1
|
Mabry ME, Abrahams RS, Al-Shehbaz IA, Baker WJ, Barak S, Barker MS, Barrett RL, Beric A, Bhattacharya S, Carey SB, Conant GC, Conran JG, Dassanayake M, Edger PP, Hall JC, Hao Y, Hendriks KP, Hibberd JM, King GJ, Kliebenstein DJ, Koch MA, Leitch IJ, Lens F, Lysak MA, McAlvay AC, McKibben MTW, Mercati F, Moore RC, Mummenhoff K, Murphy DJ, Nikolov LA, Pisias M, Roalson EH, Schranz ME, Thomas SK, Yu Q, Yocca A, Pires JC, Harkess AE. Complementing model species with model clades. THE PLANT CELL 2024; 36:1205-1226. [PMID: 37824826 PMCID: PMC11062466 DOI: 10.1093/plcell/koad260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/07/2023] [Accepted: 09/22/2023] [Indexed: 10/14/2023]
Abstract
Model species continue to underpin groundbreaking plant science research. At the same time, the phylogenetic resolution of the land plant tree of life continues to improve. The intersection of these 2 research paths creates a unique opportunity to further extend the usefulness of model species across larger taxonomic groups. Here we promote the utility of the Arabidopsis thaliana model species, especially the ability to connect its genetic and functional resources, to species across the entire Brassicales order. We focus on the utility of using genomics and phylogenomics to bridge the evolution and diversification of several traits across the Brassicales to the resources in Arabidopsis, thereby extending scope from a model species by establishing a "model clade." These Brassicales-wide traits are discussed in the context of both the model species Arabidopsis and the family Brassicaceae. We promote the utility of such a "model clade" and make suggestions for building global networks to support future studies in the model order Brassicales.
Collapse
Affiliation(s)
- Makenzie E Mabry
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - R Shawn Abrahams
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN 47906, USA
| | | | | | - Simon Barak
- Ben-Gurion University of the Negev, French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Midreshet Ben-Gurion, 8499000, Israel
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Russell L Barrett
- National Herbarium of New South Wales, Australian Botanic Garden, Locked Bag 6002, Mount Annan, NSW 2567, Australia
| | - Aleksandra Beric
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, St. Louis, MO 63110, USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, St. Louis, MO 63108, USA
| | - Samik Bhattacharya
- Department of Biology, Botany, University of Osnabrück, D-49076 Osnabrück, Germany
| | - Sarah B Carey
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Gavin C Conant
- Department of Biological Sciences, Bioinformatics Research Center, Program in Genetics, North Carolina State University, Raleigh, NC 27695, USA
| | - John G Conran
- ACEBB and SGC, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Maheshi Dassanayake
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI 48864, USA
| | - Jocelyn C Hall
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Yue Hao
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Kasper P Hendriks
- Department of Biology, Botany, University of Osnabrück, D-49076 Osnabrück, Germany
- Functional Traits, Naturalis Biodiversity Center, PO Box 9517, Leiden 2300 RA, the Netherlands
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 1TN, UK
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia
| | | | - Marcus A Koch
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany
| | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Frederic Lens
- Functional Traits, Naturalis Biodiversity Center, PO Box 9517, Leiden 2300 RA, the Netherlands
- Institute of Biology Leiden, Plant Sciences, Leiden University, 2333 BE Leiden, the Netherlands
| | - Martin A Lysak
- CEITEC, and NCBR, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Alex C McAlvay
- Institute of Economic Botany, New York Botanical Garden, The Bronx, NY 10458, USA
| | - Michael T W McKibben
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Francesco Mercati
- National Research Council (CNR), Institute of Biosciences and Bioresource (IBBR), Palermo 90129, Italy
| | | | - Klaus Mummenhoff
- Department of Biology, Botany, University of Osnabrück, D-49076 Osnabrück, Germany
| | - Daniel J Murphy
- Royal Botanic Gardens Victoria, Melbourne, VIC 3004, Australia
| | | | - Michael Pisias
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Eric H Roalson
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - M Eric Schranz
- Biosystematics Group, Wageningen University, 6708 PB Wageningen, the Netherlands
| | - Shawn K Thomas
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
- Bioinformatics and Analytics Core, University of Missouri, Columbia, MO 65211, USA
| | - Qingyi Yu
- Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Hilo, HI 96720, USA
| | - Alan Yocca
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - J Chris Pires
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523-1170, USA
| | - Alex E Harkess
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| |
Collapse
|
2
|
Thomas SK, Hoek KV, Ogoti T, Duong H, Angelovici R, Pires JC, Mendoza-Cozatl D, Washburn J, Schenck CA. Halophytes and heavy metals: A multi-omics approach to understand the role of gene and genome duplication in the abiotic stress tolerance of Cakile maritima. AMERICAN JOURNAL OF BOTANY 2024:e16310. [PMID: 38600732 DOI: 10.1002/ajb2.16310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 04/12/2024]
Abstract
PREMISE The origin of diversity is a fundamental biological question. Gene duplications are one mechanism that provides raw material for the emergence of novel traits, but evolutionary outcomes depend on which genes are retained and how they become functionalized. Yet, following different duplication types (polyploidy and tandem duplication), the events driving gene retention and functionalization remain poorly understood. Here we used Cakile maritima, a species that is tolerant to salt and heavy metals and shares an ancient whole-genome triplication with closely related salt-sensitive mustard crops (Brassica), as a model to explore the evolution of abiotic stress tolerance following polyploidy. METHODS Using a combination of ionomics, free amino acid profiling, and comparative genomics, we characterize aspects of salt stress response in C. maritima and identify retained duplicate genes that have likely enabled adaptation to salt and mild levels of cadmium. RESULTS Cakile maritima is tolerant to both cadmium and salt treatments through uptake of cadmium in the roots. Proline constitutes greater than 30% of the free amino acid pool in C. maritima and likely contributes to abiotic stress tolerance. We find duplicated gene families are enriched in metabolic and transport processes and identify key transport genes that may be involved in C. maritima abiotic stress tolerance. CONCLUSIONS These findings identify pathways and genes that could be used to enhance plant resilience and provide a putative understanding of the roles of duplication types and retention on the evolution of abiotic stress response.
Collapse
Affiliation(s)
- Shawn K Thomas
- Division of Biological Sciences, University of Missouri, Columbia, 65211, MO, USA
- Bioinformatics and Analytics Core, University of Missouri, Columbia, 65211, MO, USA
- Interdisciplinary Plant Group, University of Missouri, Columbia, 65211, MO, USA
| | - Kathryn Vanden Hoek
- Department of Biochemistry, University of Missouri, Columbia, 65211, MO, USA
| | - Tasha Ogoti
- Department of Computer Science, University of Missouri, Columbia, 65211, MO, USA
| | - Ha Duong
- Interdisciplinary Plant Group, University of Missouri, Columbia, 65211, MO, USA
- Department of Biochemistry, University of Missouri, Columbia, 65211, MO, USA
| | - Ruthie Angelovici
- Division of Biological Sciences, University of Missouri, Columbia, 65211, MO, USA
- Interdisciplinary Plant Group, University of Missouri, Columbia, 65211, MO, USA
| | - J Chris Pires
- Soil and Crop Sciences, Colorado State University, Fort Collins, 80523-1170, CO, USA
| | - David Mendoza-Cozatl
- Interdisciplinary Plant Group, University of Missouri, Columbia, 65211, MO, USA
- Division of Plant Sciences and Technology, University of Missouri, Columbia, 65211, MO, USA
| | - Jacob Washburn
- Interdisciplinary Plant Group, University of Missouri, Columbia, 65211, MO, USA
- Plant Genetics Research Unit, USDA-ARS, Columbia, 65211, MO, USA
| | - Craig A Schenck
- Interdisciplinary Plant Group, University of Missouri, Columbia, 65211, MO, USA
- Department of Biochemistry, University of Missouri, Columbia, 65211, MO, USA
| |
Collapse
|
3
|
Tran KN, Pantha P, Wang G, Kumar N, Wijesinghege C, Oh DH, Wimalagunasekara S, Duppen N, Li H, Hong H, Johnson JC, Kelt R, Matherne MG, Nguyen TT, Garcia JR, Clement A, Tran D, Crain C, Adhikari P, Zhang Y, Foroozani M, Sessa G, Larkin JC, Smith AP, Longstreth D, Finnegan P, Testerink C, Barak S, Dassanayake M. Balancing growth amidst salt stress - lifestyle perspectives from the extremophyte model Schrenkiella parvula. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:921-941. [PMID: 37609706 DOI: 10.1111/tpj.16396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 07/08/2023] [Indexed: 08/24/2023]
Abstract
Schrenkiella parvula, a leading extremophyte model in Brassicaceae, can grow and complete its lifecycle under multiple environmental stresses, including high salinity. Yet, the key physiological and structural traits underlying its stress-adapted lifestyle are unknown along with trade-offs when surviving salt stress at the expense of growth and reproduction. We aimed to identify the influential adaptive trait responses that lead to stress-resilient and uncompromised growth across developmental stages when treated with salt at levels known to inhibit growth in Arabidopsis and most crops. Its resilient growth was promoted by traits that synergistically allowed primary root growth in seedlings, the expansion of xylem vessels across the root-shoot continuum, and a high capacity to maintain tissue water levels by developing thicker succulent leaves while enabling photosynthesis during salt stress. A successful transition from vegetative to reproductive phase was initiated by salt-induced early flowering, resulting in viable seeds. Self-fertilization in salt-induced early flowering was dependent upon filament elongation in flowers otherwise aborted in the absence of salt during comparable plant ages. The maintenance of leaf water status promoting growth, and early flowering to ensure reproductive success in a changing environment, were among the most influential traits that contributed to the extremophytic lifestyle of S. parvula.
Collapse
Affiliation(s)
- Kieu-Nga Tran
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803, USA
| | - Pramod Pantha
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803, USA
| | - Guannan Wang
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803, USA
| | - Narender Kumar
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803, USA
| | - Chathura Wijesinghege
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803, USA
| | - Dong-Ha Oh
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803, USA
| | - Samadhi Wimalagunasekara
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803, USA
| | - Nick Duppen
- Albert Katz International School for Desert Studies, Ben-Gurion University of the Negev, Sde Boqer Campus, Beersheba, 8499000, Israel
| | - Hongfei Li
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University and Research, 6708PB, Wageningen, The Netherlands
| | - Hyewon Hong
- Department of Plant Biology, University of Illinois, Urbana-Champaign, Illinois, 61801, USA
| | - John C Johnson
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803, USA
| | - Ross Kelt
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803, USA
| | - Megan G Matherne
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803, USA
| | - Thu T Nguyen
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803, USA
| | - Jason R Garcia
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803, USA
| | - Ashley Clement
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803, USA
| | - David Tran
- Department of Biochemistry & Department of Psychology, University of Miami, Coral Gables, Florida, 33146, USA
| | - Colt Crain
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803, USA
- Louisiana School for Math, Science and the Arts, Natchitoches, Louisiana, 71457, USA
| | - Prava Adhikari
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803, USA
| | - Yanxia Zhang
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University and Research, 6708PB, Wageningen, The Netherlands
| | - Maryam Foroozani
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803, USA
| | - Guido Sessa
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - John C Larkin
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803, USA
| | - Aaron P Smith
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803, USA
| | - David Longstreth
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803, USA
| | - Patrick Finnegan
- School of Biological Sciences, University of Western Australia, Perth, 6009, Australia
| | - Christa Testerink
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University and Research, 6708PB, Wageningen, The Netherlands
| | - Simon Barak
- French Associates' Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sde Boqer Campus, Beersheba, 8499000, Israel
| | - Maheshi Dassanayake
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803, USA
| |
Collapse
|
4
|
Du L, Ma Z, Mao H. Duplicate Genes Contribute to Variability in Abiotic Stress Resistance in Allopolyploid Wheat. PLANTS (BASEL, SWITZERLAND) 2023; 12:2465. [PMID: 37447026 DOI: 10.3390/plants12132465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 07/15/2023]
Abstract
Gene duplication is a universal biological phenomenon that drives genomic variation and diversity, plays a crucial role in plant evolution, and contributes to innovations in genetic engineering and crop development. Duplicated genes participate in the emergence of novel functionality, such as adaptability to new or more severe abiotic stress resistance. Future crop research will benefit from advanced, mechanistic understanding of the effects of gene duplication, especially in the development and deployment of high-performance, stress-resistant, elite wheat lines. In this review, we summarize the current knowledge of gene duplication in wheat, including the principle of gene duplication and its effects on gene function, the diversity of duplicated genes, and how they have functionally diverged. Then, we discuss how duplicated genes contribute to abiotic stress response and the mechanisms of duplication. Finally, we have a future prospects section that discusses the direction of future efforts in the short term regarding the elucidation of replication and retention mechanisms of repetitive genes related to abiotic stress response in wheat, excellent gene function research, and practical applications.
Collapse
Affiliation(s)
- Linying Du
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Science, Northwest A&F University, Yangling 712100, China
| | - Zhenbing Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Science, Northwest A&F University, Yangling 712100, China
| | - Hude Mao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| |
Collapse
|
5
|
Li H, Duijts K, Pasini C, van Santen JE, Lamers J, de Zeeuw T, Verstappen F, Wang N, Zeeman SC, Santelia D, Zhang Y, Testerink C. Effective root responses to salinity stress include maintained cell expansion and carbon allocation. THE NEW PHYTOLOGIST 2023; 238:1942-1956. [PMID: 36908088 DOI: 10.1111/nph.18873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 02/25/2023] [Indexed: 05/04/2023]
Abstract
Acclimation of root growth is vital for plants to survive salt stress. Halophytes are great examples of plants that thrive even under severe salinity, but their salt tolerance mechanisms, especially those mediated by root responses, are still largely unknown. We compared root growth responses of the halophyte Schrenkiella parvula with its glycophytic relative species Arabidopsis thaliana under salt stress and performed transcriptomic analysis of S. parvula roots to identify possible gene regulatory networks underlying their physiological responses. Schrenkiella parvula roots do not avoid salt and experience less growth inhibition under salt stress. Salt-induced abscisic acid levels were higher in S. parvula roots compared with Arabidopsis. Root transcriptomic analysis of S. parvula revealed the induction of sugar transporters and genes regulating cell expansion and suberization under salt stress. 14 C-labeled carbon partitioning analyses showed that S. parvula continued allocating carbon to roots from shoots under salt stress while carbon barely allocated to Arabidopsis roots. Further physiological investigation revealed that S. parvula roots maintained root cell expansion and enhanced suberization under severe salt stress. In summary, roots of S. parvula deploy multiple physiological and developmental adjustments under salt stress to maintain growth, providing new avenues to improve salt tolerance of plants using root-specific strategies.
Collapse
Affiliation(s)
- Hongfei Li
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University & Research, 6708PB, Wageningen, the Netherlands
| | - Kilian Duijts
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University & Research, 6708PB, Wageningen, the Netherlands
| | - Carlo Pasini
- Institute of Integrative Biology, ETH Zurich, 8092, Zurich, Switzerland
| | - Joyce E van Santen
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University & Research, 6708PB, Wageningen, the Netherlands
| | - Jasper Lamers
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University & Research, 6708PB, Wageningen, the Netherlands
| | - Thijs de Zeeuw
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University & Research, 6708PB, Wageningen, the Netherlands
| | - Francel Verstappen
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University & Research, 6708PB, Wageningen, the Netherlands
| | - Nan Wang
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University & Research, 6708PB, Wageningen, the Netherlands
| | - Samuel C Zeeman
- Institute of Molecular Plant Biology, ETH Zurich, 8092, Zurich, Switzerland
| | - Diana Santelia
- Institute of Integrative Biology, ETH Zurich, 8092, Zurich, Switzerland
| | - Yanxia Zhang
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University & Research, 6708PB, Wageningen, the Netherlands
| | - Christa Testerink
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University & Research, 6708PB, Wageningen, the Netherlands
| |
Collapse
|
6
|
Pantha P, Oh DH, Longstreth D, Dassanayake M. Living with high potassium: Balance between nutrient acquisition and K-induced salt stress signaling. PLANT PHYSIOLOGY 2023; 191:1102-1121. [PMID: 36493387 PMCID: PMC9922392 DOI: 10.1093/plphys/kiac564] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/08/2022] [Accepted: 12/07/2022] [Indexed: 05/12/2023]
Abstract
High potassium (K) in the growth medium induces salinity stress in plants. However, the molecular mechanisms underlying plant responses to K-induced salt stress are virtually unknown. We examined Arabidopsis (Arabidopsis thaliana) and its extremophyte relative Schrenkiella parvula using a comparative multiomics approach to identify cellular processes affected by excess K and understand which deterministic regulatory pathways are active to avoid tissue damages while sustaining growth. Arabidopsis showed limited capacity to curb excess K accumulation and prevent nutrient depletion, contrasting to S. parvula which could limit excess K accumulation without restricting nutrient uptake. A targeted transcriptomic response in S. parvula promoted nitrogen uptake along with other key nutrients followed by uninterrupted N assimilation into primary metabolites during excess K-stress. This resulted in larger antioxidant and osmolyte pools and corresponded with sustained growth in S. parvula. Antithetically, Arabidopsis showed increased reactive oxygen species levels, reduced photosynthesis, and transcriptional responses indicative of a poor balance between stress signaling, subsequently leading to growth limitations. Our results indicate that the ability to regulate independent nutrient uptake and a coordinated transcriptomic response to avoid nonspecific stress signaling are two main deterministic steps toward building stress resilience to excess K+-induced salt stress.
Collapse
Affiliation(s)
- Pramod Pantha
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Dong-Ha Oh
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - David Longstreth
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | | |
Collapse
|
7
|
Moinoddini F, Mirshamsi Kakhki A, Bagheri A, Jalilian A. Genome-wide analysis of annexin gene family in Schrenkiella parvula and Eutrema salsugineum suggests their roles in salt stress response. PLoS One 2023; 18:e0280246. [PMID: 36652493 PMCID: PMC9847905 DOI: 10.1371/journal.pone.0280246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 12/24/2022] [Indexed: 01/19/2023] Open
Abstract
Annexins (Anns) play an important role in plant development, growth and responses to various stresses. Although Ann genes have been characterized in some plants, their role in adaptation mechanisms and tolerance to environmental stresses have not been studied in extremophile plants. In this study, Ann genes in Schrenkiella parvula and Eutrema salsugineum were identified using a genome-wide method and phylogenetic relationships, subcellular distribution, gene structures, conserved residues and motifs and also promoter prediction have been studied through bioinformatics analysis. We identified ten and eight encoding putative Ann genes in S. parvula and E. salsugineum genome respectively, which were divided into six subfamilies according to phylogenetic relationships. By observing conservation in gene structures and protein motifs we found that the majority of Ann members in two extremophile plants are similar. Furthermore, promoter analysis revealed a greater number of GATA, Dof, bHLH and NAC transcription factor binding sites, as well as ABRE, ABRE3a, ABRE4, MYB and Myc cis-acting elements in compare to Arabidopsis thaliana. To gain additional insight into the putative roles of candidate Ann genes, the expression of SpAnn1, SpAnn2 and SpAnn6 in S. parvula was studied in response to salt stress, which indicated that their expression level in shoot increased. Similarly, salt stress induced expression of EsAnn1, 5 and 7, in roots and EsAnn1, 2 and 5 in leaves of E. salsugineum. Our comparative analysis implies that both halophytes have different regulatory mechanisms compared to A. thaliana and suggest SpAnn2 gene play important roles in mediating salt stress.
Collapse
Affiliation(s)
- Fatemeh Moinoddini
- Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Amin Mirshamsi Kakhki
- Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
- * E-mail:
| | - Abdolreza Bagheri
- Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Ahmad Jalilian
- Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| |
Collapse
|
8
|
Xu S, Guo Z, Feng X, Shao S, Yang Y, Li J, Zhong C, He Z, Shi S. Where whole-genome duplication is most beneficial: Adaptation of mangroves to a wide salinity range between land and sea. Mol Ecol 2023; 32:460-475. [PMID: 34882881 DOI: 10.1111/mec.16320] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 11/08/2021] [Accepted: 12/01/2021] [Indexed: 01/11/2023]
Abstract
Whole-genome duplication (WGD) is believed to increase the chance of adaptation to a new environment. This conjecture may apply particularly well to new environments that are not only different but also more variable than ancestral habitats. One such prominent environment is the interface between land and sea, which has been invaded by woody plants, collectively referred as mangroves, multiple times. Here, we use two distantly related mangrove species (Avicennia marina and Rhizophora apiculata) to explore the effects of WGD on the adaptive process. We found that a high proportion of duplicated genes retained after WGD have acquired derived differential expression in response to salt gradient treatment. The WGD duplicates differentially expressed in at least one copy usually (>90%) diverge from their paralogues' expression profiles. Furthermore, both species evolved in parallel to have one paralogue expressed at a high level in both fresh water and hypersaline conditions but at a lower level at medium salinity. The pattern contrasts with the conventional view of monotone increase/decrease as salinity increases. Differentially expressed copies have thus probably acquired a new role in salinity tolerance. Our results indicate that the WGD duplicates may have evolved to function collaboratively in coping with different salinity levels, rather than specializing in the intermediate salinity optimal for mangrove plants. In conclusion, WGD and the retained duplicates appear to be an effective solution for adaptation to new and unstable environments.
Collapse
Affiliation(s)
- Shaohua Xu
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Zixiao Guo
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Xiao Feng
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Shao Shao
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Yuchen Yang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
| | - Jianfang Li
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Cairong Zhong
- Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou, China
| | - Ziwen He
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Suhua Shi
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| |
Collapse
|
9
|
Eshel G, Duppen N, Wang G, Oh D, Kazachkova Y, Herzyk P, Amtmann A, Gordon M, Chalifa‐Caspi V, Oscar MA, Bar‐David S, Marshall‐Colon A, Dassanayake M, Barak S. Positive selection and heat-response transcriptomes reveal adaptive features of the Brassicaceae desert model, Anastatica hierochuntica. THE NEW PHYTOLOGIST 2022; 236:1006-1026. [PMID: 35909295 PMCID: PMC9804903 DOI: 10.1111/nph.18411] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Plant adaptation to a desert environment and its endemic heat stress is poorly understood at the molecular level. The naturally heat-tolerant Brassicaceae species Anastatica hierochuntica is an ideal extremophyte model to identify genetic adaptations that have evolved to allow plants to tolerate heat stress and thrive in deserts. We generated an A. hierochuntica reference transcriptome and identified extremophyte adaptations by comparing Arabidopsis thaliana and A. hierochuntica transcriptome responses to heat, and detecting positively selected genes in A. hierochuntica. The two species exhibit similar transcriptome adjustment in response to heat and the A. hierochuntica transcriptome does not exist in a constitutive heat 'stress-ready' state. Furthermore, the A. hierochuntica global transcriptome as well as heat-responsive orthologs, display a lower basal and higher heat-induced expression than in A. thaliana. Genes positively selected in multiple extremophytes are associated with stomatal opening, nutrient acquisition, and UV-B induced DNA repair while those unique to A. hierochuntica are consistent with its photoperiod-insensitive, early-flowering phenotype. We suggest that evolution of a flexible transcriptome confers the ability to quickly react to extreme diurnal temperature fluctuations characteristic of a desert environment while positive selection of genes involved in stress tolerance and early flowering could facilitate an opportunistic desert lifestyle.
Collapse
Affiliation(s)
- Gil Eshel
- Albert Katz International School for Desert StudiesBen‐Gurion University of the NegevSde Boqer CampusMidreshet Ben‐Gurion8499000Israel
| | - Nick Duppen
- Albert Katz International School for Desert StudiesBen‐Gurion University of the NegevSde Boqer CampusMidreshet Ben‐Gurion8499000Israel
| | - Guannan Wang
- Department of Biological SciencesLouisiana State UniversityBaton RougeLA70803USA
| | - Dong‐Ha Oh
- Department of Biological SciencesLouisiana State UniversityBaton RougeLA70803USA
| | - Yana Kazachkova
- Albert Katz International School for Desert StudiesBen‐Gurion University of the NegevSde Boqer CampusMidreshet Ben‐Gurion8499000Israel
| | - Pawel Herzyk
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowG12 8QQUK
| | - Anna Amtmann
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowG12 8QQUK
| | - Michal Gordon
- Bioinformatics Core Facility, The National Institute for Biotechnology in the NegevBen‐Gurion University of the NegevBeer‐Sheva8410501Israel
| | - Vered Chalifa‐Caspi
- Bioinformatics Core Facility, The National Institute for Biotechnology in the NegevBen‐Gurion University of the NegevBeer‐Sheva8410501Israel
| | - Michelle Arland Oscar
- Blaustein Center for Scientific CooperationBen‐Gurion University of the NegevSde Boqer CampusMidreshet Ben‐Gurion8499000Israel
| | - Shirli Bar‐David
- Mitrani Department of Desert Ecology, Jacob Blaustein Institutes for Desert ResearchBen‐Gurion University of the NegevSde Boqer CampusMidreshet Ben‐Gurion8499000Israel
| | - Amy Marshall‐Colon
- Department of Plant BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIL61801USA
| | - Maheshi Dassanayake
- Department of Biological SciencesLouisiana State UniversityBaton RougeLA70803USA
| | - Simon Barak
- French Associates' Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert ResearchBen‐Gurion University of the NegevSde Boqer CampusMidreshet Ben‐Gurion8499000Israel
| |
Collapse
|
10
|
Palos K, Nelson Dittrich AC, Yu L, Brock JR, Railey CE, Wu HYL, Sokolowska E, Skirycz A, Hsu PY, Gregory BD, Lyons E, Beilstein MA, Nelson ADL. Identification and functional annotation of long intergenic non-coding RNAs in Brassicaceae. THE PLANT CELL 2022; 34:3233-3260. [PMID: 35666179 PMCID: PMC9421480 DOI: 10.1093/plcell/koac166] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 05/05/2022] [Indexed: 06/01/2023]
Abstract
Long intergenic noncoding RNAs (lincRNAs) are a large yet enigmatic class of eukaryotic transcripts that can have critical biological functions. The wealth of RNA-sequencing (RNA-seq) data available for plants provides the opportunity to implement a harmonized identification and annotation effort for lincRNAs that enables cross-species functional and genomic comparisons as well as prioritization of functional candidates. In this study, we processed >24 Tera base pairs of RNA-seq data from >16,000 experiments to identify ∼130,000 lincRNAs in four Brassicaceae: Arabidopsis thaliana, Camelina sativa, Brassica rapa, and Eutrema salsugineum. We used nanopore RNA-seq, transcriptome-wide structural information, peptide data, and epigenomic data to characterize these lincRNAs and identify conserved motifs. We then used comparative genomic and transcriptomic approaches to highlight lincRNAs in our data set with sequence or transcriptional conservation. Finally, we used guilt-by-association analyses to assign putative functions to lincRNAs within our data set. We tested this approach on a subset of lincRNAs associated with germination and seed development, observing germination defects for Arabidopsis lines harboring T-DNA insertions at these loci. LincRNAs with Brassicaceae-conserved putative miRNA binding motifs, small open reading frames, or abiotic-stress modulated expression are a few of the annotations that will guide functional analyses into this cryptic portion of the transcriptome.
Collapse
Affiliation(s)
- Kyle Palos
- The Boyce Thompson Institute, Cornell University, Ithaca, New York, USA
| | | | - Li’ang Yu
- The Boyce Thompson Institute, Cornell University, Ithaca, New York, USA
| | - Jordan R Brock
- Department of Horticulture, Michigan State University, East Lansing, Michigan, USA
| | - Caylyn E Railey
- The Boyce Thompson Institute, Cornell University, Ithaca, New York, USA
| | - Hsin-Yen Larry Wu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | | | | | - Polly Yingshan Hsu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Eric Lyons
- The School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Mark A Beilstein
- The School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | | |
Collapse
|
11
|
Sun Y, Oh DH, Duan L, Ramachandran P, Ramirez A, Bartlett A, Tran KN, Wang G, Dassanayake M, Dinneny JR. Divergence in the ABA gene regulatory network underlies differential growth control. NATURE PLANTS 2022; 8:549-560. [PMID: 35501452 DOI: 10.1038/s41477-022-01139-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
The phytohormone abscisic acid (ABA) is a central regulator of acclimation to environmental stress; however, its contribution to differences in stress tolerance between species is unclear. To establish a comparative framework for understanding how stress hormone signalling pathways diverge across species, we studied the growth response of four Brassicaceae species to ABA treatment and generated transcriptomic and DNA affinity purification and sequencing datasets to construct a cross-species gene regulatory network (GRN) for ABA. Comparison of genes bound directly by ABA-responsive element binding factors suggests that cis-factors are most important for determining the target loci represented in the ABA GRN of a particular species. Using this GRN, we reveal how rewiring of growth hormone subnetworks contributes to stark differences in the response to ABA in the extremophyte Schrenkiella parvula. Our study provides a model for understanding how divergence in gene regulation can lead to species-specific physiological outcomes in response to hormonal cues.
Collapse
Affiliation(s)
- Ying Sun
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Dong-Ha Oh
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Lina Duan
- Department of Biology, Stanford University, Stanford, CA, USA
| | | | - Andrea Ramirez
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Anna Bartlett
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Kieu-Nga Tran
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Guannan Wang
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Maheshi Dassanayake
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - José R Dinneny
- Department of Biology, Stanford University, Stanford, CA, USA.
| |
Collapse
|
12
|
Shen J, Li Z, Fu Y, Liang J. Identification and molecular characterization of the alternative spliced variants of beta carbonic anhydrase 1 (βCA1) from Arabidopsis thaliana. PeerJ 2022; 9:e12673. [PMID: 35036152 PMCID: PMC8710251 DOI: 10.7717/peerj.12673] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 12/02/2021] [Indexed: 12/17/2022] Open
Abstract
Carbonic anhydrases (CAs) are ubiquitous zinc metalloenzymes that catalyze the interconversion of carbon dioxide and bicarbonate. Higher plants mainly contain the three evolutionarily distinct CA families αCA, βCA, and γCA, with each represented by multiple isoforms. Alternative splicing (AS) of the CA transcripts is common. However, there is little information on the spliced variants of individual CA isoforms. In this study, we focused on the characterization of spliced variants of βCA1 from Arabidopsis. The expression patterns and subcellular localization of the individual spliced variants of βCA1 were examined. The results showed that the spliced variants of βCA1 possessed different subcellular and tissue distributions and responded differently to environmental stimuli. Additionally, we addressed the physiological role of βCA1 in heat stress response and its protein-protein interaction (PPI) network. Our results showed that βCA1 was regulated by heat stresses, and βca1 mutant was hypersensitive to heat stress, indicating a role for βCA1 in heat stress response. Furthermore, PPI network analysis revealed that βCA1 interacts with multiple proteins involved in several processes, including photosynthesis, metabolism, and the stress response, and these will provide new avenues for future investigations of βCA1.
Collapse
Affiliation(s)
- Jinyu Shen
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Zhiyong Li
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China.,Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Yajuan Fu
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Jiansheng Liang
- Department of Biology, Southern University of Science and Technology, Shenzhen, China.,Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Southern University of Science and Technology, Shenzhen, China
| |
Collapse
|
13
|
Genies L, Martin L, Kanno S, Chiarenza S, Carasco L, Camilleri V, Vavasseur A, Henner P, Leonhardt N. Disruption of AtHAK/KT/KUP9 enhances plant cesium accumulation under low potassium supply. PHYSIOLOGIA PLANTARUM 2021; 173:1230-1243. [PMID: 34342899 DOI: 10.1111/ppl.13518] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
Understanding the molecular mechanisms that underlie cesium (Cs+ ) transport in plants is important to limit the entry of its radioisotopes from contaminated areas into the food chain. The potentially toxic element Cs+ , which is not involved in any biological process, is chemically closed to the macronutrient potassium (K+ ). Among the multiple K+ carriers, the high-affinity K+ transporters family HAK/KT/KUP is thought to be relevant in mediating opportunistic Cs+ transport. Of the 13 KUP identified in A. thaliana, only HAK5, the major contributor to root K+ acquisition under low K+ supply, has been functionally demonstrated to be involved in Cs+ uptake in planta. In the present study, we showed that accumulation of Cs+ increased by up to 30% in two A. thaliana mutant lines lacking KUP9 and grown under low K+ supply. Since further experiments revealed that Cs+ release from contaminated plants to the external medium is proportionally lower in the two kup9 mutant alleles, we proposed that KUP9 disruption could impair Cs+ efflux. By contrast, K+ status in kup9 mutants is not affected, suggesting that KUP9 disruption does not alter substantially K+ transport in experimental conditions used. The putative primary role of KUP9 in plants is further discussed.
Collapse
Affiliation(s)
- Laure Genies
- Aix Marseille University, French Alternative Energies and Atomic Energy Commission (CEA), National Center for Scientific Research (CNRS), Bioscience and Biotechnology Institute of Aix-Marseille (BIAM), Laboratory of Signaling for the Adaptation to their Environment (SAVE), Saint-Paul-lez-Durance, France
- Laboratory of Research on Radionuclides Transfer Within Terrestrial Ecosystems (LR2T), Institute for Radiological Protection and Nuclear Safety (IRSN), Cadarache, France
| | - Ludovic Martin
- Aix Marseille University, French Alternative Energies and Atomic Energy Commission (CEA), National Center for Scientific Research (CNRS), Bioscience and Biotechnology Institute of Aix-Marseille (BIAM), Laboratory of Signaling for the Adaptation to their Environment (SAVE), Saint-Paul-lez-Durance, France
| | - Satomi Kanno
- Aix Marseille University, French Alternative Energies and Atomic Energy Commission (CEA), National Center for Scientific Research (CNRS), Bioscience and Biotechnology Institute of Aix-Marseille (BIAM), Laboratory of Signaling for the Adaptation to their Environment (SAVE), Saint-Paul-lez-Durance, France
| | - Serge Chiarenza
- Aix Marseille University, French Alternative Energies and Atomic Energy Commission (CEA), National Center for Scientific Research (CNRS), Bioscience and Biotechnology Institute of Aix-Marseille (BIAM), Laboratory of Signaling for the Adaptation to their Environment (SAVE), Saint-Paul-lez-Durance, France
| | - Loïc Carasco
- Laboratory of Research on Radionuclides Transfer Within Terrestrial Ecosystems (LR2T), Institute for Radiological Protection and Nuclear Safety (IRSN), Cadarache, France
| | - Virginie Camilleri
- Laboratory for Radionuclide Ecotoxicology (LECO), Institute for Radiological Protection and Nuclear Safety (IRSN), Cadarache, France
| | - Alain Vavasseur
- Aix Marseille University, French Alternative Energies and Atomic Energy Commission (CEA), National Center for Scientific Research (CNRS), Bioscience and Biotechnology Institute of Aix-Marseille (BIAM), Laboratory of Signaling for the Adaptation to their Environment (SAVE), Saint-Paul-lez-Durance, France
| | - Pascale Henner
- Laboratory of Research on Radionuclides Transfer Within Terrestrial Ecosystems (LR2T), Institute for Radiological Protection and Nuclear Safety (IRSN), Cadarache, France
| | - Nathalie Leonhardt
- Aix Marseille University, French Alternative Energies and Atomic Energy Commission (CEA), National Center for Scientific Research (CNRS), Bioscience and Biotechnology Institute of Aix-Marseille (BIAM), Laboratory of Signaling for the Adaptation to their Environment (SAVE), Saint-Paul-lez-Durance, France
| |
Collapse
|
14
|
Wang G, DiTusa SF, Oh DH, Herrmann AD, Mendoza-Cozatl DG, O'Neill MA, Smith AP, Dassanayake M. Cross species multi-omics reveals cell wall sequestration and elevated global transcript abundance as mechanisms of boron tolerance in plants. THE NEW PHYTOLOGIST 2021; 230:1985-2000. [PMID: 33629348 DOI: 10.1111/nph.17295] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 02/18/2021] [Indexed: 06/12/2023]
Abstract
Boron toxicity is a world-wide problem for crops, yet we have a limited understanding of the genetic responses and adaptive mechanisms to this stress in plants. We employed a cross-species comparison between boron stress-sensitive Arabidopsis thaliana and its boron stress-tolerant extremophyte relative Schrenkiella parvula, and a multi-omics approach integrating genomics, transcriptomics, metabolomics and ionomics to assess plant responses and adaptations to boron stress. Schrenkiella parvula maintains lower concentrations of total boron and free boric acid than Arabidopsis when grown with excess boron. Schrenkiella parvula excludes excess boron more efficiently than Arabidopsis, which we propose is partly driven by SpBOR5, a boron transporter that we functionally characterize in this study. Both species use cell walls as a partial sink for excess boron. When accumulated in the cytoplasm, excess boron appears to interrupt RNA metabolism. The extremophyte S. parvula facilitates critical cellular processes while maintaining the pool of ribose-containing compounds that can bind with boric acid. The S. parvula transcriptome is pre-adapted to boron toxicity. It exhibits substantial overlaps with the Arabidopsis boron-stress responsive transcriptome. Cell wall sequestration and increases in global transcript levels under excess boron conditions emerge as key mechanisms for sustaining plant growth under boron toxicity.
Collapse
Affiliation(s)
- Guannan Wang
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Sandra Feuer DiTusa
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Dong-Ha Oh
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Achim D Herrmann
- Department of Geology & Geophysics and Coastal Studies Institute, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - David G Mendoza-Cozatl
- Division of Plant Sciences, Interdisciplinary Plant Group, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Malcolm A O'Neill
- Complex Carbohydrate Research Center, The University of Georgia, Athens, GA, 30602, USA
| | - Aaron P Smith
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Maheshi Dassanayake
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| |
Collapse
|
15
|
A comparison of shared patterns of differential gene expression and gene ontologies in response to water-stress in roots and leaves of four diverse genotypes of Lolium and Festuca spp. temperate pasture grasses. PLoS One 2021; 16:e0249636. [PMID: 33831050 PMCID: PMC8031407 DOI: 10.1371/journal.pone.0249636] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/22/2021] [Indexed: 12/13/2022] Open
Abstract
Ryegrasses (Lolium spp.) and fescues (Festuca spp.) are closely related and widely cultivated perennial forage grasses. As such, resilience in the face of abiotic stresses is an important component of their traits. We have compared patterns of differentially expressed genes (DEGs) in roots and leaves of two perennial ryegrass genotypes and a single genotype of each of a festulolium (predominantly Italian ryegrass) and meadow fescue with the onset of water stress, focussing on overall patterns of DEGs and gene ontology terms (GOs) shared by all four genotypes. Plants were established in a growing medium of vermiculite watered with nutrient solution. Leaf and root material were sampled at 35% (saturation) and, as the medium dried, at 15%, 5% and 1% estimated water contents (EWCs) and RNA extracted. Differential gene expression was evaluated comparing the EWC sampling points from RNAseq data using a combination of analysis methods. For all genotypes, the greatest numbers of DEGs were identified in the 35/1 and 5/1 comparisons in both leaves and roots. In total, 566 leaf and 643 root DEGs were common to all 4 genotypes, though a third of these leaf DEGs were not regulated in the same up/down direction in all 4 genotypes. For roots, the equivalent figure was 1% of the DEGs. GO terms shared by all four genotypes were often enriched by both up- and down-regulated DEGs in the leaf, whereas generally, only by either up- or down-regulated DEGs in the root. Overall, up-regulated leaf DEGs tended to be more genotype-specific than down-regulated leaf DEGs or root DEGs and were also associated with fewer GOs. On average, only 5–15% of the DEGs enriching common GO terms were shared by all 4 genotypes, suggesting considerable variation in DEGs between related genotypes in enacting similar biological processes.
Collapse
|
16
|
Ali A, Raddatz N, Pardo JM, Yun D. HKT sodium and potassium transporters in Arabidopsis thaliana and related halophyte species. PHYSIOLOGIA PLANTARUM 2021; 171:546-558. [PMID: 32652584 PMCID: PMC8048799 DOI: 10.1111/ppl.13166] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 06/30/2020] [Accepted: 07/06/2020] [Indexed: 05/10/2023]
Abstract
High salinity induces osmotic stress and often leads to sodium ion-specific toxicity, with inhibitory effects on physiological, biochemical and developmental pathways. To cope with increased Na+ in soil water, plants restrict influx, compartmentalize ions into vacuoles, export excess Na+ from the cell, and distribute ions between the aerial and root organs. In this review, we discuss our current understanding of how high-affinity K+ transporters (HKT) contribute to salinity tolerance, focusing on HKT1-like family members primarily involved in long-distance transport, and in the recent research in the model plant Arabidopsis and its halophytic counterparts of the Eutrema genus. Functional characterization of the salt overly sensitive (SOS) pathway and HKT1-type transporters in these species indicate that they utilize similar approaches to deal with salinity, regardless of their tolerance.
Collapse
Affiliation(s)
- Akhtar Ali
- Institute of Glocal Disease ControlKonkuk UniversitySeoul05029South Korea
- Department of Biomedical Science & EngineeringKonkuk UniversitySeoul05029South Korea
| | - Natalia Raddatz
- Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, CSIC‐Universidad de SevillaAmerico Vespucio 49, Sevilla41092Spain
| | - Jose M. Pardo
- Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, CSIC‐Universidad de SevillaAmerico Vespucio 49, Sevilla41092Spain
| | - Dae‐Jin Yun
- Department of Biomedical Science & EngineeringKonkuk UniversitySeoul05029South Korea
| |
Collapse
|
17
|
Das Laha S, Dutta S, Schäffner AR, Das M. Gene duplication and stress genomics in Brassicas: Current understanding and future prospects. JOURNAL OF PLANT PHYSIOLOGY 2020; 255:153293. [PMID: 33181457 DOI: 10.1016/j.jplph.2020.153293] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 09/09/2020] [Accepted: 09/21/2020] [Indexed: 06/11/2023]
Abstract
Polyploidy or whole genome duplication (WGD) is an evolutionary phenomenon that happened in all angiosperms multiple times over millions of years. Extensive studies on the model plant Arabidopsis thaliana genome have revealed that it has undergone five rounds of WGDs followed, in the Brassicaceae tribe, by a characteristic whole genome triplication (WGT). In addition, small-scale events such as tandem or segmental duplications and retrotransposition also enable plants to reshape their genomes. Over the decades, extensive research efforts have been undertaken to understand the evolutionary significance of polyploidy. On the other hand, much less attention has been paid to understanding the impact of gene duplication on the diversification of important stress response genes. The main objective of this review is to discuss key aspects of gene and genome duplications with a focus on genes primarily regulated by osmotic stresses. The focal family is the Brassicaceae, since it (i) underwent multiple rounds of WGDs plus WGTs, (ii) hosts many economically important crops and wild relatives that are tolerant to a range of stresses, and (iii) comprises many species that have already been sequenced. Diverse molecular mechanisms that lead to structural and regulatory alterations of duplicated genes are discussed. Examples are drawn from recent literature to elucidate expanded, stress responsive gene families identified from different Brassica crops. A combined bioinformatic and transcriptomic method has been proposed and tested on a known stress-responsive gene pair to prove that stress-responsive duplicated allelic variants can be identified by this method. Finally, future prospects for engineering these genes into crops to enhance stress tolerance are discussed, and important resources for Brassica genome research are provided.
Collapse
Affiliation(s)
- Shayani Das Laha
- Department of Life Sciences, Presidency University, Kolkata, India
| | - Smritikana Dutta
- Department of Life Sciences, Presidency University, Kolkata, India
| | - Anton R Schäffner
- Institute of Biochemical Plant Pathology, Department of Environmental Sciences, Helmholtz Zentrum München, München, Germany
| | - Malay Das
- Department of Life Sciences, Presidency University, Kolkata, India.
| |
Collapse
|
18
|
Xu S, Wang J, Guo Z, He Z, Shi S. Genomic Convergence in the Adaptation to Extreme Environments. PLANT COMMUNICATIONS 2020; 1:100117. [PMID: 33367270 PMCID: PMC7747959 DOI: 10.1016/j.xplc.2020.100117] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 10/12/2020] [Accepted: 10/28/2020] [Indexed: 05/08/2023]
Abstract
Convergent evolution is especially common in plants that have independently adapted to the same extreme environments (i.e., extremophile plants). The recent burst of omics data has alleviated many limitations that have hampered molecular convergence studies of non-model extremophile plants. In this review, we summarize cases of genomic convergence in these taxa to examine the extent and type of genomic convergence during the process of adaptation to extreme environments. Despite being well studied by candidate gene approaches, convergent evolution at individual sites is rare and often has a high false-positive rate when assessed in whole genomes. By contrast, genomic convergence at higher genetic levels has been detected during adaptation to the same extreme environments. Examples include the convergence of biological pathways and changes in gene expression, gene copy number, amino acid usage, and GC content. Higher convergence levels play important roles in the adaptive evolution of extremophiles and may be more frequent and involve more genes. In several cases, multiple types of convergence events have been found to co-occur. However, empirical and theoretical studies of this higher level convergent evolution are still limited. In conclusion, both the development of powerful approaches and the detection of convergence at various genetic levels are needed to further reveal the genetic mechanisms of plant adaptation to extreme environments.
Collapse
Affiliation(s)
- Shaohua Xu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jiayan Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zixiao Guo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Ziwen He
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Suhua Shi
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| |
Collapse
|
19
|
Monihan SM, Magness CA, Ryu CH, McMahon MM, Beilstein MA, Schumaker KS. Duplication and functional divergence of a calcium sensor in the Brassicaceae. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2782-2795. [PMID: 31989164 PMCID: PMC7210777 DOI: 10.1093/jxb/eraa031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 01/27/2020] [Indexed: 05/09/2023]
Abstract
The presence of varied numbers of CALCINEURIN B-LIKE10 (CBL10) calcium sensor genes in species across the Brassicaceae and the demonstrated role of CBL10 in salt tolerance in Arabidopsis thaliana and Eutrema salsugineum provided a unique opportunity to determine if CBL10 function is modified in different species and linked to salt tolerance. Salinity effects on species growth and cross-species complementation were used to determine the extent of conservation and divergence of CBL10 function in four species representing major lineages within the core Brassicaceae (A. thaliana, E. salsugineum, Schrenkiella parvula, and Sisymbrium irio) as well as the first diverging lineage (Aethionema arabicum). Evolutionary and functional analyses indicate that CBL10 duplicated within expanded lineage II of the Brassicaceae and that, while portions of CBL10 function are conserved across the family, there are species-specific variations in CBL10 function. Paralogous CBL10 genes within a species diverged in expression and function probably contributing to the maintenance of the duplicated gene pairs. Orthologous CBL10 genes diverged in function in a species-specific manner, suggesting that functions arose post-speciation. Multiple CBL10 genes and their functional divergence may have expanded calcium-mediated signaling responses and contributed to the ability of certain members of the Brassicaceae to maintain growth in salt-affected soils.
Collapse
Affiliation(s)
- Shea M Monihan
- School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | | | - Choong-Hwan Ryu
- School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | | | - Mark A Beilstein
- School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Karen S Schumaker
- School of Plant Sciences, University of Arizona, Tucson, AZ, USA
- Correspondence:
| |
Collapse
|
20
|
Abstract
Crop loss due to soil salinization is an increasing threat to agriculture worldwide. This review provides an overview of cellular and physiological mechanisms in plant responses to salt. We place cellular responses in a time- and tissue-dependent context in order to link them to observed phases in growth rate that occur in response to stress. Recent advances in phenotyping can now functionally or genetically link cellular signaling responses, ion transport, water management, and gene expression to growth, development, and survival. Halophytes, which are naturally salt-tolerant plants, are highlighted as success stories to learn from. We emphasize that (a) filling the major knowledge gaps in salt-induced signaling pathways, (b) increasing the spatial and temporal resolution of our knowledge of salt stress responses, (c) discovering and considering crop-specific responses, and (d) including halophytes in our comparative studies are all essential in order to take our approaches to increasing crop yields in saline soils to the next level.
Collapse
Affiliation(s)
- Eva van Zelm
- Laboratory of Plant Physiology, Wageningen University, 6700 AA Wageningen, The Netherlands;
| | - Yanxia Zhang
- Laboratory of Plant Physiology, Wageningen University, 6700 AA Wageningen, The Netherlands;
| | - Christa Testerink
- Laboratory of Plant Physiology, Wageningen University, 6700 AA Wageningen, The Netherlands;
| |
Collapse
|
21
|
Vithanage M, Kumarathilaka P, Oze C, Karunatilake S, Seneviratne M, Hseu ZY, Gunarathne V, Dassanayake M, Ok YS, Rinklebe J. Occurrence and cycling of trace elements in ultramafic soils and their impacts on human health: A critical review. ENVIRONMENT INTERNATIONAL 2019; 131:104974. [PMID: 31376597 DOI: 10.1016/j.envint.2019.104974] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 06/26/2019] [Accepted: 06/27/2019] [Indexed: 06/10/2023]
Abstract
The transformation of trace metals (TMs) in natural environmental systems has created significant concerns in recent decades. Ultramafic environments lead to potential risks to the agricultural products and, subsequently, to human health. This unique review presents geochemistry of ultramafic soils, TM fractionation (i.e. sequential and single extraction techniques), TM uptake and accumulation mechanisms of ultramafic flora, and ultramafic-associated health risks to human and agricultural crops. Ultramafic soils contain high levels of TMs (i.e. Cr, Ni, Mn, and Co) and have a low Ca:Mg ratio together with deficiencies in essential macronutrients required for the growth of crops. Even though a higher portion of TMs bind with the residual fraction of ultramafic soils, environmental changes (i.e. natural or anthropogenic) may increase the levels of TMs in the bioavailable or extractable fractions of ultramafic soils. Extremophile plants that have evolved to thrive in ultramafic soils present clear examples of evolutionary adaptations to TM resistance. The release of TMs into water sources and accumulation in food crops in and around ultramafic localities increases health risks for humans. Therefore, more focused investigations need to be implemented to understand the mechanisms related to the mobility and bioavailability of TMs in different ultramafic environments. Research gaps and directions for future studies are also discussed in this review. Lastly, we consider the importance of characterizing terrestrial ultramafic soil and its effect on crop plants in the context of multi-decadal plans by NASA and other space agencies to establish human colonies on Mars.
Collapse
Affiliation(s)
- Meththika Vithanage
- Ecosphere Resilience Research Center, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda 10250, Sri Lanka; School of Civil Engineering and Surveying, Faculty of Health, Engineering and Sciences, University of Southern Queensland, West Street, Toowoomba, Queensland 4350, Australia.
| | - Prasanna Kumarathilaka
- School of Civil Engineering and Surveying, Faculty of Health, Engineering and Sciences, University of Southern Queensland, West Street, Toowoomba, Queensland 4350, Australia
| | - Christopher Oze
- Department of Geology, Occidental College, Los Angeles, CA 90041, USA
| | - Suniti Karunatilake
- Planetary Science Lab, Geology & Geophysics, Louisiana State University, USA
| | - Mihiri Seneviratne
- Department of Botany, The Open University of Sri Lanka, Nawala, Sri Lanka
| | - Zeng-Yei Hseu
- Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan
| | - Viraj Gunarathne
- Ecosphere Resilience Research Center, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda 10250, Sri Lanka
| | | | - Yong Sik Ok
- Korea Biochar Research Center, O-Jeong Eco-Resilience Institute, Division of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea.
| | - Jörg Rinklebe
- University of Wuppertal, School of Architecture and Civil Engineering, Institute of Foundation Engineering, Water- and Waste-Management, Laboratory of Soil- and Groundwater-Management, Pauluskirchstraße 7, 42285 Wuppertal, Germany; University of Sejong, Department of Environment and Energy, Seoul 05006, Republic of Korea.
| |
Collapse
|
22
|
Oh DH, Dassanayake M. Landscape of gene transposition-duplication within the Brassicaceae family. DNA Res 2019; 26:21-36. [PMID: 30380026 PMCID: PMC6379040 DOI: 10.1093/dnares/dsy035] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 10/03/2018] [Indexed: 11/12/2022] Open
Abstract
We developed the CLfinder-OrthNet pipeline that detects co-linearity among multiple closely related genomes, finds orthologous gene groups, and encodes the evolutionary history of each orthologue group into a representative network (OrthNet). Using a search based on network topology, we identified 1,394 OrthNets that included gene transposition-duplication (tr-d) events, out of 17,432 identified in six Brassicaceae genomes. Occurrences of tr-d shared by subsets of Brassicaceae genomes mirrored the divergence times between the genomes and their repeat contents. The majority of tr-d events resulted in truncated open reading frames (ORFs) in the duplicated loci. However, the duplicates with complete ORFs were significantly more frequent than expected from random events. These were derived from older tr-d events and had a higher chance of being expressed. We also found an enrichment of tr-d events with complete loss of intergenic sequence conservation between the original and duplicated loci. Finally, we identified tr-d events uniquely found in two extremophytes among the six Brassicaceae genomes, including tr-d of SALT TOLERANCE 32 and ZINC TRANSPORTER 3 that relate to their adaptive evolution. CLfinder-OrthNet provides a flexible toolkit to compare gene order, visualize evolutionary paths among orthologues as networks, and identify gene loci that share an evolutionary history.
Collapse
Affiliation(s)
- Dong-Ha Oh
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Maheshi Dassanayake
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| |
Collapse
|
23
|
Ali A, Maggio A, Bressan RA, Yun DJ. Role and Functional Differences of HKT1-Type Transporters in Plants under Salt Stress. Int J Mol Sci 2019; 20:E1059. [PMID: 30823627 PMCID: PMC6429402 DOI: 10.3390/ijms20051059] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 02/17/2019] [Accepted: 02/25/2019] [Indexed: 02/03/2023] Open
Abstract
Abiotic stresses generally cause a series of morphological, biochemical and molecular changes that unfavorably affect plant growth and productivity. Among these stresses, soil salinity is a major threat that can seriously impair crop yield. To cope with the effects of high salinity on plants, it is important to understand the mechanisms that plants use to deal with it, including those activated in response to disturbed Na⁺ and K⁺ homeostasis at cellular and molecular levels. HKT1-type transporters are key determinants of Na⁺ and K⁺ homeostasis under salt stress and they contribute to reduce Na⁺-specific toxicity in plants. In this review, we provide a brief overview of the function of HKT1-type transporters and their importance in different plant species under salt stress. Comparison between HKT1 homologs in different plant species will shed light on different approaches plants may use to cope with salinity.
Collapse
Affiliation(s)
- Akhtar Ali
- Department of Biomedical Science & Engineering, Konkuk University, Seoul 05029, Korea.
| | - Albino Maggio
- Department of Agriculture, University of Naples Federico II, Via Universita 100, I-80055 Portici, Italy.
| | - Ray A Bressan
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907-2010, USA.
| | - Dae-Jin Yun
- Department of Biomedical Science & Engineering, Konkuk University, Seoul 05029, Korea.
| |
Collapse
|
24
|
Hajiboland R, Bahrami-Rad S, Akhani H, Poschenrieder C. Salt tolerance mechanisms in three Irano-Turanian Brassicaceae halophytes relatives of Arabidopsis thaliana. JOURNAL OF PLANT RESEARCH 2018; 131:1029-1046. [PMID: 29967980 DOI: 10.1007/s10265-018-1053-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 06/15/2018] [Indexed: 06/08/2023]
Abstract
Salt tolerance mechanisms were studied in three Irano-Turanian halophytic species from the Brassicaceae (Lepidium latifolium, L. perfoliatum and Schrenkiella parvula) and compared with the glycophyte Arabidopsis thaliana. According to seed germination under salt stress, L. perfoliatum was the most tolerant species, while L. latifolium and S. parvula were rather susceptible. Contrastingly, based on biomass production L. perfoliatum was more salt sensitive than the other two species. In S. parvula biomass was increased up to 2.8-fold by 100 mM NaCl; no significant growth reduction was observed even when exposed to 400 mM NaCl. Stable activities of antioxidative defense enzymes, nil or negligible accumulation of superoxide anion and hydrogen peroxide, as well as stable membrane integrity in the three halophytes revealed that no oxidative stress occurred in these tolerant species under salt stress. Proline levels increased in response to salt treatment. However, it contributed only by 0.3‒2.0% to the total osmolyte concentration in the three halophytes (at 400 mM NaCl) and even less (0.04%) in the glycophyte, A. thaliana (at 100 mM NaCl). Soluble sugars in all three halophytes and free amino acids pool in S. parvula decreased under salt treatment in contrast to the glycophyte, A. thaliana. The contribution of organic osmolytes to the total osmolyte pool increased by salt treatment in the roots, while decreased in halophyte and glycophyte, A. thaliana leaves. Interestingly, this reduction was compensated by a higher relative contribution of K in the leaves of the halophytes, but of Na in A. thaliana. Taken together, biomass data and biochemical indicators show that S. parvula is more salt tolerant than the two Lepidium species. Our data indicate that L. latifolium, as a perennial halophyte with a large biomass, is highly suitable for both restoration of saline habitats and saline agriculture.
Collapse
Affiliation(s)
- Roghieh Hajiboland
- Department of Plant Science, University of Tabriz, Tabriz, 51666-16471, Iran.
| | - Sara Bahrami-Rad
- Department of Plant Science, University of Tabriz, Tabriz, 51666-16471, Iran
| | - Hossein Akhani
- Halophytes and C4 Plants Research Laboratory, Department of Plant Science, School of Biology, University of Tehran, P.O. Box 14155-6455, Tehran, Iran
| | - Charlotte Poschenrieder
- Plant Physiology Laboratory, Bioscience Faculty, Universidad Autónoma de Barcelona, 08193, Bellaterra, Spain
| |
Collapse
|
25
|
Kazachkova Y, Eshel G, Pantha P, Cheeseman JM, Dassanayake M, Barak S. Halophytism: What Have We Learnt From Arabidopsis thaliana Relative Model Systems? PLANT PHYSIOLOGY 2018; 178:972-988. [PMID: 30237204 PMCID: PMC6236594 DOI: 10.1104/pp.18.00863] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 08/31/2018] [Indexed: 05/06/2023]
Abstract
Halophytes are able to thrive in salt concentrations that would kill 99% of other plant species, and identifying their salt-adaptive mechanisms has great potential for improving the tolerance of crop plants to salinized soils. Much research has focused on the physiological basis of halophyte salt tolerance, whereas the elucidation of molecular mechanisms has traditionally lagged behind due to the absence of a model halophyte system. However, over the last decade and a half, two Arabidopsis (Arabidopsis thaliana) relatives, Eutrema salsugineum and Schrenkiella parvula, have been established as transformation-competent models with various genetic resources including high-quality genome assemblies. These models have facilitated powerful comparative analyses with salt-sensitive Arabidopsis to unravel the genetic adaptations that enable a halophytic lifestyle. The aim of this review is to explore what has been learned about halophytism using E. salsugineum and S. parvula We consider evidence from physiological and molecular studies suggesting that differences in salt tolerance between related halophytes and salt-sensitive plants are associated with alterations in the regulation of basic physiological, biochemical, and molecular processes. Furthermore, we discuss how salt tolerance mechanisms of the halophytic models are reflected at the level of their genomes, where evolutionary processes such as subfunctionalization and/or neofunctionalization have altered the expression and/or functions of genes to facilitate adaptation to saline conditions. Lastly, we summarize the many areas of research still to be addressed with E. salsugineum and S. parvula as well as obstacles hindering further progress in understanding halophytism.
Collapse
Affiliation(s)
- Yana Kazachkova
- French Associates' Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion 8499000, Israel
| | - Gil Eshel
- French Associates' Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion 8499000, Israel
| | - Pramod Pantha
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - John M Cheeseman
- Department of Plant Biology, University of Illinois, Urbana, Illinois 61801
| | - Maheshi Dassanayake
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Simon Barak
- French Associates' Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion 8499000, Israel
| |
Collapse
|
26
|
Fan L, Wang G, Hu W, Pantha P, Tran KN, Zhang H, An L, Dassanayake M, Qiu QS. Transcriptomic view of survival during early seedling growth of the extremophyte Haloxylon ammodendron. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 132:475-489. [PMID: 30292980 DOI: 10.1016/j.plaphy.2018.09.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/08/2018] [Accepted: 09/18/2018] [Indexed: 05/27/2023]
Abstract
Seedling establishment in an extreme environment requires an integrated genomic and physiological response to survive multiple abiotic stresses. The extremophyte, Haloxylon ammodendron is a pioneer species capable of colonizing temperate desert sand dunes. We investigated the induced and basal transcriptomes in H. ammodendron under water-deficit stress during early seedling establishment. We find that not only drought-responsive genes, but multiple genes in pathways associated with salt, osmotic, cold, UV, and high-light stresses were induced, suggesting an altered regulatory stress response system. Additionally, H. ammodendron exhibited enhanced biotic stress tolerance by down-regulation of genes that were generally up-regulated during pathogen entry in susceptible plants. By comparing the H. ammodendron basal transcriptome to six closely related transcriptomes in Amaranthaceae, we detected enriched basal level transcripts in H. ammodendron that shows preadaptation to abiotic stress and pathogens. We found transcripts that were generally maintained at low levels and some induced only under abiotic stress in the stress-sensitive model, Arabidopsis thaliana to be highly expressed under basal conditions in the Amaranthaceae transcriptomes including H. ammodendron. H. ammodendron shows coordinated expression of genes that regulate stress tolerance and seedling development resource allocation to support survival against multiple stresses in a sand dune dominated temperate desert environment.
Collapse
Affiliation(s)
- Ligang Fan
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, 222 South Tianshui Road, Lanzhou, Gansu, 730000, China
| | - Guannan Wang
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA, 70803, USA
| | - Wei Hu
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, 222 South Tianshui Road, Lanzhou, Gansu, 730000, China
| | - Pramod Pantha
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA, 70803, USA
| | - Kieu-Nga Tran
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA, 70803, USA
| | - Hua Zhang
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, 222 South Tianshui Road, Lanzhou, Gansu, 730000, China
| | - Lizhe An
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, 222 South Tianshui Road, Lanzhou, Gansu, 730000, China
| | - Maheshi Dassanayake
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA, 70803, USA.
| | - Quan-Sheng Qiu
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, 222 South Tianshui Road, Lanzhou, Gansu, 730000, China.
| |
Collapse
|
27
|
Ali A, Khan IU, Jan M, Khan HA, Hussain S, Nisar M, Chung WS, Yun DJ. The High-Affinity Potassium Transporter EpHKT1;2 From the Extremophile Eutrema parvula Mediates Salt Tolerance. FRONTIERS IN PLANT SCIENCE 2018; 9:1108. [PMID: 30105045 PMCID: PMC6077265 DOI: 10.3389/fpls.2018.01108] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 07/09/2018] [Indexed: 05/23/2023]
Abstract
To survive salt stress, plants must maintain a balance between sodium and potassium ions. High-affinity potassium transporters (HKTs) play a key role in reducing Na+ toxicity through K+ uptake. Eutrema parvula (formerly known as Thellungiella parvula), a halophyte closely related to Arabidopsis, has two HKT1 genes that encode EpHKT1;1 and EpHKT1;2. In response to high salinity, the EpHKT1;2 transcript level increased rapidly; by contrast, the EpHKT1;1 transcript increased more slowly in response to salt treatment. Yeast cells expressing EpHKT1;2 were able to tolerate high concentrations of NaCl, whereas EpHKT1;1-expressing yeast cells remained sensitive to NaCl. Amino acid sequence alignment with other plant HKTs showed that EpHKT1;1 contains an asparagine residue (Asn-213) in the second pore-loop domain, but EpHKT1;2 contains an aspartic acid residue (Asp-205) at the same position. Yeast cells expressing EpHKT1;1, in which Asn-213 was substituted with Asp, were able to tolerate high concentrations of NaCl. In contrast, substitution of Asp-205 by Asn in EpHKT1;2 did not enhance salt tolerance and rather resulted in a similar function to that of AtHKT1 (Na+ influx but no K+ influx), indicating that the presence of Asn or Asp determines the mode of cation selectivity of the HKT1-type transporters. Moreover, Arabidopsis plants (Col-gl) overexpressing EpHKT1;2 showed significantly higher tolerance to salt stress and accumulated less Na+ and more K+ compared to those overexpressing EpHKT1;1 or AtHKT1. Taken together, these results suggest that EpHKT1;2 mediates tolerance to Na+ ion toxicity in E. parvula and is a major contributor to its halophytic nature.
Collapse
Affiliation(s)
- Akhtar Ali
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, South Korea
| | - Irfan Ullah Khan
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, South Korea
- Division of Applied Life Science (BK21plus program), Gyeongsang National University, Jinju, South Korea
| | - Masood Jan
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, South Korea
- Division of Applied Life Science (BK21plus program), Gyeongsang National University, Jinju, South Korea
| | - Haris Ali Khan
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, South Korea
| | - Shah Hussain
- Division of Applied Life Science (BK21plus program), Gyeongsang National University, Jinju, South Korea
| | - Muhammad Nisar
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, South Korea
- Department of Botany, University of Malakand, Chakdara, Pakistan
| | - Woo Sik Chung
- Division of Applied Life Science (BK21plus program), Gyeongsang National University, Jinju, South Korea
| | - Dae-Jin Yun
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, South Korea
| |
Collapse
|
28
|
Oscar MA, Barak S, Winters G. The Tropical Invasive Seagrass, Halophila stipulacea, Has a Superior Ability to Tolerate Dynamic Changes in Salinity Levels Compared to Its Freshwater Relative, Vallisneria americana. FRONTIERS IN PLANT SCIENCE 2018; 9:950. [PMID: 30022993 PMCID: PMC6040085 DOI: 10.3389/fpls.2018.00950] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 06/12/2018] [Indexed: 05/30/2023]
Abstract
The tropical seagrass species, Halophila stipulacea, originated from the Indian Ocean and the Red Sea, subsequently invading the Mediterranean and has recently established itself in the Caribbean Sea. Due to its invasive nature, there is growing interest in understanding this species' capacity to adapt to new conditions. One approach to understanding the natural tolerance of a plant is to compare the tolerant species with a closely related non-tolerant species. We compared the physiological responses of H. stipulacea exposed to different salinities, with that of its nearest freshwater relative, Vallisneria americana. To achieve this goal, H. stipulacea and V. americana plants were grown in dedicated microcosms, and exposed to the following salt regimes: (i) H. stipulacea: control (40 PSU, practical salinity units), hyposalinity (25 PSU) and hypersalinity (60 PSU) for 3 weeks followed by a 4-week recovery phase (back to 40 PSU); (ii) V. americana: control (1 PSU), and hypersalinity (12 PSU) for 3 weeks, followed by a 4-week recovery phase (back to 1 PSU). In H. stipulacea, leaf number and chlorophyll content showed no significant differences between control plants and plants under hypo and hypersalinities, but a significant decrease in leaf area under hypersalinity was observed. In addition, compared with control plants, H. stipulacea plants exposed to hypo and hypersalinity were found to have reduced below-ground biomass and C/N ratios, suggesting changes in the allocation of resources in response to both stresses. There was no significant effect of hypo/hypersalinity on dark-adapted quantum yield of photosystem II (Fv/Fm) suggesting that H. stipulacea photochemistry is resilient to hypo/hypersalinity stress. In contrast to the seagrass, V. americana exposed to hypersalinity displayed significant decreases in above-ground biomass, shoot number, leaf number, blade length and Fv/Fm, followed by significant recoveries of all these parameters upon return of the plants to non-saline control conditions. These data suggest that H. stipulacea shows remarkable tolerance to both hypo and hypersalinity. Resilience to a relatively wide range of salinities may be one of the traits explaining the invasive nature of this species in the Mediterranean and Caribbean Seas.
Collapse
Affiliation(s)
- Michelle A. Oscar
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
- Dead-Sea & Arava Science Center, Neve Zohar, Israel
| | - Simon Barak
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
| | | |
Collapse
|
29
|
Abstract
A gene regulatory network (GRN) describes the hierarchical relationship between transcription factors, associated proteins, and their target genes. Studying GRNs allows us to understand how a plant's genotype and environment are integrated to regulate downstream physiological responses. Current efforts in plants have focused on defining the GRNs that regulate functions such as development and stress response and have been performed primarily in genetically tractable model plant species such as Arabidopsis thaliana. Future studies will likely focus on how GRNs function in non-model plants and change over evolutionary time to allow for adaptation to extreme environments. This broader understanding will inform efforts to engineer GRNs to create tailored crop traits.
Collapse
Affiliation(s)
- Ying Sun
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA, 94305, USA
| | - José R Dinneny
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA, 94305, USA. .,Department of Plant Biology, Carnegie Institution for Science, 260 Panama St, Stanford, CA, 94305, USA.
| |
Collapse
|
30
|
Krämer U. Conceptualizing plant systems evolution. CURRENT OPINION IN PLANT BIOLOGY 2018; 42:66-75. [PMID: 29579731 DOI: 10.1016/j.pbi.2018.02.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 02/22/2018] [Accepted: 02/26/2018] [Indexed: 06/08/2023]
Abstract
Organisms inhabiting extreme environments are emerging models in systems evolution, enabling us to identify the molecular alterations effecting major phenotypic divergence through comparative approaches. Here I discuss possible physiological mechanisms underlying evolutionary adaptations to extreme environments both theoretically and in relation to experimental observations. Reasoning leads me to the 'conserved steady-state' hypothesis of evolutionary adaptation: Between closely related plants adapted to differently composed soils, the homeostatically controlled steady-state set point cytosolic (buffered) concentrations of mineral ions are conserved. Subsequently, I compare molecular alterations expected to contribute to physiological adaptations with our present knowledge. Key roles of enhanced gene product dosage in plant evolutionary adaptations question the widespread stimulus response-centric paradigm. As a broader implication, co-regulation networks can lack decisive functional network elements. With this article, I hope to stimulate a discussion across research fields and provide an initial conceptual framework for future experimental testing and for quantitative modelling.
Collapse
Affiliation(s)
- Ute Krämer
- Molecular Genetics and Physiology of Plants, Ruhr University Bochum, Universitätsstraße 150, ND3/30, D-44801 Bochum, Germany.
| |
Collapse
|
31
|
Hawkins AK, Garza ER, Dietz VA, Hernandez OJ, Hawkins WD, Burrell AM, Pepper AE. Transcriptome Signatures of Selection, Drift, Introgression, and Gene Duplication in the Evolution of an Extremophile Endemic Plant. Genome Biol Evol 2017; 9:3478-3494. [PMID: 29220486 PMCID: PMC5751042 DOI: 10.1093/gbe/evx259] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2017] [Indexed: 12/26/2022] Open
Abstract
Plants on serpentine soils provide extreme examples of adaptation to environment, and thus offer excellent models for the study of evolution at the molecular and genomic level. Serpentine outcrops are derived from ultramafic rock and have extremely low levels of essential plant nutrients (e.g., N, P, K, and Ca), as well as toxic levels of heavy metals (e.g., Ni, Cr, and Co) and low moisture availability. These outcrops provide habitat to a number of endemic plant species, including the annual mustard Caulanthus amplexicaulis var. barbarae (Cab) (Brassicaceae). Its sister taxon, C. amplexicaulis var. amplexicaulis (Caa), is intolerant to serpentine soils. Here, we assembled and annotated comprehensive reference transcriptomes of both Caa and Cab for use in protein coding sequence comparisons. A set of 29,443 reciprocal best Blast hit (RBH) orthologs between Caa and Cab was compared with identify coding sequence variants, revealing a high genome-wide dN/dS ratio between the two taxa (mean = 0.346). We show that elevated dN/dS likely results from the composite effects of genetic drift, positive selection, and the relaxation of negative selection. Further, analysis of paralogs within each taxon revealed the signature of a period of elevated gene duplication (∼10 Ma) that is shared with other species of the tribe Thelypodieae, and may have played a role in the striking morphological and ecological diversity of this tribe. In addition, distribution of the synonymous substitution rate, dS, is strongly bimodal, indicating a history of reticulate evolution that may have contributed to serpentine adaptation.
Collapse
|
32
|
Zhao P, Wang L, Zhao X, Chen G, Ma XF. A comparative transcriptomic analysis reveals the core genetic components of salt and osmotic stress responses in Braya humilis. PLoS One 2017; 12:e0183778. [PMID: 28859098 PMCID: PMC5578489 DOI: 10.1371/journal.pone.0183778] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Accepted: 08/10/2017] [Indexed: 11/25/2022] Open
Abstract
Braya humilis is a member of the Euclidieae tribe within the family Brassicaceae. This species exhibits a broad range of adaptations to different climatic zones and latitudes as it has a distribution that ranges from northern Asia to the arctic-alpine regions of northern North America. In China, B. humilis is mainly found on the Qinghai-Tibetan Plateau (QTP) and in adjacent arid regions. In this study, we sequenced a sample from an arid region adjacent to the QTP using the Illumina platform generating a total of 46,485 highly accurate unigenes, of which 78.41% were annotated by BLASTing versus public protein databases. The B. humilis transcriptome is characterized by a high level of sequence conservation compared with its close relative, Arabidopsis thaliana. We also used reciprocal blast to identify shared orthologous genes between B. humilis and four other sequenced Brassicaceae species (i.e. A. thaliana, A. lyrata, Capsella rubella, and Thellungiella parvula). To enable precise characterization of orthologous genes, the early-diverging basal angiosperm Amborella trichopoda was also included. A total of 6,689 orthologous genes were identified before stricter criteria for the determination of e-values, amino acid hit lengths, and identity values was applied to further reduce this list. This led to a final list of 381 core orthologous genes for B. humilis; 39 out of these genes are involved in salt and osmotic stress responses and estimations of nonsynonymous/synonymous substitution ratios for this species and A. thaliana orthologs show that these genes are under purifying selection in B. humilis. Expression of six genes was detected in B. humilis seedlings under salt and osmotic stress treatments. Comparable expression patterns to their counterparts in Arabidopsis suggest that these orthologous genes are both sequence and functional conservation. The results of this study demonstrate that the environmental adaptations of B. humilis are mainly the results of preexisting genetic components. Future work will be required to characterize the expression patterns of these orthologous genes in natural populations and will provide further insights into the adaptive mechanisms underlying the wide range of B. humilis adaptations.
Collapse
Affiliation(s)
- Pengshan Zhao
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, P. R. China
- Shapotou Desert Research and Experimental Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, P. R. China
| | - Lirong Wang
- College of Forestry, Gansu Agricultural University, Lanzhou, Gansu Province, P. R. China
| | - Xin Zhao
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, P. R. China
- Shapotou Desert Research and Experimental Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, P. R. China
| | - Guoxiong Chen
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, P. R. China
- Shapotou Desert Research and Experimental Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, P. R. China
| | - Xiao-Fei Ma
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, P. R. China
- Shapotou Desert Research and Experimental Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, P. R. China
| |
Collapse
|
33
|
Eshel G, Shaked R, Kazachkova Y, Khan A, Eppel A, Cisneros A, Acuna T, Gutterman Y, Tel-Zur N, Rachmilevitch S, Fait A, Barak S. Anastatica hierochuntica, an Arabidopsis Desert Relative, Is Tolerant to Multiple Abiotic Stresses and Exhibits Species-Specific and Common Stress Tolerance Strategies with Its Halophytic Relative, Eutrema ( Thellungiella) salsugineum. FRONTIERS IN PLANT SCIENCE 2017; 7:1992. [PMID: 28144244 PMCID: PMC5239783 DOI: 10.3389/fpls.2016.01992] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 12/15/2016] [Indexed: 05/08/2023]
Abstract
The search for novel stress tolerance determinants has led to increasing interest in plants native to extreme environments - so called "extremophytes." One successful strategy has been comparative studies between Arabidopsis thaliana and extremophyte Brassicaceae relatives such as the halophyte Eutrema salsugineum located in areas including cold, salty coastal regions of China. Here, we investigate stress tolerance in the desert species, Anastatica hierochuntica (True Rose of Jericho), a member of the poorly investigated lineage III Brassicaceae. We show that A. hierochuntica has a genome approximately 4.5-fold larger than Arabidopsis, divided into 22 diploid chromosomes, and demonstrate that A. hierochuntica exhibits tolerance to heat, low N and salt stresses that are characteristic of its habitat. Taking salt tolerance as a case study, we show that A. hierochuntica shares common salt tolerance mechanisms with E. salsugineum such as tight control of shoot Na+ accumulation and resilient photochemistry features. Furthermore, metabolic profiling of E. salsugineum and A. hierochuntica shoots demonstrates that the extremophytes exhibit both species-specific and common metabolic strategies to cope with salt stress including constitutive up-regulation (under control and salt stress conditions) of ascorbate and dehydroascorbate, two metabolites involved in ROS scavenging. Accordingly, A. hierochuntica displays tolerance to methyl viologen-induced oxidative stress suggesting that a highly active antioxidant system is essential to cope with multiple abiotic stresses. We suggest that A. hierochuntica presents an excellent extremophyte Arabidopsis relative model system for understanding plant survival in harsh desert conditions.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Simon Barak
- French Associates Institute for Biotechnology and Agriculture of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the NegevSde Boker, Israel
| |
Collapse
|
34
|
DiMario RJ, Clayton H, Mukherjee A, Ludwig M, Moroney JV. Plant Carbonic Anhydrases: Structures, Locations, Evolution, and Physiological Roles. MOLECULAR PLANT 2017; 10:30-46. [PMID: 27646307 PMCID: PMC5226100 DOI: 10.1016/j.molp.2016.09.001] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 08/30/2016] [Accepted: 09/04/2016] [Indexed: 05/19/2023]
Abstract
Carbonic anhydrases (CAs) are zinc metalloenzymes that catalyze the interconversion of CO2 and HCO3- and are ubiquitous in nature. Higher plants contain three evolutionarily distinct CA families, αCAs, βCAs, and γCAs, where each family is represented by multiple isoforms in all species. Alternative splicing of CA transcripts appears common; consequently, the number of functional CA isoforms in a species may exceed the number of genes. CAs are expressed in numerous plant tissues and in different cellular locations. The most prevalent CAs are those in the chloroplast, cytosol, and mitochondria. This diversity in location is paralleled in the many physiological and biochemical roles that CAs play in plants. In this review, the number and types of CAs in C3, C4, and crassulacean acid metabolism (CAM) plants are considered, and the roles of the α and γCAs are briefly discussed. The remainder of the review focuses on plant βCAs and includes the identification of homologs between species using phylogenetic approaches, a consideration of the inter- and intracellular localization of the proteins, along with the evidence for alternative splice forms. Current understanding of βCA tissue-specific expression patterns and what controls them are reviewed, and the physiological roles for which βCAs have been implicated are presented.
Collapse
Affiliation(s)
- Robert J DiMario
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Harmony Clayton
- School of Chemistry and Biochemistry, University of Western Australia, Perth, WA 6009 Australia
| | - Ananya Mukherjee
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Martha Ludwig
- School of Chemistry and Biochemistry, University of Western Australia, Perth, WA 6009 Australia
| | - James V Moroney
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
| |
Collapse
|
35
|
Rigó G, Valkai I, Faragó D, Kiss E, Van Houdt S, Van de Steene N, Hannah MA, Szabados L. Gene mining in halophytes: functional identification of stress tolerance genes in Lepidium crassifolium. PLANT, CELL & ENVIRONMENT 2016; 39:2074-84. [PMID: 27343166 DOI: 10.1111/pce.12768] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 05/08/2016] [Indexed: 05/27/2023]
Abstract
Extremophile plants are valuable sources of genes conferring tolerance traits, which can be explored to improve stress tolerance of crops. Lepidium crassifolium is a halophytic relative of the model plant Arabidopsis thaliana, and displays tolerance to salt, osmotic and oxidative stresses. We have employed the modified Conditional cDNA Overexpression System to transfer a cDNA library from L. crassifolium to the glycophyte A. thaliana. By screening for salt, osmotic and oxidative stress tolerance through in vitro growth assays and non-destructive chlorophyll fluorescence imaging, 20 Arabidopsis lines were identified with superior performance under restrictive conditions. Several cDNA inserts were cloned and confirmed to be responsible for the enhanced tolerance by analysing independent transgenic lines. Examples include full-length cDNAs encoding proteins with high homologies to GDSL-lipase/esterase or acyl CoA-binding protein or proteins without known function, which could confer tolerance to one or several stress conditions. Our results confirm that random gene transfer from stress tolerant to sensitive plant species is a valuable tool to discover novel genes with potential for biotechnological applications.
Collapse
Affiliation(s)
- Gábor Rigó
- Biological Research Centre, Institute of Plant Biology, 6726, Szeged, Hungary
| | - Ildikó Valkai
- Biological Research Centre, Institute of Plant Biology, 6726, Szeged, Hungary
| | - Dóra Faragó
- Biological Research Centre, Institute of Plant Biology, 6726, Szeged, Hungary
| | - Edina Kiss
- Biological Research Centre, Institute of Plant Biology, 6726, Szeged, Hungary
| | | | | | | | - László Szabados
- Biological Research Centre, Institute of Plant Biology, 6726, Szeged, Hungary
| |
Collapse
|
36
|
Park HJ, Kim WY, Yun DJ. A New Insight of Salt Stress Signaling in Plant. Mol Cells 2016; 39:447-59. [PMID: 27239814 PMCID: PMC4916396 DOI: 10.14348/molcells.2016.0083] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 05/06/2016] [Accepted: 05/16/2016] [Indexed: 12/12/2022] Open
Abstract
Many studies have been conducted to understand plant stress responses to salinity because irrigation-dependent salt accumulation compromises crop productivity and also to understand the mechanism through which some plants thrive under saline conditions. As mechanistic understanding has increased during the last decades, discovery-oriented approaches have begun to identify genetic determinants of salt tolerance. In addition to osmolytes, osmoprotectants, radical detoxification, ion transport systems, and changes in hormone levels and hormone-guided communications, the Salt Overly Sensitive (SOS) pathway has emerged to be a major defense mechanism. However, the mechanism by which the components of the SOS pathway are integrated to ultimately orchestrate plant-wide tolerance to salinity stress remains unclear. A higher-level control mechanism has recently emerged as a result of recognizing the involvement of GIGANTEA (GI), a protein involved in maintaining the plant circadian clock and control switch in flowering. The loss of GI function confers high tolerance to salt stress via its interaction with the components of the SOS pathway. The mechanism underlying this observation indicates the association between GI and the SOS pathway and thus, given the key influence of the circadian clock and the pathway on photoperiodic flowering, the association between GI and SOS can regulate growth and stress tolerance. In this review, we will analyze the components of the SOS pathways, with emphasis on the integration of components recognized as hallmarks of a halophytic lifestyle.
Collapse
Affiliation(s)
- Hee Jin Park
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Jinju 52828,
Korea
| | - Woe-Yeon Kim
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Jinju 52828,
Korea
- Institute of Agriculture & Life Sciences, Graduate School of Gyeongsang National University, Jinju 52828,
Korea
| | - Dae-Jin Yun
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Jinju 52828,
Korea
| |
Collapse
|
37
|
DiMario RJ, Quebedeaux JC, Longstreth DJ, Dassanayake M, Hartman MM, Moroney JV. The Cytoplasmic Carbonic Anhydrases βCA2 and βCA4 Are Required for Optimal Plant Growth at Low CO2. PLANT PHYSIOLOGY 2016; 171:280-93. [PMID: 26993617 PMCID: PMC4854698 DOI: 10.1104/pp.15.01990] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 03/16/2016] [Indexed: 05/23/2023]
Abstract
Carbonic anhydrases (CAs) are zinc metalloenzymes that interconvert CO2 and HCO3 (-) In plants, both α- and β-type CAs are present. We hypothesize that cytoplasmic βCAs are required to modulate inorganic carbon forms needed in leaf cells for carbon-requiring reactions such as photosynthesis and amino acid biosynthesis. In this report, we present evidence that βCA2 and βCA4 are the two most abundant cytoplasmic CAs in Arabidopsis (Arabidopsis thaliana) leaves. Previously, βCA4 was reported to be localized to the plasma membrane, but here, we show that two forms of βCA4 are expressed in a tissue-specific manner and that the two proteins encoded by βCA4 localize to two different regions of the cell. Comparing transfer DNA knockout lines with wild-type plants, there was no reduction in the growth rates of the single mutants, βca2 and βca4 However, the growth rate of the double mutant, βca2βca4, was reduced significantly when grown at 200 μL L(-1) CO2 The reduction in growth of the double mutant was not linked to a reduction in photosynthetic rate. The amino acid content of leaves from the double mutant showed marked reduction in aspartate when compared with the wild type and the single mutants. This suggests the cytoplasmic CAs play an important but not previously appreciated role in amino acid biosynthesis.
Collapse
Affiliation(s)
- Robert J DiMario
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70808
| | - Jennifer C Quebedeaux
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70808
| | - David J Longstreth
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70808
| | - Maheshi Dassanayake
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70808
| | - Monica M Hartman
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70808
| | - James V Moroney
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70808
| |
Collapse
|
38
|
Ferreira de Carvalho J, Oplaat C, Pappas N, Derks M, de Ridder D, Verhoeven KJF. Heritable gene expression differences between apomictic clone members in Taraxacum officinale: Insights into early stages of evolutionary divergence in asexual plants. BMC Genomics 2016; 17:203. [PMID: 26956152 PMCID: PMC4782324 DOI: 10.1186/s12864-016-2524-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 02/24/2016] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Asexual reproduction has the potential to enhance deleterious mutation accumulation and to constrain adaptive evolution. One source of mutations that can be especially relevant in recent asexuals is activity of transposable elements (TEs), which may have experienced selection for high transposition rates in sexual ancestor populations. Predictions of genomic divergence under asexual reproduction therefore likely include a large contribution of transposable elements but limited adaptive divergence. For plants empirical insight into genome divergence under asexual reproduction remains limited. Here, we characterize expression divergence between clone members of a single apomictic lineage of the common dandelion (Taraxacum officinale) to contribute to our knowledge of genome evolution under asexuality. RESULTS Using RNA-Seq, we show that about one third of heritable divergence within the apomictic lineage is driven by TEs and TE-related gene activity. In addition, we identify non-random transcriptional differences in pathways related to acyl-lipid and abscisic acid metabolisms which might reflect functional divergence within the apomictic lineage. We analyze SNPs in the transcriptome to assess genetic divergence between the apomictic clone members and reveal that heritable expression differences between the accessions are not explained simply by genome-wide genetic divergence. CONCLUSION The present study depicts a first effort towards a more complete understanding of apomictic plant genome evolution. We identify abundant TE activity and ecologically relevant functional genes and pathways affecting heritable within-lineage expression divergence. These findings offer valuable resources for future work looking at epigenetic silencing and Cis-regulation of gene expression with particular emphasis on the effects of TE activity on asexual species' genome.
Collapse
Affiliation(s)
- Julie Ferreira de Carvalho
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands.
| | - Carla Oplaat
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands.
| | - Nikolaos Pappas
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
| | - Martijn Derks
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
| | - Koen J F Verhoeven
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands.
| |
Collapse
|
39
|
Fischer I, Diévart A, Droc G, Dufayard JF, Chantret N. Evolutionary Dynamics of the Leucine-Rich Repeat Receptor-Like Kinase (LRR-RLK) Subfamily in Angiosperms. PLANT PHYSIOLOGY 2016; 170:1595-610. [PMID: 26773008 PMCID: PMC4775120 DOI: 10.1104/pp.15.01470] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 01/14/2016] [Indexed: 05/20/2023]
Abstract
Gene duplications are an important factor in plant evolution, and lineage-specific expanded (LSE) genes are of particular interest. Receptor-like kinases expanded massively in land plants, and leucine-rich repeat receptor-like kinases (LRR-RLK) constitute the largest receptor-like kinases family. Based on the phylogeny of 7,554 LRR-RLK genes from 31 fully sequenced flowering plant genomes, the complex evolutionary dynamics of this family was characterized in depth. We studied the involvement of selection during the expansion of this family among angiosperms. LRR-RLK subgroups harbor extremely contrasting rates of duplication, retention, or loss, and LSE copies are predominantly found in subgroups involved in environmental interactions. Expansion rates also differ significantly depending on the time when rounds of expansion or loss occurred on the angiosperm phylogenetic tree. Finally, using a dN/dS-based test in a phylogenetic framework, we searched for selection footprints on LSE and single-copy LRR-RLK genes. Selective constraint appeared to be globally relaxed at LSE genes, and codons under positive selection were detected in 50% of them. Moreover, the leucine-rich repeat domains, and specifically four amino acids in them, were found to be the main targets of positive selection. Here, we provide an extensive overview of the expansion and evolution of this very large gene family.
Collapse
Affiliation(s)
- Iris Fischer
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, F-34060 Montpellier, France (I.F., N.C.); andCentre de Coopération Internationale en Recherche Agronomique Pour le Développement, Unité Mixte de Recherche AGAP, F-34398 Montpellier, France (A.D., G.D., J.-F.D.)
| | - Anne Diévart
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, F-34060 Montpellier, France (I.F., N.C.); andCentre de Coopération Internationale en Recherche Agronomique Pour le Développement, Unité Mixte de Recherche AGAP, F-34398 Montpellier, France (A.D., G.D., J.-F.D.)
| | - Gaetan Droc
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, F-34060 Montpellier, France (I.F., N.C.); andCentre de Coopération Internationale en Recherche Agronomique Pour le Développement, Unité Mixte de Recherche AGAP, F-34398 Montpellier, France (A.D., G.D., J.-F.D.)
| | - Jean-François Dufayard
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, F-34060 Montpellier, France (I.F., N.C.); andCentre de Coopération Internationale en Recherche Agronomique Pour le Développement, Unité Mixte de Recherche AGAP, F-34398 Montpellier, France (A.D., G.D., J.-F.D.)
| | - Nathalie Chantret
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, F-34060 Montpellier, France (I.F., N.C.); andCentre de Coopération Internationale en Recherche Agronomique Pour le Développement, Unité Mixte de Recherche AGAP, F-34398 Montpellier, France (A.D., G.D., J.-F.D.)
| |
Collapse
|
40
|
Kumar N, Harashima H, Kalve S, Bramsiepe J, Wang K, Sizani BL, Bertrand LL, Johnson MC, Faulk C, Dale R, Simmons LA, Churchman ML, Sugimoto K, Kato N, Dasanayake M, Beemster G, Schnittger A, Larkin JC. Functional Conservation in the SIAMESE-RELATED Family of Cyclin-Dependent Kinase Inhibitors in Land Plants. THE PLANT CELL 2015; 27:3065-80. [PMID: 26546445 PMCID: PMC4682297 DOI: 10.1105/tpc.15.00489] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/16/2015] [Indexed: 05/03/2023]
Abstract
The best-characterized members of the plant-specific SIAMESE-RELATED (SMR) family of cyclin-dependent kinase inhibitors regulate the transition from the mitotic cell cycle to endoreplication, also known as endoreduplication, an altered version of the cell cycle in which DNA is replicated without cell division. Some other family members are implicated in cell cycle responses to biotic and abiotic stresses. However, the functions of most SMRs remain unknown, and the specific cyclin-dependent kinase complexes inhibited by SMRs are unclear. Here, we demonstrate that a diverse group of SMRs, including an SMR from the bryophyte Physcomitrella patens, can complement an Arabidopsis thaliana siamese (sim) mutant and that both Arabidopsis SIM and P. patens SMR can inhibit CDK activity in vitro. Furthermore, we show that Arabidopsis SIM can bind to and inhibit both CDKA;1 and CDKB1;1. Finally, we show that SMR2 acts to restrict cell proliferation during leaf growth in Arabidopsis and that SIM, SMR1/LGO, and SMR2 play overlapping roles in controlling the transition from cell division to endoreplication during leaf development. These results indicate that differences in SMR function in plant growth and development are primarily due to differences in transcriptional and posttranscriptional regulation, rather than to differences in fundamental biochemical function.
Collapse
Affiliation(s)
- Narender Kumar
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Hirofumi Harashima
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Shweta Kalve
- Department of Biology, Molecular Plant Physiology, and Biotechnology, University of Antwerp, 2020 Antwerp, Belgium
| | - Jonathan Bramsiepe
- Institut de Biologie Moléculaire des Plantes du CNRS, IBMP-CNRS-UPR2357, Université de Strasbourg, F-67084 Strasbourg Cedex, France
| | - Kai Wang
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Bulelani L Sizani
- Department of Biology, Molecular Plant Physiology, and Biotechnology, University of Antwerp, 2020 Antwerp, Belgium
| | - Laura L Bertrand
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Matthew C Johnson
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Christopher Faulk
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Renee Dale
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - L Alice Simmons
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Michelle L Churchman
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Keiko Sugimoto
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Naohiro Kato
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Maheshi Dasanayake
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Gerrit Beemster
- Department of Biology, Molecular Plant Physiology, and Biotechnology, University of Antwerp, 2020 Antwerp, Belgium
| | - Arp Schnittger
- Institut de Biologie Moléculaire des Plantes du CNRS, IBMP-CNRS-UPR2357, Université de Strasbourg, F-67084 Strasbourg Cedex, France
| | - John C Larkin
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| |
Collapse
|
41
|
Rawat V, Abdelsamad A, Pietzenuk B, Seymour DK, Koenig D, Weigel D, Pecinka A, Schneeberger K. Improving the Annotation of Arabidopsis lyrata Using RNA-Seq Data. PLoS One 2015; 10:e0137391. [PMID: 26382944 PMCID: PMC4575116 DOI: 10.1371/journal.pone.0137391] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 08/17/2015] [Indexed: 11/19/2022] Open
Abstract
Gene model annotations are important community resources that ensure comparability and reproducibility of analyses and are typically the first step for functional annotation of genomic regions. Without up-to-date genome annotations, genome sequences cannot be used to maximum advantage. It is therefore essential to regularly update gene annotations by integrating the latest information to guarantee that reference annotations can remain a common basis for various types of analyses. Here, we report an improvement of the Arabidopsis lyrata gene annotation using extensive RNA-seq data. This new annotation consists of 31,132 protein coding gene models in addition to 2,089 genes with high similarity to transposable elements. Overall, ~87% of the gene models are corroborated by evidence of expression and 2,235 of these models feature multiple transcripts. Our updated gene annotation corrects hundreds of incorrectly split or merged gene models in the original annotation, and as a result the identification of alternative splicing events and differential isoform usage are vastly improved.
Collapse
Affiliation(s)
- Vimal Rawat
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Ahmed Abdelsamad
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
- Department of Genetics, Cairo University, 12613, Giza, Egypt
| | - Björn Pietzenuk
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Danelle K. Seymour
- Department for Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35–39, 72076, Tübingen, Germany
| | - Daniel Koenig
- Department for Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35–39, 72076, Tübingen, Germany
| | - Detlef Weigel
- Department for Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35–39, 72076, Tübingen, Germany
| | - Ales Pecinka
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
- * E-mail: (KS); (AP)
| | - Korbinian Schneeberger
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
- * E-mail: (KS); (AP)
| |
Collapse
|
42
|
Frades I, Abreha KB, Proux-Wéra E, Lankinen Å, Andreasson E, Alexandersson E. A novel workflow correlating RNA-seq data to Phythophthora infestans resistance levels in wild Solanum species and potato clones. FRONTIERS IN PLANT SCIENCE 2015; 6:718. [PMID: 26442032 PMCID: PMC4585127 DOI: 10.3389/fpls.2015.00718] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 08/27/2015] [Indexed: 05/18/2023]
Abstract
Comparative transcriptomics between species can provide valuable understanding of plant-pathogen interactions. Here, we focus on wild Solanum species and potato clones with varying degree of resistance against Phytophthora infestans, which causes the devastating late blight disease in potato. The transcriptomes of three wild Solanum species native to Southern Sweden, Solanum dulcamara, Solanum nigrum, and Solanum physalifolium were compared to three potato clones, Desiree (cv.), SW93-1015 and Sarpo Mira. Desiree and S. physalifolium are susceptible to P. infestans whereas the other four have different degrees of resistance. By building transcript families based on de novo assembled RNA-seq across species and clones and correlating these to resistance phenotypes, we created a novel workflow to identify families with expanded or depleted number of transcripts in relation to the P. infestans resistance level. Analysis was facilitated by inferring functional annotations based on the family structure and semantic clustering. More transcript families were expanded in the resistant clones and species and the enriched functions of these were associated to expected gene ontology (GO) terms for resistance mechanisms such as hypersensitive response, host programmed cell death and endopeptidase activity. However, a number of unexpected functions and transcripts were also identified, for example transmembrane transport and protein acylation expanded in the susceptible group and a cluster of Zinc knuckle family proteins expanded in the resistant group. Over 400 expressed putative resistance (R-)genes were identified and resistant clones Sarpo Mira and SW93-1015 had ca 25% more expressed putative R-genes than susceptible cultivar Desiree. However, no differences in numbers of susceptibility (S-)gene homologs were seen between species and clones. In addition, we identified P. infestans transcripts including effectors in the early stages of P. infestans-Solanum interactions.
Collapse
Affiliation(s)
| | | | | | | | | | - Erik Alexandersson
- Department of Plant Protection Biology, Swedish University of Agricultural SciencesAlnarp, Sweden
| |
Collapse
|
43
|
He Q, Hao G, Wang X, Bi H, Li Y, Guo X, Ma T. The complete chloroplast genome of Schrenkiella parvula (Brassicaceae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3527-8. [PMID: 26260181 DOI: 10.3109/19401736.2015.1074202] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Schrenkiella parvula is an Arabidopsis-related model species used here for studying plant stress tolerance. In this study, the complete chloroplast genome sequence of S. parvula has been reported for the first time. The total length of the chloroplast genome was 153 979 bp, which had a typical quadripartite structure. The annotated plastid genome includes 87 protein-coding genes, 39 tRNA genes and 8 ribosomal RNA genes. The evolutionary relationships revealed by our phylogenetic analysis indicated that S. parvula is closer to the Brassiceae species when compared with Eutrema salsugineum.
Collapse
Affiliation(s)
- Qi He
- a MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Science, Sichuan University , Chengdu , China
| | - Guoqian Hao
- a MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Science, Sichuan University , Chengdu , China
| | - Xiaojuan Wang
- a MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Science, Sichuan University , Chengdu , China
| | - Hao Bi
- a MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Science, Sichuan University , Chengdu , China
| | - Yuanshuo Li
- a MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Science, Sichuan University , Chengdu , China
| | - Xinyi Guo
- a MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Science, Sichuan University , Chengdu , China
| | - Tao Ma
- a MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Science, Sichuan University , Chengdu , China
| |
Collapse
|
44
|
Oh DH, Barkla BJ, Vera-Estrella R, Pantoja O, Lee SY, Bohnert HJ, Dassanayake M. Cell type-specific responses to salinity - the epidermal bladder cell transcriptome of Mesembryanthemum crystallinum. THE NEW PHYTOLOGIST 2015; 207:627-44. [PMID: 25944243 DOI: 10.1111/nph.13414] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 03/08/2015] [Indexed: 05/18/2023]
Abstract
Mesembryanthemum crystallinum (ice plant) exhibits extreme tolerance to salt. Epidermal bladder cells (EBCs), developing on the surface of aerial tissues and specialized in sodium sequestration and other protective functions, are critical for the plant's stress adaptation. We present the first transcriptome analysis of EBCs isolated from intact plants, to investigate cell type-specific responses during plant salt adaptation. We developed a de novo assembled, nonredundant EBC reference transcriptome. Using RNAseq, we compared the expression patterns of the EBC-specific transcriptome between control and salt-treated plants. The EBC reference transcriptome consists of 37 341 transcript-contigs, of which 7% showed significantly different expression between salt-treated and control samples. We identified significant changes in ion transport, metabolism related to energy generation and osmolyte accumulation, stress signalling, and organelle functions, as well as a number of lineage-specific genes of unknown function, in response to salt treatment. The salinity-induced EBC transcriptome includes active transcript clusters, refuting the view of EBCs as passive storage compartments in the whole-plant stress response. EBC transcriptomes, differing from those of whole plants or leaf tissue, exemplify the importance of cell type-specific resolution in understanding stress adaptive mechanisms.
Collapse
Affiliation(s)
- Dong-Ha Oh
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Bronwyn J Barkla
- Southern Cross Plant Science, Southern Cross University, PO Box 157, Lismore, NSW, 2480, Australia
| | - Rosario Vera-Estrella
- Instituto de Biotecnología, UNAM, A.P. 510-3, Colonia Miraval, Cuernavaca, MOR, 62250, México
| | - Omar Pantoja
- Instituto de Biotecnología, UNAM, A.P. 510-3, Colonia Miraval, Cuernavaca, MOR, 62250, México
| | - Sang-Yeol Lee
- Division of Applied Life Science, Gyeongsang National University, Jinju, 660-701, South Korea
| | - Hans J Bohnert
- Departments of Plant Biology and of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Maheshi Dassanayake
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| |
Collapse
|
45
|
Cheeseman JM. The evolution of halophytes, glycophytes and crops, and its implications for food security under saline conditions. THE NEW PHYTOLOGIST 2015; 206:557-70. [PMID: 25495078 DOI: 10.1111/nph.13217] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 11/12/2014] [Indexed: 05/09/2023]
Abstract
The effective development of salt tolerant crops requires an understanding that the evolution of halophytes, glycophytes and our major grain crops has involved significantly different processes. Halophytes (and other edaphic endemics) generally arose through colonization of habitats in severe disequilibrium by pre-adapted individuals, rather than by gradual adaptation from populations of 'glycophytes'. Glycophytes, by contrast, occur in low sodium ecosystems, where sodium was and is the major limiting nutrient in herbivore diets, suggesting that their evolution reflects the fact that low sodium individuals experienced lower herbivory and had higher fitness. For domestication/evolution of crop plants, the selective pressure was human imposed and involved humans co-opting functions of defense and reproductive security. Unintended consequences of this included loss of tolerance to various stresses and loss of the genetic variability needed to correct that. Understanding, combining and manipulating all three modes of evolution are now critical to the development of salt tolerant crops, particularly those that will offer food security in countries with few economic resources and limited infrastructure. Such efforts will require exploiting the genetic structures of recently evolved halophytes, the genetic variability of model plants, and endemic halophytes and 'minor' crops that already exist.
Collapse
Affiliation(s)
- John M Cheeseman
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| |
Collapse
|
46
|
Mickelbart MV, Hasegawa PM, Bailey-Serres J. Genetic mechanisms of abiotic stress tolerance that translate to crop yield stability. Nat Rev Genet 2015; 16:237-51. [PMID: 25752530 DOI: 10.1038/nrg3901] [Citation(s) in RCA: 405] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Crop yield reduction as a consequence of increasingly severe climatic events threatens global food security. Genetic loci that ensure productivity in challenging environments exist within the germplasm of crops, their wild relatives and species that are adapted to extreme environments. Selective breeding for the combination of beneficial loci in germplasm has improved yields in diverse environments throughout the history of agriculture. An effective new paradigm is the targeted identification of specific genetic determinants of stress adaptation that have evolved in nature and their precise introgression into elite varieties. These loci are often associated with distinct regulation or function, duplication and/or neofunctionalization of genes that maintain plant homeostasis.
Collapse
Affiliation(s)
- Michael V Mickelbart
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA
| | - Paul M Hasegawa
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907, USA
| | - Julia Bailey-Serres
- 1] Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California Riverside, California 92521, USA. [2] Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| |
Collapse
|
47
|
Narang A, Jha P, Kumar D, Kutum R, Mondal AK, Dash D, Mukerji M. Extensive copy number variations in admixed Indian population of African ancestry: potential involvement in adaptation. Genome Biol Evol 2014; 6:3171-81. [PMID: 25398783 PMCID: PMC4986450 DOI: 10.1093/gbe/evu250] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Admixture mapping has been enormously resourceful in identifying genetic variations linked to phenotypes, adaptation, and diseases. In this study through analysis of copy number variable regions (CNVRs), we report extensive restructuring in the genomes of the recently admixed African-Indian population (OG-W-IP) that inhabits a highly saline environment in Western India. The study included subjects from OG-W-IP (OG), five different Indian and three HapMap populations that were genotyped using Affymetrix version 6.0 arrays. Copy number variations (CNVs) detected using Birdsuite were used to define CNVRs. Population structure with respect to CNVRs was delineated using random forest approach. OG genomes have a surprising excess of CNVs in comparison to other studied populations. Individual ancestry proportions computed using STRUCTURE also reveals a unique genetic component in OGs. Population structure analysis with CNV genotypes indicates OG to be distant from both the African and Indian ancestral populations. Interestingly, it shows genetic proximity with respect to CNVs to only one Indian population IE-W-LP4, which also happens to reside in the same geographical region. We also observe a significant enrichment of molecular processes related to ion binding and receptor activity in genes encompassing OG-specific CNVRs. Our results suggest that retention of CNVRs from ancestral natives and de novo acquisition of CNVRs could accelerate the process of adaptation especially in an extreme environment. Additionally, this population would be enormously useful for dissecting genes and delineating the involvement of CNVs in salt adaptation.
Collapse
Affiliation(s)
- Ankita Narang
- G.N. Ramachandran Knowledge Centre for Genome Informatics, Council of Scientific and Industrial Research, Institute of Genomics and Integrative Biology, New Delhi, India
| | - Pankaj Jha
- Genomics and Molecular Medicine, Council of Scientific and Industrial Research, Institute of Genomics and Integrative Biology, New Delhi, India
| | - Dhirendra Kumar
- G.N. Ramachandran Knowledge Centre for Genome Informatics, Council of Scientific and Industrial Research, Institute of Genomics and Integrative Biology, New Delhi, India
| | - Rintu Kutum
- G.N. Ramachandran Knowledge Centre for Genome Informatics, Council of Scientific and Industrial Research, Institute of Genomics and Integrative Biology, New Delhi, India
| | - Anupam Kumar Mondal
- G.N. Ramachandran Knowledge Centre for Genome Informatics, Council of Scientific and Industrial Research, Institute of Genomics and Integrative Biology, New Delhi, India
| | | | - Debasis Dash
- G.N. Ramachandran Knowledge Centre for Genome Informatics, Council of Scientific and Industrial Research, Institute of Genomics and Integrative Biology, New Delhi, India
| | - Mitali Mukerji
- G.N. Ramachandran Knowledge Centre for Genome Informatics, Council of Scientific and Industrial Research, Institute of Genomics and Integrative Biology, New Delhi, India Genomics and Molecular Medicine, Council of Scientific and Industrial Research, Institute of Genomics and Integrative Biology, New Delhi, India
| |
Collapse
|
48
|
Zhao P, Capella-Gutiérrez S, Shi Y, Zhao X, Chen G, Gabaldón T, Ma XF. Transcriptomic analysis of a psammophyte food crop, sand rice (Agriophyllum squarrosum) and identification of candidate genes essential for sand dune adaptation. BMC Genomics 2014; 15:872. [PMID: 25287394 PMCID: PMC4459065 DOI: 10.1186/1471-2164-15-872] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Accepted: 09/29/2014] [Indexed: 12/22/2022] Open
Abstract
Background Sand rice (Agriophyllum squarrosum) is an annual desert plant adapted to
mobile sand dunes in arid and semi-arid regions of Central Asia. The sand rice
seeds have excellent nutrition value and have been historically consumed by local
populations in the desert regions of northwest China. Sand rice is a potential
food crop resilient to ongoing climate change; however, partly due to the scarcity
of genetic information, this species has undergone only little agronomic
modifications through classical breeding during recent years. Results We generated a deep transcriptomic sequencing of sand rice, which uncovers 67,741
unigenes. Phylogenetic analysis based on 221 single-copy genes showed close
relationship between sand rice and the recently domesticated crop sugar beet.
Transcriptomic comparisons also showed a high level of global sequence
conservation between these two species. Conservation of sand rice and sugar beet
orthologs assigned to response to salt stress gene ontology term suggests that
sand rice is also a potential salt tolerant plant. Furthermore, sand rice is far
more tolerant to high temperature. A set of genes likely relevant for resistance
to heat stress, was functionally annotated according to expression levels,
sequence annotation, and comparisons corresponding transcriptome profiling results
in Arabidopsis. Conclusions The present work provides abundant genomic information for functional dissection
of the important traits in sand rice. Future screening the genetic variation among
different ecotypes and constructing a draft genome sequence will further
facilitate agronomic trait improvement and final domestication of sand rice. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-872) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Pengshan Zhao
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China. .,Shapotou Desert Research and Experimental Station, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China.
| | - Salvador Capella-Gutiérrez
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader, 88, 08003, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain. .,Yeast and Basidiomycete Research Group, CBS Fungal Biodiversity Centre, Uppsalalaan 8, 3584, LT, Utrecht, The Netherlands.
| | - Yong Shi
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China. .,Shapotou Desert Research and Experimental Station, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China.
| | - Xin Zhao
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China. .,Shapotou Desert Research and Experimental Station, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China.
| | - Guoxiong Chen
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China. .,Shapotou Desert Research and Experimental Station, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China.
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader, 88, 08003, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain. .,Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain.
| | - Xiao-Fei Ma
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China. .,Shapotou Desert Research and Experimental Station, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China.
| |
Collapse
|
49
|
Transcriptome sequencing and analysis of leaf tissue of Avicennia marina using the Illumina platform. PLoS One 2014; 9:e108785. [PMID: 25265387 PMCID: PMC4181315 DOI: 10.1371/journal.pone.0108785] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 08/25/2014] [Indexed: 12/12/2022] Open
Abstract
Avicennia marina is a widely distributed mangrove species that thrives in high-salinity habitats. It plays a significant role in supporting coastal ecosystem and holds unique potential for studying molecular mechanisms underlying ecological adaptation. Despite and sometimes because of its numerous merits, this species is facing increasing pressure of exploitation and deforestation. Both study on adaptation mechanisms and conservation efforts necessitate more genomic resources for A. marina. In this study, we used Illumina sequencing of an A. marina foliar cDNA library to generate a transcriptome dataset for gene and marker discovery. We obtained 40 million high-quality reads and assembled them into 91,125 unigenes with a mean length of 463 bp. These unigenes covered most of the publicly available A. marina Sanger ESTs and greatly extended the repertoire of transcripts for this species. A total of 54,497 and 32,637 unigenes were annotated based on homology to sequences in the NCBI non-redundant and the Swiss-prot protein databases, respectively. Both Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed some transcriptomic signatures of stress adaptation for this halophytic species. We also detected an extraordinary amount of transcripts derived from fungal endophytes and demonstrated the utility of transcriptome sequencing in surveying endophyte diversity without isolating them out of plant tissues. Additionally, we identified 3,423 candidate simple sequence repeats (SSRs) from 3,141 unigenes with a density of one SSR locus every 8.25 kb sequence. Our transcriptomic data will provide valuable resources for ecological, genetic and evolutionary studies in A. marina.
Collapse
|