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Huang R, Snedden WA, diCenzo GC. Reference nodule transcriptomes for Melilotus officinalis and Medicago sativa cv. Algonquin. PLANT DIRECT 2022; 6:e408. [PMID: 35774624 PMCID: PMC9219011 DOI: 10.1002/pld3.408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 05/14/2022] [Accepted: 05/19/2022] [Indexed: 05/10/2023]
Abstract
Host/symbiont compatibility is a hallmark of the symbiotic nitrogen-fixing interaction between rhizobia and legumes, mediated in part by plant-produced nodule-specific cysteine-rich (NCR) peptides and the bacterial BacA membrane protein that can act as a NCR peptide transporter. In addition, the genetic and metabolic properties supporting symbiotic nitrogen fixation often differ between compatible partners, including those sharing a common partner, highlighting the need for multiple study systems. Here, we report high-quality nodule transcriptome assemblies for Medicago sativa cv. Algonquin and Melilotus officinalis, two legumes able to form compatible symbioses with Sinorhizobium meliloti. The compressed M. sativa and M. officinalis assemblies consisted of 79,978 and 64,593 contigs, respectively, of which 33,341 and 28,278 were assigned putative annotations, respectively. As expected, the two transcriptomes showed broad similarity at a global level. We were particularly interested in the NCR peptide profiles of these plants, as these peptides drive bacterial differentiation during the symbiosis. A total of 412 and 308 NCR peptides were predicted from the M. sativa and M. officinalis transcriptomes, respectively, with approximately 9% of the transcriptome of both species consisting of NCR transcripts. Notably, transcripts encoding highly cationic NCR peptides (isoelectric point > 9.5), which are known to have antimicrobial properties, were ∼2-fold more abundant in M. sativa than in M. officinalis, and ∼27-fold more abundant when considering only NCR peptides in the six-cysteine class. We hypothesize that the difference in abundance of highly cationic NCR peptides explains our previous observation that some rhizobial bacA alleles which can support symbiosis with M. officinalis are unable to support symbiosis with M. sativa.
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Affiliation(s)
- Rui Huang
- Department of BiologyQueen's UniversityKingstonOntarioCanada
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Genomics Associated Interventions for Heat Stress Tolerance in Cool Season Adapted Grain Legumes. Int J Mol Sci 2021; 23:ijms23010399. [PMID: 35008831 PMCID: PMC8745526 DOI: 10.3390/ijms23010399] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 12/22/2021] [Accepted: 12/27/2021] [Indexed: 11/16/2022] Open
Abstract
Cool season grain legumes occupy an important place among the agricultural crops and essentially provide multiple benefits including food supply, nutrition security, soil fertility improvement and revenue for farmers all over the world. However, owing to climate change, the average temperature is steadily rising, which negatively affects crop performance and limits their yield. Terminal heat stress that mainly occurred during grain development phases severely harms grain quality and weight in legumes adapted to the cool season, such as lentils, faba beans, chickpeas, field peas, etc. Although, traditional breeding approaches with advanced screening procedures have been employed to identify heat tolerant legume cultivars. Unfortunately, traditional breeding pipelines alone are no longer enough to meet global demands. Genomics-assisted interventions including new-generation sequencing technologies and genotyping platforms have facilitated the development of high-resolution molecular maps, QTL/gene discovery and marker-assisted introgression, thereby improving the efficiency in legumes breeding to develop stress-resilient varieties. Based on the current scenario, we attempted to review the intervention of genomics to decipher different components of tolerance to heat stress and future possibilities of using newly developed genomics-based interventions in cool season adapted grain legumes.
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Circadian Rhythms in Legumes: What Do We Know and What Else Should We Explore? Int J Mol Sci 2021; 22:ijms22094588. [PMID: 33925559 PMCID: PMC8123782 DOI: 10.3390/ijms22094588] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/16/2021] [Accepted: 04/21/2021] [Indexed: 12/15/2022] Open
Abstract
The natural timing devices of organisms, commonly known as biological clocks, are composed of specific complex folding molecules that interact to regulate the circadian rhythms. Circadian rhythms, the changes or processes that follow a 24-h light–dark cycle, while endogenously programmed, are also influenced by environmental factors, especially in sessile organisms such as plants, which can impact ecosystems and crop productivity. Current knowledge of plant clocks emanates primarily from research on Arabidopsis, which identified the main components of the circadian gene regulation network. Nonetheless, there remain critical knowledge gaps related to the molecular components of circadian rhythms in important crop groups, including the nitrogen-fixing legumes. Additionally, little is known about the synergies and trade-offs between environmental factors and circadian rhythm regulation, especially how these interactions fine-tune the physiological adaptations of the current and future crops in a rapidly changing world. This review highlights what is known so far about the circadian rhythms in legumes, which include major as well as potential future pulse crops that are packed with nutrients, particularly protein. Based on existing literature, this review also identifies the knowledge gaps that should be addressed to build a sustainable food future with the reputed “poor man’s meat”.
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Afonin AM, Leppyanen IV, Kulaeva OA, Shtark OY, Tikhonovich IA, Dolgikh EA, Zhukov VA. A high coverage reference transcriptome assembly of pea (Pisum sativum L.) mycorrhizal roots. Vavilovskii Zhurnal Genet Selektsii 2021; 24:331-339. [PMID: 33659815 PMCID: PMC7716550 DOI: 10.18699/vj20.625] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Arbuscular mycorrhiza (AM) is an ancient mutualistic symbiosis formed by 80–90 % of land plant species with
the obligatorily biotrophic fungi that belong to the phylum Glomeromycota. This symbiosis is mutually beneficial, as
AM fungi feed on plant photosynthesis products, in turn improving the efficiency of nutrient uptake from the environment. The garden pea (Pisum sativum L.), a widely cultivated crop and an important model for genetics, is capable of
forming triple symbiotic systems consisting of the plant, AM fungi and nodule bacteria. As transcriptomic and proteomic approaches are being implemented for studying the mutualistic symbioses of pea, a need for a reference transcriptome of genes expressed under these specific conditions for increasing the resolution and the accuracy of other
methods arose. Numerous transcriptome assemblies constructed for pea did not include mycorrhizal roots, hence the
aim of the study to construct a reference transcriptome assembly of pea mycorrhizal roots. The combined transcriptome of mycorrhizal roots of Pisum sativum cv. Frisson inoculated with Rhizophagus irregularis BEG144 was investigated,
and for both the organisms independent transcriptomes were assembled (coverage 177x for pea and 45x for fungus).
Genes specific to mycorrhizal roots were found in the assembly, their expression patterns were examined with qPCR on
two pea cultivars, Frisson and Finale. The gene expression depended on the inoculation stage and on the pea cultivar.
The investigated genes may serve as markers for early stages of inoculation in genetically diverse pea cultivars.
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Affiliation(s)
- A M Afonin
- All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg, Russia
| | - I V Leppyanen
- All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg, Russia
| | - O A Kulaeva
- All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg, Russia
| | - O Y Shtark
- All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg, Russia
| | - I A Tikhonovich
- All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg, Russia Faculty of Biology, St. Petersburg State University, St. Petersburg, Russia
| | - E A Dolgikh
- All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg, Russia
| | - V A Zhukov
- All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg, Russia
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Popovic I, Bierne N, Gaiti F, Tanurdžić M, Riginos C. Pre-introduction introgression contributes to parallel differentiation and contrasting hybridization outcomes between invasive and native marine mussels. J Evol Biol 2020; 34:175-192. [PMID: 33251632 DOI: 10.1111/jeb.13746] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 11/01/2020] [Accepted: 11/11/2020] [Indexed: 12/28/2022]
Abstract
Non-native species experience novel selection pressures in introduced environments and may interbreed with native lineages. Species introductions therefore provide opportunities to investigate repeated patterns of adaptation and introgression across replicated contact zones. Here, we investigate genetic parallelism between multiple introduced populations of the invasive marine mussel, Mytilus galloprovincialis, in the absence (South Africa and California) and presence of hybridization with a native congener (Mytilus planulatus in Batemans Bay and Sydney Harbour, Australia). Repeatability in post-introduction differentiation from native-range populations varied between genetically distinct Atlantic and Mediterranean lineages, with Atlantic-derived introductions displaying high differentiation (maxFST > 0.4) and parallelism at outlier loci. Identification of long noncoding RNA transcripts (lncRNA) additionally allowed us to clarify that parallel responses are largely limited to protein-coding loci, with lncRNAs likely evolving under evolutionary constraints. Comparisons of independent hybrid zones revealed differential introgression most strongly in Batemans Bay, with an excess of M. galloprovincialis ancestry and resistance to introgression at loci differentiating parental lineages (M. planulatus and Atlantic M. galloprovincialis). Additionally, contigs putatively introgressed with divergent alleles from a closely related species, Mytilus edulis, showed stronger introgression asymmetries compared with genome-wide trends and also diverged in parallel in both Atlantic-derived introductions. These results suggest that divergent demographic histories experienced by introduced lineages, including pre-introduction introgression, influence contemporary admixture dynamics. Our findings build on previous investigations reporting contributions of historical introgression to intrinsic reproductive architectures shared between marine lineages and illustrate that interspecific introgression history can shape differentiation between colonizing populations and their hybridization with native congeners.
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Affiliation(s)
- Iva Popovic
- School of Biological Sciences, University of Queensland, St Lucia, Qld, Australia
| | - Nicolas Bierne
- Institut des Sciences de l'Evolution UMR 5554, Université de Montpellier, CNRS-IRD-EPHE-UM, Montpellier, France
| | - Federico Gaiti
- Weill Cornell Medicine, New York, NY, USA.,New York Genome Center, New York, NY, USA
| | - Miloš Tanurdžić
- School of Biological Sciences, University of Queensland, St Lucia, Qld, Australia
| | - Cynthia Riginos
- School of Biological Sciences, University of Queensland, St Lucia, Qld, Australia
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The Utility of Genomic and Transcriptomic Data in the Construction of Proxy Protein Sequence Databases for Unsequenced Tree Nuts. BIOLOGY 2020; 9:biology9050104. [PMID: 32438695 PMCID: PMC7284556 DOI: 10.3390/biology9050104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/07/2020] [Accepted: 05/12/2020] [Indexed: 01/04/2023]
Abstract
As the apparent incidence of tree nut allergies rises, the development of MS methods that accurately identify tree nuts in food is critical. However, analyses are limited by few available tree nut protein sequences. We assess the utility of translated genomic and transcriptomic data for library construction with Juglans regia, walnut, as a model. Extracted walnuts were subjected to nano-liquid chromatography-mass spectrometry (n-LC-MS/MS), and spectra were searched against databases made from a six-frame translation of the genome (6FT), a transcriptome, and three proteomes. Searches against proteomic databases yielded a variable number of peptides (1156-1275), and only ten additional unique peptides were identified in the 6FT database. Searches against a transcriptomic database yielded results similar to those of the National Center for Biotechnology Information (NCBI) proteome (1200 and 1275 peptides, respectively). Performance of the transcriptomic database was improved via the adjustment of RNA-Seq read processing methods, which increased the number of identified peptides which align to seed allergen proteins by ~20%. Together, these findings establish a path towards the construction of robust proxy protein databases for tree nut species and other non-model organisms.
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Smolikova G, Shiroglazova O, Vinogradova G, Leppyanen I, Dinastiya E, Yakovleva O, Dolgikh E, Titova G, Frolov A, Medvedev S. Comparative analysis of the plastid conversion, photochemical activity and chlorophyll degradation in developing embryos of green-seeded and yellow-seeded pea (Pisum sativum) cultivars. FUNCTIONAL PLANT BIOLOGY : FPB 2020; 47:409-424. [PMID: 32209205 DOI: 10.1071/fp19270] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/08/2019] [Indexed: 05/13/2023]
Abstract
Developing seeds of some higher plants are photosynthetically active and contain chlorophylls (Chl), which are typically destroyed at the late stages of seed maturation. However, in some crop plant cultivars, degradation of embryonic Chl remains incomplete, and mature seeds preserve green colour, as it is known for green-seeded cultivars of pea (Pisum sativum L.). The residual Chl compromise seed quality and represent a severe challenge for farmers. Hence, comprehensive understanding of the molecular mechanisms, underlying incomplete Chl degradation is required for maintaining sustainable agriculture. Therefore, here we address dynamics of plastid conversion and photochemical activity alterations, accompanying degradation of Chl in embryos of yellow- and green-seeded cultivars Frisson and Rondo respectively. The yellow-seeded cultivar demonstrated higher rate of Chl degradation at later maturation stage, accompanied with termination of photochemical activity, seed dehydration and conversion of green plastids into amyloplasts. In agreement with this, expression of genes encoding enzymes of Chl degradation was lower in the green seeded cultivar, with the major differences in the levels of Chl b reductase (NYC1) and pheophytinase (PPH) transcripts. Thus, the difference between yellow and green seeds can be attributed to incomplete Chl degradation in the latter at the end of maturation period.
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Affiliation(s)
- Galina Smolikova
- Department of Plant Physiology and Biochemistry, Saint Petersburg State University, Saint Petersburg, Russian Federation; and Corresponding author.
| | - Olga Shiroglazova
- Department of Plant Physiology and Biochemistry, Saint Petersburg State University, Saint Petersburg, Russian Federation
| | - Galina Vinogradova
- Laboratory of Embryology and Reproductive Biology, Komarov Botanical Institute, Russian Academy of Sciences, Saint Petersburg, Russian Federation
| | - Irina Leppyanen
- Laboratory of Signal Regulation, All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russian Federation
| | - Ekaterina Dinastiya
- Department of Biochemistry, Saint Petersburg State University, Saint Petersburg, Russian Federation; and Postovsky Institute of Organic Synthesis, Ural Branch of Russian Academy of Sciences, Ekaterinburg, Russian Federation; and Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | - Olga Yakovleva
- Laboratory of Anatomy and Morphology, Komarov Botanical Institute, Russian Academy of Sciences, Saint Petersburg, Russian Federation
| | - Elena Dolgikh
- Laboratory of Signal Regulation, All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russian Federation
| | - Galina Titova
- Laboratory of Embryology and Reproductive Biology, Komarov Botanical Institute, Russian Academy of Sciences, Saint Petersburg, Russian Federation
| | - Andrej Frolov
- Department of Biochemistry, Saint Petersburg State University, Saint Petersburg, Russian Federation; and Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | - Sergei Medvedev
- Department of Plant Physiology and Biochemistry, Saint Petersburg State University, Saint Petersburg, Russian Federation
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Rai MI, Alam M, Lightfoot DA, Gurha P, Afzal AJ. Classification and experimental identification of plant long non-coding RNAs. Genomics 2019; 111:997-1005. [DOI: 10.1016/j.ygeno.2018.04.014] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/13/2018] [Accepted: 04/17/2018] [Indexed: 02/07/2023]
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9
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Samarth, Jameson PE. Selection of reference genes for flowering pathway analysis in the masting plants, Celmisia lyallii and Chionochloa pallens, under variable environmental conditions. Sci Rep 2019; 9:9767. [PMID: 31278277 PMCID: PMC6611903 DOI: 10.1038/s41598-019-45780-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 06/13/2019] [Indexed: 12/20/2022] Open
Abstract
Mast flowering is characterised by mass synchronised flowering at irregular intervals over a wide geographical area. An understanding of the molecular drivers of mast flowering requires expression analysis of key developmentally regulated gene(s). Reverse transcription-quantitative PCR is the gold standard technique used to assess expression of target gene(s) and to validate high-throughput sequencing data. Selection and validation of appropriate reference gene(s), used as normalisation factors in transcript abundance analysis, is an essential step to avoid ambiguous expression results. Eight candidate reference genes were assessed to select the best internal normalisation factors in naturally growing masting plants Chionochloa pallens and Celmisia lyallii. Statistical packages geNorm, Normfinder, BestKeeper, ΔCt and RefFinder were used to determine the expression stability in plants translocated to different altitudes and sampled across the season. GAPDH and PP2a in Celmisia and ExP and THP in Chionochloa were found to be the best pairs of reference genes for normalisation of the gene expression data. Our study revealed environmentally-induced changes in reference gene expression, information that will be utilised as we investigate flowering phenology of masting plants under global climatic change.
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Affiliation(s)
- Samarth
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Paula E Jameson
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
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Tian T, Liu Y, Yan H, You Q, Yi X, Du Z, Xu W, Su Z. agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update. Nucleic Acids Res 2019; 45:W122-W129. [PMID: 28472432 PMCID: PMC5793732 DOI: 10.1093/nar/gkx382] [Citation(s) in RCA: 1324] [Impact Index Per Article: 264.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 04/25/2017] [Indexed: 01/30/2023] Open
Abstract
The agriGO platform, which has been serving the scientific community for >10 years, specifically focuses on gene ontology (GO) enrichment analyses of plant and agricultural species. We continuously maintain and update the databases and accommodate the various requests of our global users. Here, we present our updated agriGO that has a largely expanded number of supporting species (394) and datatypes (865). In addition, a larger number of species have been classified into groups covering crops, vegetables, fish, birds and insects closely related to the agricultural community. We further improved the computational efficiency, including the batch analysis and P-value distribution (PVD), and the user-friendliness of the web pages. More visualization features were added to the platform, including SEACOMPARE (cross comparison of singular enrichment analysis), direct acyclic graph (DAG) and Scatter Plots, which can be merged by choosing any significant GO term. The updated platform agriGO v2.0 is now publicly accessible at http://systemsbiology.cau.edu.cn/agriGOv2/.
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Affiliation(s)
- Tian Tian
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yue Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Hengyu Yan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Qi You
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xin Yi
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Zhou Du
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Wenying Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Zhen Su
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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Barbier FF, Chabikwa TG, Ahsan MU, Cook SE, Powell R, Tanurdzic M, Beveridge CA. A phenol/chloroform-free method to extract nucleic acids from recalcitrant, woody tropical species for gene expression and sequencing. PLANT METHODS 2019; 15:62. [PMID: 31171930 PMCID: PMC6549277 DOI: 10.1186/s13007-019-0447-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 05/27/2019] [Indexed: 05/10/2023]
Abstract
BACKGROUND Woody tropical plants contain high levels of complex organic compounds that inhibit the chemical procedures needed to extract RNA or DNA, thus compromising downstream applications such as RNA sequencing and analysis of gene expression. To overcome this issue, researchers must use extraction protocols using CTAB/PVP buffer instead of commercially available DNA/RNA extraction kits. However, these protocols are time-consuming, use toxic chemicals like phenol and chloroform, and can only be used to process a small number of samples at a time. To overcome these issues, we developed a new CTAB/PVP based protocol for RNA or DNA extraction that eliminates the traditional phenol/chloroform step. Furthermore, the protocol was developed for 96-well plates to speed up processing. RESULTS Our new protocol enabled us to successfully extract RNA from macadamia, avocado, and mango tissues that are traditionally difficult to work with. This RNA was then successfully used to synthesise cDNA for real-time quantitative PCR and to generate good quality RNA-Seq libraries. Our protocol can be easily converted for rapid DNA extraction from different tropical and sub-tropical tree species. CONCLUSION This method enables safer and faster DNA and RNA extraction from recalcitrant species, thus facilitating future work on tropical trees.
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Affiliation(s)
- François F. Barbier
- School of Biological Sciences, and The Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072 Australia
| | - Tinashe G. Chabikwa
- School of Biological Sciences, and The Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072 Australia
| | - Muhammad U. Ahsan
- School of Biological Sciences, and The Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072 Australia
| | - Stacey E. Cook
- School of Biological Sciences, and The Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072 Australia
| | - Rosanna Powell
- School of Biological Sciences, and The Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072 Australia
| | - Milos Tanurdzic
- School of Biological Sciences, and The Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072 Australia
| | - Christine A. Beveridge
- School of Biological Sciences, and The Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072 Australia
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Kerr SC, Gaiti F, Tanurdzic M. De Novo Plant Transcriptome Assembly and Annotation Using Illumina RNA-Seq Reads. Methods Mol Biol 2019; 1933:265-275. [PMID: 30945191 DOI: 10.1007/978-1-4939-9045-0_16] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The ability to identify and quantify transcribed sequences from a multitude of organisms using high-throughput RNA sequencing has revolutionized our understanding of genetics and plant biology. However, a number of computational tools used in these analyses still require a reference genome sequence, something that is seldom available for non-model organisms. Computational tools employing de Bruijn graphs to reconstruct full-length transcripts from short sequence reads allow for de novo transcriptome assembly. Here we provide detailed methods for generating and annotating de novo transcriptome assembly from plant RNA-seq data.
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Affiliation(s)
- Stephanie C Kerr
- School of Biological Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - Federico Gaiti
- New York Genome Center and Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Milos Tanurdzic
- School of Biological Sciences, The University of Queensland, St Lucia, QLD, Australia.
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13
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Zaman MSU, Malik AI, Erskine W, Kaur P. Changes in gene expression during germination reveal pea genotypes with either "quiescence" or "escape" mechanisms of waterlogging tolerance. PLANT, CELL & ENVIRONMENT 2019; 42:245-258. [PMID: 29761495 DOI: 10.1111/pce.13338] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 05/01/2018] [Accepted: 05/01/2018] [Indexed: 05/12/2023]
Abstract
Waterlogging causes germination failure in pea (Pisum sativum L.). Three genotypes (BARI Motorshuti-3, Natore local-2 [NL-2], and Kaspa) contrasting in ability to germinate in waterlogged soil were exposed to different durations of waterlogging. Whole genome RNAseq was employed to capture differentially expressing genes. The ability to germinate in waterlogged soil was associated with testa colour and testa membrane integrity as confirmed by electrical conductivity measurements. Genotypes Kaspa and NL-2 displayed different mechanisms of tolerance. In Kaspa, an energy conserving strategy was indicated by a strong upregulation of tyrosine protein kinsase and down regulation of linoleate 9S-lipoxygenase 5, a fat metabolism gene. In contrast, a faster energy utilization strategy was suggested in NL-2 by the marked upregulation of a subtilase family protein and peroxisomal adenine nucleotide carrier 2, a fat metabolizing gene. Waterlogging susceptibility in germinating seeds of genotype BARI Motorshuti-3 was linked to upregulation of a kunitz-type trypsin/protease inhibitor that blocks protein metabolism and may lead to excessive lipid metabolism and the membrane leakage associated with waterlogging damage. Pathway analyses based on gene ontologies showed seed storage protein metabolism as upregulated in tolerant genotypes and downregulated in the sensitive genotype. Understanding the tolerance mechanism provides a platform to breed for adaptation to waterlogging stress at germination in pea.
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Affiliation(s)
- Md Shahin Uz Zaman
- Centre for Plant Genetics and Breeding, UWA School of Agriculture and Environment, The University of Western Australia, Crawley, Western Australia, 6009, Australia
- Institute of Agriculture, The University of Western Australia, Crawley, Western Australia, 6009, Australia
| | - Al Imran Malik
- Centre for Plant Genetics and Breeding, UWA School of Agriculture and Environment, The University of Western Australia, Crawley, Western Australia, 6009, Australia
| | - William Erskine
- Centre for Plant Genetics and Breeding, UWA School of Agriculture and Environment, The University of Western Australia, Crawley, Western Australia, 6009, Australia
- Institute of Agriculture, The University of Western Australia, Crawley, Western Australia, 6009, Australia
| | - Parwinder Kaur
- Centre for Plant Genetics and Breeding, UWA School of Agriculture and Environment, The University of Western Australia, Crawley, Western Australia, 6009, Australia
- Institute of Agriculture, The University of Western Australia, Crawley, Western Australia, 6009, Australia
- Telethon Kids Institute, Subiaco, Western Australia, 6008, Australia
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14
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Ju Y, Feng L, Wu J, Ye Y, Zheng T, Cai M, Cheng T, Wang J, Zhang Q, Pan H. Transcriptome analysis of the genes regulating phytohormone and cellular patterning in Lagerstroemia plant architecture. Sci Rep 2018; 8:15162. [PMID: 30310123 PMCID: PMC6181930 DOI: 10.1038/s41598-018-33506-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 10/01/2018] [Indexed: 11/16/2022] Open
Abstract
Plant architecture is a popular research topic because plants with different growth habits that may generate economic or ornamental value are in great demand by orchards and nurseries. However, the molecular basis of the architecture of woody perennial plants is poorly understood due to the complexity of the phenotypic and regulatory relationships. Here, transcriptional profiling of dwarf and non-dwarf crapemyrtles was performed, and potential target genes were identified based on the phenotype, histology and phytohormone metabolite levels. An integrated analysis demonstrated that the internode length was explained mainly by cell number and secondarily by cell length and revealed important hormones in regulatory pathway of Lagerstroemia architecture. Differentially expressed genes (DEGs) involved in phytohormone pathways and cellular patterning regulation were analysed, and the regulatory relationships between these parameters were evaluated at the transcriptional level. Exogenous indole-3-acetic acid (IAA) and gibberellin A4 (GA4) treatments further indicated the pivotal role of auxin in cell division within the shoot apical meristem (SAM) and suggested an interaction between auxin and GA4 in regulating the internode length of Lagerstroemia. These results provide insights for further functional genomic studies on the regulatory mechanisms underlying Lagerstroemia plant architecture and may improve the efficiency of woody plant molecular breeding.
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Affiliation(s)
- Yiqian Ju
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Lu Feng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Jiyang Wu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Yuanjun Ye
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Tangchun Zheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Ming Cai
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Tangren Cheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Jia Wang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Huitang Pan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China.
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15
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Chang H, Sang H, Wang J, McPhee KE, Zhuang X, Porter LD, Chilvers MI. Exploring the genetics of lesion and nodal resistance in pea ( Pisum sativum L.) to Sclerotinia sclerotiorum using genome-wide association studies and RNA-Seq. PLANT DIRECT 2018; 2:e00064. [PMID: 31245727 PMCID: PMC6508546 DOI: 10.1002/pld3.64] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 05/09/2018] [Accepted: 05/21/2018] [Indexed: 05/30/2023]
Abstract
The disease white mold caused by the fungus Sclerotinia sclerotiorum is a significant threat to pea production, and improved resistance to this disease is needed. Nodal resistance in plants is a phenomenon where a fungal infection is prevented from passing through a node, and the infection is limited to an internode region. Nodal resistance has been observed in some pathosystems such as the pea (Pisum sativum L.)-S. sclerotiorum pathosystem. In addition to nodal resistance, different pea lines display different levels of stem lesion size restriction, referred to as lesion resistance. It is unclear whether the genetics of lesion resistance and nodal resistance are identical or different. This study applied genome-wide association studies (GWAS) and RNA-Seq to understand the genetic makeup of these two types of resistance. The time series RNA-Seq experiment consisted of two pea lines (the susceptible 'Lifter' and the partially resistant PI 240515), two treatments (mock inoculated samples and S. sclerotiorum-inoculated samples), and three time points (12, 24, and 48 hr post inoculation). Integrated results from GWAS and RNA-Seq analyses identified different redox-related transcripts for lesion and nodal resistances. A transcript encoding a glutathione S-transferase was the only shared resistance variant for both phenotypes. There were more leucine rich-repeat containing transcripts found for lesion resistance, while different candidate resistance transcripts such as a VQ motif-containing protein and a myo-inositol oxygenase were found for nodal resistance. This study demonstrated the robustness of combining GWAS and RNA-Seq for identifying white mold resistance in pea, and results suggest different genetics underlying lesion and nodal resistance.
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Affiliation(s)
- Hao‐Xun Chang
- Department of Plant, Soil and Microbial SciencesMichigan State UniversityEast LansingMichigan
| | - Hyunkyu Sang
- Department of Plant, Soil and Microbial SciencesMichigan State UniversityEast LansingMichigan
| | - Jie Wang
- Department of Plant BiologyMichigan State UniversityEast LansingMichigan
| | - Kevin E. McPhee
- Department of Plant Sciences and Plant PathologyMontana State UniversityBozemanMontana
| | - Xiaofeng Zhuang
- Department of Horticulture and Crop ScienceThe Ohio State UniversityWoosterOhio
| | | | - Martin I. Chilvers
- Department of Plant, Soil and Microbial SciencesMichigan State UniversityEast LansingMichigan
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16
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Martín-Fontecha ES, Tarancón C, Cubas P. To grow or not to grow, a power-saving program induced in dormant buds. CURRENT OPINION IN PLANT BIOLOGY 2018; 41:102-109. [PMID: 29125947 DOI: 10.1016/j.pbi.2017.10.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 10/07/2017] [Accepted: 10/09/2017] [Indexed: 05/06/2023]
Abstract
Plant shoot branching patterns determine leaf, flower and fruit production, and thus reproductive success and yield. Branch primordia, or axillary buds, arise in the axils of leaves and their decision to either grow or enter dormancy is coordinated at the whole plant level. Comparisons of transcriptional profiles of axillary buds entering dormancy have identified a shared set of responses that closely resemble a Low Energy Syndrome. This syndrome is aimed at saving carbon use to support essential maintenance functions, rather than additional growth, and involves growth arrest (thus dormancy), metabolic reprogramming and hormone signalling. This response is widely conserved in distantly related woody and herbaceous species, and not only underlies but also precedes the growth-to-dormancy transition induced in buds by different stimuli.
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Affiliation(s)
- Elena Sánchez Martín-Fontecha
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología/CSIC, Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Carlos Tarancón
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología/CSIC, Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Pilar Cubas
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología/CSIC, Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain.
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17
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Leppyanen IV, Shakhnazarova VY, Shtark OY, Vishnevskaya NA, Tikhonovich IA, Dolgikh EA. Receptor-Like Kinase LYK9 in Pisum sativum L. Is the CERK1-Like Receptor that Controls Both Plant Immunity and AM Symbiosis Development. Int J Mol Sci 2017; 19:E8. [PMID: 29267197 PMCID: PMC5795960 DOI: 10.3390/ijms19010008] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 12/13/2017] [Accepted: 12/16/2017] [Indexed: 01/24/2023] Open
Abstract
Plants are able to discriminate and respond to structurally related chitooligosaccharide (CO) signals from pathogenic and symbiotic fungi. In model plants Arabidopsis thaliana and Oryza sativa LysM-receptor like kinases (LysM-RLK) AtCERK1 and OsCERK1 (chitin elicitor receptor kinase 1) were shown to be involved in response to CO signals. Based on phylogenetic analysis, the pea Pisum sativum L. LysM-RLK PsLYK9 was chosen as a possible candidate given its role on the CERK1-like receptor. The knockdown regulation of the PsLyk9 gene by RNA interference led to increased susceptibility to fungal pathogen Fusarium culmorum. Transcript levels of PsPAL2, PsPR10 defense-response genes were significantly reduced in PsLyk9 RNAi roots. PsLYK9's involvement in recognizing short-chain COs as most numerous signals of arbuscular mycorrhizal (AM) fungi, was also evaluated. In transgenic roots with PsLyk9 knockdown treated with short-chain CO5, downregulation of AM symbiosis marker genes (PsDELLA3, PsNSP2, PsDWARF27) was observed. These results clearly indicate that PsLYK9 appears to be involved in the perception of COs and subsequent signal transduction in pea roots. It allows us to conclude that PsLYK9 is the most likely CERK1-like receptor in pea to be involved in the control of plant immunity and AM symbiosis formation.
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Affiliation(s)
- Irina V Leppyanen
- All Russia Research Institute for Agricultural Microbiology, 196608, Podbelsky Shosse 3, St.-Petersburg, 196608 Pushkin, Russia.
| | - Vlada Y Shakhnazarova
- All Russia Research Institute for Agricultural Microbiology, 196608, Podbelsky Shosse 3, St.-Petersburg, 196608 Pushkin, Russia.
| | - Oksana Y Shtark
- All Russia Research Institute for Agricultural Microbiology, 196608, Podbelsky Shosse 3, St.-Petersburg, 196608 Pushkin, Russia.
| | - Nadezhda A Vishnevskaya
- All Russia Research Institute for Agricultural Microbiology, 196608, Podbelsky Shosse 3, St.-Petersburg, 196608 Pushkin, Russia.
| | - Igor A Tikhonovich
- All Russia Research Institute for Agricultural Microbiology, 196608, Podbelsky Shosse 3, St.-Petersburg, 196608 Pushkin, Russia.
| | - Elena A Dolgikh
- All Russia Research Institute for Agricultural Microbiology, 196608, Podbelsky Shosse 3, St.-Petersburg, 196608 Pushkin, Russia.
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18
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Jiao K, Li X, Guo W, Su S, Luo D. High-Throughput RNA-Seq Data Analysis of the Single Nucleotide Polymorphisms (SNPs) and Zygomorphic Flower Development in Pea (Pisum sativum L.). Int J Mol Sci 2017; 18:E2710. [PMID: 29261120 PMCID: PMC5751311 DOI: 10.3390/ijms18122710] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 12/10/2017] [Accepted: 12/12/2017] [Indexed: 11/17/2022] Open
Abstract
Pea (Pisum sativum L.) is a model plant that has been used in classical genetics and organ development studies. However, its large and complex genome has hindered research investigations in pea. Here, we generated transcriptomes from different tissues or organs of three pea accessions using next-generation sequencing to assess single nucleotide polymorphisms (SNPs), and further investigated petal differentially expressed genes to elucidate the mechanisms regulating floral zygomorphy. Eighteen samples were sequenced, which yielded a total of 617 million clean reads, and de novo assembly resulted in 87,137 unigenes. A total of 9044 high-quality SNPs were obtained among the three accessions, and a consensus map was constructed. We further discovered several dorsoventral asymmetrically expressed genes that were confirmed by qRT-PCR among different petals, including previously reported three CYC-like proliferating cell factor (TCP) genes. One MADS-box gene was highly expressed in dorsal petals, and several MYB factors were predominantly expressed among dorsal, lateral, and/or ventral petals, together with a ventrally expressed TCP gene. In sum, our comprehensive database complements the existing resources for comparative genetic mapping and facilitates future investigations in legume zygomorphic flower development.
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Affiliation(s)
- Keyuan Jiao
- Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
| | - Xin Li
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing 210014, China.
| | - Wuxiu Guo
- Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
| | - Shihao Su
- Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
| | - Da Luo
- Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
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