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Xia L, Li M, Chen Y, Dai Y, Li H, Zhang S. Sexually dimorphic acetyl-CoA biosynthesis and utilization in response to drought and exogenous acetic acid. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:1967-1985. [PMID: 38944754 DOI: 10.1111/tpj.16901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 04/19/2024] [Accepted: 06/14/2024] [Indexed: 07/01/2024]
Abstract
Female willows exhibit greater drought tolerance and benefit more from exogenous acetic acid (AA)-improved drought tolerance than males. However, the potential mechanisms driving these sex-specific responses remain unclear. To comprehensively investigate the sexually dimorphic responsive mechanisms of willows to drought and exogenous AA, here, we performed physiological, proteomic, Lys-acetylproteomic, and transgenic analyses in female and male Salix myrtillacea exposed to drought and AA-applicated drought treatments, focusing on protein abundance and lysine acetylation (LysAc) changes. Drought-tolerant females suffered less drought-induced photosynthetic and oxidative damage, did not activate AA and acetyl-CoA biosynthesis, TCA cycle, fatty acid metabolism, and jasmonic acid signaling as strongly as drought-sensitive males. Exogenous AA caused overaccumulation of endogenous AA and inhibition of acetyl-CoA biosynthesis and utilization in males. However, exogenous AA greatly enhanced acetyl-CoA biosynthesis and utilization and further enhanced drought performance of females, possibly determining that AA improved drought tolerance more in females than in males. Interestingly, overexpression of acetyl-CoA synthetase (ACS) could reprogram fatty acids, increase LysAc levels, and improve drought tolerance, highlighting the involvement of ACS-derived acetyl-CoA in drought responses. In addition, drought and exogenous AA induced sexually dimorphic LysAc associated with histones, transcription factors, and metabolic enzymes in willows. Especially, exogenous AA may greatly improve the photosynthetic capacity of S. myrtillacea males by decreasing LysAc levels and increasing the abundances of photosynthetic proteins. While hyperacetylation in glycolysis, TCA cycle, and fatty acid biosynthesis potentially possibly serve as negative feedback to acclimate acetyl-CoA biosynthesis and utilization in drought-stressed males and AA-applicated females. Thus, acetyl-CoA biosynthesis and utilization determine the sexually dimorphic responses of S. myrtillacea to drought and exogenous AA.
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Affiliation(s)
- Linchao Xia
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Menghan Li
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yao Chen
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yujie Dai
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Huanhuan Li
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Sheng Zhang
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
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Shen W, Pan L, Fu Y, Suo Y, Zhang Y, Liu H, Su X, Zhao J. Comparative Study on the Effectiveness of Three Inoculation Methods for Valsa sordida in Populus alba var. pyramidalis. BIOLOGY 2024; 13:251. [PMID: 38666863 PMCID: PMC11047983 DOI: 10.3390/biology13040251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 03/29/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024]
Abstract
A key step in the study of tree pathology is the identification of an appropriate method for inoculating pathogens of diseases in branches and trunks. Pathogens of diseases in branches and trunks are commonly inoculated through punching, burning, and toothpick inoculation. However, there is a lack of comparative analyses of the inoculation outcomes of these three methods. In this work, six-year-old P. alba var. pyramidalis were inoculated with V. sordida using punching, burning, and toothpick techniques to investigate the differences in the effectiveness of these inoculation methods. Results reveal that the incidence rate was 93.55% in the toothpick inoculation group, significantly higher than the 80.65% in the burning inoculation group (chi-square, n = 90, p = 0.007), while punching inoculation exhibited significant pathological responses in the early stages, with spontaneous healing in the later stage. Additionally, toothpick inoculation was more efficient in inducing Valsa canker when inoculating the pathogen at the bottom of the tree, with lower intra- and inter-row spacing (stand density) providing better outcomes than higher intra- and inter-row spacing. The results of this study demonstrate that toothpick inoculation is an optimal option for studying the artificial inoculation of V. sordida in six-year-old P. alba var. pyramidalis, providing technical support for research on poplar diseases and offering a theoretical basis for the inoculation of other diseases in the branch and trunk.
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Affiliation(s)
- Wanna Shen
- State Key Laboratory of Tree Genetics and Breeding, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China
| | - Long Pan
- State Key Laboratory of Tree Genetics and Breeding, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China
| | - Yuchen Fu
- State Key Laboratory of Tree Genetics and Breeding, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China
| | - Yutian Suo
- State Key Laboratory of Tree Genetics and Breeding, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China
| | - Yinan Zhang
- State Key Laboratory of Tree Genetics and Breeding, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China
| | - Huixiang Liu
- Shandong Research Center for Forestry Harmful Biological Control Engineering and Technology, College of Plant Protection, Shandong Agricultural University, Taian 271002, China
| | - Xiaohua Su
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Jiaping Zhao
- State Key Laboratory of Tree Genetics and Breeding, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China
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3
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Zhou R, Jenkins JW, Zeng Y, Shu S, Jang H, Harding SA, Williams M, Plott C, Barry KW, Koriabine M, Amirebrahimi M, Talag J, Rajasekar S, Grimwood J, Schmitz RJ, Dawe RK, Schmutz J, Tsai CJ. Haplotype-resolved genome assembly of Populus tremula × P. alba reveals aspen-specific megabase satellite DNA. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1003-1017. [PMID: 37675609 DOI: 10.1111/tpj.16454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 09/08/2023]
Abstract
Populus species play a foundational role in diverse ecosystems and are important renewable feedstocks for bioenergy and bioproducts. Hybrid aspen Populus tremula × P. alba INRA 717-1B4 is a widely used transformation model in tree functional genomics and biotechnology research. As an outcrossing interspecific hybrid, its genome is riddled with sequence polymorphisms which present a challenge for sequence-sensitive analyses. Here we report a telomere-to-telomere genome for this hybrid aspen with two chromosome-scale, haplotype-resolved assemblies. We performed a comprehensive analysis of the repetitive landscape and identified both tandem repeat array-based and array-less centromeres. Unexpectedly, the most abundant satellite repeats in both haplotypes lie outside of the centromeres, consist of a 147 bp monomer PtaM147, frequently span >1 megabases, and form heterochromatic knobs. PtaM147 repeats are detected exclusively in aspens (section Populus) but PtaM147-like sequences occur in LTR-retrotransposons of closely related species, suggesting their origin from the retrotransposons. The genomic resource generated for this transformation model genotype has greatly improved the design and analysis of genome editing experiments that are highly sensitive to sequence polymorphisms. The work should motivate future hypothesis-driven research to probe into the function of the abundant and aspen-specific PtaM147 satellite DNA.
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Affiliation(s)
- Ran Zhou
- School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, USA
- Department of Genetics, University of Georgia, Athens, Georgia, USA
- Department of Plant Biology, University of Georgia, Athens, Georgia, USA
| | - Jerry W Jenkins
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama, USA
| | - Yibing Zeng
- Department of Genetics, University of Georgia, Athens, Georgia, USA
| | - Shengqiang Shu
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Hosung Jang
- Department of Genetics, University of Georgia, Athens, Georgia, USA
| | - Scott A Harding
- School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, USA
- Department of Genetics, University of Georgia, Athens, Georgia, USA
- Department of Plant Biology, University of Georgia, Athens, Georgia, USA
| | - Melissa Williams
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama, USA
| | | | - Kerrie W Barry
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Maxim Koriabine
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Mojgan Amirebrahimi
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Jayson Talag
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Shanmugam Rajasekar
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Jane Grimwood
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, Georgia, USA
| | - R Kelly Dawe
- Department of Genetics, University of Georgia, Athens, Georgia, USA
- Department of Plant Biology, University of Georgia, Athens, Georgia, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama, USA
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Chung-Jui Tsai
- School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, USA
- Department of Genetics, University of Georgia, Athens, Georgia, USA
- Department of Plant Biology, University of Georgia, Athens, Georgia, USA
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4
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Bai Q, Niu Z, Chen Q, Gao C, Zhu M, Bai J, Liu M, He L, Liu J, Jiang Y, Wan D. The C 2 H 2 -type zinc finger transcription factor OSIC1 positively regulates stomatal closure under osmotic stress in poplar. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:943-960. [PMID: 36632734 PMCID: PMC10106854 DOI: 10.1111/pbi.14007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 12/30/2022] [Accepted: 12/23/2022] [Indexed: 05/04/2023]
Abstract
Salt and drought impair plant osmotic homeostasis and greatly limit plant growth and development. Plants decrease stomatal aperture to reduce water loss and maintain osmotic homeostasis, leading to improved stress tolerance. Herein, we identified the C2 H2 transcription factor gene OSMOTIC STRESS INDUCED C2 H2 1 (OSIC1) from Populus alba var. pyramidalis to be induced by salt, drought, polyethylene glycol 6000 (PEG6000) and abscisic acid (ABA). Overexpression of OSIC1 conferred transgenic poplar more tolerance to high salinity, drought and PEG6000 treatment by reducing stomatal aperture, while its mutant generated by the CRISPR/Cas9 system showed the opposite phenotype. Furthermore, OSIC1 directly up-regulates PalCuAOζ in vitro and in vivo, encoding a copper-containing polyamine oxidase, to enhance H2 O2 accumulation in guard cells and thus modulates stomatal closure when stresses occur. Additionally, ABA-, drought- and salt-induced PalMPK3 phosphorylates OSIC1 to increase its transcriptional activity to PalCuAOζ. This regulation of OSIC1 at the transcriptional and protein levels guarantees rapid stomatal closure when poplar responds to osmotic stress. Our results revealed a novel transcriptional regulatory mechanism of H2 O2 production in guard cells mediated by the OSIC1-PalCuAOζ module. These findings deepen our understanding of how perennial woody plants, like poplar, respond to osmotic stress caused by salt and drought and provide potential targets for breeding.
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Affiliation(s)
- Qiuxian Bai
- State Key Laboratory of Grassland Agro‐Ecosystem, College of EcologyLanzhou UniversityLanzhouChina
- Department of PharmacologyNingxia Medical UniversityYinchuanChina
| | - Zhimin Niu
- State Key Laboratory of Grassland Agro‐Ecosystem, College of EcologyLanzhou UniversityLanzhouChina
| | - Qingyuan Chen
- State Key Laboratory of Grassland Agro‐Ecosystem, College of EcologyLanzhou UniversityLanzhouChina
| | - Chengyu Gao
- State Key Laboratory of Grassland Agro‐Ecosystem, College of EcologyLanzhou UniversityLanzhouChina
| | - Mingjia Zhu
- State Key Laboratory of Grassland Agro‐Ecosystem, College of EcologyLanzhou UniversityLanzhouChina
| | - Jiexian Bai
- College of Computer Information Engineering,Shanxi Technology and Business CollegeTaiyuanChina
| | - Meijun Liu
- State Key Laboratory of Grassland Agro‐Ecosystem, College of EcologyLanzhou UniversityLanzhouChina
| | - Ling He
- State Key Laboratory of Grassland Agro‐Ecosystem, College of EcologyLanzhou UniversityLanzhouChina
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro‐Ecosystem, College of EcologyLanzhou UniversityLanzhouChina
| | - Yuanzhong Jiang
- Key Laboratory for Bio‐resources and Eco‐environment of Ministry of Education, College of Life ScienceSichuan UniversityChengduChina
| | - Dongshi Wan
- State Key Laboratory of Grassland Agro‐Ecosystem, College of EcologyLanzhou UniversityLanzhouChina
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5
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Yuan G, Liu Y, Yao T, Muchero W, Chen JG, Tuskan GA, Yang X. eYGFPuv-Assisted Transgenic Selection in Populus deltoides WV94 and Multiplex Genome Editing in Protoplasts of P. trichocarpa × P. deltoides Clone '52-225'. PLANTS (BASEL, SWITZERLAND) 2023; 12:1657. [PMID: 37111880 PMCID: PMC10145771 DOI: 10.3390/plants12081657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 03/16/2023] [Accepted: 03/30/2023] [Indexed: 06/19/2023]
Abstract
Although CRISPR/Cas-based genome editing has been widely used for plant genetic engineering, its application in the genetic improvement of trees has been limited, partly because of challenges in Agrobacterium-mediated transformation. As an important model for poplar genomics and biotechnology research, eastern cottonwood (Populus deltoides) clone WV94 can be transformed by A. tumefaciens, but several challenges remain unresolved, including the relatively low transformation efficiency and the relatively high rate of false positives from antibiotic-based selection of transgenic events. Moreover, the efficacy of CRISPR-Cas system has not been explored in P. deltoides yet. Here, we first optimized the protocol for Agrobacterium-mediated stable transformation in P. deltoides WV94 and applied a UV-visible reporter called eYGFPuv in transformation. Our results showed that the transgenic events in the early stage of transformation could be easily recognized and counted in a non-invasive manner to narrow down the number of regenerated shoots for further molecular characterization (at the DNA or mRNA level) using PCR. We found that approximately 8.7% of explants regenerated transgenic shoots with green fluorescence within two months. Next, we examined the efficacy of multiplex CRISPR-based genome editing in the protoplasts derived from P. deltoides WV94 and hybrid poplar clone '52-225' (P. trichocarpa × P. deltoides clone '52-225'). The two constructs expressing the Trex2-Cas9 system resulted in mutation efficiency ranging from 31% to 57% in hybrid poplar clone 52-225, but no editing events were observed in P. deltoides WV94 transient assay. The eYGFPuv-assisted plant transformation and genome editing approach demonstrated in this study has great potential for accelerating the genome editing-based breeding process in poplar and other non-model plants species and point to the need for additional CRISPR work in P. deltoides.
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Affiliation(s)
- Guoliang Yuan
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Chemical and Biological Process Development Group, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99352, USA
| | - Yang Liu
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN 37831, USA
| | - Tao Yao
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Wellington Muchero
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jin-Gui Chen
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Gerald A. Tuskan
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Xiaohan Yang
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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6
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Sidharthan VK, Rajeswari V, Baranwal VK. Broadening the host range and genetic diversity of waikaviruses. Virology 2023; 582:106-113. [PMID: 37043910 DOI: 10.1016/j.virol.2023.03.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/07/2023] [Accepted: 03/30/2023] [Indexed: 04/14/2023]
Abstract
Waikaviruses are monopartite, positive sense, single-stranded RNA viruses that cause economically important plant diseases. Despite their importance, waikaviruses are poorly understood and only ten members are currently recognized. The present study on Sequence Read Archive (SRA)-based data-driven virus discovery (DDVD) identified 22 putative new waikaviruses, nearly doubling the number of known waikaviruses, in SRA libraries of diverse plant species, from ferns to trees. Besides, a highly divergent secoviral sequence with distinct genome features was identified in a wheat transcriptome. Other significant findings of the study include identification of a new waikavirus in a library derived from diseased water chestnut sample wherein a caulimovirus was reported, prediction of coiled-coils in hypothetical protein region of waikaviral polyprotein alignment and phylogenetic clustering of tree-infecting waikaviruses. The study not only reiterates the importance of DDVD in unveiling hitherto hidden viral sequences in plant SRA libraries but also deepens our understanding of waikaviral diversity.
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Affiliation(s)
- V Kavi Sidharthan
- Division of Genetics and Tree Improvement, ICFRE-Institute of Forest Biodiversity, Hyderabad, India.
| | - V Rajeswari
- School of Agricultural Sciences, Malla Reddy University, Hyderabad, India
| | - V K Baranwal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India.
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7
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Li G, Chen Q, Bai Q, Feng Y, Mao K, Yang M, He L, Liu M, Liu J, Wan D. LncRNA expression analysis by comparative transcriptomics among closely related poplars and their regulatory roles in response to salt stress. TREE PHYSIOLOGY 2023:tpad041. [PMID: 37017317 DOI: 10.1093/treephys/tpad041] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 03/13/2023] [Indexed: 06/19/2023]
Abstract
Long noncoding RNAs (lncRNAs) play crucial roles in regulating key biological processes; however, our knowledge of lncRNAs' roles in plant adaptive evolution is still limited. Here, we determined the divergence of conserved lncRNAs in closely related poplar species that were either tolerant or sensitive to salt stress by comparative transcriptome analysis. Among the 34,363 identified lncRNAs, approximately 3% were shared among poplar species with conserved sequences but diversified in their function, copy number, originating genomic region and expression patterns. Further cluster analysis revealed that the conserved lncRNAs showed more similar expression patterns within salt-tolerant poplars (P. euphratica and P. pruinosa) than between salt-tolerant and salt-sensitive poplars. Among these lncRNAs, the antisense lncRNA lncERF024 was induced by salt and differentiated expression between salt-sensitive and salt-tolerant poplars. Overexpression of lncERF024 in P. alba var. pyramidalis enhanced poplar tolerance to salt stress. Furthermore, RNA pull-down and RNA-seq analysis showed that numerous candidate genes or proteins associated with stress response and photosynthesis might be involved in salt resistance in PeulncERF024-OE poplars. Altogether, our study provided novel insight into how the diversification of lncRNA expression contributes to plant adaptation traits and showed that lncERF024 may be involved in the regulation both of gene expression and protein function conferring salt tolerance in Populus.
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Affiliation(s)
- Guiting Li
- State Key Laboratory Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Qingyuan Chen
- State Key Laboratory Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Qiuxian Bai
- State Key Laboratory Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
- Department of Pharmacology, Ningxia Medical University, Yinchuan,750004, China
| | - Yannan Feng
- State Key Laboratory Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Kaili Mao
- State Key Laboratory Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Mengran Yang
- State Key Laboratory Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Ling He
- State Key Laboratory Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Meijun Liu
- State Key Laboratory Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Jianquan Liu
- State Key Laboratory Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Dongshi Wan
- State Key Laboratory Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
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Comprehensive Genome-Wide Analyses of Poplar R2R3-MYB Transcription Factors and Tissue-Specific Expression Patterns under Drought Stress. Int J Mol Sci 2023; 24:ijms24065389. [PMID: 36982459 PMCID: PMC10049292 DOI: 10.3390/ijms24065389] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/03/2023] [Accepted: 03/09/2023] [Indexed: 03/14/2023] Open
Abstract
R2R3-type MYB transcription factors are implicated in drought stress, which is a primary factor limiting the growth and development of woody plants. The identification of R2R3-MYB genes in the Populus trichocarpa genome has been previously reported. Nevertheless, the diversity and complexity of the conserved domain of the MYB gene caused inconsistencies in these identification results. There is still a lack of drought-responsive expression patterns and functional studies of R2R3-MYB transcription factors in Populus species. In this study, we identified a total of 210 R2R3-MYB genes in the P. trichocarpa genome, of which 207 genes were unevenly distributed across all 19 chromosomes. These poplar R2R3-MYB genes were phylogenetically divided into 23 subgroups. Collinear analysis demonstrated that the poplar R2R3-MYB genes underwent rapid expansion and that whole-genome duplication events were a dominant factor in the process of rapid gene expansion. Subcellular localization assays indicated that poplar R2R3-MYB TFs mainly played a transcriptional regulatory role in the nucleus. Ten R2R3-MYB genes were cloned from P. deltoides × P. euramericana cv. Nanlin895, and their expression patterns were tissue-specific. A majority of the genes showed similar drought-responsive expression patterns in two out of three tissues. This study provides a valid cue for further functional characterization of drought-responsive R2R3-MYB genes in poplar and provides support for the development of new poplar genotypes with elevated drought tolerance.
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Li Y, Wang D, Wang W, Yang W, Gao J, Zhang W, Shan L, Kang M, Chen Y, Ma T. A chromosome-level Populus qiongdaoensis genome assembly provides insights into tropical adaptation and a cryptic turnover of sex determination. Mol Ecol 2023; 32:1366-1380. [PMID: 35712997 DOI: 10.1111/mec.16566] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 05/24/2022] [Accepted: 06/10/2022] [Indexed: 01/17/2023]
Abstract
Populus species have long been used as model organisms to study the adaptability of trees and the evolution of sex chromosomes. As a species belonging to the section Populus and limited to tropical areas, the P. qiongdaoensis genome contains important information for tropical poplar studies and protection. Here, we report a chromosome-level genome assembly and annotation of a female P. qiongdaoensis. Gene family clustering, positive selection detection and historical reconstruction of population dynamics revealed the tropical adaptation of P. qiongdaoensis, and showed convergent evolution with another tropical poplar, P. ilicifolia, at the molecular level, especially on some functional genes (e.g., PIF3 and PIL1). In addition, we also identified a ZW sex determination system on chromosome 19 of P. qiongdaoensis, and inferred that it seems to have a similar sex determination mechanism to other poplars, controlled by a type-A cytokinin response regulator (RR) gene. However, comparison and phylogenetic analysis of the sex determination regions confirmed a cryptic sex turnover event in the section Populus, which may be caused by the translocation and duplication of the RR gene driven by Helitron-like transposable elements. Our study provides new insights into the environmental adaptation and sex chromosome evolution of poplars, and emphasizes the importance of using long read sequencing in ecological and evolutionary inferences of plants.
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Affiliation(s)
- Yiling Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu, China
| | - Deyan Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu, China
| | - Weiwei Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu, China
| | - Wenlu Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jinwen Gao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu, China
| | - Wenyan Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu, China
| | - Lanxing Shan
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu, China
| | - Minghui Kang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yang Chen
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu, China
| | - Tao Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu, China
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10
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Chen S, Yu Y, Wang X, Wang S, Zhang T, Zhou Y, He R, Meng N, Wang Y, Liu W, Liu Z, Liu J, Guo Q, Huang H, Sederoff RR, Wang G, Qu G, Chen S. Chromosome-level genome assembly of a triploid poplar Populus alba 'Berolinensis'. Mol Ecol Resour 2023. [PMID: 36789493 DOI: 10.1111/1755-0998.13770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/16/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023]
Abstract
Many recent studies have provided significant insights into polyploid breeding, but limited research has been carried out on trees. The genomic information needed to understand growth and response to abiotic stress in polyploidy trees is largely unknown, but has become critical due to the threats to forests imposed by climate change. Populus alba 'Berolinensis,' also known "Yinzhong poplar," is a triploid poplar from northeast China. This hybrid triploid poplar is widely used as a landscape ornamental and in urban forestry owing to its adaptation to adverse environments and faster growth than its parental diploid. It is an artificially synthesized male allotriploid hybrid, with three haploid genomes of P. alba 'Berolinensis' originating from different poplar species, so it is attractive for studying polyploidy genomic mechanisms in heterosis. In this study, we focused on the allelic genomic interactions in P. alba 'Berolinensis,' and generated a high-quality chromosome-level genome assembly consisting of 19 allelic chromosomes. Its three haploid chromosome sets are polymorphic with an average of 25.73 nucleotide polymorphism sites per kilobase. We found that some stress-related genes such as RD22 and LEA7 exhibited sequence differences between different haploid genomes. The genome assembly has been deposited in our polyploid genome online analysis website TreeGenomes (https://www.treegenomes.com). These polyploid genome-related resources will provide a critical foundation for the molecular breeding of P. alba 'Berolinensis' and help us uncover the allopolyploidization effects of heterosis and abiotic stress resistance and traits of polyploidy species in the future.
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Affiliation(s)
- Song Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Yue Yu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Xinyu Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Sui Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China.,Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Tianjiao Zhang
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
| | - Yan Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Ruihan He
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Nan Meng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Yiran Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Wenxuan Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Zhijie Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Jinwen Liu
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou, China
| | - Qiwen Guo
- Department of Forest and Soil Sciences, Institute of Forest Ecology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Haijiao Huang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Ronald R Sederoff
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China.,Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina, USA
| | - Guohua Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China.,College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
| | - Guanzheng Qu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Su Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
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11
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Li M, Song Z, Li Z, Qiao R, Zhang P, Ding C, Xie J, Chen Y, Guo H. Populus root exudates are associated with rhizosphere microbial communities and symbiotic patterns. Front Microbiol 2022; 13:1042944. [PMID: 36619999 PMCID: PMC9812961 DOI: 10.3389/fmicb.2022.1042944] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Introduction Microbial communities in the plant rhizosphere are critical for nutrient cycling and ecosystem stability. However, how root exudates and soil physicochemical characteristics affect microbial community composition in Populus rhizosphere is not well understood. Methods This study measured soil physiochemistry properties and root exudates in a representative forest consists of four Populus species. The composition of rhizosphere bacterial and fungal communities was determined by metabolomics and high-throughput sequencing. Results Luvangetin, salicylic acid, gentisic acid, oleuropein, strigol, chrysin, and linoleic acid were the differential root exudates extracted in the rhizosphere of four Populus species, which explained 48.40, 82.80, 48.73, and 59.64% of the variance for the dominant and key bacterial or fungal communities, respectively. Data showed that differential root exudates were the main drivers of the changes in the rhizosphere microbial communities. Nitrosospira, Microvirga, Trichoderma, Cortinarius, and Beauveria were the keystone taxa in the rhizosphere microbial communities, and are thus important for maintaining a stable Populus microbial rhizosphere. The differential root exudates had strong impact on key bacteria than dominant bacteria, key fungi, and dominant fungi. Moreover, strigol had positively effects with bacteria, whereas phenolic compounds and chrysin were negatively correlated with rhizosphere microorganisms. The assembly process of the community structure (keystone taxa and bacterial dominant taxa) was mostly determined by stochastic processes. Discussion This study showed the association of rhizosphere microorganisms (dominant and keystone taxa) with differential root exudates in the rhizosphere of Populus plants, and revealed the assembly process of the dominant and keystone taxa. It provides a theoretical basis for the identification and utilization of beneficial microorganisms in Populus rhizosphere.
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Affiliation(s)
- Mengjie Li
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Zhen Song
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhanbiao Li
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Rongye Qiao
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Pingdong Zhang
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Changjun Ding
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Jianbo Xie
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yinglong Chen
- UWA School of Agriculture and Environment, UWA Institute of Agriculture, Perth, WA, Australia
| | - Hui Guo
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China,National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing, China,*Correspondence: Hui Guo,
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12
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The Current Developments in Medicinal Plant Genomics Enabled the Diversification of Secondary Metabolites' Biosynthesis. Int J Mol Sci 2022; 23:ijms232415932. [PMID: 36555572 PMCID: PMC9781956 DOI: 10.3390/ijms232415932] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/04/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Medicinal plants produce important substrates for their adaptation and defenses against environmental factors and, at the same time, are used for traditional medicine and industrial additives. Plants have relatively little in the way of secondary metabolites via biosynthesis. Recently, the whole-genome sequencing of medicinal plants and the identification of secondary metabolite production were revolutionized by the rapid development and cheap cost of sequencing technology. Advances in functional genomics, such as transcriptomics, proteomics, and metabolomics, pave the way for discoveries in secondary metabolites and related key genes. The multi-omics approaches can offer tremendous insight into the variety, distribution, and development of biosynthetic gene clusters (BGCs). Although many reviews have reported on the plant and medicinal plant genome, chemistry, and pharmacology, there is no review giving a comprehensive report about the medicinal plant genome and multi-omics approaches to study the biosynthesis pathway of secondary metabolites. Here, we introduce the medicinal plant genome and the application of multi-omics tools for identifying genes related to the biosynthesis pathway of secondary metabolites. Moreover, we explore comparative genomics and polyploidy for gene family analysis in medicinal plants. This study promotes medicinal plant genomics, which contributes to the biosynthesis and screening of plant substrates and plant-based drugs and prompts the research efficiency of traditional medicine.
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13
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He X, Wang Y, Lian J, Zheng J, Zhou J, Li J, Jiao Z, Niu Y, Wang W, Zhang J, Wang B, Zhuge Q. The whole-genome assembly of an endangered Salicaceae species: Chosenia arbutifolia (Pall.) A. Skv. Gigascience 2022; 11:6827246. [PMID: 36374197 PMCID: PMC9661892 DOI: 10.1093/gigascience/giac109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/22/2022] [Accepted: 10/14/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND As a fast-growing tree species, Chosenia arbutifolia has a unique but controversial taxonomic status in the family Salicaceae. Despite its importance as an industrial material, in ecological protection, and in landscaping, C. arbutifolia is seriously endangered in Northeast China because of artificial destruction and its low reproductive capability. RESULTS To clarify its phylogenetic relationships with other Salicaceae species, we assembled a high-quality chromosome-level genome of C. arbutifolia using PacBio High-Fidelity reads and Hi-C sequencing data, with a total size of 338.93 Mb and contig N50 of 1.68 Mb. Repetitive sequences, which accounted for 42.34% of the assembly length, were identified. In total, 33,229 protein-coding genes and 11,474 small noncoding RNAs were predicted. Phylogenetic analysis suggested that C. arbutifolia and poplars diverged approximately 15.3 million years ago, and a large interchromosomal recombination between C. arbutifolia and other Salicaceae species was discovered. CONCLUSIONS Our study provides insights into the genome architecture and systematic evolution of C. arbutifolia, as well as comprehensive information for germplasm protection and future functional genomic studies.
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Affiliation(s)
- Xudong He
- Willow Engineering Technology Research Center of National Forestry and Grassland Administration, Jiangsu Academy of Forestry, Nanjing 211153, China.,Willow Nursery of the Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Jiangsu Academy of Forestry, Nanjing 211153, China
| | - Yu Wang
- Willow Engineering Technology Research Center of National Forestry and Grassland Administration, Jiangsu Academy of Forestry, Nanjing 211153, China.,College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Jinmin Lian
- Biozeron Shenzhen, Inc., Shenzhen 518000, China
| | - Jiwei Zheng
- Willow Engineering Technology Research Center of National Forestry and Grassland Administration, Jiangsu Academy of Forestry, Nanjing 211153, China.,Willow Nursery of the Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Jiangsu Academy of Forestry, Nanjing 211153, China
| | - Jie Zhou
- Willow Engineering Technology Research Center of National Forestry and Grassland Administration, Jiangsu Academy of Forestry, Nanjing 211153, China.,Willow Nursery of the Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Jiangsu Academy of Forestry, Nanjing 211153, China
| | - Jiang Li
- Biozeron Shenzhen, Inc., Shenzhen 518000, China
| | - Zhongyi Jiao
- Willow Engineering Technology Research Center of National Forestry and Grassland Administration, Jiangsu Academy of Forestry, Nanjing 211153, China.,Willow Nursery of the Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Jiangsu Academy of Forestry, Nanjing 211153, China
| | | | - Weiwei Wang
- Willow Engineering Technology Research Center of National Forestry and Grassland Administration, Jiangsu Academy of Forestry, Nanjing 211153, China.,Willow Nursery of the Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Jiangsu Academy of Forestry, Nanjing 211153, China
| | - Jun Zhang
- Willow Engineering Technology Research Center of National Forestry and Grassland Administration, Jiangsu Academy of Forestry, Nanjing 211153, China.,Willow Nursery of the Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Jiangsu Academy of Forestry, Nanjing 211153, China
| | - Baosong Wang
- Willow Engineering Technology Research Center of National Forestry and Grassland Administration, Jiangsu Academy of Forestry, Nanjing 211153, China.,Willow Nursery of the Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Jiangsu Academy of Forestry, Nanjing 211153, China
| | - Qiang Zhuge
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
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14
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Zheng Z, Hu H, Lei W, Zhang J, Zhu M, Li Y, Zhang X, Ma J, Wan D, Ma T, Ren G, Ru D. Somatic mutations during rapid clonal domestication of Populus alba var. pyramidalis. Evol Appl 2022; 15:1875-1887. [PMID: 36426122 PMCID: PMC9679227 DOI: 10.1111/eva.13486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 09/08/2022] [Accepted: 09/15/2022] [Indexed: 12/01/2022] Open
Abstract
For many clonally propagated species, the accumulation of somatic mutations is the principal driver of declines in yield and quality. However, somatic mutations may also promote genetic diversification. Thus, elucidating somatic mutation rates and patterns is important to understand the genetic basis undergirding the emergence of commercially valuable traits and developmental processes. In this study, we studied the effect of short-time clonal domestication of Populus alba var. pyramidalis, a species that has been propagated by cutting for the last 67 years. We found that: (1) the somatic mutation rate for P. alba var. pyramidalis is 9.24 × 10-9, which is higher than rates observed in related species; (2) there were more mutations near heterozygous regions, and a larger proportion of CpG and CHG sites were associated with somatic mutations, which may be related to the blocking of DNA repair by methylation; and (3) deleterious mutations were not shared by multiple individuals, and all occurred in heterozygous states, demonstrating the strong selective pressures that act against deleterious mutations. Taken together, the results of our study provide a global view of somatic mutation that will aid efforts to understand the genetic basis of commercially valuable traits and to improve clonally breeding species.
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Affiliation(s)
- Zeyu Zheng
- State Key Laboratory of Grassland Agro‐Ecosystems, College of EcologyLanzhou UniversityLanzhouChina
| | - Hongyin Hu
- State Key Laboratory of Grassland Agro‐Ecosystems, College of EcologyLanzhou UniversityLanzhouChina
| | - Weixiao Lei
- State Key Laboratory of Grassland Agro‐Ecosystems, College of EcologyLanzhou UniversityLanzhouChina
| | - Jin Zhang
- State Key Laboratory of Grassland Agro‐Ecosystems, College of EcologyLanzhou UniversityLanzhouChina
| | - Mingjia Zhu
- State Key Laboratory of Grassland Agro‐Ecosystems, College of EcologyLanzhou UniversityLanzhouChina
| | - Ying Li
- State Key Laboratory of Grassland Agro‐Ecosystems, College of EcologyLanzhou UniversityLanzhouChina
| | - Xu Zhang
- State Key Laboratory of Grassland Agro‐Ecosystems, College of EcologyLanzhou UniversityLanzhouChina
| | - Jianchao Ma
- State Key Laboratory of Grassland Agro‐Ecosystems, College of EcologyLanzhou UniversityLanzhouChina
| | - Dongshi Wan
- State Key Laboratory of Grassland Agro‐Ecosystems, College of EcologyLanzhou UniversityLanzhouChina
| | - Tao Ma
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River EngineeringSichuan UniversityChengduChina
| | - Guangpeng Ren
- State Key Laboratory of Grassland Agro‐Ecosystems, College of EcologyLanzhou UniversityLanzhouChina
| | - Dafu Ru
- State Key Laboratory of Grassland Agro‐Ecosystems, College of EcologyLanzhou UniversityLanzhouChina
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15
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Yang Y, Shao Y, Chaffin TA, Lee JH, Poindexter MR, Ahkami AH, Blumwald E, Stewart CN. Performance of abiotic stress-inducible synthetic promoters in genetically engineered hybrid poplar ( Populus tremula × Populus alba). FRONTIERS IN PLANT SCIENCE 2022; 13:1011939. [PMID: 36330242 PMCID: PMC9623294 DOI: 10.3389/fpls.2022.1011939] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/28/2022] [Indexed: 05/27/2023]
Abstract
Abiotic stresses can cause significant damage to plants. For sustainable bioenergy crop production, it is critical to generate resistant crops to such stress. Engineering promoters to control the precise expression of stress resistance genes is a very effective way to address the problem. Here we developed stably transformed Populus tremula × Populus alba hybrid poplar (INRA 717-1B4) containing one-of-six synthetic drought stress-inducible promoters (SDs; SD9-1, SD9-2, SD9-3, SD13-1, SD18-1, and SD18-3) identified previously by transient transformation assays. We screened green fluorescent protein (GFP) induction in poplar under osmotic stress conditions. Of six transgenic lines containing synthetic promoter, three lines (SD18-1, 9-2, and 9-3) had significant GFP expression in both salt and osmotic stress treatments. Each synthetic promoter employed heptamerized repeats of specific and short cis-regulatory elements (7 repeats of 7-8 bases). To verify whether the repeats of longer sequences can improve osmotic stress responsiveness, a transgenic poplar containing the synthetic promoter of the heptamerized entire SD9 motif (20 bases, containing all partial SD9 motifs) was generated and measured for GFP induction under osmotic stress. The heptamerized entire SD9 motif did not result in higher GFP expression than the shorter promoters consisting of heptamerized SD9-1, 9-2, and 9-3 (partial SD9) motifs. This result indicates that shorter synthetic promoters (~50 bp) can be used for versatile control of gene expression in transgenic poplar. These synthetic promoters will be useful tools to engineer stress-resilient bioenergy tree crops in the future.
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Affiliation(s)
- Yongil Yang
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
- Department of Plant Sciences, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
| | - Yuanhua Shao
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
- Department of Plant Sciences, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
| | - Timothy A. Chaffin
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
- Department of Plant Sciences, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
| | - Jun Hyung Lee
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
- Department of Plant Sciences, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Magen R. Poindexter
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
- Department of Plant Sciences, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
| | - Amir H. Ahkami
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, WA, United States
| | - Eduardo Blumwald
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - C. Neal Stewart
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
- Department of Plant Sciences, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
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16
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Wang D, Li Y, Li M, Yang W, Ma X, Zhang L, Wang Y, Feng Y, Zhang Y, Zhou R, Sanderson BJ, Keefover-Ring K, Yin T, Smart LB, DiFazio SP, Liu J, Olson M, Ma T. Repeated turnovers keep sex chromosomes young in willows. Genome Biol 2022; 23:200. [PMID: 36151581 PMCID: PMC9502649 DOI: 10.1186/s13059-022-02769-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 09/08/2022] [Indexed: 01/10/2023] Open
Abstract
Background Salicaceae species have diverse sex determination systems and frequent sex chromosome turnovers. However, compared with poplars, the diversity of sex determination in willows is poorly understood, and little is known about the evolutionary forces driving their turnover. Here, we characterized the sex determination in two Salix species, S. chaenomeloides and S. arbutifolia, which have an XY system on chromosome 7 and 15, respectively. Results Based on the assemblies of their sex determination regions, we found that the sex determination mechanism of willows may have underlying similarities with poplars, both involving intact and/or partial homologs of a type A cytokinin response regulator (RR) gene. Comparative analyses suggested that at least two sex turnover events have occurred in Salix, one preserving the ancestral pattern of male heterogamety, and the other changing heterogametic sex from XY to ZW, which could be partly explained by the “deleterious mutation load” and “sexually antagonistic selection” theoretical models. We hypothesize that these repeated turnovers keep sex chromosomes of willow species in a perpetually young state, leading to limited degeneration. Conclusions Our findings further improve the evolutionary trajectory of sex chromosomes in Salicaceae species, explore the evolutionary forces driving the repeated turnovers of their sex chromosomes, and provide a valuable reference for the study of sex chromosomes in other species. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02769-w.
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Affiliation(s)
- Deyan Wang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Yiling Li
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Mengmeng Li
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Wenlu Yang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Xinzhi Ma
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Lei Zhang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Yubo Wang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Yanlin Feng
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Yuanyuan Zhang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Ran Zhou
- Department of Biology, West Virginia University, Morgantown, WV, USA
| | - Brian J Sanderson
- Department of Biology, West Virginia University, Morgantown, WV, USA.,Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Ken Keefover-Ring
- Departments of Botany and Geography, University of Wisconsin-Madison, Madison, WI, USA
| | - Tongming Yin
- The Key Laboratory of Tree Genetics and Biotechnology of Jiangsu Province and Education Department of China, Nanjing Forestry University, Nanjing, China
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, WV, USA
| | - Jianquan Liu
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China.
| | - Matthew Olson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA.
| | - Tao Ma
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China.
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17
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Grünhofer P, Stöcker T, Guo Y, Li R, Lin J, Ranathunge K, Schoof H, Schreiber L. Populus × canescens root suberization in reaction to osmotic and salt stress is limited to the developing younger root tip region. PHYSIOLOGIA PLANTARUM 2022; 174:e13765. [PMID: 36281836 DOI: 10.1111/ppl.13765] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/05/2022] [Accepted: 08/12/2022] [Indexed: 06/16/2023]
Abstract
Populus is a valuable and fast-growing tree species commonly cultivated for economic and scientific purposes. But most of the poplar species are sensitive to drought and salt stress. Thus, we compared the physiological effects of osmotic stress (PEG8000) and salt treatment (NaCl) on poplar roots to identify potential strategies for future breeding or genetic engineering approaches. We investigated root anatomy using epifluorescence microscopy, changes in root suberin composition and amount using gas chromatography, transcriptional reprogramming using RNA sequencing, and modifications of root transport physiology using a pressure chamber. Poplar roots reacted to the imposed stress conditions, especially in the developing younger root tip region, with remarkable differences between both types of stress. Overall, the increase in suberin content was surprisingly small, but the expression of key suberin biosynthesis genes was strongly induced. Significant reductions of the radial water transport in roots were only observed for the osmotic and not the hydrostatic hydraulic conductivity. Our data indicate that the genetic enhancement of root suberization processes in poplar might be a promising target to convey increased tolerance, especially against toxic sodium chloride.
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Affiliation(s)
- Paul Grünhofer
- Department of Ecophysiology, Institute of Cellular and Molecular Botany, University of Bonn, Bonn, Germany
| | - Tyll Stöcker
- Department of Crop Bioinformatics, Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, Germany
| | - Yayu Guo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- College of Biological Science and Technology, Beijing Forestry University, Beijing, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing, China
| | - Ruili Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- College of Biological Science and Technology, Beijing Forestry University, Beijing, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing, China
| | - Jinxing Lin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- College of Biological Science and Technology, Beijing Forestry University, Beijing, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing, China
| | - Kosala Ranathunge
- UWA School of Biological Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Heiko Schoof
- Department of Crop Bioinformatics, Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, Germany
| | - Lukas Schreiber
- Department of Ecophysiology, Institute of Cellular and Molecular Botany, University of Bonn, Bonn, Germany
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18
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Advanced Breeding for Biotic Stress Resistance in Poplar. PLANTS 2022; 11:plants11152032. [PMID: 35956510 PMCID: PMC9370193 DOI: 10.3390/plants11152032] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 07/29/2022] [Accepted: 08/01/2022] [Indexed: 12/20/2022]
Abstract
Poplar is one of the most important forest trees because of its high economic value. Thanks to the fast-growing rate, easy vegetative propagation and transformation, and availability of genomic resources, poplar has been considered the model species for forest genetics, genomics, and breeding. Being a field-growing tree, poplar is exposed to environmental threats, including biotic stresses that are becoming more intense and diffused because of global warming. Current poplar farming is mainly based on monocultures of a few elite clones and the expensive and long-term conventional breeding programmes of perennial tree species cannot face current climate-change challenges. Consequently, new tools and methods are necessary to reduce the limits of traditional breeding related to the long generation time and to discover new sources of resistance. Recent advances in genomics, marker-assisted selection, genomic prediction, and genome editing offer powerful tools to efficiently exploit the Populus genetic diversity and allow enabling molecular breeding to support accurate early selection, increasing the efficiency, and reducing the time and costs of poplar breeding, that, in turn, will improve our capacity to face or prevent the emergence of new diseases or pests.
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Tong S, Wang Y, Chen N, Wang D, Liu B, Wang W, Chen Y, Liu J, Ma T, Jiang Y. PtoNF-YC9-SRMT-PtoRD26 module regulates the high saline tolerance of a triploid poplar. Genome Biol 2022; 23:148. [PMID: 35799188 PMCID: PMC9264554 DOI: 10.1186/s13059-022-02718-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 06/25/2022] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Sensing and responding to stresses determine the tolerance of plants to adverse environments. The triploid Chinese white poplar is widely cultivated in North China because of its adaptation to a wide range of habitats including highly saline ones. However, its triploid genome complicates any detailed investigation of the molecular mechanisms underlying its adaptations. RESULTS We report a haplotype-resolved genome of this triploid poplar and characterize, using reverse genetics and biochemical approaches, a MYB gene, SALT RESPONSIVE MYB TRANSCRIPTION FACTOR (SRMT), which combines NUCLEAR FACTOR Y SUBUNIT C 9 (PtoNF-YC9) and RESPONSIVE TO DESICCATION 26 (PtoRD26), to regulate an ABA-dependent salt-stress response signaling. We reveal that the salt-inducible PtoRD26 is dependent on ABA signaling. We demonstrate that ABA or salt drives PtoNF-YC9 shuttling into the nucleus where it interacts with SRMT, resulting in the rapid expression of PtoRD26 which in turn directly regulates SRMT. This positive feedback loop of SRMT-PtoRD26 can rapidly amplify salt-stress signaling. Interference with either component of this regulatory module reduces the salt tolerance of this triploid poplar. CONCLUSION Our findings reveal a novel ABA-dependent salt-responsive mechanism, which is mediated by the PtoNF-YC9-SRMT-PtoRD26 module that confers salt tolerance to this triploid poplar. These genes may therefore also serve as potential and important modification targets in breeding programs.
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Affiliation(s)
- Shaofei Tong
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, China
| | - Yubo Wang
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, China
| | - Ningning Chen
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, China
| | - Deyan Wang
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, China
| | - Bao Liu
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, China
| | - Weiwei Wang
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, China
| | - Yang Chen
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, China
| | - Jianquan Liu
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, China.
| | - Tao Ma
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, China.
| | - Yuanzhong Jiang
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, China.
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20
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Hou Z, Li A. Genomic Differentiation and Demographic Histories of Two Closely Related Salicaceae Species. FRONTIERS IN PLANT SCIENCE 2022; 13:911467. [PMID: 35747877 PMCID: PMC9210983 DOI: 10.3389/fpls.2022.911467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 05/06/2022] [Indexed: 06/15/2023]
Abstract
Populus alba (P. alba) and Populus davidiana (P. davidiana) are important plant species for answering a variety of issues on species evolution due to their wide distribution and ability to adapt to a variety of environments and climates. Even though P. alba and P. davidiana belong to ecologically and economically important forest trees in the Northern Hemisphere, little is known about their genomic landscape and genome divergence during speciation. We re-sequenced 20 and 19 members of P. davidiana and P. alba, respectively, and found that the Dxy value between P. alba and P. davidiana was 0.2658, whereas the F ST values were 0.2988, indicating that the genetic divergence was fairly clear. Populus davidiana and P. alba diverged from the ancestor in the middle Pleistocene, c. 0.80 Ma (95% HPD: 0.79-0.81 Ma). The population sizes of P. davidiana increased ~20,000 years ago after a considerable long-term decline following divergence. However, after differentiation, the effective population size of P. alba expanded slightly before experiencing a long-term bottleneck effect. According to the expectation of allopatric speciation, we found a significant number of genomic differentiation sites in both species' speciation events, and the majority of these genomic differentiation regions can be attributed to neutral evolutionary processes. Nevertheless, the regions with extreme divergence exist in abundance, indicating that natural selection has had an impact. Positive selection can be found in highly differentiated regions, while long-term balancing selection traits can be easily observed in low differentiated regions. According to these findings, climate differences over the Quaternary, as well as variance in linked selection and recombination, all contributed significantly to genomic divergence during allopatric speciation of the two aspens.
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21
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Grünhofer P, Herzig L, Sent S, Zeisler-Diehl VV, Schreiber L. Increased cuticular wax deposition does not change residual foliar transpiration. PLANT, CELL & ENVIRONMENT 2022; 45:1157-1171. [PMID: 35102563 DOI: 10.1111/pce.14274] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 01/19/2022] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
The effect of contrasting environmental growth conditions (in vitro tissue culture, ex vitro acclimatisation, climate chamber, greenhouse and outdoor) on leaf development, cuticular wax composition, and foliar transpiration of detached leaves of the Populus × canescens clone 84 K were investigated. Our results show that total amounts of cuticular wax increased more than 10-fold when cultivated in different growth conditions, whereas qualitative wax composition did not change. With exception of plants directly taken from tissue culture showing rapid dehydration, rates of water loss (residual foliar transpiration) of intact but detached leaves were constant and independent from growth conditions and thus independent from increasing wax amounts. Since cuticular transpiration measured with isolated astomatous P. × canescens cuticles was identical to residual foliar transpiration rates of detached leaves, our results confirm that cuticular transpiration of P. × canescens leaves can be predicted with high accuracy from residual transpiration of detached leaves after stomatal closure. Our results convincingly show that more than 10-fold increased wax amounts in P. × canescens cuticles do not lead to decreased rates of residual (cuticular) transpiration.
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Affiliation(s)
- Paul Grünhofer
- Department of Ecophysiology, Institute of Cellular and Molecular Botany, University of Bonn, Bonn, Germany
| | - Lena Herzig
- Department of Ecophysiology, Institute of Cellular and Molecular Botany, University of Bonn, Bonn, Germany
| | - Sophie Sent
- Department of Ecophysiology, Institute of Cellular and Molecular Botany, University of Bonn, Bonn, Germany
| | - Viktoria V Zeisler-Diehl
- Department of Ecophysiology, Institute of Cellular and Molecular Botany, University of Bonn, Bonn, Germany
| | - Lukas Schreiber
- Department of Ecophysiology, Institute of Cellular and Molecular Botany, University of Bonn, Bonn, Germany
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22
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Comprehensive Genome-Wide Identification and Transcript Profiling of GABA Pathway Gene Family in Apple ( Malus domestica). Genes (Basel) 2021; 12:genes12121973. [PMID: 34946926 PMCID: PMC8700813 DOI: 10.3390/genes12121973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/07/2021] [Accepted: 12/10/2021] [Indexed: 11/16/2022] Open
Abstract
γ-Aminobutyric Acid (GABA), a four-carbon non-protein amino acid, is a significant component of the free amino acid pool in most prokaryotic and eukaryotic organisms. GABA is involved in pH regulation, maintaining C/N balance, plant development and defence, as well as a compatible osmolyte and an alternative pathway for glutamate utilization via anion flux. Glutamate decarboxylase (GAD, EC 4.1.1.15) and GABA transaminase (GABA-T, EC 2.6.1.19) are two key enzymes involved in the synthesis and metabolism of GABA. Recently, GABA transporters (GATs), protein and aluminium-activated malate transporter (ALMT) proteins which function as GABA receptors, have been shown to be involved in GABA regulation. However, there is no report on the characterization of apple GABA pathway genes. In this study, we performed a genome-wide analysis and expression profiling of the GABA pathway gene family in the apple genome. A total of 24 genes were identified including five GAD genes (namely MdGAD 1–5), two GABA-T genes (namely MdGABA-T 1,2), 10 GAT genes (namely GAT 1–10) and seven ALMT genes (namely MdALMT1–7). These genes were randomly distributed on 12 chromosomes. Phylogenetic analyses grouped GABA shunt genes into three clusters—cluster I, cluster II, and cluster III—which had three, four, and five genes, respectively. The expression profile analysis revealed significant MdGAD4 expression levels in both fruit and flower organs, except pollen. However, there were no significant differences in the expression of other GABA shunt genes in different tissues. This work provides the first characterization of the GABA shunt gene family in apple and suggests their importance in apple response to abiotic stress. These results can serve as a guide for future studies on the understanding and functional characterization of these gene families.
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23
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Tong S, Chen N, Wang D, Ai F, Liu B, Ren L, Chen Y, Zhang J, Lou S, Liu H, Liu J, Ma T, Jiang Y. The U-box E3 ubiquitin ligase PalPUB79 positively regulates ABA-dependent drought tolerance via ubiquitination of PalWRKY77 in Populus. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2561-2575. [PMID: 34382303 PMCID: PMC8633511 DOI: 10.1111/pbi.13681] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 08/09/2021] [Indexed: 05/22/2023]
Abstract
The abscisic acid (ABA) signalling pathway is involved in the plant response to osmotic stress caused by drought and/or salinity. Although the ABA signalling pathway has been elucidated in Arabidopsis, it remains elusive in woody poplars. In this study, genome-wide analyses of U-box genes in poplars revealed that a U-box E3 ubiquitin ligase gene, PalPUB79, is significantly induced following drought, salinity and ABA signalling. PalPUB79 overexpression enhanced drought tolerance in transgenic poplars, while PalPUB79 RNAi lines were more sensitive to drought. PalPUB79 positively regulated ABA signalling pathway. Furthermore, PalPUB79 interacted with PalWRKY77, a negative transcriptional regulator of ABA signalling, and mediated its ubiquitination for degradation, therefore counteracting its inhibitory effect on PalRD26 transcription. However, the finding that PalWRKY77 negatively regulates PalPUB79 expression was indicative of a negative feedback loop between PalWRKY77 and PalPUB79 during ABA signalling in poplar. These findings provide novel insight into the mechanism through which PalPUB79 enhances the ABA-mediated stress response in woody poplars.
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Affiliation(s)
- Shaofei Tong
- Key Laboratory for Bio‐resources and Eco‐environment of Ministry of EducationCollege of Life ScienceSichuan UniversityChengduChina
| | - Ningning Chen
- Key Laboratory for Bio‐resources and Eco‐environment of Ministry of EducationCollege of Life ScienceSichuan UniversityChengduChina
| | - Deyan Wang
- Key Laboratory for Bio‐resources and Eco‐environment of Ministry of EducationCollege of Life ScienceSichuan UniversityChengduChina
| | - Fandi Ai
- Key Laboratory for Bio‐resources and Eco‐environment of Ministry of EducationCollege of Life ScienceSichuan UniversityChengduChina
| | - Bao Liu
- Key Laboratory for Bio‐resources and Eco‐environment of Ministry of EducationCollege of Life ScienceSichuan UniversityChengduChina
| | - Liwen Ren
- Key Laboratory for Bio‐resources and Eco‐environment of Ministry of EducationCollege of Life ScienceSichuan UniversityChengduChina
| | - Yang Chen
- Key Laboratory for Bio‐resources and Eco‐environment of Ministry of EducationCollege of Life ScienceSichuan UniversityChengduChina
| | - Junlin Zhang
- Key Laboratory for Bio‐resources and Eco‐environment of Ministry of EducationCollege of Life ScienceSichuan UniversityChengduChina
| | - Shangling Lou
- Key Laboratory for Bio‐resources and Eco‐environment of Ministry of EducationCollege of Life ScienceSichuan UniversityChengduChina
| | - Huanhuan Liu
- Key Laboratory for Bio‐resources and Eco‐environment of Ministry of EducationCollege of Life ScienceSichuan UniversityChengduChina
| | - Jianquan Liu
- Key Laboratory for Bio‐resources and Eco‐environment of Ministry of EducationCollege of Life ScienceSichuan UniversityChengduChina
- State Key Laboratory of Grassland Agro‐EcosystemInstitute of Innovation Ecology & College of Life ScienceLanzhou UniversityLanzhouChina
| | - Tao Ma
- Key Laboratory for Bio‐resources and Eco‐environment of Ministry of EducationCollege of Life ScienceSichuan UniversityChengduChina
| | - Yuanzhong Jiang
- Key Laboratory for Bio‐resources and Eco‐environment of Ministry of EducationCollege of Life ScienceSichuan UniversityChengduChina
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24
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An X, Gao K, Chen Z, Li J, Yang X, Yang X, Zhou J, Guo T, Zhao T, Huang S, Miao D, Ullah Khan W, Rao P, Ye M, Lei B, Liao W, Wang J, Ji L, Li Y, Guo B, Siddig Mustafa N, Li S, Yun Q, Keller SR, Mao JF, Zhang RG, Strauss SH. High quality haplotype-resolved genome assemblies of Populus tomentosa Carr., a stabilized interspecific hybrid species widespread in Asia. Mol Ecol Resour 2021; 22:786-802. [PMID: 34549890 DOI: 10.1111/1755-0998.13507] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 08/19/2021] [Accepted: 09/09/2021] [Indexed: 11/30/2022]
Abstract
Populus has a wide ecogeographical range spanning the Northern Hemisphere, and interspecific hybrids are common. Populus tomentosa Carr. is widely distributed and cultivated in the eastern region of Asia, where it plays multiple important roles in forestry, agriculture, conservation, and urban horticulture. Reference genomes are available for several Populus species, however, our goals were to produce a very high quality de novo chromosome-level genome assembly in P. tomentosa genome that could serve as a reference for evolutionary and ecological studies of hybrid speciation throughout the genus. Here, combining long-read sequencing and Hi-C scaffolding, we present a high-quality, haplotype-resolved genome assembly. The genome size was 740.2 Mb, with a contig N50 size of 5.47 Mb and a scaffold N50 size of 46.68 Mb, consisting of 38 chromosomes, as expected with the known diploid chromosome number (2n = 2x = 38). A total of 59,124 protein-coding genes were identified. Phylogenomic analyses revealed that P. tomentosa is comprised of two distinct subgenomes, which we deomonstrate is likely to have resulted from hybridization between Populus adenopoda as the female parent and Populus alba var. pyramidalis as the male parent, with an origin of approximately 3.93 Ma. Although highly colinear, significant structural variation was found between the two subgenomes. Our study provides a valuable resource for ecological genetics and forest biotechnology.
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Affiliation(s)
- Xinmin An
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China.,National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, MOE, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Kai Gao
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, MOE, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Zhong Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China.,National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, MOE, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Juan Li
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, MOE, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xiong Yang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, MOE, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xiaoyu Yang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, MOE, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Jing Zhou
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, MOE, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Ting Guo
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, MOE, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Tianyun Zhao
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, MOE, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Sai Huang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, MOE, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Deyu Miao
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, MOE, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Wasif Ullah Khan
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, MOE, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Pian Rao
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, MOE, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Meixia Ye
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, MOE, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Bingqi Lei
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, MOE, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Weihua Liao
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, MOE, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Jia Wang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, MOE, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Lexiang Ji
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, MOE, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Ying Li
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, MOE, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Bin Guo
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, MOE, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.,Shanxi Academy of Forestry, Taiyuan, China
| | - Nada Siddig Mustafa
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, MOE, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Shanwen Li
- Shandong Academy of Forestry, Jinan, China
| | | | - Stephen R Keller
- Department of Plant Biology, University of Vermont, Burlington, Vermont, USA
| | - Jian-Feng Mao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China.,National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, MOE, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | | | - Steven H Strauss
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, Oregon, USA
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25
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Niu Z, Li G, Hu H, Lv J, Zheng Q, Liu J, Wan D. A gene that underwent adaptive evolution, LAC2 (LACCASE), in Populus euphratica improves drought tolerance by improving water transport capacity. HORTICULTURE RESEARCH 2021; 8:88. [PMID: 33795664 PMCID: PMC8016922 DOI: 10.1038/s41438-021-00518-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 12/20/2020] [Accepted: 02/06/2021] [Indexed: 05/16/2023]
Abstract
Drought severely limits plant development and growth; accordingly, plants have evolved strategies to prevent water loss and adapt to water deficit conditions. However, experimental cases that corroborate these evolutionary processes are limited. The LACCASEs (LACs) family is involved in various plant development and growth processes. Here, we performed an evolutionary analysis of LACs from Populus euphratica and characterized the functions of LACs in Arabidopsis and poplar. The results showed that in PeuLACs, multiple gene duplications led to apparent functional redundancy as the result of various selective pressures. Among them, PeuLAC2 underwent strong positive selection. Heterologous expression analyses showed that the overexpression of PeuLAC2 alters the xylem structure of plants, including thickening the secondary cell wall (SCW) and increasing the fiber cell length and stem tensile strength. Altogether, these changes improve the water transport capacity of plants. The analysis of the physiological experimental results showed that PeuLAC2-OE lines exhibited a stronger antioxidant response and greater drought tolerance than WT. Three genes screened by transcriptome analysis, NAC025, BG1, and UGT, that are associated with SCW synthesis and drought stress were all upregulated in the PeuLAC2-OE lines, implying that the overexpression of PeuLAC2 thickened the SCW, improved the water transport capacity of the plant, and further enhanced its drought tolerance. Our study highlights that genes that have undergone adaptive evolution may participate in the development of adaptive traits in P. euphratica and that PeuLAC2 could be a candidate gene for molecular genetic breeding in trees.
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Affiliation(s)
- Zhimin Niu
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, People's Republic of China
| | - Guiting Li
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, People's Republic of China
| | - Hongyin Hu
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, People's Republic of China
| | - Jiaojiao Lv
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, People's Republic of China
| | - Qiwei Zheng
- Laboratory of Cell Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, People's Republic of China
| | - Dongshi Wan
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, People's Republic of China.
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26
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Zhang L, Zhao J, Bi H, Yang X, Zhang Z, Su Y, Li Z, Zhang L, Sanderson BJ, Liu J, Ma T. Bioinformatic analysis of chromatin organization and biased expression of duplicated genes between two poplars with a common whole-genome duplication. HORTICULTURE RESEARCH 2021; 8:62. [PMID: 33750794 PMCID: PMC7943600 DOI: 10.1038/s41438-021-00494-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 12/07/2020] [Accepted: 01/03/2021] [Indexed: 05/20/2023]
Abstract
The nonrandom three-dimensional organization of chromatin plays an important role in the regulation of gene expression. However, it remains unclear whether this organization is conserved and whether it is involved in regulating gene expression during speciation after whole-genome duplication (WGD) in plants. In this study, high-resolution interaction maps were generated using high-throughput chromatin conformation capture (Hi-C) techniques for two poplar species, Populus euphratica and Populus alba var. pyramidalis, which diverged ~14 Mya after a common WGD. We examined the similarities and differences in the hierarchical chromatin organization between the two species, including A/B compartment regions and topologically associating domains (TADs), as well as in their DNA methylation and gene expression patterns. We found that chromatin status was strongly associated with epigenetic modifications and gene transcriptional activity, yet the conservation of hierarchical chromatin organization across the two species was low. The divergence of gene expression between WGD-derived paralogs was associated with the strength of chromatin interactions, and colocalized paralogs exhibited strong similarities in epigenetic modifications and expression levels. Thus, the spatial localization of duplicated genes is highly correlated with biased expression during the diploidization process. This study provides new insights into the evolution of chromatin organization and transcriptional regulation during the speciation process of poplars after WGD.
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Affiliation(s)
- Le Zhang
- College of Computer Science & Medical Big Data Center of Sichuan University & Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & College of Life Sciences, Sichuan University, 610065, Chengdu, China.
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 310024, Hangzhou, China.
| | - Jingtian Zhao
- College of Computer Science & Medical Big Data Center of Sichuan University & Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & College of Life Sciences, Sichuan University, 610065, Chengdu, China
| | - Hao Bi
- College of Computer Science & Medical Big Data Center of Sichuan University & Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & College of Life Sciences, Sichuan University, 610065, Chengdu, China
| | - Xiangyu Yang
- College of Computer Science & Medical Big Data Center of Sichuan University & Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & College of Life Sciences, Sichuan University, 610065, Chengdu, China
| | - Zhiyang Zhang
- College of Computer Science & Medical Big Data Center of Sichuan University & Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & College of Life Sciences, Sichuan University, 610065, Chengdu, China
| | - Yutao Su
- College of Computer Science & Medical Big Data Center of Sichuan University & Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & College of Life Sciences, Sichuan University, 610065, Chengdu, China
| | - Zhenghao Li
- College of Computer Science & Medical Big Data Center of Sichuan University & Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & College of Life Sciences, Sichuan University, 610065, Chengdu, China
| | - Lei Zhang
- College of Computer Science & Medical Big Data Center of Sichuan University & Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & College of Life Sciences, Sichuan University, 610065, Chengdu, China
| | - Brian J Sanderson
- Department of Biology, West Virginia University, Morgantown, WV, 26506, USA
| | - Jianquan Liu
- College of Computer Science & Medical Big Data Center of Sichuan University & Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & College of Life Sciences, Sichuan University, 610065, Chengdu, China
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & College of Life Sciences, Lanzhou University, 730000, Lanzhou, China
| | - Tao Ma
- College of Computer Science & Medical Big Data Center of Sichuan University & Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & College of Life Sciences, Sichuan University, 610065, Chengdu, China.
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Yang W, Wang D, Li Y, Zhang Z, Tong S, Li M, Zhang X, Zhang L, Ren L, Ma X, Zhou R, Sanderson BJ, Keefover-Ring K, Yin T, Smart LB, Liu J, DiFazio SP, Olson M, Ma T. A General Model to Explain Repeated Turnovers of Sex Determination in the Salicaceae. Mol Biol Evol 2021; 38:968-980. [PMID: 33027519 PMCID: PMC7947767 DOI: 10.1093/molbev/msaa261] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Dioecy, the presence of separate sexes on distinct individuals, has evolved repeatedly in multiple plant lineages. However, the specific mechanisms by which sex systems evolve and their commonalities among plant species remain poorly understood. With both XY and ZW sex systems, the family Salicaceae provides a system to uncover the evolutionary forces driving sex chromosome turnovers. In this study, we performed a genome-wide association study to characterize sex determination in two Populus species, P. euphratica and P. alba. Our results reveal an XY system of sex determination on chromosome 14 of P. euphratica, and a ZW system on chromosome 19 of P. alba. We further assembled the corresponding sex-determination regions, and found that their sex chromosome turnovers may be driven by the repeated translocations of a Helitron-like transposon. During the translocation, this factor may have captured partial or intact sequences that are orthologous to a type-A cytokinin response regulator gene. Based on results from this and other recently published studies, we hypothesize that this gene may act as a master regulator of sex determination for the entire family. We propose a general model to explain how the XY and ZW sex systems in this family can be determined by the same RR gene. Our study provides new insights into the diversification of incipient sex chromosomes in flowering plants by showing how transposition and rearrangement of a single gene can control sex in both XY and ZW systems.
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Affiliation(s)
- Wenlu Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Deyan Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yiling Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Zhiyang Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Shaofei Tong
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Mengmeng Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xu Zhang
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, China
| | - Lei Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Liwen Ren
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xinzhi Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Ran Zhou
- Department of Biology, West Virginia University, Morgantown, WV
| | - Brian J Sanderson
- Department of Biology, West Virginia University, Morgantown, WV
- Department of Biological Sciences, Texas Tech University, Lubbock, TX
| | - Ken Keefover-Ring
- Departments of Botany and Geography, University of Wisconsin—Madison, Madison, WI
| | - Tongming Yin
- The Key Laboratory of Tree Genetics and Biotechnology of Jiangsu Province and Education Department of China, Nanjing Forestry University, Nanjing, China
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY
| | - Jianquan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, China
| | | | - Matthew Olson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX
| | - Tao Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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Jiang Y, Tong S, Chen N, Liu B, Bai Q, Chen Y, Bi H, Zhang Z, Lou S, Tang H, Liu J, Ma T, Liu H. The PalWRKY77 transcription factor negatively regulates salt tolerance and abscisic acid signaling in Populus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:1258-1273. [PMID: 33264467 DOI: 10.1111/tpj.15109] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/28/2020] [Accepted: 11/04/2020] [Indexed: 06/12/2023]
Abstract
High salinity, one of the most widespread abiotic stresses, inhibits photosynthesis, reduces vegetation growth, blocks respiration and disrupts metabolism in plants. In order to survive their long-term lifecycle, trees, such as Populus species, recruit the abscisic acid (ABA) signaling pathway to adapt to a saline environment. However, the molecular mechanism behind the ABA-mediated salt stress response in woody plants remains elusive. We have isolated a WRKY transcription factor gene, PalWRKY77, from Populus alba var. pyramidalis (poplar), the expression of which is repressed by salt stress. PalWRKY77 decreases salt tolerance in poplar. Furthermore, PalWRKY77 negatively regulated ABA-responsive genes and relieved ABA-mediated growth inhibition, indicating that PalWRKY77 is a repressor of the ABA response. In vivo and in vitro assays revealed that PalWRKY77 targets the ABA- and salt-induced PalNAC002 and PalRD26 genes by binding to the W-boxes in their promoters. In addition, overexpression of both PalNAC002 and PalRD26 could elevate salt tolerance in transgenic poplars. These findings reveal a novel negative regulation mechanism for the ABA signaling pathway mediated by PalWRKY77 that results in more sensitivity to salt stress in poplar. This deepens our understanding of the complex responses of woody species to salt stress.
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Affiliation(s)
- Yuanzhong Jiang
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Shaofei Tong
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Ningning Chen
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Bao Liu
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Qiuxian Bai
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and College of Life Science, Lanzhou University, Lanzhou, 730000, China
| | - Yang Chen
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Hao Bi
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Zhiyang Zhang
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Shangling Lou
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Hu Tang
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Jianquan Liu
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610065, China
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and College of Life Science, Lanzhou University, Lanzhou, 730000, China
| | - Tao Ma
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610065, China
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and College of Life Science, Lanzhou University, Lanzhou, 730000, China
| | - Huanhuan Liu
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610065, China
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29
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Zheng L, Yang J, Chen Y, Ding L, Wei J, Wang H. An improved and efficient method of Agrobacterium syringe infiltration for transient transformation and its application in the elucidation of gene function in poplar. BMC PLANT BIOLOGY 2021; 21:54. [PMID: 33478390 PMCID: PMC7818742 DOI: 10.1186/s12870-021-02833-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 01/11/2021] [Indexed: 05/23/2023]
Abstract
BACKGROUND Forest trees have important economic and ecological value. As a model tree, poplar has played a significant role in elucidating the molecular mechanisms underlying tree biology. However, a lack of mutant libraries and time-consuming stable genetic transformation processes severely limit progress into the functional characterization of poplar genes. A convenient and fast transient transformation method is therefore needed to enhance progress on functional genomics in poplar. METHODS A total of 11 poplar clones were screened for amenability to syringe infiltration. Syringe infiltration was performed on the lower side of the leaves of young soil-grown plants. Transient expression was evaluated by visualizing the reporters β-glucuronidase (GUS) and green fluorescent protein (GFP). The experimental parameters of the syringe agroinfiltration were optimized based on the expression levels of the reporter luciferase (LUC). Stably transformed plants were regenerated from transiently transformed leaf explants through callus-induced organogenesis. The functions of Populus genes in secondary cell wall-thickening were characterized by visualizing lignin deposition therein after staining with basic fuchsin. RESULTS We greatly improved the transient transformation efficiency of syringe Agrobacterium infiltration in poplar through screening for a suitable poplar clone from a variety of clones and optimizing the syringe infiltration procedure. The selected poplar clone, Populus davidiana × P. bolleana, is amenable to Agrobacterium syringe infiltration, as indicated by the easy diffusion of the bacterial suspension inside the leaf tissues. Using this technique, we localized a variety of poplar proteins in specific intracellular organelles and illustrated the protein-protein and protein-DNA interactions. The transiently transformed leaves could be used to generate stably transformed plants with high efficiency through callus induction and differentiation processes. Furthermore, transdifferentiation of the protoxylem-like vessel element and ectopic secondary wall thickening were induced in the agroinfiltrated leaves via the transient overexpression of genes associated with secondary wall formation. CONCLUSIONS The application of P. davidiana × P. bolleana in Agrobacterium syringe infiltration provides a foundation for the rapid and high-throughput functional characterization of Populus genes in intact poplar plants, including those involved in wood formation, and provides an effective alternative to Populus stable genetic transformation.
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Affiliation(s)
- Lin Zheng
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agricultural and Forestry Sciences, No. 9, Shuguang Huayuan Middle Road, Haidian District, Beijing, 100097, People's Republic of China
| | - Jixiu Yang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agricultural and Forestry Sciences, No. 9, Shuguang Huayuan Middle Road, Haidian District, Beijing, 100097, People's Republic of China
- College of Bioscience and Resources Environment, Beijing University of Agriculture, No. 7, Beinong Road, Huilongguan, Changping District, Beijing, 102206, People's Republic of China
| | - Yajuan Chen
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agricultural and Forestry Sciences, No. 9, Shuguang Huayuan Middle Road, Haidian District, Beijing, 100097, People's Republic of China
| | - Liping Ding
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agricultural and Forestry Sciences, No. 9, Shuguang Huayuan Middle Road, Haidian District, Beijing, 100097, People's Republic of China
| | - Jianhua Wei
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agricultural and Forestry Sciences, No. 9, Shuguang Huayuan Middle Road, Haidian District, Beijing, 100097, People's Republic of China.
| | - Hongzhi Wang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agricultural and Forestry Sciences, No. 9, Shuguang Huayuan Middle Road, Haidian District, Beijing, 100097, People's Republic of China.
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30
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Bryant ND, Pu Y, Tschaplinski TJ, Tuskan GA, Muchero W, Kalluri UC, Yoo CG, Ragauskas AJ. Transgenic Poplar Designed for Biofuels. TRENDS IN PLANT SCIENCE 2020; 25:881-896. [PMID: 32482346 DOI: 10.1016/j.tplants.2020.03.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 03/19/2020] [Accepted: 03/25/2020] [Indexed: 05/12/2023]
Abstract
Members of the genus Populus (i.e., cottonwood, hybrid poplar) represent a promising source of lignocellulosic biomass for biofuels. However, one of the major factors negatively affecting poplar's efficient conversion to biofuel is the inherent recalcitrance to enzymatic saccharification due to cell wall components such as lignin. To this effect, there have been efforts to modify gene expression to reduce biomass recalcitrance by changing cell wall properties. Here, we review recent genetic modifications of poplar that led to change cell wall properties and the resulting effects on subsequent pretreatment efficacy and saccharification. Although genetic engineering's impacts on cell wall properties are not fully predictable, recent studies have shown promising improvement in the biological conversion of transgenic poplar to biofuels.
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Affiliation(s)
- Nathan D Bryant
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, USA
| | - Yunqiao Pu
- Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Joint Institute for Biological Science, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Timothy J Tschaplinski
- Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Gerald A Tuskan
- Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Wellington Muchero
- Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Udaya C Kalluri
- Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Chang Geun Yoo
- Department of Paper and Bioprocess Engineering, State University of New York College of Environmental Science and Forestry, Syracuse, NY 13210, USA
| | - Arthur J Ragauskas
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, USA; Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Joint Institute for Biological Science, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Center for Renewable Carbon, Department of Forestry, Wildlife, and Fisheries, University of Tennessee Institute of Agriculture, Knoxville, TN 37996, USA.
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31
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Chen Z, Ai F, Zhang J, Ma X, Yang W, Wang W, Su Y, Wang M, Yang Y, Mao K, Wang Q, Lascoux M, Liu J, Ma T. Survival in the Tropics despite isolation, inbreeding and asexual reproduction: insights from the genome of the world's southernmost poplar (Populus ilicifolia). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:430-442. [PMID: 32168389 DOI: 10.1111/tpj.14744] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 02/04/2020] [Accepted: 03/02/2020] [Indexed: 05/16/2023]
Abstract
Species are becoming extinct at unprecedented rates as a consequence of human activity. Hence it is important to understand the evolutionary dynamics of species with already small population sizes. Populus ilicifolia is a vulnerable poplar species that is isolated from other poplar species and is uniquely adapted to the Tropics. It has a very limited size, reproduces partly clonally and is therefore an excellent case study for conservation genomics. We present here the first annotated draft genome of P. ilicifolia, characterize genome-wide patterns of polymorphisms and compare those to other poplar species with larger natural ranges. P. ilicifolia experienced a more prolonged and severe decline of effective population size (Ne ) and signs of genetic erosion than any other poplar species with which it was compared. At present, the species has the lowest genome-wide genetic diversity, the highest abundance of long runs of homozygosity, high inbreeding levels as well as a high overall accumulation of deleterious variants. However, more effective purging of severely deleterious variants and adaptation to the Tropics may have contributed to its survival. Hence, in spite of its limited genetic variation, it is certainly worth pursuing the conservation efforts of this unique species.
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Affiliation(s)
- Zeyuan Chen
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Fandi Ai
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Junlin Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Xinzhi Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Wenlu Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Weiwei Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Yutao Su
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Mingcheng Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Yongzhi Yang
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Kangshan Mao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Qingfeng Wang
- Key Laboratory of Aquatic Botany and Watershed Ecology, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen, 18D 75326, Uppsala, Sweden
| | - Jianquan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Tao Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
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Chen N, Tong S, Tang H, Zhang Z, Liu B, Lou S, Liu J, Liu H, Ma T, Jiang Y. The PalERF109 transcription factor positively regulates salt tolerance via PalHKT1;2 in Populus alba var. pyramidalis. TREE PHYSIOLOGY 2020; 40:717-730. [PMID: 32083670 DOI: 10.1093/treephys/tpaa018] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 01/01/2020] [Accepted: 01/31/2020] [Indexed: 05/19/2023]
Abstract
Salinity restricts the growth of trees to varying extents, but the regulatory mechanisms involved in their varying salt tolerance are largely unknown. In an effort to elucidate these mechanisms, we identified a total of 99 genes in the Ethylene Responsive Factor (ERF) family of transcription factors and examined their expression patterns under salt stress in Populus alba var. pyramidalis. We found that a B4 group gene, PalERF109, was rapidly induced by salt treatment and preferentially expressed in stems and petioles, where it is probably involved in transport of ions and water in xylem. Overexpression of PalERF109 enhanced the salt tolerance of the poplar, and further analysis showed that it directly upregulated a high-affinity K+transporter (HKT) gene, PalHKT1;2. The results clearly indicate that PalERF109 enhances salt tolerance at least partially through direct activation of PalHKT1;2 and extends understanding of the roles of ERF genes in tree stress responses.
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Affiliation(s)
- Ningning Chen
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu 610065, China
| | - Shaofei Tong
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu 610065, China
| | - Hu Tang
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu 610065, China
| | - Zhiyang Zhang
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu 610065, China
| | - Bao Liu
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu 610065, China
| | - Shangling Lou
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu 610065, China
| | - Jianquan Liu
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu 610065, China
- State Key Laboratory of Grassland Agro-Ecosystem, College of Life Science, Institute of Innovation Ecology, Lanzhou University, Lanzhou 730000, China
| | - Huanhuan Liu
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu 610065, China
| | - Tao Ma
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu 610065, China
| | - Yuanzhong Jiang
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu 610065, China
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Nvsvrot T, Xia W, Xiao Z, Zhan C, Liu M, Yang X, Zhang Y, Wang N. Combining QTL Mapping with Genome Resequencing Identifies an Indel in an R Gene that is Associated with Variation in Leaf Rust Disease Resistance in Poplar. PHYTOPATHOLOGY 2020; 110:900-906. [PMID: 31958037 DOI: 10.1094/phyto-10-19-0402-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Poplar trees (Populus spp.) are important and are widely grown worldwide. However, the extensive occurrence of leaf rust disease caused by Melampsora spp. seriously inhibits their growth and reduces their biomass. In our previous study, a high-quality genetic map was constructed for the poplar F1 population I-69 × XYY by using next-generation sequencing-based genotyping-by-sequencing. Here, we collected phenotypic data on leaf rust disease resistance on three different dates for all 300 progenies of the F1 population. Combining a high-quality genetic map and phenotypic data, we were able to detect 11 major quantitative trait loci (QTLs) for leaf rust disease resistance. Among these 11 QTLs, two pairs were detected on at least two dates. In the corresponding genomic sequence, we found that resistance (R) gene clusters were located in these two QTL regions. By using genome resequencing, PCR confirmation and statistical analysis, a 611-bp deletion within an R gene in one QTL region was found to be associated with variation in leaf rust disease resistance. A PCR-based examination of this 611-bp deletion was performed. This 611-bp deletion was also found to affect mRNA splicing and form a new protein with the loss of some key protein domains. Based on this study, we were able to determine the genetic architecture of variation in poplar leaf rust disease resistance, and the 611-bp deletion in the R gene could be used as a diagnostic marker for future poplar molecular breeding.
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Affiliation(s)
- Tashbek Nvsvrot
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenxiu Xia
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Logistics Service Group, Wuhan University, Wuhan, 430070, China
| | - Zheng'ang Xiao
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chang Zhan
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Meifeng Liu
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaoqing Yang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yan Zhang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Nian Wang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan, 430070, China
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Wei S, Yang Y, Yin T. The chromosome-scale assembly of the willow genome provides insight into Salicaceae genome evolution. HORTICULTURE RESEARCH 2020; 7:45. [PMID: 32257231 PMCID: PMC7109076 DOI: 10.1038/s41438-020-0268-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 02/03/2020] [Accepted: 02/07/2020] [Indexed: 05/11/2023]
Abstract
Salix suchowensis is an early-flowering shrub willow that provides a desirable system for studies on the basic biology of woody plants. The current reference genome of S. suchowensis was assembled with 454 sequencing reads. Here, we report a chromosome-scale assembly of S. suchowensis generated by combining PacBio sequencing with Hi-C technologies. The obtained genome assemblies covered a total length of 356 Mb. The contig N50 of these assemblies was 263,908 bp, which was ~65-fold higher than that reported previously. The contiguity and completeness of the genome were significantly improved. By applying Hi-C data, 339.67 Mb (95.29%) of the assembled sequences were allocated to the 19 chromosomes of haploid willow. With the chromosome-scale assembly, we revealed a series of major chromosomal fissions and fusions that explain the genome divergence between the sister genera of Salix and Populus. The more complete and accurate willow reference genome obtained in this study provides a fundamental resource for studying many genetic and genomic characteristics of woody plants.
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Affiliation(s)
- Suyun Wei
- Key Laboratory for Tree Breeding and Germplasm Improvement, Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037 China
| | - Yonghua Yang
- College of Life Sciences, Nanjing University, Nanjing, 210093 China
| | - Tongming Yin
- Key Laboratory for Tree Breeding and Germplasm Improvement, Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
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35
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Qiu D, Bai S, Ma J, Zhang L, Shao F, Zhang K, Yang Y, Sun T, Huang J, Zhou Y, Galbraith DW, Wang Z, Sun G. The genome of Populus alba x Populus tremula var. glandulosa clone 84K. DNA Res 2020; 26:423-431. [PMID: 31580414 PMCID: PMC6796506 DOI: 10.1093/dnares/dsz020] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 09/09/2019] [Indexed: 01/22/2023] Open
Abstract
Poplar 84K (Populus alba x P. tremula var. glandulosa) is a fast-growing poplar hybrid. Originated in South Korea, this hybrid has been extensively cultivated in northern China. Due to the economic and ecological importance of this hybrid and high transformability, we now report the de novo sequencing and assembly of a male individual of poplar 84K using PacBio and Hi-C technologies. The final reference nuclear genome (747.5 Mb) has a contig N50 size of 1.99 Mb and a scaffold N50 size of 19.6 Mb. Complete chloroplast and mitochondrial genomes were also assembled from the sequencing data. Based on similarities to the genomes of P. alba var. pyramidalis and P. tremula, we were able to identify two subgenomes, representing 356 Mb from P. alba (subgenome A) and 354 Mb from P. tremula var. glandulosa (subgenome G). The phased assembly allowed us to detect the transcriptional bias between the two subgenomes, and we found that the subgenome from P. tremula displayed dominant expression in both 84K and another widely used hybrid, P. tremula x P. alba. This high-quality poplar 84K genome will be a valuable resource for poplar breeding and for molecular biology studies.
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Affiliation(s)
- Deyou Qiu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, The Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Shenglong Bai
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Jianchao Ma
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Lisha Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, The Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Fenjuan Shao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, The Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Kaikai Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, The Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,College of Horticulture, Agricultural University of Hebei, Baoding, China
| | - Yanfang Yang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, The Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Ting Sun
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Jinling Huang
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Yun Zhou
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - David W Galbraith
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China.,School of Plant Sciences and Bio5 Institute, The University of Arizona, Tucson, AZ, USA
| | - Zhaoshan Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, The Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Guiling Sun
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
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36
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Zhang Z, Chen Y, Zhang J, Ma X, Li Y, Li M, Wang D, Kang M, Wu H, Yang Y, Olson MS, DiFazio SP, Wan D, Liu J, Ma T. Improved genome assembly provides new insights into genome evolution in a desert poplar (Populus euphratica). Mol Ecol Resour 2020; 20. [PMID: 32034885 DOI: 10.1111/1755-0998.13142] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 01/21/2020] [Accepted: 02/03/2020] [Indexed: 12/30/2022]
Abstract
Populus euphratica is well adapted to extreme desert environments and is an important model species for elucidating the mechanisms of abiotic stress resistance in trees. The current assembly of P. euphratica genome is highly fragmented with many gaps and errors, thereby impeding downstream applications. Here, we report an improved chromosome-level reference genome of P. euphratica (v2.0) using single-molecule sequencing and chromosome conformation capture (Hi-C) technologies. Relative to the previous reference genome, our assembly represents a nearly 60-fold improvement in contiguity, with a scaffold N50 size of 28.59 Mb. Using this genome, we have found that extensive expansion of Gypsy elements in P. euphratica led to its rapid increase in genome size compared to any other Salicaceae species studied to date, and potentially contributed to adaptive divergence driven by insertions near genes involved in stress tolerance. We also detected a wide range of unique structural rearrangements in P. euphratica, including 2,549 translocations, 454 inversions, 121 tandem and 14 segmental duplications. Several key genes likely to be involved in tolerance to abiotic stress were identified within these regions. This high-quality genome represents a valuable resource for poplar breeding and genetic improvement in the future, as well as comparative genomic analysis with other Salicaceae species.
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Affiliation(s)
- Zhiyang Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Yang Chen
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Junlin Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Xinzhi Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Yiling Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Mengmeng Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Deyan Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Minghui Kang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Haolin Wu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Yongzhi Yang
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & College of Life Sciences, Lanzhou University, Lanzhou, China
| | - Matthew S Olson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, WV, USA
| | - Dongshi Wan
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & College of Life Sciences, Lanzhou University, Lanzhou, China
| | - Jianquan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China.,State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & College of Life Sciences, Lanzhou University, Lanzhou, China
| | - Tao Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
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Hu H, Yang W, Zheng Z, Niu Z, Yang Y, Wan D, Liu J, Ma T. Analysis of Alternative Splicing and Alternative Polyadenylation in Populus alba var. pyramidalis by Single-Molecular Long-Read Sequencing. Front Genet 2020; 11:48. [PMID: 32117458 PMCID: PMC7020888 DOI: 10.3389/fgene.2020.00048] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 01/16/2020] [Indexed: 11/29/2022] Open
Abstract
Poplars are worldwidely cultivated with ecologically and economically important value. Populus alba var. pyramidalis (= P. bolleana) is a main tree of the farmland shelter-belt system in the arid region of Northwest China due to its rapid growth, erect stems, and high biomass production. However, the full-length messenger RNA (mRNA) sequences and complete structure of P. alba var. pyramidalis remain unclear. In this study, using single-molecular real-time (SMRT) and next-generation high-throughput sequencing (NGS) platform, we sequenced transcripts from leaf, root, xylem, and phloem of P. alba var. pyramidalis, to obtain the full-length mRNA transcripts and annotate the complete structure. In total, 86,327 mapped full-length non-chimeric (FLNC) reads were identified, with 705 previously unannotated loci and 3,410 long noncoding RNAs (lncRNAs) and 174 fusion genes found. Alternative spicing (AS) events were detected in 7,536 genes, of which 4,652 genes had multiple AS events. A total of 10,213 alternative polyadenylation (APA) sites were identified, with two or more APA sites observed in 2,212 genes. Our transcriptome data provided the full-length sequences and gene isoforms of transcripts for P. alba var. pyramidalis, which will be helpful in improving our understanding for the genome annotation and gene structures of P. alba var. pyramidalis.
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Affiliation(s)
- Hongyin Hu
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Wenlu Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Zeyu Zheng
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Zhimin Niu
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Yongzhi Yang
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Dongshi Wan
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China.,Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Tao Ma
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China.,Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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38
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Wu H, Yao D, Chen Y, Yang W, Zhao W, Gao H, Tong C. De Novo Genome Assembly of Populus simonii Further Supports That Populus simonii and Populus trichocarpa Belong to Different Sections. G3 (BETHESDA, MD.) 2020; 10:455-466. [PMID: 31806765 PMCID: PMC7003099 DOI: 10.1534/g3.119.400913] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 12/03/2019] [Indexed: 11/18/2022]
Abstract
Populus simonii is an important tree in the genus Populus, widely distributed in the Northern Hemisphere and having a long cultivation history. Although this species has ecologically and economically important values, its genome sequence is currently not available, hindering the development of new varieties with wider adaptive and commercial traits. Here, we report a chromosome-level genome assembly of P. simonii using PacBio long-read sequencing data aided by Illumina paired-end reads and related genetic linkage maps. The assembly is 441.38 Mb in length and contain 686 contigs with a contig N50 of 1.94 Mb. With the linkage maps, 336 contigs were successfully anchored into 19 pseudochromosomes, accounting for 90.2% of the assembled genome size. Genomic integrity assessment showed that 1,347 (97.9%) of the 1,375 genes conserved among all embryophytes can be found in the P. simonii assembly. Genomic repeat analysis revealed that 41.47% of the P. simonii genome is composed of repetitive elements, of which 40.17% contained interspersed repeats. A total of 45,459 genes were predicted from the P. simonii genome sequence and 39,833 (87.6%) of the genes were annotated with one or more related functions. Phylogenetic analysis indicated that P. simonii and Populus trichocarpa should be placed in different sections, contrary to the previous classification according to morphology. The genome assembly not only provides an important genetic resource for the comparative and functional genomics of different Populus species, but also furnishes one of the closest reference sequences for identifying genomic variants in an F1 hybrid population derived by crossing P. simonii with other Populus species.
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Affiliation(s)
- Hainan Wu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Dan Yao
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Yuhua Chen
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Wenguo Yang
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Wei Zhao
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Hua Gao
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Chunfa Tong
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
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39
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Poplar PdPTP1 Gene Negatively Regulates Salt Tolerance by Affecting Ion and ROS Homeostasis in Populus. Int J Mol Sci 2020; 21:ijms21031065. [PMID: 32033494 PMCID: PMC7037657 DOI: 10.3390/ijms21031065] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/29/2020] [Accepted: 02/04/2020] [Indexed: 12/18/2022] Open
Abstract
High concentrations of Na+ in saline soil impair plant growth and agricultural production. Protein tyrosine phosphorylation is crucial in many cellular regulatory mechanisms. However, regulatory mechanisms of plant protein tyrosine phosphatases (PTPs) in controlling responses to abiotic stress remain limited. We report here the identification of a Tyrosine (Tyr)-specific phosphatase, PdPTP1, from NE19 (Populus nigra × (P. deltoides × P. nigra). Transcript levels of PdPTP1 were upregulated significantly by NaCl treatment and oxidative stress. PdPTP1 was found both in the nucleus and cytoplasm. Under NaCl treatment, transgenic plants overexpressing PdPTP1 (OxPdPTP1) accumulated more Na+ and less K+. In addition, OxPdPTP1 poplars accumulated more H2O2 and O2·-, which is consistent with the downregulation of enzymatic ROS-scavengers activity. Furthermore, PdPTP1 interacted with PdMAPK3/6 in vivo and in vitro. In conclusion, our findings demonstrate that PdPTP1 functions as a negative regulator of salt tolerance via a mechanism of affecting Na+/K+ and ROS homeostasis.
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40
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Wang M, Zhang L, Zhang Z, Li M, Wang D, Zhang X, Xi Z, Keefover-Ring K, Smart LB, DiFazio SP, Olson MS, Yin T, Liu J, Ma T. Phylogenomics of the genus Populus reveals extensive interspecific gene flow and balancing selection. THE NEW PHYTOLOGIST 2020; 225:1370-1382. [PMID: 31550399 DOI: 10.1111/nph.16215] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Accepted: 09/16/2019] [Indexed: 05/10/2023]
Abstract
Phylogenetic analysis is complicated by interspecific gene flow and the presence of shared ancestral polymorphisms, particularly those maintained by balancing selection. In this study, we aimed to examine the prevalence of these factors during the diversification of Populus, a model tree genus in the Northern Hemisphere. We constructed phylogenetic trees of 29 Populus taxa using 80 individuals based on re-sequenced genomes. Our species tree analyses recovered four main clades in the genus based on consensus nuclear phylogenies, but in conflict with the plastome phylogeny. A few interspecific relationships remained unresolved within the multiple-species clade because of inconsistent gene trees. Our results indicated that gene flow has been widespread within each clade and also occurred among the four clades during their early divergence. We identified 45 candidate genes with ancient polymorphisms maintained by balancing selection. These genes were mainly associated with mating compatibility, growth and stress resistance. Both gene flow and selection-mediated ancient polymorphisms are prevalent in the genus Populus. These are potentially important contributors to adaptive variation. Our results provide a framework for the diversification of model tree genus that will facilitate future comparative studies.
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Affiliation(s)
- Mingcheng Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Lei Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Zhiyang Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Mengmeng Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Deyan Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Xu Zhang
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Zhenxiang Xi
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Ken Keefover-Ring
- Departments of Botany and Geography, University of Wisconsin-Madison, 430 Lincoln Dr., Madison, WI, 53706, USA
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, New York State Agricultural Experiment Station, Cornell University, Geneva, NY, 14456, USA
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, WV, 25606, USA
| | - Matthew S Olson
- Department of Biological Sciences, Texas Tech University, Box 43131, Lubbock, TX, 79409-3131, USA
| | - Tongming Yin
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Jianquan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Tao Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
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Xin H, Zhang T, Wu Y, Zhang W, Zhang P, Xi M, Jiang J. An extraordinarily stable karyotype of the woody Populus species revealed by chromosome painting. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:253-264. [PMID: 31529535 DOI: 10.1111/tpj.14536] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 08/25/2019] [Accepted: 09/02/2019] [Indexed: 05/22/2023]
Abstract
The karyotype represents the basic genetic make-up of a eukaryotic species. Comparative cytogenetic analysis of related species based on individually identified chromosomes has been conducted in only a few plant groups and not yet in woody plants. We have developed a complete set of 19 chromosome painting probes based on the reference genome of the model woody plant Populus trichocarpa. Using sequential fluorescence in situ hybridization we were able to identify all poplar chromosomes in the same metaphase cells, which led to the development of poplar karyotypes based on individually identified chromosomes. We demonstrate that five Populus species, belonging to five different sections within Populus, have maintained a remarkably conserved karyotype. No inter-chromosomal structural rearrangements were observed on any of the 19 chromosomes among the five species. Thus, the chromosomal synteny in Populus has been remarkably maintained after nearly 14 million years of divergence. We propose that the karyotypes of woody species are more stable than those of herbaceous plants since it may take a longer period of time for woody plants to fix chromosome number or structural variants in natural populations.
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Affiliation(s)
- Haoyang Xin
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, Nanjing Forestry University, Nanjing, 210037, China
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, 48824, USA
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Co-Innovation Centre for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Yufeng Wu
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenli Zhang
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Pingdong Zhang
- National Engineering Laboratory for Tree Breeding, College of Bioscience and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Mengli Xi
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, Nanjing Forestry University, Nanjing, 210037, China
| | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, 48824, USA
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Michigan State University AgBioResearch, East Lansing, MI, 48824, USA
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Bai X, Xu J, Shao X, Luo W, Niu Z, Gao C, Wan D. A Novel Gene Coding γ-Aminobutyric Acid Transporter May Improve the Tolerance of Populus euphratica to Adverse Environments. FRONTIERS IN PLANT SCIENCE 2019; 10:1083. [PMID: 31572409 PMCID: PMC6749060 DOI: 10.3389/fpls.2019.01083] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 08/08/2019] [Indexed: 05/28/2023]
Abstract
Novel genes provide important genetic resource for organism innovation. However, the evidence from genetic experiment is limited. In plants, γ-aminobutyric acid (GABA) transporters (GATs) primarily transport GABA and further involve in plant growth, development, and response to various stresses. In this study, we have identified the GATs family in Populus species and characterized their functional evolution and divergence in a desert poplar species (Populus euphratica). We found that the GATs underwent genus-specific expansion via multiple whole-genome duplications in Populus species. The purifying selection were identified across those GATs evolution and divergence in poplar diversity, except two paralogous PeuGAT2 and PeuGAT3 from P. euphratica. The both genes arose from a tandem duplication event about 49 million years ago and have experienced strong positive selection, suggesting that the divergence in PeuGAT3 protein function/structure might define gene function better than in expression pattern. Both PeuGAT genes were functionally characterized in Arabidopsis and poplar, respectively. The overexpression of PeuGAT3 increased the thickness of xylem cells walls in both Arabidopsis and poplar and enhanced the lignin content of xylem tissues and the proline accumulation in poplar leaves, all of which may improve tolerance of salt/drought stress in desert poplars. Our findings help clarify the genetic mechanisms underpinning high tolerance in desert poplars and suggest that PeuGAT3 could be an attractive candidate gene for engineering trees with improved brown-rot resistance.
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43
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Ma J, Bai X, Luo W, Feng Y, Shao X, Bai Q, Sun S, Long Q, Wan D. Genome-Wide Identification of Long Noncoding RNAs and Their Responses to Salt Stress in Two Closely Related Poplars. Front Genet 2019; 10:777. [PMID: 31543901 PMCID: PMC6739720 DOI: 10.3389/fgene.2019.00777] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 07/23/2019] [Indexed: 12/23/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are involved in various biological regulatory processes, but their roles in plants resistance to salt stress remain largely unknown. To systematically explore the characteristics of lncRNAs and their roles in plant salt responses, we conducted strand-specific RNA-sequencing of four tissue types with salt treatments in two closely related poplars (Populus euphratica and Populus alba var. pyramidalis), and a total of 10,646 and 10,531 lncRNAs were identified, respectively. These lncRNAs showed significantly lower values in terms of length, expression, and expression correction than with mRNA. We further found that about 40% and 60% of these identified lncRNAs responded to salt stress with tissue-specific expression patterns across the two poplars. Furthermore, lncRNAs showed weak evolutionary conservation in sequences and exhibited diverse regulatory styles; in particular, tissue- and species-specific responses to salt stress varied greatly in two poplars, for example, 322 lncRNAs were found highly expressed in P. euphratica but not in P. alba var. pyramidalis and 3,425 lncRNAs were identified to be species-specific in P. euphratica in response to salt stress. Moreover, tissue-specific expression of lncRNAs in two poplars were identified with predicted target genes included Aux/IAA, NAC, MYB, involved in regulating plant growth and the plant stress response. Taken together, the systematic analysis of lncRNAs between sister species enhances our understanding of the characteristics of lncRNAs and their roles in plant growth and salt response.
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Affiliation(s)
- Jianchao Ma
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China.,Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Xiaotao Bai
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Wenchun Luo
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Yannan Feng
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Xuemin Shao
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Qiuxian Bai
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Shujiao Sun
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Qiming Long
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Dongshi Wan
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
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Bruegmann T, Deecke K, Fladung M. Evaluating the Efficiency of gRNAs in CRISPR/Cas9 Mediated Genome Editing in Poplars. Int J Mol Sci 2019; 20:E3623. [PMID: 31344908 PMCID: PMC6696231 DOI: 10.3390/ijms20153623] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/12/2019] [Accepted: 07/21/2019] [Indexed: 01/23/2023] Open
Abstract
CRISPR/Cas9 has become one of the most promising techniques for genome editing in plants and works very well in poplars with an Agrobacterium-mediated transformation system. We selected twelve genes, including SOC1, FUL, and their paralogous genes, four NFP-like genes and TOZ19 for three different research topics. The gRNAs were designed for editing, and, together with a constitutively expressed Cas9 nuclease, transferred either into the poplar hybrid Populus × canescens or into P. tremula. The regenerated lines showed different types of editing and revealed several homozygous editing events which are of special interest in perennial species because of limited back-cross ability. Through a time series, we could show that despite the constitutive expression of the Cas9 nuclease, no secondary editing of the target region occurred. Thus, constitutive Cas9 expression does not seem to pose any risk to additional editing events. Based on various criteria, we obtained evidence for a relationship between the structure of gRNA and the efficiency of gene editing. In particular, the GC content, purine residues in the gRNA end, and the free accessibility of the seed region seemed to be highly important for genome editing in poplars. Based on our findings on nine different poplar genes, efficient gRNAs can be designed for future efficient editing applications in poplars.
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Affiliation(s)
- Tobias Bruegmann
- Thuenen Institute of Forest Genetics, Sieker Landstrasse 2, D-22927 Grosshansdorf, Germany.
| | - Khira Deecke
- Thuenen Institute of Forest Genetics, Sieker Landstrasse 2, D-22927 Grosshansdorf, Germany
| | - Matthias Fladung
- Thuenen Institute of Forest Genetics, Sieker Landstrasse 2, D-22927 Grosshansdorf, Germany.
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Brenner WG, Mader M, Müller NA, Hoenicka H, Schroeder H, Zorn I, Fladung M, Kersten B. High Level of Conservation of Mitochondrial RNA Editing Sites Among Four Populus Species. G3 (BETHESDA, MD.) 2019; 9:709-717. [PMID: 30617214 PMCID: PMC6404595 DOI: 10.1534/g3.118.200763] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/01/2019] [Indexed: 01/29/2023]
Abstract
RNA editing occurs in the endosymbiont organelles of higher plants as C-to-U conversions of defined nucleotides. The availability of large quantities of RNA sequencing data makes it possible to identify RNA editing sites and to quantify their editing extent. We have investigated RNA editing in 34 protein-coding mitochondrial transcripts of four Populus species, a genus noteworthy for its remarkably small number of RNA editing sites compared to other angiosperms. 27 of these transcripts were subject to RNA editing in at least one species. In total, 355 RNA editing sites were identified with high confidence, their editing extents ranging from 10 to 100%. The most heavily edited transcripts were ccmB with the highest density of RNA editing sites (53.7 sites / kb) and ccmFn with the highest number of sites (39 sites). Most of the editing events are at position 1 or 2 of the codons, usually altering the encoded amino acid, and are highly conserved among the species, also with regard to their editing extent. However, one SNP was found in the newly sequenced and annotated mitochondrial genome of P. alba resulting in the loss of an RNA editing site compared to P. tremula and P. davidiana This SNP causes a C-to-T transition and an amino acid exchange from Ser to Phe, highlighting the widely discussed role of RNA editing in compensating mutations.
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Affiliation(s)
| | - Malte Mader
- Thünen Institute of Forest Genetics, 22927 Grosshansdorf, Germany
| | | | - Hans Hoenicka
- Thünen Institute of Forest Genetics, 22927 Grosshansdorf, Germany
| | - Hilke Schroeder
- Thünen Institute of Forest Genetics, 22927 Grosshansdorf, Germany
| | - Ingo Zorn
- Thünen Institute of Forest Genetics, 22927 Grosshansdorf, Germany
| | - Matthias Fladung
- Thünen Institute of Forest Genetics, 22927 Grosshansdorf, Germany
| | - Birgit Kersten
- Thünen Institute of Forest Genetics, 22927 Grosshansdorf, Germany
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Bai Q, Duan B, Ma J, Fen Y, Sun S, Long Q, Lv J, Wan D. Coexpression of PalbHLH1 and PalMYB90 Genes From Populus alba Enhances Pathogen Resistance in Poplar by Increasing the Flavonoid Content. FRONTIERS IN PLANT SCIENCE 2019; 10:1772. [PMID: 32174927 PMCID: PMC7054340 DOI: 10.3389/fpls.2019.01772] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 12/18/2019] [Indexed: 05/20/2023]
Abstract
Secondary metabolites of the flavonoid pathway participate in plant defense, and bHLH and MYB transcription factors regulate the synthesis of these metabolites. Here, we define the regulatory mechanisms in response to pathogens. Two transcription factors from Populus alba var. pyramidalis, PalbHLH1 and PalMYB90, were overexpressed together in poplar, and transcriptome analysis revealed differences in response to pathogen infection. The transgenic plants showed elevated levels of several key flavonoid pathway components: total phenols, proanthocyanidins (PAs), and anthocyanins and intermediates quercetin and kaempferol. Furthermore, PalbHLH1 and PalMYB90 overexpression in poplar enhanced antioxidase activities and H2O2 release and also increased resistance to Botrytis cinerea and Dothiorella gregaria infection. Gene expression profile analysis showed most genes involved in the flavonoid biosynthesis pathway or antioxidant response to be upregulated in MYB90/bHLH1-OE poplar, but significant differential expression occurred in response to pathogen infection. Specifically, expression of PalF3H (flavanone 3-hydroxylase), PalDFR (dihydroflavonol 4-seductase), PalANS (anthocyanin synthase), and PalANR (anthocyanin reductase), which function in initial, middle, and final steps of anthocyanin and PA biosynthesis, respectively, was significantly upregulated in D. gregaria-infected MYB90/bHLH1-OE poplar. Our results highlight that PalbHLH1 and PalMYB90 function as transcriptional activators of flavonoid pathway secondary-metabolite synthesis genes, with differential mechanisms in response to bacterial or fungal infection.
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Hou J, Wei S, Pan H, Zhuge Q, Yin T. Uneven selection pressure accelerating divergence of Populus and Salix. HORTICULTURE RESEARCH 2019; 6:37. [PMID: 30962934 PMCID: PMC6450953 DOI: 10.1038/s41438-019-0121-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 12/17/2018] [Accepted: 12/30/2018] [Indexed: 05/22/2023]
Abstract
Populus (poplars) and Salix (willows) are sister genera in the Salicaceae family that arise from a common tetraploid ancestor. The karyotypes of these two lineages are distinguished by two major interchromosomal and some minor intrachromosomal rearrangements, but which one is evolutionarily more primitive remains debatable. In this study, we compare the selection pressure acting on the paralogous genes resulting from salicoid duplication (PGRS) within and between the genomes of the two lineages. Purifying selection was determined to act more strongly on the PGRS in willow than on those in poplar, which would cause a faster loss of paralogous duplicates in willow. Therefore, Salix species are supposed to evolve faster than Populus species, which is consistent with the observation that the former are taxonomically and morphologically more diverse than the latter. In these two lineages, different autosomes were found to have been evolving into sex chromosomes. Examining the ω ratio and the PGRS in the sex determination regions in willow and poplar revealed higher convergent selection pressure and a faster loss of PGRS in the sex determination regions of both lineages. At the chromosome level, the sex chromosome in poplar is characterized by the lowest gene density among all chromosome members, while this feature is not observed on the sex chromosome in willow, suggesting that Populus species may inherit the more incipient sex chromosome from their progenitor. Taken together, Salix is supposed to be the nascent lineage arising from the additional round of genome reorganization that distinguishes the karyotypes of the two sister genera. In this study, assessment of ω ratios also detected a list of paralogous genes under unusual selection pressure, which could have special consequences for the adaptive evolution of Salicaceae species. In conclusion, the results of this study provide unique information for better understanding the genetic mechanism accelerating the divergence of these two closely related lineages.
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Affiliation(s)
- Jing Hou
- The Key Laboratory for Cultivar Innovation and Germplasm Improvement for Salicaceae Species, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
| | - Suyun Wei
- The Key Laboratory for Cultivar Innovation and Germplasm Improvement for Salicaceae Species, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
| | - Huixin Pan
- The Key Laboratory for Cultivar Innovation and Germplasm Improvement for Salicaceae Species, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
| | - Qiang Zhuge
- The Key Laboratory for Cultivar Innovation and Germplasm Improvement for Salicaceae Species, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
| | - Tongming Yin
- The Key Laboratory for Cultivar Innovation and Germplasm Improvement for Salicaceae Species, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
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