometry (LC-MS) method. METHODS Four genotypes of each of common bean, chickpea, pea, lentil and faba bean seed coats were selected for analysis. Following extraction, polyphenols were quantified using LC-MS. RESULTS An LC-MS method was developed to quantify 98 polyphenols from 13 different classes in 30 min. The low-tannin seed coats had the lowest concentrations of all polyphenols. Chickpea and pea seed coats had the most similar polyphenolic profiles. The black common bean showed the most diverse seed coat polyphenol profile, including several anthocyanins not detected in any of the other seed coats. CONCLUSION The LC-MS method reported herein was used to show polyphenol diversity within several polyphenol classes among the pulse crop seed coats. Detected in all seed coats, flavonols and hydroxybenzoic acids appear well-conserved in the edible Fabaceae. The presence of anthocyanins, flavan-3-ols and proanthocyanins in the coloured seed coats suggests that unique divergent branches were introduced in the flavonoid biosynthetic pathway, possibly in response to environmental stressors.
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Affiliation(s)
- Fatma M Elessawy
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Navid Bazghaleh
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Albert Vandenberg
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Randy W Purves
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Centre for Veterinary Drug Residues, Canadian Food Inspection Agency, Saskatoon, Saskatchewan, Canada
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Teplyakova SB, Volkov VA, Dzyubenko EА, Potokina EК. Variability of the photoperiod response in guar (Cyamopsis tetragonoloba (L.) Taub.) genotypes of different geographic origin. Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj19.547] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- S. B. Teplyakova
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR)
| | - V. A. Volkov
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR)
| | - E. А. Dzyubenko
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR)
| | - E. К. Potokina
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR); St. Petersburg State University
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Dubois O, Allanic C, Charvet CL, Guégnard F, Février H, Théry-Koné I, Cortet J, Koch C, Bouvier F, Fassier T, Marcon D, Magnin-Robert JB, Peineau N, Courtot E, Huau C, Meynadier A, Enguehard-Gueiffier C, Neveu C, Boudesocque-Delaye L, Sallé G. Lupin (Lupinus spp.) seeds exert anthelmintic activity associated with their alkaloid content. Sci Rep 2019; 9:9070. [PMID: 31227784 PMCID: PMC6588613 DOI: 10.1038/s41598-019-45654-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 06/12/2019] [Indexed: 12/20/2022] Open
Abstract
The growing range of drug resistant parasitic nematode populations threatens the sustainability of ruminant farming worldwide. In this context, nutraceuticals, animal feed that provides necessary dietary requirements while ensuring parasite control, could contribute to increase farming sustainability in developed and low resource settings. In this study, we evaluated the anthelmintic potential of lupin seed extracts against the major ruminant trichostrongylids, Haemonchus contortus and Teladorsagia circumcincta. In vitro observations showed that seed extracts from commercially available lupin varieties could significantly but moderately inhibit larval migration. This anthelmintic effect was mediated by the seed alkaloid content and was potent against both fully susceptible and multidrug resistant H. contortus isolates as well as a susceptible T. circumcincta isolate. Analytical chemistry revealed a set of four lupanine and sparteine-derivatives with anthelmintic activity, and electrophysiology assays on recombinant nematode acetylcholine receptors suggested an antagonistic mode of action for lupin alkaloids. An in vivo trial in H. contortus infected lupin-fed ewes and goats failed to demonstrate any direct anthelmintic effect of crude lupin seeds but infected lupin-fed goats suffered significantly less parasite-mediated blood losses. Altogether, our findings suggest that the anthelmintic potential of lupin remains limited. However, the potent alkaloids identified could lead to the development of novel drugs or may be used in combination with current anthelmintics to improve their efficacy.
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Affiliation(s)
- O Dubois
- UMR1282 Infectiologie et Santé Publique, INRA, Université de Tours, F-37380, Nouzilly, France.,EA 7502 SIMBA, Université de Tours, Faculté de Pharmacie, F-37000, Tours, France
| | - C Allanic
- UMR1282 Infectiologie et Santé Publique, INRA, Université de Tours, F-37380, Nouzilly, France
| | - C L Charvet
- UMR1282 Infectiologie et Santé Publique, INRA, Université de Tours, F-37380, Nouzilly, France
| | - F Guégnard
- UMR1282 Infectiologie et Santé Publique, INRA, Université de Tours, F-37380, Nouzilly, France
| | - H Février
- UMR1282 Infectiologie et Santé Publique, INRA, Université de Tours, F-37380, Nouzilly, France
| | - I Théry-Koné
- EA 7502 SIMBA, Université de Tours, Faculté de Pharmacie, F-37000, Tours, France
| | - J Cortet
- UMR1282 Infectiologie et Santé Publique, INRA, Université de Tours, F-37380, Nouzilly, France
| | - C Koch
- UMR1282 Infectiologie et Santé Publique, INRA, Université de Tours, F-37380, Nouzilly, France
| | - F Bouvier
- UE332 La Sapinière, INRA, F-18174, Osmoy, France
| | - T Fassier
- UE332 La Sapinière, INRA, F-18174, Osmoy, France
| | - D Marcon
- UE332 La Sapinière, INRA, F-18174, Osmoy, France
| | - J B Magnin-Robert
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France
| | - N Peineau
- Département Physiologie Animale, Université de Tours, Faculté des Sciences et Techniques, F-37000, Tours, France
| | - E Courtot
- UMR1282 Infectiologie et Santé Publique, INRA, Université de Tours, F-37380, Nouzilly, France
| | - C Huau
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, F-31326, Castanet-Tolosan, France
| | - A Meynadier
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, F-31326, Castanet-Tolosan, France
| | | | - C Neveu
- UMR1282 Infectiologie et Santé Publique, INRA, Université de Tours, F-37380, Nouzilly, France
| | - L Boudesocque-Delaye
- EA 7502 SIMBA, Université de Tours, Faculté de Pharmacie, F-37000, Tours, France
| | - G Sallé
- UMR1282 Infectiologie et Santé Publique, INRA, Université de Tours, F-37380, Nouzilly, France.
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Dorman HE, Wallace LE. Diversity of Nitrogen-Fixing Symbionts of Chamaecrista fasciculata (Partridge Pea) Across Variable Soils. SOUTHEAST NAT 2019. [DOI: 10.1656/058.018.0110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Hanna E. Dorman
- Department of Biology, University of Massachusetts, 611 North Pleasant Street, Morrill Science Center, RM 427, Amherst, MA 01007
| | - Lisa E. Wallace
- Department of Biological Sciences, Old Dominion University, Mills Godwin Building 110, Norfolk, VA 23529
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Chronopoulou EG, Papageorgiou AC, Ataya F, Nianiou-Obeidat I, Madesis P, Labrou NE. Expanding the Plant GSTome Through Directed Evolution: DNA Shuffling for the Generation of New Synthetic Enzymes With Engineered Catalytic and Binding Properties. FRONTIERS IN PLANT SCIENCE 2018; 9:1737. [PMID: 30555496 PMCID: PMC6284010 DOI: 10.3389/fpls.2018.01737] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 11/08/2018] [Indexed: 06/09/2023]
Abstract
Glutathione transferases (GSTs, EC. 2.5.1.18) are inducible multifunctional enzymes that are essential in the detoxification and degradation of toxic compounds. GSTs have considerable biotechnological potential. In the present work, a new method for the generation of synthetic GSTs was developed. Abiotic stress treatment of Phaseolus vulgaris and Glycine max plants led to the induction of total GST activity and allowed the creation of a GST-enriched cDNA library using degenerated GST-specific primers and reverse transcription-PCR. This library was further diversified by employing directed evolution through DNA shuffling. Activity screening of the evolved library led to the identification of a novel tau class GST enzyme (PvGmGSTUG). The enzyme was purified by affinity chromatography, characterized by kinetic analysis, and its structure was determined by X-ray crystallography. Interestingly, PvGmGSTUG displayed enhanced glutathione hydroperoxidase activity, which was significantly greater than that reported so far for natural tau class GSTs. In addition, the enzyme displayed unusual cooperative kinetics toward 1-chloro-2,4-dinitrochlorobenzene (CDNB) but not toward glutathione. The present work provides an easy approach for the simultaneous shuffling of GST genes from different plants, thus allowing the directed evolution of plants GSTome. This may permit the generation of new synthetic enzymes with interesting properties that are valuable in biotechnology.
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Affiliation(s)
- Evangelia G. Chronopoulou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, Athens, Greece
| | | | - Farid Ataya
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Irini Nianiou-Obeidat
- Laboratory of Genetics and Plant Breeding, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Panagiotis Madesis
- Institute of Applied Biosciences, Centre for Research and Technology Hellas (CERTH), Thessaloniki, Greece
| | - Nikolaos E. Labrou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, Athens, Greece
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Keller J, Imperial J, Ruiz-Argüeso T, Privet K, Lima O, Michon-Coudouel S, Biget M, Salmon A, Aïnouche A, Cabello-Hurtado F. RNA sequencing and analysis of three Lupinus nodulomes provide new insights into specific host-symbiont relationships with compatible and incompatible Bradyrhizobium strains. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 266:102-116. [PMID: 29241560 DOI: 10.1016/j.plantsci.2017.10.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 10/11/2017] [Accepted: 10/27/2017] [Indexed: 06/07/2023]
Abstract
Nitrogen fixation in the legume root-nodule symbiosis has a critical importance in natural and agricultural ecosystems and depends on the proper choice of the symbiotic partners. However, the genetic determinism of symbiotic specificity remains unclear. To study this process, we inoculated three Lupinus species (L. albus, L. luteus, L. mariae-josephae), belonging to the under-investigated tribe of Genistoids, with two Bradyrhizobium strains (B. japonicum, B. valentinum) presenting contrasted degrees of symbiotic specificity depending on the host. We produced the first transcriptomes (RNA-Seq) from lupine nodules in a context of symbiotic specificity. For each lupine species, we compared gene expression between functional and non-functional interactions and determined differentially expressed (DE) genes. This revealed that L. luteus and L. mariae-josephae (nodulated by only one of the Bradyrhizobium strains) specific nodulomes were richest in DE genes than L. albus (nodulation with both microsymbionts, but non-functional with B. valentinum) and share a higher number of these genes between them than with L. albus. In addition, a functional analysis of DE genes highlighted the central role of the genetic pathways controlling infection and nodule organogenesis, hormones, secondary, carbon and nitrogen metabolisms, as well as the implication of plant defence in response to compatible or incompatible Bradyrhizobium strains.
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Affiliation(s)
- J Keller
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France
| | - J Imperial
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223 Pozuelo de Alarcón, Madrid, Spain; Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas (CSIC), 28006 Madrid, Spain
| | - T Ruiz-Argüeso
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223 Pozuelo de Alarcón, Madrid, Spain
| | - K Privet
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France
| | - O Lima
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France
| | - S Michon-Coudouel
- Environmental and Human Genomics Platform, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France
| | - M Biget
- Environmental and Human Genomics Platform, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France
| | - A Salmon
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France
| | - A Aïnouche
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France
| | - F Cabello-Hurtado
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France.
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12
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Jiao K, Li X, Guo W, Su S, Luo D. High-Throughput RNA-Seq Data Analysis of the Single Nucleotide Polymorphisms (SNPs) and Zygomorphic Flower Development in Pea (Pisum sativum L.). Int J Mol Sci 2017; 18:E2710. [PMID: 29261120 PMCID: PMC5751311 DOI: 10.3390/ijms18122710] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 12/10/2017] [Accepted: 12/12/2017] [Indexed: 11/17/2022] Open
Abstract
Pea (Pisum sativum L.) is a model plant that has been used in classical genetics and organ development studies. However, its large and complex genome has hindered research investigations in pea. Here, we generated transcriptomes from different tissues or organs of three pea accessions using next-generation sequencing to assess single nucleotide polymorphisms (SNPs), and further investigated petal differentially expressed genes to elucidate the mechanisms regulating floral zygomorphy. Eighteen samples were sequenced, which yielded a total of 617 million clean reads, and de novo assembly resulted in 87,137 unigenes. A total of 9044 high-quality SNPs were obtained among the three accessions, and a consensus map was constructed. We further discovered several dorsoventral asymmetrically expressed genes that were confirmed by qRT-PCR among different petals, including previously reported three CYC-like proliferating cell factor (TCP) genes. One MADS-box gene was highly expressed in dorsal petals, and several MYB factors were predominantly expressed among dorsal, lateral, and/or ventral petals, together with a ventrally expressed TCP gene. In sum, our comprehensive database complements the existing resources for comparative genetic mapping and facilitates future investigations in legume zygomorphic flower development.
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Affiliation(s)
- Keyuan Jiao
- Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
| | - Xin Li
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing 210014, China.
| | - Wuxiu Guo
- Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
| | - Shihao Su
- Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
| | - Da Luo
- Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
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13
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Keller J, Rousseau-Gueutin M, Martin GE, Morice J, Boutte J, Coissac E, Ourari M, Aïnouche M, Salmon A, Cabello-Hurtado F, Aïnouche A. The evolutionary fate of the chloroplast and nuclear rps16 genes as revealed through the sequencing and comparative analyses of four novel legume chloroplast genomes from Lupinus. DNA Res 2017; 24:343-358. [PMID: 28338826 PMCID: PMC5737547 DOI: 10.1093/dnares/dsx006] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 02/02/2017] [Indexed: 01/21/2023] Open
Abstract
The Fabaceae family is considered as a model system for understanding chloroplast genome evolution due to the presence of extensive structural rearrangements, gene losses and localized hypermutable regions. Here, we provide sequences of four chloroplast genomes from the Lupinus genus, belonging to the underinvestigated Genistoid clade. Notably, we found in Lupinus species the functional loss of the essential rps16 gene, which was most likely replaced by the nuclear rps16 gene that encodes chloroplast and mitochondrion targeted RPS16 proteins. To study the evolutionary fate of the rps16 gene, we explored all available plant chloroplast, mitochondrial and nuclear genomes. Whereas no plant mitochondrial genomes carry an rps16 gene, many plants still have a functional nuclear and chloroplast rps16 gene. Ka/Ks ratios revealed that both chloroplast and nuclear rps16 copies were under purifying selection. However, due to the dual targeting of the nuclear rps16 gene product and the absence of a mitochondrial copy, the chloroplast gene may be lost. We also performed comparative analyses of lupine plastomes (SNPs, indels and repeat elements), identified the most variable regions and examined their phylogenetic utility. The markers identified here will help to reveal the evolutionary history of lupines, Genistoids and closely related clades.
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Affiliation(s)
- J Keller
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France
| | - M Rousseau-Gueutin
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France.,IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, BP35327, 35653 Le Rheu Cedex, France
| | - G E Martin
- CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398 Montpellier, France
| | - J Morice
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, BP35327, 35653 Le Rheu Cedex, France
| | - J Boutte
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France
| | - E Coissac
- Laboratoire d'Ecologie Alpine, CNRS - Université de Grenoble 1 - Université de Savoie, 38041 Grenoble, France
| | - M Ourari
- Département des Sciences Biologiques, Faculté des Sciences de la Nature et de la Vie, Université Abderrahmane Mira, 06000 Bejaia, Algeria
| | - M Aïnouche
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France
| | - A Salmon
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France
| | - F Cabello-Hurtado
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France
| | - A Aïnouche
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France
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14
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Chloroplast Genome Sequence of Clusterbean (Cyamopsis tetragonoloba L.): Genome Structure and Comparative Analysis. Genes (Basel) 2017; 8:genes8090212. [PMID: 28925932 PMCID: PMC5615346 DOI: 10.3390/genes8090212] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 08/16/2017] [Accepted: 08/21/2017] [Indexed: 12/23/2022] Open
Abstract
Clusterbean (Cyamopsis tetragonoloba L.), also known as guar, belongs to the family Leguminosae, and is an annual herbaceous legume. Guar is the main source of galactomannan for gas mining industries. In the present study, the draft chloroplast genome of clusterbean was generated and compared to some of the previously reported legume chloroplast genomes. The chloroplast genome of clusterbean is 152,530 bp in length, with a quadripartite structure consisting of large single copy (LSC) and small single copy (SSC) of 83,025 bp and 17,879 bp in size, respectively, and a pair of inverted repeats (IRs) of 25,790 bp in size. The chloroplast genome contains 114 unique genes, which includes 78 protein coding genes, 30 tRNAs, 4 rRNAs genes, and 2 pseudogenes. It also harbors a 50 kb inversion, typical of the Leguminosae family. The IR region of the clusterbean chloroplast genome has undergone an expansion, and hence, the whole rps19 gene is included in the IR, as compared to other legume plastid genomes. A total of 220 simple sequence repeats (SSRs) were detected in the clusterbean plastid genome. The analysis of the clusterbean plastid genome will provide useful insights for evolutionary, molecular and genetic engineering studies.
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15
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Zhang X, Zhai H, Wang Y, Tian X, Zhang Y, Wu H, Lü S, Yang G, Li Y, Wang L, Hu B, Bu Q, Xia Z. Functional conservation and diversification of the soybean maturity gene E1 and its homologs in legumes. Sci Rep 2016; 6:29548. [PMID: 27405888 PMCID: PMC4942777 DOI: 10.1038/srep29548] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 06/03/2016] [Indexed: 12/14/2022] Open
Abstract
Gene regulatory networks involved in flowering time and photoperiodic responses in legumes remain unknown. Although the major maturity gene E1 has been successfully deciphered in soybean, knowledge on the functional conservation of this gene is limited to a certain extent to E1 homologs in legumes. The ectopic expression of Phvul.009G204600 (PvE1L), an E1 homolog from common bean, delayed the onset of flowering in soybean. By contrast, the ectopic expression of Medtr2g058520 (MtE1L) from Medicago truncatula did not affect the flowering of soybean. Characterization of the late-flowering mte1l mutant indicated that MtE1L promoted flowering in Medicago truncatula. Moreover, all transgenic E1, PvE1L and MtE1L soybean lines exhibited phenotypic changes in terms of plant height. Transgenic E1 or PvE1L plants were taller than the wild-type, whereas transgenic MtE1L plants produced dwarf phenotype with few nodes and short internode. Thus, functional conservation and diversification of E1 family genes from legumes in the regulation of flowering and plant growth may be associated with lineage specification and genomic duplication.
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Affiliation(s)
- Xingzheng Zhang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Hong Zhai
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Yaying Wang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Xiaojie Tian
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Yupeng Zhang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Hongyan Wu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Shixiang Lü
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
- Information Center of Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
| | - Guang Yang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Yuqiu Li
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Lu Wang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Bo Hu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Qingyun Bu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Zhengjun Xia
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
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16
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Cabello-Hurtado F, Keller J, Ley J, Sanchez-Lucas R, Jorrín-Novo JV, Aïnouche A. Proteomics for exploiting diversity of lupin seed storage proteins and their use as nutraceuticals for health and welfare. J Proteomics 2016; 143:57-68. [PMID: 26996462 DOI: 10.1016/j.jprot.2016.03.026] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 03/07/2016] [Accepted: 03/09/2016] [Indexed: 02/07/2023]
Abstract
UNLABELLED Lupins have a variety of both traditional and modern uses. In the last decade, reports assessing the benefits of lupin seed proteins have proliferated and, nowadays, the pharmaceutical industry is interested in lupin proteins for human health. Modern genomics and proteomics have hugely contributed to describing the diversity of lupin storage genes and, above all, proteins. Most of these studies have been centered on few edible lupin species. However, Lupinus genus comprises hundreds of species spread throughout the Old and New Worlds, and these resources have been scarcely explored and exploited. We present here a detailed review of the literature on the potential of lupin seed proteins as nutraceuticals, and the use of -omic tools to analyze seed storage polypeptides in main edible lupins and their diversity at the Lupinus inter- and intra-species level. In this sense, proteomics, more than any other, has been a key approach. Proteomics has shown that lupin seed protein diversity, where post-translational modifications yield a large number of peptide variants with a potential concern in bioactivity, goes far beyond gene diversity. The future extended use of second and third generation proteomics should definitely help to go deeper into coverage and characterization of lupin seed proteome. BIOLOGICAL SIGNIFICANCE Some important topics concerning storage proteins from lupin seeds are presented and analyzed in an integrated way in this review. Proteomic approaches have been essential in characterizing lupin seed protein diversity, which goes far beyond gene diversity since the protein level adds to the latter differential proteolytic cleavage of conglutin pro-proteins and a diverse array of glycosylation forms and sites. Proteomics has also proved helpful for screening and studying Lupinus germplasm with the future aim of exploiting and improving food production, quality, and nutritional values.
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Affiliation(s)
- Francisco Cabello-Hurtado
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), University of Rennes 1, 263 av. du Général Leclerc, 35042 Rennes, France.
| | - Jean Keller
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), University of Rennes 1, 263 av. du Général Leclerc, 35042 Rennes, France
| | - José Ley
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), University of Rennes 1, 263 av. du Général Leclerc, 35042 Rennes, France
| | - Rosa Sanchez-Lucas
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Dpt. Biochemistry and Molecular Biology, University of Cordoba-CeiA3, Cordoba, Spain
| | - Jesús V Jorrín-Novo
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Dpt. Biochemistry and Molecular Biology, University of Cordoba-CeiA3, Cordoba, Spain
| | - Abdelkader Aïnouche
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), University of Rennes 1, 263 av. du Général Leclerc, 35042 Rennes, France
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17
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Karaki L, Da Silva P, Rizk F, Chouabe C, Chantret N, Eyraud V, Gressent F, Sivignon C, Rahioui I, Kahn D, Brochier-Armanet C, Rahbé Y, Royer C. Genome-wide analysis identifies gain and loss/change of function within the small multigenic insecticidal Albumin 1 family of Medicago truncatula. BMC PLANT BIOLOGY 2016; 16:63. [PMID: 26964738 PMCID: PMC4785745 DOI: 10.1186/s12870-016-0745-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 02/25/2016] [Indexed: 05/25/2023]
Abstract
BACKGROUND Albumin 1b peptides (A1b) are small disulfide-knotted insecticidal peptides produced by Fabaceae (also called Leguminosae). To date, their diversity among this plant family has been essentially investigated through biochemical and PCR-based approaches. The availability of high-quality genomic resources for several fabaceae species, among which the model species Medicago truncatula (Mtr), allowed for a genomic analysis of this protein family aimed at i) deciphering the evolutionary history of A1b proteins and their links with A1b-nodulins that are short non-insecticidal disulfide-bonded peptides involved in root nodule signaling and ii) exploring the functional diversity of A1b for novel bioactive molecules. RESULTS Investigating the Mtr genome revealed a remarkable expansion, mainly through tandem duplications, of albumin1 (A1) genes, retaining nearly all of the same canonical structure at both gene and protein levels. Phylogenetic analysis revealed that the ancestral molecule was most probably insecticidal giving rise to, among others, A1b-nodulins. Expression meta-analysis revealed that many A1b coding genes are silent and a wide tissue distribution of the A1 transcripts/peptides within plant organs. Evolutionary rate analyses highlighted branches and sites with positive selection signatures, including two sites shown to be critical for insecticidal activity. Seven peptides were chemically synthesized and folded in vitro, then assayed for their biological activity. Among these, AG41 (aka MtrA1013 isoform, encoded by the orphan TA24778 contig.), showed an unexpectedly high insecticidal activity. The study highlights the unique burst of diversity of A1 peptides within the Medicago genus compared to the other taxa for which full-genomes are available: no A1 member in Lotus, or in red clover to date, while only a few are present in chick pea, soybean or pigeon pea genomes. CONCLUSION The expansion of the A1 family in the Medicago genus is reminiscent of the situation described for another disulfide-rich peptide family, the "Nodule-specific Cysteine-Rich" (NCR), discovered within the same species. The oldest insecticidal A1b toxin was described from the Sophorae, dating the birth of this seed-defense function to more than 58 million years, and making this model of plant/insect toxin/receptor (A1b/insect v-ATPase) one of the oldest known.
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Affiliation(s)
- L. Karaki
- />INRA, UMR0203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621 Villeurbanne, France
- />Insa-Lyon, UMR0203 BF2I, F-69621 Villeurbanne, France
- />ER030-EDST; Department of Life and Earth Sciences, Faculty of Sciences II, Lebanese University, Beirut, Lebanon
- />Université de Lyon, F-69000 Lyon, France
| | - P. Da Silva
- />INRA, UMR0203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621 Villeurbanne, France
- />Insa-Lyon, UMR0203 BF2I, F-69621 Villeurbanne, France
- />Université de Lyon, F-69000 Lyon, France
| | - F. Rizk
- />ER030-EDST; Department of Life and Earth Sciences, Faculty of Sciences II, Lebanese University, Beirut, Lebanon
| | - C. Chouabe
- />Université de Lyon, F-69000 Lyon, France
- />UCBL, CarMeN Laboratory, INSERM UMR-1060, Cardioprotection Team, Faculté de Médecine, Univ Lyon-1, Université Claude Bernard Lyon1, 8 Avenue Rockefeller, 69373 Lyon Cedex 08, France
| | - N. Chantret
- />INRA, UMR1334 AGAP, 2 Place Pierre Viala, 34060 Montpellier, France
- />Supagro Montpellier, 2 Place Pierre Viala, 34060 Montpellier, France
| | - V. Eyraud
- />INRA, UMR0203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621 Villeurbanne, France
- />Insa-Lyon, UMR0203 BF2I, F-69621 Villeurbanne, France
- />Université de Lyon, F-69000 Lyon, France
| | - F. Gressent
- />INRA, UMR0203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621 Villeurbanne, France
- />Insa-Lyon, UMR0203 BF2I, F-69621 Villeurbanne, France
- />Université de Lyon, F-69000 Lyon, France
| | - C. Sivignon
- />INRA, UMR0203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621 Villeurbanne, France
- />Insa-Lyon, UMR0203 BF2I, F-69621 Villeurbanne, France
- />Université de Lyon, F-69000 Lyon, France
| | - I. Rahioui
- />INRA, UMR0203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621 Villeurbanne, France
- />Insa-Lyon, UMR0203 BF2I, F-69621 Villeurbanne, France
- />Université de Lyon, F-69000 Lyon, France
| | - D. Kahn
- />Université de Lyon, F-69000 Lyon, France
- />Université Claude Bernard Lyon 1; CNRS; INRA; UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, 43 boulevard du 11 novembre 1918, F-69622 Villeurbanne, France
| | - C. Brochier-Armanet
- />Université de Lyon, F-69000 Lyon, France
- />Université Claude Bernard Lyon 1; CNRS; INRA; UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, 43 boulevard du 11 novembre 1918, F-69622 Villeurbanne, France
| | - Y. Rahbé
- />INRA, UMR0203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621 Villeurbanne, France
- />Insa-Lyon, UMR0203 BF2I, F-69621 Villeurbanne, France
- />Université de Lyon, F-69000 Lyon, France
| | - C. Royer
- />INRA, UMR0203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621 Villeurbanne, France
- />Insa-Lyon, UMR0203 BF2I, F-69621 Villeurbanne, France
- />Université de Lyon, F-69000 Lyon, France
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18
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Savković U, ĐorĐević M, Šešlija Jovanović D, Lazarević J, Tucić N, Stojković B. Experimentally induced host-shift changes life-history strategy in a seed beetle. J Evol Biol 2016; 29:837-47. [DOI: 10.1111/jeb.12831] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 01/12/2016] [Accepted: 01/13/2016] [Indexed: 11/27/2022]
Affiliation(s)
- Uroš Savković
- Institute for Biological Research “Siniša Stanković”; University of Belgrade; Belgrade Serbia
| | - Mirko ĐorĐević
- Institute for Biological Research “Siniša Stanković”; University of Belgrade; Belgrade Serbia
| | - Darka Šešlija Jovanović
- Institute for Biological Research “Siniša Stanković”; University of Belgrade; Belgrade Serbia
| | - Jelica Lazarević
- Institute for Biological Research “Siniša Stanković”; University of Belgrade; Belgrade Serbia
| | - Nikola Tucić
- Institute for Biological Research “Siniša Stanković”; University of Belgrade; Belgrade Serbia
| | - Biljana Stojković
- Institute for Biological Research “Siniša Stanković”; University of Belgrade; Belgrade Serbia
- Faculty of Biology; University of Belgrade; Belgrade Serbia
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19
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Kaila T, Chaduvla PK, Saxena S, Bahadur K, Gahukar SJ, Chaudhury A, Sharma TR, Singh NK, Gaikwad K. Chloroplast Genome Sequence of Pigeonpea ( Cajanus cajan (L.) Millspaugh) and Cajanus scarabaeoides (L.) Thouars: Genome Organization and Comparison with Other Legumes. FRONTIERS IN PLANT SCIENCE 2016; 7:1847. [PMID: 28018385 PMCID: PMC5145887 DOI: 10.3389/fpls.2016.01847] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 11/23/2016] [Indexed: 05/09/2023]
Abstract
Pigeonpea (Cajanus cajan (L.) Millspaugh), a diploid (2n = 22) legume crop with a genome size of 852 Mbp, serves as an important source of human dietary protein especially in South East Asian and African regions. In this study, the draft chloroplast genomes of Cajanus cajan and Cajanus scarabaeoides (L.) Thouars were generated. Cajanus scarabaeoides is an important species of the Cajanus gene pool and has also been used for developing promising CMS system by different groups. A male sterile genotype harboring the C. scarabaeoides cytoplasm was used for sequencing the plastid genome. The cp genome of C. cajan is 152,242bp long, having a quadripartite structure with LSC of 83,455 bp and SSC of 17,871 bp separated by IRs of 25,398 bp. Similarly, the cp genome of C. scarabaeoides is 152,201bp long, having a quadripartite structure in which IRs of 25,402 bp length separates 83,423 bp of LSC and 17,854 bp of SSC. The pigeonpea cp genome contains 116 unique genes, including 30 tRNA, 4 rRNA, 78 predicted protein coding genes and 5 pseudogenes. A 50 kb inversion was observed in the LSC region of pigeonpea cp genome, consistent with other legumes. Comparison of cp genome with other legumes revealed the contraction of IR boundaries due to the absence of rps19 gene in the IR region. Chloroplast SSRs were mined and a total of 280 and 292 cpSSRs were identified in C. scarabaeoides and C. cajan respectively. RNA editing was observed at 37 sites in both C. scarabaeoides and C. cajan, with maximum occurrence in the ndh genes. The pigeonpea cp genome sequence would be beneficial in providing informative molecular markers which can be utilized for genetic diversity analysis and aid in understanding the plant systematics studies among major grain legumes.
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Affiliation(s)
- Tanvi Kaila
- ICAR-National Research Centre on Plant BiotechnologyNew Delhi, India
- Department of Bio & Nanotechnology, Guru Jambheshwar University of Science & TechnologyHisar, India
| | - Pavan K. Chaduvla
- ICAR-National Research Centre on Plant BiotechnologyNew Delhi, India
| | - Swati Saxena
- ICAR-National Research Centre on Plant BiotechnologyNew Delhi, India
| | | | - Santosh J. Gahukar
- Biotechnology Department, Biotechnology Centre, Dr. Panjabrao Deshmukh Krishi VidyapeethAkola, India
| | - Ashok Chaudhury
- Department of Bio & Nanotechnology, Guru Jambheshwar University of Science & TechnologyHisar, India
| | - T. R. Sharma
- ICAR-National Research Centre on Plant BiotechnologyNew Delhi, India
| | - N. K. Singh
- ICAR-National Research Centre on Plant BiotechnologyNew Delhi, India
| | - Kishor Gaikwad
- ICAR-National Research Centre on Plant BiotechnologyNew Delhi, India
- *Correspondence: Kishor Gaikwad
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Kigel J, Rosental L, Fait A. Seed Physiology and Germination of Grain Legumes. GRAIN LEGUMES 2015. [DOI: 10.1007/978-1-4939-2797-5_11] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Weller JL, Ortega R. Genetic control of flowering time in legumes. FRONTIERS IN PLANT SCIENCE 2015; 6:207. [PMID: 25914700 PMCID: PMC4391241 DOI: 10.3389/fpls.2015.00207] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 03/15/2015] [Indexed: 05/18/2023]
Abstract
The timing of flowering, and in particular the degree to which it is responsive to the environment, is a key factor in the adaptation of a given species to various eco-geographic locations and agricultural practices. Flowering time variation has been documented in many crop legumes, and selection for specific variants has permitted significant expansion and improvement in cultivation, from prehistoric times to the present day. Recent advances in legume genomics have accelerated the process of gene identification and functional analysis, and opened up new prospects for a molecular understanding of flowering time adaptation in this important crop group. Within the legumes, two species have been prominent in flowering time studies; the vernalization-responsive long-day species pea (Pisum sativum) and the warm-season short-day plant soybean (Glycine max). Analysis of flowering in these species is now being complemented by reverse genetics capabilities in the model legumes Medicago truncatula and Lotus japonicus, and the emergence of genome-scale resources in a range of other legumes. This review will outline the insights gained from detailed forward genetic analysis of flowering time in pea and soybean, highlighting the importance of light perception, the circadian clock and the FT family of flowering integrators. It discusses the current state of knowledge on genetic mechanisms for photoperiod and vernalization response, and concludes with a broader discussion of flowering time adaptation across legumes generally.
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Affiliation(s)
- James L. Weller
- *Correspondence: James L. Weller, School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia
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Martin GE, Rousseau-Gueutin M, Cordonnier S, Lima O, Michon-Coudouel S, Naquin D, de Carvalho JF, Aïnouche M, Salmon A, Aïnouche A. The first complete chloroplast genome of the Genistoid legume Lupinus luteus: evidence for a novel major lineage-specific rearrangement and new insights regarding plastome evolution in the legume family. ANNALS OF BOTANY 2014; 113:1197-210. [PMID: 24769537 PMCID: PMC4030815 DOI: 10.1093/aob/mcu050] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
BACKGROUND AND AIMS To date chloroplast genomes are available only for members of the non-protein amino acid-accumulating clade (NPAAA) Papilionoid lineages in the legume family (i.e. Millettioids, Robinoids and the 'inverted repeat-lacking clade', IRLC). It is thus very important to sequence plastomes from other lineages in order to better understand the unusual evolution observed in this model flowering plant family. To this end, the plastome of a lupine species, Lupinus luteus, was sequenced to represent the Genistoid lineage, a noteworthy but poorly studied legume group. METHODS The plastome of L. luteus was reconstructed using Roche-454 and Illumina next-generation sequencing. Its structure, repetitive sequences, gene content and sequence divergence were compared with those of other Fabaceae plastomes. PCR screening and sequencing were performed in other allied legumes in order to determine the origin of a large inversion identified in L. luteus. KEY RESULTS The first sequenced Genistoid plastome (L. luteus: 155 894 bp) resulted in the discovery of a 36-kb inversion, embedded within the already known 50-kb inversion in the large single-copy (LSC) region of the Papilionoideae. This inversion occurs at the base or soon after the Genistoid emergence, and most probably resulted from a flip-flop recombination between identical 29-bp inverted repeats within two trnS genes. Comparative analyses of the chloroplast gene content of L. luteus vs. Fabaceae and extra-Fabales plastomes revealed the loss of the plastid rpl22 gene, and its functional relocation to the nucleus was verified using lupine transcriptomic data. An investigation into the evolutionary rate of coding and non-coding sequences among legume plastomes resulted in the identification of remarkably variable regions. CONCLUSIONS This study resulted in the discovery of a novel, major 36-kb inversion, specific to the Genistoids. Chloroplast mutational hotspots were also identified, which contain novel and potentially informative regions for molecular evolutionary studies at various taxonomic levels in the legumes. Taken together, the results provide new insights into the evolutionary landscape of the legume plastome.
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Affiliation(s)
- Guillaume E Martin
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1/Université Européenne de Bretagne, 35 042 Rennes, France
| | - Mathieu Rousseau-Gueutin
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1/Université Européenne de Bretagne, 35 042 Rennes, France
| | - Solenn Cordonnier
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1/Université Européenne de Bretagne, 35 042 Rennes, France
| | - Oscar Lima
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1/Université Européenne de Bretagne, 35 042 Rennes, France
| | - Sophie Michon-Coudouel
- Plate-forme Génomique Environnementale et Fonctionnelle, OSUR-CNRS, Université de Rennes 1, 35042 Rennes, France
| | - Delphine Naquin
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1/Université Européenne de Bretagne, 35 042 Rennes, France
| | - Julie Ferreira de Carvalho
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1/Université Européenne de Bretagne, 35 042 Rennes, France
| | - Malika Aïnouche
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1/Université Européenne de Bretagne, 35 042 Rennes, France
| | - Armel Salmon
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1/Université Européenne de Bretagne, 35 042 Rennes, France
| | - Abdelkader Aïnouche
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1/Université Européenne de Bretagne, 35 042 Rennes, France
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Schubert M, Koteyeva NK, Zdyb A, Santos P, Voitsekhovskaja OV, Demchenko KN, Pawlowski K. Lignification of cell walls of infected cells in Casuarina glauca nodules that depend on symplastic sugar supply is accompanied by reduction of plasmodesmata number and narrowing of plasmodesmata. PHYSIOLOGIA PLANTARUM 2013; 147:524-40. [PMID: 22924772 DOI: 10.1111/j.1399-3054.2012.01685.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Revised: 06/05/2012] [Accepted: 06/24/2012] [Indexed: 05/03/2023]
Abstract
The oxygen protection system for the bacterial nitrogen-fixing enzyme complex nitrogenase in actinorhizal nodules of Casuarina glauca resembles that of legume nodules: infected cells contain large amounts of the oxygen-binding protein hemoglobin and are surrounded by an oxygen diffusion barrier. However, while in legume nodules infected cells are located in the central tissue, actinorhizal nodules are composed of modified lateral roots with infected cells in the expanded cortex. Since an oxygen diffusion barrier around the entire cortex would also block oxygen access to the central vascular system where it is required to provide energy for transport processes, here each individual infected cell is surrounded with an oxygen diffusion barrier. In order to assess the effect of these oxygen diffusion barriers on oxygen supply for energy production for transport processes, apoplastic and symplastic sugar transport pathways in C. glauca nodules were examined. The results support the idea that sugar transport to and within the nodule cortex relies to a large extent on the less energy-demanding symplastic mechanism. This is in line with the assumption that oxygen access to the nodule vascular system is substantially restricted. In spite of this dependence on symplastic transport processes to supply sugars to infected cells, plasmodesmal connections between infected cells, and to a lesser degree with uninfected cells, were reduced during the differentiation of infected cells.
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Affiliation(s)
- Maria Schubert
- Department of Plant Biochemistry, Albrecht von Haller Institute for Plant Sciences, Göttingen University, Göttingen, Germany
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Manzanilla V, Bruneau A. Phylogeny reconstruction in the Caesalpinieae grade (Leguminosae) based on duplicated copies of the sucrose synthase gene and plastid markers. Mol Phylogenet Evol 2012; 65:149-62. [DOI: 10.1016/j.ympev.2012.05.035] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Revised: 05/30/2012] [Accepted: 05/31/2012] [Indexed: 01/05/2023]
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Tek AL, Kashihara K, Murata M, Nagaki K. Functional centromeres in Astragalus sinicus include a compact centromere-specific histone H3 and a 20-bp tandem repeat. Chromosome Res 2011; 19:969-78. [PMID: 22065151 DOI: 10.1007/s10577-011-9247-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Revised: 09/16/2011] [Accepted: 10/03/2011] [Indexed: 11/30/2022]
Abstract
The centromere plays an essential role for proper chromosome segregation during cell division and usually harbors long arrays of tandem repeated satellite DNA sequences. Although this function is conserved among eukaryotes, the sequences of centromeric DNA repeats are variable. Most of our understanding of functional centromeres, which are defined by localization of a centromere-specific histone H3 (CENH3) protein, comes from model organisms. The components of the functional centromere in legumes are poorly known. The genus Astragalus is a member of the legumes and bears the largest numbers of species among angiosperms. Therefore, we studied the components of centromeres in Astragalus sinicus. We identified the CenH3 homolog of A. sinicus, AsCenH3 that is the most compact in size among higher eukaryotes. A CENH3-based assay revealed the functional centromeric DNA sequences from A. sinicus, called CentAs. The CentAs repeat is localized in A. sinicus centromeres, and comprises an AT-rich tandem repeat with a monomer size of 20 nucleotides.
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Affiliation(s)
- Ahmet L Tek
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan.
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Bensmihen S, de Billy F, Gough C. Contribution of NFP LysM domains to the recognition of Nod factors during the Medicago truncatula/Sinorhizobium meliloti symbiosis. PLoS One 2011; 6:e26114. [PMID: 22087221 PMCID: PMC3210742 DOI: 10.1371/journal.pone.0026114] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2011] [Accepted: 09/19/2011] [Indexed: 12/24/2022] Open
Abstract
The root nodule nitrogen fixing symbiosis between legume plants and soil bacteria called rhizobia is of great agronomical and ecological interest since it provides the plant with fixed atmospheric nitrogen. The establishment of this symbiosis is mediated by the recognition by the host plant of lipo-chitooligosaccharides called Nod Factors (NFs), produced by the rhizobia. This recognition is highly specific, as precise NF structures are required depending on the host plant. Here, we study the importance of different LysM domains of a LysM-Receptor Like Kinase (LysM-RLK) from Medicago truncatula called Nod factor perception (NFP) in the recognition of different substitutions of NFs produced by its symbiont Sinorhizobium meliloti. These substitutions are a sulphate group at the reducing end, which is essential for host specificity, and a specific acyl chain at the non-reducing end, that is critical for the infection process. The NFP extracellular domain (ECD) contains 3 LysM domains that are predicted to bind NFs. By swapping the whole ECD or individual LysM domains of NFP for those of its orthologous gene from pea, SYM10 (a legume plant that interacts with another strain of rhizobium producing NFs with different substitutions), we showed that NFP is not directly responsible for specific recognition of the sulphate substitution of S. meliloti NFs, but probably interacts with the acyl substitution. Moreover, we have demonstrated the importance of the NFP LysM2 domain for rhizobial infection and we have pinpointed the importance of a single leucine residue of LysM2 in that step of the symbiosis. Together, our data put into new perspective the recognition of NFs in the different steps of symbiosis in M. truncatula, emphasising the probable existence of a missing component for early NF recognition and reinforcing the important role of NFP for NF recognition during rhizobial infection.
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Affiliation(s)
- Sandra Bensmihen
- Laboratoire des Interactions Plantes-Microorganismes, Institut National de la Recherche Agronomique, Castanet-Tolosan, France.
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Francia D, Chiltz A, Lo Schiavo F, Pugin A, Bonfante P, Cardinale F. AM fungal exudates activate MAP kinases in plant cells in dependence from cytosolic Ca(2+) increase. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2011; 49:963-9. [PMID: 21561784 DOI: 10.1016/j.plaphy.2011.04.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2011] [Accepted: 04/18/2011] [Indexed: 05/30/2023]
Abstract
The molecular dialogue occurring prior to direct contact between the fungal and plant partners of arbuscular-mycorrhizal (AM) symbioses begins with the release of fungal elicitors, so far only partially identified chemically, which can activate specific signaling pathways in the host plant. We show here that the activation of MAPK is also induced by exudates of germinating spores of Gigaspora margarita in cultured cells of the non-leguminous species tobacco (Nicotiana tabacum), as well as in those of the model legume Lotus japonicus. MAPK activity peaked about 15 min after the exposure of the host cells to the fungal exudates (FE). FE were also responsible for a rapid and transient increase in free cytosolic Ca(2+) in Nicotiana plumbaginifolia and tobacco cells, and pre-treatment with a Ca(2+)-channel blocker (La(3+)) showed that in these cells, MAPK activation was dependent on the cytosolic Ca(2+) increase. A partial dependence of MAPK activity on the common Sym pathway could be demonstrated for a cell line of L. japonicus defective for LjSym4 and hence unable to establish an AM symbiosis. Our results show that MAPK activation is triggered by an FE-induced cytosolic Ca(2+) transient, and that a Sym genetic determinant acts to modulate the intensity and duration of this activity.
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Affiliation(s)
- Doriana Francia
- DiVaPRA, Patologia Vegetale, Università degli Studi di Torino, Via L. da Vinci, 44, 10095 Grugliasco (TO), Italy
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Kaur S, Cogan NOI, Pembleton LW, Shinozuka M, Savin KW, Materne M, Forster JW. Transcriptome sequencing of lentil based on second-generation technology permits large-scale unigene assembly and SSR marker discovery. BMC Genomics 2011; 12:265. [PMID: 21609489 PMCID: PMC3113791 DOI: 10.1186/1471-2164-12-265] [Citation(s) in RCA: 150] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2011] [Accepted: 05/25/2011] [Indexed: 12/05/2022] Open
Abstract
Background Lentil (Lens culinaris Medik.) is a cool-season grain legume which provides a rich source of protein for human consumption. In terms of genomic resources, lentil is relatively underdeveloped, in comparison to other Fabaceae species, with limited available data. There is hence a significant need to enhance such resources in order to identify novel genes and alleles for molecular breeding to increase crop productivity and quality. Results Tissue-specific cDNA samples from six distinct lentil genotypes were sequenced using Roche 454 GS-FLX Titanium technology, generating c. 1.38 × 106 expressed sequence tags (ESTs). De novo assembly generated a total of 15,354 contigs and 68,715 singletons. The complete unigene set was sequence-analysed against genome drafts of the model legume species Medicago truncatula and Arabidopsis thaliana to identify 12,639, and 7,476 unique matches, respectively. When compared to the genome of Glycine max, a total of 20,419 unique hits were observed corresponding to c. 31% of the known gene space. A total of 25,592 lentil unigenes were subsequently annoated from GenBank. Simple sequence repeat (SSR)-containing ESTs were identified from consensus sequences and a total of 2,393 primer pairs were designed. A subset of 192 EST-SSR markers was screened for validation across a panel 12 cultivated lentil genotypes and one wild relative species. A total of 166 primer pairs obtained successful amplification, of which 47.5% detected genetic polymorphism. Conclusions A substantial collection of ESTs has been developed from sequence analysis of lentil genotypes using second-generation technology, permitting unigene definition across a broad range of functional categories. As well as providing resources for functional genomics studies, the unigene set has permitted significant enhancement of the number of publicly-available molecular genetic markers as tools for improvement of this species.
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Affiliation(s)
- Sukhjiwan Kaur
- Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, La Trobe University Research and Development Park, Bundoora, Australia
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Franssen SU, Shrestha RP, Bräutigam A, Bornberg-Bauer E, Weber APM. Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing. BMC Genomics 2011; 12:227. [PMID: 21569327 PMCID: PMC3224338 DOI: 10.1186/1471-2164-12-227] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2010] [Accepted: 05/11/2011] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The garden pea, Pisum sativum, is among the best-investigated legume plants and of significant agro-commercial relevance. Pisum sativum has a large and complex genome and accordingly few comprehensive genomic resources exist. RESULTS We analyzed the pea transcriptome at the highest possible amount of accuracy by current technology. We used next generation sequencing with the Roche/454 platform and evaluated and compared a variety of approaches, including diverse tissue libraries, normalization, alternative sequencing technologies, saturation estimation and diverse assembly strategies. We generated libraries from flowers, leaves, cotyledons, epi- and hypocotyl, and etiolated and light treated etiolated seedlings, comprising a total of 450 megabases. Libraries were assembled into 324,428 unigenes in a first pass assembly.A second pass assembly reduced the amount to 81,449 unigenes but caused a significant number of chimeras. Analyses of the assemblies identified the assembly step as a major possibility for improvement. By recording frequencies of Arabidopsis orthologs hit by randomly drawn reads and fitting parameters of the saturation curve we concluded that sequencing was exhaustive. For leaf libraries we found normalization allows partial recovery of expression strength aside the desired effect of increased coverage. Based on theoretical and biological considerations we concluded that the sequence reads in the database tagged the vast majority of transcripts in the aerial tissues. A pathway representation analysis showed the merits of sampling multiple aerial tissues to increase the number of tagged genes. All results have been made available as a fully annotated database in fasta format. CONCLUSIONS We conclude that the approach taken resulted in a high quality - dataset which serves well as a first comprehensive reference set for the model legume pea. We suggest future deep sequencing transcriptome projects of species lacking a genomics backbone will need to concentrate mainly on resolving the issues of redundancy and paralogy during transcriptome assembly.
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Affiliation(s)
- Susanne U Franssen
- Institute for Evolution and Biodiversity, Westfalian Wilhelms University, Hüfferstrasse 1, 48149 Münster, Germany
| | - Roshan P Shrestha
- Department of Plant Biology, Michigan State University, 48823 East Lansing, MI, USA
| | - Andrea Bräutigam
- Department of Plant Biology, Michigan State University, 48823 East Lansing, MI, USA
- Institute of Plant Biochemistry, Heinrich Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, Westfalian Wilhelms University, Hüfferstrasse 1, 48149 Münster, Germany
| | - Andreas PM Weber
- Department of Plant Biology, Michigan State University, 48823 East Lansing, MI, USA
- Institute of Plant Biochemistry, Heinrich Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany
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Genomic resources in horticultural crops: Status, utility and challenges. Biotechnol Adv 2011; 29:199-209. [DOI: 10.1016/j.biotechadv.2010.11.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2010] [Revised: 09/04/2010] [Accepted: 09/26/2010] [Indexed: 01/02/2023]
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Rüping B, Ernst AM, Jekat SB, Nordzieke S, Reineke AR, Müller B, Bornberg-Bauer E, Prüfer D, Noll GA. Molecular and phylogenetic characterization of the sieve element occlusion gene family in Fabaceae and non-Fabaceae plants. BMC PLANT BIOLOGY 2010; 10:219. [PMID: 20932300 PMCID: PMC3017817 DOI: 10.1186/1471-2229-10-219] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2010] [Accepted: 10/08/2010] [Indexed: 05/18/2023]
Abstract
BACKGROUND The phloem of dicotyledonous plants contains specialized P-proteins (phloem proteins) that accumulate during sieve element differentiation and remain parietally associated with the cisternae of the endoplasmic reticulum in mature sieve elements. Wounding causes P-protein filaments to accumulate at the sieve plates and block the translocation of photosynthate. Specialized, spindle-shaped P-proteins known as forisomes that undergo reversible calcium-dependent conformational changes have evolved exclusively in the Fabaceae. Recently, the molecular characterization of three genes encoding forisome components in the model legume Medicago truncatula (MtSEO1, MtSEO2 and MtSEO3; SEO = sieve element occlusion) was reported, but little is known about the molecular characteristics of P-proteins in non-Fabaceae. RESULTS We performed a comprehensive genome-wide comparative analysis by screening the M. truncatula, Glycine max, Arabidopsis thaliana, Vitis vinifera and Solanum phureja genomes, and a Malus domestica EST library for homologs of MtSEO1, MtSEO2 and MtSEO3 and identified numerous novel SEO genes in Fabaceae and even non-Fabaceae plants, which do not possess forisomes. Even in Fabaceae some SEO genes appear to not encode forisome components. All SEO genes have a similar exon-intron structure and are expressed predominantly in the phloem. Phylogenetic analysis revealed the presence of several subgroups with Fabaceae-specific subgroups containing all of the known as well as newly identified forisome component proteins. We constructed Hidden Markov Models that identified three conserved protein domains, which characterize SEO proteins when present in combination. In addition, one common and three subgroup specific protein motifs were found in the amino acid sequences of SEO proteins. SEO genes are organized in genomic clusters and the conserved synteny allowed us to identify several M. truncatula vs G. max orthologs as well as paralogs within the G. max genome. CONCLUSIONS The unexpected occurrence of forisome-like genes in non-Fabaceae plants may indicate that these proteins encode species-specific P-proteins, which is backed up by the phloem-specific expression profiles. The conservation of gene structure, the presence of specific motifs and domains and the genomic synteny argue for a common phylogenetic origin of forisomes and other P-proteins.
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Affiliation(s)
- Boris Rüping
- Institut für Biochemie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Hindenburgplatz 55, D-48143 Münster, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Forckenbeckstraße 6, D-52074 Aachen, Germany
| | - Antonia M Ernst
- Institut für Biochemie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Hindenburgplatz 55, D-48143 Münster, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Forckenbeckstraße 6, D-52074 Aachen, Germany
| | - Stephan B Jekat
- Institut für Biochemie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Hindenburgplatz 55, D-48143 Münster, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Forckenbeckstraße 6, D-52074 Aachen, Germany
| | - Steffen Nordzieke
- Institut für Biochemie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Hindenburgplatz 55, D-48143 Münster, Germany
| | - Anna R Reineke
- Institut für Evolution und Biodiversität, Westfälische Wilhelms-Universität Münster, Hüfferstraße 1, D-48149 Münster, Germany
| | - Boje Müller
- Institut für Biochemie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Hindenburgplatz 55, D-48143 Münster, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Forckenbeckstraße 6, D-52074 Aachen, Germany
| | - Erich Bornberg-Bauer
- Institut für Evolution und Biodiversität, Westfälische Wilhelms-Universität Münster, Hüfferstraße 1, D-48149 Münster, Germany
| | - Dirk Prüfer
- Institut für Biochemie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Hindenburgplatz 55, D-48143 Münster, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Forckenbeckstraße 6, D-52074 Aachen, Germany
| | - Gundula A Noll
- Institut für Biochemie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Hindenburgplatz 55, D-48143 Münster, Germany
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Li X, Zhuang LL, Ambrose M, Rameau C, Hu XH, Yang J, Luo D. Genetic analysis of ele mutants and comparative mapping of ele1 locus in the control of organ internal asymmetry in garden pea. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2010; 52:528-35. [PMID: 20590983 DOI: 10.1111/j.1744-7909.2010.00949.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Previous study has shown that during zygomorphic development in garden pea (Pisum sativum L.), the organ internal (IN) asymmetry of lateral and ventral petals was regulated by a genetic locus, SYMMETRIC PETAL 1 (SYP1), while the dorsoventral (DV) asymmetry was determined by two CYC-like TCP genes or the PsCYC genes, KEELED WINGS (K) and LOBED STANDARD 1 (LST1). In this study, two novel loci, ELEPHANT EAR-LIKE LEAF 1 (ELE1) and ELE2 were characterized. These mutants exhibit a similar defect of IN asymmetry as syp1 in lateral and ventral petals, but also display pleiotropic effects of enlarged organ size. Genetic analysis showed that ELE1 and ELE2 were involved in same genetic pathway and the enlarged size of petals but not compound leaves in ele2 was suppressed by introducing k and lst1, indicating that the enlargement of dorsal petal in ele2 requires the activities of K and LST1. An experimental framework of comparative genomic mapping approach was set up to map and clone LjELE1 locus in Lotus japonicus. Cloning the ELE1 gene will shed light on the underlying molecular mechanism during zygomorphic development and further provide the molecular basis for genetic improvement on legume crops.
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Affiliation(s)
- Xin Li
- School of Life Science and Biotechnology, Shanghai JiaoTong University, Shanghai 200030, China
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David P, des Francs-Small CC, Sévignac M, Thareau V, Macadré C, Langin T, Geffroy V. Three highly similar formate dehydrogenase genes located in the vicinity of the B4 resistance gene cluster are differentially expressed under biotic and abiotic stresses in Phaseolus vulgaris. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 121:87-103. [PMID: 20182695 DOI: 10.1007/s00122-010-1293-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2009] [Accepted: 01/28/2010] [Indexed: 05/06/2023]
Abstract
In higher plants, formate dehydrogenase (FDH, EC1.2.1.2.) catalyzes the NAD-linked oxidation of formate to CO(2), and FDH transcript accumulation has been reported after various abiotic stresses. By sequencing a Phaseolus vulgaris BAC clone encompassing a CC-NBS-LRR gene rich region of the B4 resistance gene cluster, we identified three FDH-encoding genes. FDH is present as a single copy gene in the Arabidopsis thaliana genome, and public database searches confirm that FDH is a low copy gene in plant genomes, since only 33 FDH homologs were identified from 27 plant species. Three independent prediction programs (Predotar, TargetP and Mitoprot) used on this large subset of 33 plant FDHs, revealed that mitochondrial localization of FDH might be the rule in higher plants. A phylogenetic analysis suggests a scenario of local FDH gene duplication in an ancestor of the Phaseoleae followed by another more recent duplication event after bean/soybean divergence. The expression levels of two common bean FDH genes under different treatments were investigated by quantitative RT-PCR analysis. FDH genes are differentially up-regulated after biotic and abiotic stresses (infection with the fungus Colletotrichum lindemuthianum, and dark treatment, respectively). The present study provides the first report of FDH transcript accumulation after biotic stress, suggesting the involvement of FDH in the pathogen resistance process.
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Affiliation(s)
- Perrine David
- Institut de Biotechnologie des Plantes, UMR-CNRS 8618, bât. 630, Université Paris-Sud, 91405, Orsay, France
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David P, Chen NW, Pedrosa-Harand A, Thareau V, Sévignac M, Cannon SB, Debouck D, Langin T, Geffroy V. A nomadic subtelomeric disease resistance gene cluster in common bean. PLANT PHYSIOLOGY 2009; 151:1048-65. [PMID: 19776165 PMCID: PMC2773105 DOI: 10.1104/pp.109.142109] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Accepted: 09/17/2009] [Indexed: 05/18/2023]
Abstract
The B4 resistance (R) gene cluster is one of the largest clusters known in common bean (Phaseolus vulgaris [Pv]). It is located in a peculiar genomic environment in the subtelomeric region of the short arm of chromosome 4, adjacent to two heterochromatic blocks (knobs). We sequenced 650 kb spanning this locus and annotated 97 genes, 26 of which correspond to Coiled-Coil-Nucleotide-Binding-Site-Leucine-Rich-Repeat (CNL). Conserved microsynteny was observed between the Pv B4 locus and corresponding regions of Medicago truncatula and Lotus japonicus in chromosomes Mt6 and Lj2, respectively. The notable exception was the CNL sequences, which were completely absent in these regions. The origin of the Pv B4-CNL sequences was investigated through phylogenetic analysis, which reveals that, in the Pv genome, paralogous CNL genes are shared among nonhomologous chromosomes (4 and 11). Together, our results suggest that Pv B4-CNL was derived from CNL sequences from another cluster, the Co-2 cluster, through an ectopic recombination event. Integration of the soybean (Glycine max) genome data enables us to date more precisely this event and also to infer that a single CNL moved from the Co-2 to the B4 cluster. Moreover, we identified a new 528-bp satellite repeat, referred to as khipu, specific to the Phaseolus genus, present both between B4-CNL sequences and in the two knobs identified at the B4 R gene cluster. The khipu repeat is present on most chromosomal termini, indicating the existence of frequent ectopic recombination events in Pv subtelomeric regions. Our results highlight the importance of ectopic recombination in R gene evolution.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Valérie Geffroy
- Institut de Biotechnologie des Plantes, UMR-CNRS 8618, Université Paris-Sud, 91405 Orsay cedex, France (P.D., N.W.G.C., V.T., M.S., T.L., V.G.); Unité Mixte de Recherche de Génétique Végétale, Institut National de la Recherche Agronomique, 91190 Gif-sur-Yvette, France (V.G.); Laboratório de Citogenética Vegetal, Departamento de Botânica-Centro de Ciências Biológicas, Universidade Federal de Pernambuco, Recife-Pernambuco 50670–420, Brazil (A.P.-H.); United States Department of Agriculture-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, Iowa 50011 (S.B.C.); and Genetic Resources Unit, Centro Internacional de Agricultura Tropical, AA 6713 Cali, Colombia (D.D.)
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Illing N, Klak C, Johnson C, Brito D, Negrao N, Baine F, van Kets V, Ramchurn KR, Seoighe C, Roden L. Duplication of the Asymmetric Leaves1/Rough Sheath 2/Phantastica (ARP) gene precedes the explosive radiation of the Ruschioideae. Dev Genes Evol 2009; 219:331-8. [PMID: 19554349 DOI: 10.1007/s00427-009-0293-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Accepted: 05/31/2009] [Indexed: 11/28/2022]
Abstract
The Mesembryanthemoideae and Ruschioideae subfamilies are a major component of the Greater Cape Floristic Region in southern Africa. The Ruschioideae show an astonishing diversity of leaf shape and growth forms. Although 1,585 species are recognised within the morphologically diverse Ruschioideae, these species show minimal variation in plastid DNA sequence. We have investigated whether changes in selected leaf development transcription factors underpin the recent, rapid diversification of this large group of succulent plants. Degenerate primers designed to conserved regions of Asymmetric Leaves1/Rough Sheath 2/Phantastica (ARP) and the Class III HD-ZIP family of genes, were used to amplify sequences corresponding to these genes from several species within the Mesembryanthemoideae and Ruschioideae subfamilies. Two members of the Class III HD-ZIP family were identified in both the Mesembryanthemoideae and Ruschioideae, and were derived from an ancient gene duplication event that preceded the divergence of gymnosperms and angiosperms. While a single ARP orthologue was identified in the Mesembryanthemoideae, two paralogues, ARPa and ARPb, were identified in the Ruschioideae subfamily. ARPa was present in all species of Ruschioideae analysed in this study. ARPb has been lost from the Apatesieae and Dorotheantheae tribes, which form an early evolutionary branch from the Ruschieae tribe, as well as from selected species within the Ruschieae. The recent duplication and subsequent selected gene loss of the ARP transcription factor correlates with the rapid diversification of plant forms in the Ruschioideae.
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Affiliation(s)
- Nicola Illing
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa.
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Zhukov V, Radutoiu S, Madsen LH, Rychagova T, Ovchinnikova E, Borisov A, Tikhonovich I, Stougaard J. The pea Sym37 receptor kinase gene controls infection-thread initiation and nodule development. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2008; 21:1600-8. [PMID: 18986256 DOI: 10.1094/mpmi-21-12-1600] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Phenotypic characterization of pea symbiotic mutants has provided a detailed description of the symbiosis with Rhizobium leguminosarum bv. viciae strains. We show here that two allelic non-nodulating pea mutants, RisNod4 and K24, are affected in the PsSym37 gene, encoding a LysM receptor kinase similar to Lotus japonicus NFR1 and Medicago truncatula LYK3. Phenotypic analysis of RisNod4 and K24 suggests a role for the SYM37 in regulation of infection-thread initiation and nodule development from cortical-cell division foci. We show that RisNod4 plants carrying an L to F substitution in the LysM1 domain display a restrictive symbiotic phenotype comparable to the PsSym2(A) lines that distinguish 'European' and 'Middle East' Rhizobium leguminosarum bv. viciae strains. RisNod4 mutants develop nodules only in the presence of a 'Middle East' Rhizobium strain producing O-acetylated Nod factors indicating the SYM37 involvement in Nod-factor recognition. Along with the PsSym37, a homologous LysM receptor kinase gene, PsK1, was isolated and characterized. We show that PsK1 and PsSym37 are genetically linked to each other and to the PsSym2 locus. Allelic complementation analyses and sequencing of the extracellular regions of PsSym37 and PsK1 in several 'European' and 'Afghan' pea cultivars point towards PsK1 as possible candidate for the elusive PsSym2 gene.
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Affiliation(s)
- Vladimir Zhukov
- Laboratory of Genetics of Plant-Microbe Interactions, All-Russia Research Institute for Agricultural Microbiology, Podbelsky chausse 3, 196608 Saint-Petersburg-Pushkin, Russia
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Yuksel B, Memon AR. Comparative phylogenetic analysis of small GTP-binding genes of model legume plants and assessment of their roles in root nodules. JOURNAL OF EXPERIMENTAL BOTANY 2008; 59:3831-44. [PMID: 18849296 PMCID: PMC2576638 DOI: 10.1093/jxb/ern223] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2008] [Revised: 07/17/2008] [Accepted: 08/06/2008] [Indexed: 05/03/2023]
Abstract
Small GTP-binding genes play an essential regulatory role in a multitude of cellular processes such as vesicle-mediated intracellular trafficking, signal transduction, cytoskeletal organization, and cell division in plants and animals. Medicago truncatula and Lotus japonicus are important model plants for studying legume-specific biological processes such as nodulation. The publicly available online resources for these plants from websites such as http://www.ncbi.nih.gov, http://www.medicago.org, http://www.tigr.org, and related sites were searched to collect nucleotide sequences that encode GTP-binding protein homologues. A total of 460 small GTPase sequences from several legume species including Medicago and Lotus, Arabidopsis, human, and yeast were phyletically analysed to shed light on the evolution and functional characteristics of legume-specific homologues. One of the main emphases of this study was the elucidation of the possible involvement of some members of small GTPase homologues in the establishment and maintenance of symbiotic associations in root nodules of legumes. A high frequency of vesicle-mediated trafficking in nodules led to the idea of a probable subfunctionalization of some members of this family in legumes. As a result of the analyses, a group of 10 small GTPases that are likely to be mainly expressed in nodules was determined. The sequences determined as a result of this study could be used in more detailed molecular genetic analyses such as creation of RNA interference silencing mutants for further clarification of the role of GTPases in nodulation. This study will also assist in furthering our understanding of the evolutionary history of small GTPases in legume species.
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Affiliation(s)
- Bayram Yuksel
- Plant Molecular Biology Laboratory, Genetic Engineering and Biotechnology Institute, Marmara Research Center, TUBITAK, PO Box 21, 41400, Gebze, Kocaeli, Turkey.
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Timko MP, Rushton PJ, Laudeman TW, Bokowiec MT, Chipumuro E, Cheung F, Town CD, Chen X. Sequencing and analysis of the gene-rich space of cowpea. BMC Genomics 2008; 9:103. [PMID: 18304330 PMCID: PMC2279124 DOI: 10.1186/1471-2164-9-103] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2007] [Accepted: 02/27/2008] [Indexed: 11/16/2022] Open
Abstract
Background Cowpea, Vigna unguiculata (L.) Walp., is one of the most important food and forage legumes in the semi-arid tropics because of its drought tolerance and ability to grow on poor quality soils. Approximately 80% of cowpea production takes place in the dry savannahs of tropical West and Central Africa, mostly by poor subsistence farmers. Despite its economic and social importance in the developing world, cowpea remains to a large extent an underexploited crop. Among the major goals of cowpea breeding and improvement programs is the stacking of desirable agronomic traits, such as disease and pest resistance and response to abiotic stresses. Implementation of marker-assisted selection and breeding programs is severely limited by a paucity of trait-linked markers and a general lack of information on gene structure and organization. With a nuclear genome size estimated at ~620 Mb, the cowpea genome is an ideal target for reduced representation sequencing. Results We report here the sequencing and analysis of the gene-rich, hypomethylated portion of the cowpea genome selectively cloned by methylation filtration (MF) technology. Over 250,000 gene-space sequence reads (GSRs) with an average length of 610 bp were generated, yielding ~160 Mb of sequence information. The GSRs were assembled, annotated by BLAST homology searches of four public protein annotation databases and four plant proteomes (A. thaliana, M. truncatula, O. sativa, and P. trichocarpa), and analyzed using various domain and gene modeling tools. A total of 41,260 GSR assemblies and singletons were annotated, of which 19,786 have unique GenBank accession numbers. Within the GSR dataset, 29% of the sequences were annotated using the Arabidopsis Gene Ontology (GO) with the largest categories of assigned function being catalytic activity and metabolic processes, groups that include the majority of cellular enzymes and components of amino acid, carbohydrate and lipid metabolism. A total of 5,888 GSRs had homology to genes encoding transcription factors (TFs) and transcription associated factors (TAFs) representing about 5% of the total annotated sequences in the dataset. Sixty-two (62) of the 64 well-characterized plant transcription factor (TF) gene families are represented in the cowpea GSRs, and these families are of similar size and phylogenetic organization to those characterized in other plants. The cowpea GSRs also provides a rich source of genes involved in photoperiodic control, symbiosis, and defense-related responses. Comparisons to available databases revealed that about 74% of cowpea ESTs and 70% of all legume ESTs were represented in the GSR dataset. As approximately 12% of all GSRs contain an identifiable simple-sequence repeat, the dataset is a powerful resource for the design of microsatellite markers. Conclusion The availability of extensive publicly available genomic data for cowpea, a non-model legume with significant importance in the developing world, represents a significant step forward in legume research. Not only does the gene space sequence enable the detailed analysis of gene structure, gene family organization and phylogenetic relationships within cowpea, but it also facilitates the characterization of syntenic relationships with other cultivated and model legumes, and will contribute to determining patterns of chromosomal evolution in the Leguminosae. The micro and macrosyntenic relationships detected between cowpea and other cultivated and model legumes should simplify the identification of informative markers for marker-assisted trait selection and map-based gene isolation necessary for cowpea improvement.
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Affiliation(s)
- Michael P Timko
- Department of Biology, University of Virginia, Charlottesville, Virginia 22903, USA.
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Coram TE, Mantri NL, Ford R, Pang ECK. Functional genomics in chickpea: an emerging frontier for molecular-assisted breeding. FUNCTIONAL PLANT BIOLOGY : FPB 2007; 34:861-873. [PMID: 32689415 DOI: 10.1071/fp07169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2007] [Accepted: 08/08/2007] [Indexed: 06/11/2023]
Abstract
Chickpea is a valuable and important agricultural crop, but yield potential is limited by a series of biotic and abiotic stresses, including Ascochyta blight, Fusarium wilt, drought, cold and salinity. To accelerate molecular breeding efforts for the discovery and introgression of stress tolerance genes into cultivated chickpea, functional genomics approaches are rapidly growing. Recently a series of genetic tools for chickpea have become available that have allowed high-powered functional genomics studies to proceed, including a dense genetic map, large insert genome libraries, expressed sequence tag libraries, microarrays, serial analysis of gene expression, transgenics and reverse genetics. This review summarises the development of these genomic tools and the achievements made in initial and emerging functional genomics studies. Much of the initial research focused on Ascochyta blight resistance, and a resistance model has been synthesised based on the results of various studies. Use of the rich comparative genomics resources from the model legumes Medicago truncatula and Lotus japonicus is also discussed. Finally, perspectives on the future directions for chickpea functional genomics, with the goal of developing elite chickpea cultivars, are discussed.
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Affiliation(s)
- Tristan E Coram
- RMIT University, School of Applied Sciences, Biotechnology and Environmental Biology, Building 223, Level 1, Plenty Road, Bundoora, Victoria 3083, Australia
| | - Nitin L Mantri
- RMIT University, School of Applied Sciences, Biotechnology and Environmental Biology, Building 223, Level 1, Plenty Road, Bundoora, Victoria 3083, Australia
| | - Rebecca Ford
- BioMarka, Faculty of Land and Food Resources, The University of Melbourne, Victoria 3010, Australia
| | - Edwin C K Pang
- RMIT University, School of Applied Sciences, Biotechnology and Environmental Biology, Building 223, Level 1, Plenty Road, Bundoora, Victoria 3083, Australia
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Guo X, Castillo-Ramírez S, González V, Bustos P, Luís Fernández-Vázquez J, Santamaría RI, Arellano J, Cevallos MA, Dávila G. Rapid evolutionary change of common bean (Phaseolus vulgaris L) plastome, and the genomic diversification of legume chloroplasts. BMC Genomics 2007; 8:228. [PMID: 17623083 PMCID: PMC1940014 DOI: 10.1186/1471-2164-8-228] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2007] [Accepted: 07/10/2007] [Indexed: 12/05/2022] Open
Abstract
Background Fabaceae (legumes) is one of the largest families of flowering plants, and some members are important crops. In contrast to what we know about their great diversity or economic importance, our knowledge at the genomic level of chloroplast genomes (cpDNAs or plastomes) for these crops is limited. Results We sequenced the complete genome of the common bean (Phaseolus vulgaris cv. Negro Jamapa) chloroplast. The plastome of P. vulgaris is a 150,285 bp circular molecule. It has gene content similar to that of other legume plastomes, but contains two pseudogenes, rpl33 and rps16. A distinct inversion occurred at the junction points of trnH-GUG/rpl14 and rps19/rps8, as in adzuki bean [1]. These two pseudogenes and the inversion were confirmed in 10 varieties representing the two domestication centers of the bean. Genomic comparative analysis indicated that inversions generally occur in legume plastomes and the magnitude and localization of insertions/deletions (indels) also vary. The analysis of repeat sequences demonstrated that patterns and sequences of tandem repeats had an important impact on sequence diversification between legume plastomes and tandem repeats did not belong to dispersed repeats. Interestingly, P. vulgaris plastome had higher evolutionary rates of change on both genomic and gene levels than G. max, which could be the consequence of pressure from both mutation and natural selection. Conclusion Legume chloroplast genomes are widely diversified in gene content, gene order, indel structure, abundance and localization of repetitive sequences, intracellular sequence exchange and evolutionary rates. The P. vulgaris plastome is a rapidly evolving genome.
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Affiliation(s)
- Xianwu Guo
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Apartado Postal 565-A, C.P 62210, Cuernavaca, Morelos, México
| | - Santiago Castillo-Ramírez
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Apartado Postal 565-A, C.P 62210, Cuernavaca, Morelos, México
| | - Víctor González
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Apartado Postal 565-A, C.P 62210, Cuernavaca, Morelos, México
| | - Patricia Bustos
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Apartado Postal 565-A, C.P 62210, Cuernavaca, Morelos, México
| | - José Luís Fernández-Vázquez
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Apartado Postal 565-A, C.P 62210, Cuernavaca, Morelos, México
| | - Rosa Isela Santamaría
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Apartado Postal 565-A, C.P 62210, Cuernavaca, Morelos, México
| | - Jesús Arellano
- Programa de Genómica Funcional de Eucariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Apartado Postal 565-A, C.P 62210, Cuernavaca, Morelos, México
| | - Miguel A Cevallos
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Apartado Postal 565-A, C.P 62210, Cuernavaca, Morelos, México
| | - Guillermo Dávila
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Apartado Postal 565-A, C.P 62210, Cuernavaca, Morelos, México
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Schranz ME, Lysak MA, Mitchell-Olds T. The ABC's of comparative genomics in the Brassicaceae: building blocks of crucifer genomes. TRENDS IN PLANT SCIENCE 2006; 11:535-42. [PMID: 17029932 DOI: 10.1016/j.tplants.2006.09.002] [Citation(s) in RCA: 338] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2006] [Revised: 08/15/2006] [Accepted: 09/25/2006] [Indexed: 05/12/2023]
Abstract
In this review we summarize recent advances in our understanding of phylogenetics, polyploidization and comparative genomics in the family Brassicaceae. These findings pave the way for a unified comparative genomic framework. We integrate several of these findings into a simple system of 24 conserved chromosomal blocks (labeled A-X). The naming, order, orientation and color-coding of these blocks are based on their positions in a proposed ancestral karyotype (n=8), rather than by their position in the reduced genome of Arabidopsis thaliana (n=5). We show how these crucifer building blocks can be rearranged to model the genome structures of A. thaliana, Arabidopsis lyrata, Capsella rubella and Brassica rapa. A framework for comparison between species is timely because several crucifer genome-sequencing projects are underway.
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Affiliation(s)
- M Eric Schranz
- Department of Biology, Duke University, Durham, NC 27708, USA.
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Affiliation(s)
- Quentin C B Cronk
- Botanical Garden and Centre for Plant Research, University of British Columbia, 6804 SW Marine Drive, Vancouver, BC, Canada V6T 1Z4.
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