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Ma Y, Ratcliffe J, Bacic A, Johnson KL. Promoter and domain structures regulate FLA12 function during Arabidopsis secondary wall development. FRONTIERS IN PLANT SCIENCE 2023; 14:1275983. [PMID: 38034570 PMCID: PMC10687482 DOI: 10.3389/fpls.2023.1275983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 10/31/2023] [Indexed: 12/02/2023]
Abstract
Introduction Fasciclin-like arabinogalactan-proteins (FLAs) are a family of multi-domain glycoproteins present at the cell surface and walls of plants. Arabidopsis thaliana FLA12 and homologs in cotton, Populus, and flax have been shown to play important functions regulating secondary cell wall (SCW) development. FLA12 has been shown to have distinct roles from the closely related FLA11 that also functions during SCW development. The promoter and domain features of FLA12 that regulate functional specificity have not been well characterized. Methods In this study, promoter swap experiments of FLA11 and FLA12 were investigated. Mutation of proposed functional regions within FLA12 were used to investigate the role of post-translational modifications on sub-cellular location and trafficking. Domain swap experiments between FLA11 and FLA12 were performed to identify regions of functional specificity. Results Promote swap experiments showed that FLA12 is differentially expressed in both stem and rosette leaves compared to FLA11. Post-translational modifications, in particular addition of the glycosylphosphatidylinositol-anchor (GPI-anchor), were shown to be important for FLA12 location at the plasma membrane (PM)/cell wall interface. Domain swap experiments between FLA11 and FLA12 showed that the C-terminal arabinogalactan (AG) glycan motif acts as a key regulatory region differentiating FLA12 functions from FLA11. Discussion Understanding of FLA12 promoter and functional domains has provided new insights into the regulation of SCW development and functional specificity of FLAs for plant growth and development.
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Affiliation(s)
- Yingxuan Ma
- La Trobe Institute for Agriculture & Food, Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, VIC, Australia
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
| | - Julian Ratcliffe
- La Trobe Institute for Agriculture & Food, Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, VIC, Australia
| | - Antony Bacic
- La Trobe Institute for Agriculture & Food, Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, VIC, Australia
- Sino-Australia Plant Cell Wall Research Centre, College of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Kim L. Johnson
- La Trobe Institute for Agriculture & Food, Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, VIC, Australia
- Sino-Australia Plant Cell Wall Research Centre, College of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou, China
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Luan X, Xu W, Zhang J, Shen T, Chen C, Xi M, Zhong Y, Xu M. Genome-Scale Identification, Classification, and Expression Profiling of MYB Transcription Factor Genes in Cinnamomum camphora. Int J Mol Sci 2022; 23:14279. [PMID: 36430756 PMCID: PMC9693371 DOI: 10.3390/ijms232214279] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/10/2022] [Accepted: 11/15/2022] [Indexed: 11/19/2022] Open
Abstract
The camphor tree (Cinnamomum camphora (L.) Presl.) is the representative species of subtropical evergreen broadleaved forests in eastern Asia and an important raw material for essential oil production worldwide. Although MYBs have been comprehensively characterized and their functions have been partially resolved in many plants, it has not been explored in C. camphora. In this study, 121 CcMYBs were identified on 12 chromosomes in the whole genome of C. camphora and found that CcMYBs were mainly expanded by segmental duplication. They were divided into 28 subgroups based on phylogenetic analysis and gene structural characteristics. In the promoter regions, numerous cis-acting elements were related to biological processes. Analysis of RNA sequencing data from seven tissues showed that CcMYBs exhibited different expression profiles, suggesting that they have various roles in camphor tree development. In addition, combined with the correlation analysis of structural genes in the flavonoid synthesis pathway, we identified CcMYBs from three subgroups that might be related to the flavonoid biosynthesis pathway. This study systematically analyzed CcMYBs in C. camphora, which will set the stage for subsequent research on the functions of CcMYBs during their lifetime and provide valuable insights for the genetic improvement of camphor trees.
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Affiliation(s)
- Xiaoyue Luan
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Wenlin Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Jiaqi Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Tengfei Shen
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Caihui Chen
- Key Laboratory of Horticultural Plant Genetics and Improvement of Jiangxi Province, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang 330096, China
| | - Mengli Xi
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Yongda Zhong
- Key Laboratory of Horticultural Plant Genetics and Improvement of Jiangxi Province, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang 330096, China
| | - Meng Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
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Conaty WC, Broughton KJ, Egan LM, Li X, Li Z, Liu S, Llewellyn DJ, MacMillan CP, Moncuquet P, Rolland V, Ross B, Sargent D, Zhu QH, Pettolino FA, Stiller WN. Cotton Breeding in Australia: Meeting the Challenges of the 21st Century. FRONTIERS IN PLANT SCIENCE 2022; 13:904131. [PMID: 35646011 PMCID: PMC9136452 DOI: 10.3389/fpls.2022.904131] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 04/08/2022] [Indexed: 06/15/2023]
Abstract
The Commonwealth Scientific and Industrial Research Organisation (CSIRO) cotton breeding program is the sole breeding effort for cotton in Australia, developing high performing cultivars for the local industry which is worth∼AU$3 billion per annum. The program is supported by Cotton Breeding Australia, a Joint Venture between CSIRO and the program's commercial partner, Cotton Seed Distributors Ltd. (CSD). While the Australian industry is the focus, CSIRO cultivars have global impact in North America, South America, and Europe. The program is unique compared with many other public and commercial breeding programs because it focuses on diverse and integrated research with commercial outcomes. It represents the full research pipeline, supporting extensive long-term fundamental molecular research; native and genetically modified (GM) trait development; germplasm enhancement focused on yield and fiber quality improvements; integration of third-party GM traits; all culminating in the release of new commercial cultivars. This review presents evidence of past breeding successes and outlines current breeding efforts, in the areas of yield and fiber quality improvement, as well as the development of germplasm that is resistant to pests, diseases and abiotic stressors. The success of the program is based on the development of superior germplasm largely through field phenotyping, together with strong commercial partnerships with CSD and Bayer CropScience. These relationships assist in having a shared focus and ensuring commercial impact is maintained, while also providing access to markets, traits, and technology. The historical successes, current foci and future requirements of the CSIRO cotton breeding program have been used to develop a framework designed to augment our breeding system for the future. This will focus on utilizing emerging technologies from the genome to phenome, as well as a panomics approach with data management and integration to develop, test and incorporate new technologies into a breeding program. In addition to streamlining the breeding pipeline for increased genetic gain, this technology will increase the speed of trait and marker identification for use in genome editing, genomic selection and molecular assisted breeding, ultimately producing novel germplasm that will meet the coming challenges of the 21st Century.
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Affiliation(s)
| | | | - Lucy M. Egan
- CSIRO Agriculture and Food, Narrabri, NSW, Australia
| | - Xiaoqing Li
- CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Zitong Li
- CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Shiming Liu
- CSIRO Agriculture and Food, Narrabri, NSW, Australia
| | | | | | | | | | - Brett Ross
- Cotton Seed Distributors Ltd., Wee Waa, NSW, Australia
| | - Demi Sargent
- CSIRO Agriculture and Food, Narrabri, NSW, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, Canberra, ACT, Australia
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Burris JN, Makarem M, Slabaugh E, Chaves A, Pierce ET, Lee J, Kiemle SN, Kwansa AL, Singh A, Yingling YG, Roberts AW, Kim SH, Haigler CH. Phenotypic effects of changes in the FTVTxK region of an Arabidopsis secondary wall cellulose synthase compared with results from analogous mutations in other isoforms. PLANT DIRECT 2021; 5:e335. [PMID: 34386691 PMCID: PMC8341023 DOI: 10.1002/pld3.335] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/27/2021] [Accepted: 06/08/2021] [Indexed: 05/21/2023]
Abstract
Understanding protein structure and function relationships in cellulose synthase (CesA), including divergent isomers, is an important goal. Here, we report results from mutant complementation assays that tested the ability of sequence variants of AtCesA7, a secondary wall CesA of Arabidopsis thaliana, to rescue the collapsed vessels, short stems, and low cellulose content of the irx3-1 AtCesA7 null mutant. We tested a catalytic null mutation and seven missense or small domain changes in and near the AtCesA7 FTVTSK motif, which lies near the catalytic domain and may, analogously to bacterial CesA, exist within a substrate "gating loop." A low-to-high gradient of rescue occurred, and even inactive AtCesA7 had a small positive effect on stem cellulose content but not stem elongation. Overall, secondary wall cellulose content and stem length were moderately correlated, but the results were consistent with threshold amounts of cellulose supporting particular developmental processes. Vibrational sum frequency generation microscopy allowed tissue-specific analysis of cellulose content in stem xylem and interfascicular fibers, revealing subtle differences between selected genotypes that correlated with the extent of rescue of the collapsing xylem phenotype. Similar tests on PpCesA5 from the moss Physcomitrium (formerly Physcomitrella) patens helped us to synergize the AtCesA7 results with prior results on AtCesA1 and PpCesA5. The cumulative results show that the FTVTxK region is important for the function of an angiosperm secondary wall CesA as well as widely divergent primary wall CesAs, while differences in complementation results between isomers may reflect functional differences that can be explored in further work.
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Affiliation(s)
- Jason N. Burris
- Department of Crop and Soil SciencesNorth Carolina State UniversityRaleighNCUSA
| | - Mohamadamin Makarem
- Department of Chemical Engineering and Materials Research InstitutePennsylvania State University, University ParkState CollegePAUSA
| | - Erin Slabaugh
- Department of Crop and Soil SciencesNorth Carolina State UniversityRaleighNCUSA
| | - Arielle Chaves
- Department of Biological SciencesUniversity of Rhode IslandKingstonRIUSA
| | - Ethan T. Pierce
- Department of Crop and Soil SciencesNorth Carolina State UniversityRaleighNCUSA
| | - Jongcheol Lee
- Department of Chemical Engineering and Materials Research InstitutePennsylvania State University, University ParkState CollegePAUSA
| | - Sarah N. Kiemle
- Department of BiologyPennsylvania State University, University ParkState CollegePAUSA
| | - Albert L. Kwansa
- Department of Materials Science and EngineeringNorth Carolina State UniversityRaleighNCUSA
| | - Abhishek Singh
- Department of Materials Science and EngineeringNorth Carolina State UniversityRaleighNCUSA
| | - Yaroslava G. Yingling
- Department of Materials Science and EngineeringNorth Carolina State UniversityRaleighNCUSA
| | - Alison W. Roberts
- Department of Biological SciencesUniversity of Rhode IslandKingstonRIUSA
| | - Seong H. Kim
- Department of Chemical Engineering and Materials Research InstitutePennsylvania State University, University ParkState CollegePAUSA
| | - Candace H. Haigler
- Department of Crop and Soil SciencesNorth Carolina State UniversityRaleighNCUSA
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNCUSA
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5
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Wang A, Liang K, Yang S, Cao Y, Wang L, Zhang M, Zhou J, Zhang L. Genome-wide analysis of MYB transcription factors of Vaccinium corymbosum and their positive responses to drought stress. BMC Genomics 2021; 22:565. [PMID: 34294027 PMCID: PMC8296672 DOI: 10.1186/s12864-021-07850-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 06/25/2021] [Indexed: 01/22/2023] Open
Abstract
Background Blueberry (Vaccinium corymbosum L.) is an important species with a high content of flavonoids in fruits. As a perennial shrub, blueberry is characterized by shallow-rooted property and susceptible to drought stress. MYB transcription factor was reported to be widely involved in plant response to abiotic stresses, however, the role of MYB family in blueberry responding to drought stress remains elusive. Results In this study, we conducted a comprehensive analysis of VcMYBs in blueberry based on the genome data under drought stress, including phylogenetic relationship, identification of differentially expressed genes (DEGs), expression profiling, conserved motifs, expression correlation and protein-protein interaction prediction, etc. The results showed that 229 non-redundant MYB sequences were identified in the blueberry genome, and divided into 23 subgroups. A total of 102 MYB DEGs with a significant response to drought stress were identified, of which 72 in leaves and 69 in roots, and 8 differential expression genes with a > 20-fold change in the level of expression. 17 DEGs had a higher expression correlation with other MYB members. The interaction partners of the key VcMYB proteins were predicted by STRING analysis and in combination with physiological and morphological observation. 10 key VcMYB genes such as VcMYB8, VcMYB102 and VcMYB228 were predicted to be probably involved in reactive oxygen species (ROS) pathway, and 7 key VcMYB genes (VcMYB41, VcMYB88 and VcMYB100, etc..) probably participated in leaf regulation under drought treatment. Conclusions Our studies provide a new understanding of the regulation mechanism of VcMYB family in blueberry response to drought stress, and lay fundamental support for future studies on blueberry grown in regions with limited water supply for this crop. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07850-5.
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Affiliation(s)
- Aibin Wang
- Research & Development Center of Blueberry, Key Laboratory of Forest Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, 35 QinghuaEast Road, 100083, Beijing, China
| | - Kehao Liang
- Research & Development Center of Blueberry, Key Laboratory of Forest Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, 35 QinghuaEast Road, 100083, Beijing, China
| | - Shiwen Yang
- Research & Development Center of Blueberry, Key Laboratory of Forest Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, 35 QinghuaEast Road, 100083, Beijing, China
| | - Yibo Cao
- Research & Development Center of Blueberry, Key Laboratory of Forest Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, 35 QinghuaEast Road, 100083, Beijing, China
| | - Lei Wang
- Research & Development Center of Blueberry, Key Laboratory of Forest Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, 35 QinghuaEast Road, 100083, Beijing, China
| | - Ming Zhang
- Research & Development Center of Blueberry, Key Laboratory of Forest Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, 35 QinghuaEast Road, 100083, Beijing, China
| | - Jing Zhou
- Research & Development Center of Blueberry, Key Laboratory of Forest Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, 35 QinghuaEast Road, 100083, Beijing, China
| | - Lingyun Zhang
- Research & Development Center of Blueberry, Key Laboratory of Forest Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, 35 QinghuaEast Road, 100083, Beijing, China.
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6
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Xiao R, Zhang C, Guo X, Li H, Lu H. MYB Transcription Factors and Its Regulation in Secondary Cell Wall Formation and Lignin Biosynthesis during Xylem Development. Int J Mol Sci 2021; 22:3560. [PMID: 33808132 PMCID: PMC8037110 DOI: 10.3390/ijms22073560] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/26/2021] [Accepted: 03/26/2021] [Indexed: 01/12/2023] Open
Abstract
The secondary wall is the main part of wood and is composed of cellulose, xylan, lignin, and small amounts of structural proteins and enzymes. Lignin molecules can interact directly or indirectly with cellulose, xylan and other polysaccharide molecules in the cell wall, increasing the mechanical strength and hydrophobicity of plant cells and tissues and facilitating the long-distance transportation of water in plants. MYBs (v-myb avian myeloblastosis viral oncogene homolog) belong to one of the largest superfamilies of transcription factors, the members of which regulate secondary cell-wall formation by promoting/inhibiting the biosynthesis of lignin, cellulose, and xylan. Among them, MYB46 and MYB83, which comprise the second layer of the main switch of secondary cell-wall biosynthesis, coordinate upstream and downstream secondary wall synthesis-related transcription factors. In addition, MYB transcription factors other than MYB46/83, as well as noncoding RNAs, hormones, and other factors, interact with one another to regulate the biosynthesis of the secondary wall. Here, we discuss the biosynthesis of secondary wall, classification and functions of MYB transcription factors and their regulation of lignin polymerization and secondary cell-wall formation during wood formation.
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Affiliation(s)
- Ruixue Xiao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; (R.X.); (H.L.)
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (C.Z.); (X.G.)
| | - Chong Zhang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (C.Z.); (X.G.)
| | - Xiaorui Guo
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (C.Z.); (X.G.)
| | - Hui Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; (R.X.); (H.L.)
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (C.Z.); (X.G.)
| | - Hai Lu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; (R.X.); (H.L.)
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (C.Z.); (X.G.)
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Graham BP, Haigler CH. Microtubules exert early, partial, and variable control of cotton fiber diameter. PLANTA 2021; 253:47. [PMID: 33484350 DOI: 10.1007/s00425-020-03557-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 12/30/2020] [Indexed: 05/07/2023]
Abstract
Variable cotton fiber diameter is set early in anisotropic elongation by cell-type-specific processes involving the temporal and spatial regulation of microtubules in the apical region. Cotton fibers are single cells that originate from the seed epidermis of Gossypium species. Then, they undergo extreme anisotropic elongation and limited diametric expansion. The details of cellular morphogenesis determine the quality traits that affect fiber uses and value, such as length, strength, and diameter. Lower and more consistent diameter would increase the competitiveness of cotton fiber with synthetic fiber, but we do not know how this trait is controlled. The complexity of the question is indicated by the existence of fibers in two major width classes in the major commercial species: broad and narrow fibers exist in commonly grown G. hirsutum, whereas G. barbadense produces only narrow fiber. To further understand how fiber diameter is controlled, we used ovule cultures, morphology measurements, and microtubule immunofluorescence to observe the effects of microtubule antagonists on fiber morphology, including shape and diameter within 80 µm of the apex. The treatments were applied at either one or two days post-anthesis during different stages of fiber morphogenesis. The results showed that inhibiting the presence and/or dynamic activity of microtubules caused larger diameter tips to form, with greater effects often observed with earlier treatment. The presence and geometry of a microtubule-depleted-zone below the apex were transiently correlated with the apical diameter of the narrow tip types. Similarly, the microtubule antagonists had somewhat different effects between tip types. Overall, the results demonstrate cell-type-specific mechanisms regulating fiber expansion within 80 µm of the apex, with variation in the impact of microtubules between tip types and over developmental time.
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Affiliation(s)
- Benjamin P Graham
- Department of Crop and Soil Sciences and Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Candace H Haigler
- Department of Crop and Soil Sciences and Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA.
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Allen H, Wei D, Gu Y, Li S. A historical perspective on the regulation of cellulose biosynthesis. Carbohydr Polym 2021; 252:117022. [DOI: 10.1016/j.carbpol.2020.117022] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 08/25/2020] [Accepted: 08/25/2020] [Indexed: 01/19/2023]
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9
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Liu E, MacMillan CP, Shafee T, Ma Y, Ratcliffe J, van de Meene A, Bacic A, Humphries J, Johnson KL. Fasciclin-Like Arabinogalactan-Protein 16 (FLA16) Is Required for Stem Development in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2020; 11:615392. [PMID: 33362841 PMCID: PMC7758453 DOI: 10.3389/fpls.2020.615392] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 11/23/2020] [Indexed: 05/19/2023]
Abstract
The predominant Fascilin 1 (FAS1)-containing proteins in plants belong to the Fasciclin-Like Arabinogalactan-protein (FLA) family of extracellular glycoproteins. In addition to FAS1 domains, these multi-domain FLA proteins contain glycomotif regions predicted to direct addition of large arabinogalactan (AG) glycans and many contain signal sequences for addition of a glycosylphosphatidylinositol (GPI)-anchor to tether them to the plasma membrane. FLAs are proposed to play both structural and signaling functions by forming a range of interactions in the plant extracellular matrix, similar to FAS1-containing proteins in animals. FLA group B members contain two FAS1 domains and are not predicted to be GPI-anchored. None of the group B members have been functionally characterized or their sub-cellular location resolved, limiting understanding of their function. We investigated the group B FLA16 in Arabidopsis that is predominantly expressed in inflorescence tissues. FLA16 is the most highly expressed FLA in the stem after Group A members FLA11 and FLA12 that are stem specific. A FLA16-YFP fusion protein driven by the endogenous putative FLA16 promoter in wild type background showed expression in cells with secondary cell walls, and FLA16 displayed characteristics of cell wall glycoproteins with moderate glycosylation. Investigation of a fla16 mutant showed loss of FLA16 leads to reduced stem length and altered biomechanical properties, likely as a result of reduced levels of cellulose. Immuno-labeling indicated support for FLA16 location to the plasma-membrane and (apoplastic) cell wall of interfascicular stem fiber cells. Together these results indicate FLA16, a two-FAS1 domain FLAs, plays a role in plant secondary cell wall synthesis and function.
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Affiliation(s)
- Edgar Liu
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
| | - Colleen P. MacMillan
- CSIRO, Agriculture and Food, CSIRO Black Mountain Science and Innovation Park, Canberra, ACT, Australia
| | - Thomas Shafee
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia
| | - Yingxuan Ma
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia
| | - Julian Ratcliffe
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia
| | | | - Antony Bacic
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia
- Sino-Australia Plant Cell Wall Research Centre, College of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, China
| | - John Humphries
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia
| | - Kim L. Johnson
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia
- Sino-Australia Plant Cell Wall Research Centre, College of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, China
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10
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Shafee T, Bacic A, Johnson K. Evolution of Sequence-Diverse Disordered Regions in a Protein Family: Order within the Chaos. Mol Biol Evol 2020; 37:2155-2172. [DOI: 10.1093/molbev/msaa096] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Abstract
Approaches for studying the evolution of globular proteins are now well established yet are unsuitable for disordered sequences. Our understanding of the evolution of proteins containing disordered regions therefore lags that of globular proteins, limiting our capacity to estimate their evolutionary history, classify paralogs, and identify potential sequence–function relationships. Here, we overcome these limitations by using new analytical approaches that project representations of sequence space to dissect the evolution of proteins with both ordered and disordered regions, and the correlated changes between these. We use the fasciclin-like arabinogalactan proteins (FLAs) as a model family, since they contain a variable number of globular fasciclin domains as well as several distinct types of disordered regions: proline (Pro)-rich arabinogalactan (AG) regions and longer Pro-depleted regions.
Sequence space projections of fasciclin domains from 2019 FLAs from 78 species identified distinct clusters corresponding to different types of fasciclin domains. Clusters can be similarly identified in the seemingly random Pro-rich AG and Pro-depleted disordered regions. Sequence features of the globular and disordered regions clearly correlate with one another, implying coevolution of these distinct regions, as well as with the N-linked and O-linked glycosylation motifs. We reconstruct the overall evolutionary history of the FLAs, annotated with the changing domain architectures, glycosylation motifs, number and length of AG regions, and disordered region sequence features. Mapping these features onto the functionally characterized FLAs therefore enables their sequence–function relationships to be interrogated. These findings will inform research on the abundant disordered regions in protein families from all kingdoms of life.
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Affiliation(s)
- Thomas Shafee
- Department of Animal, Plant and Soil Sciences, La Trobe Institute for Agriculture & Food, La Trobe University, Melbourne, VIC, Australia
| | - Antony Bacic
- Department of Animal, Plant and Soil Sciences, La Trobe Institute for Agriculture & Food, La Trobe University, Melbourne, VIC, Australia
- Sino-Australia Plant Cell Wall Research Centre, College of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Lin’an, Hangzhou, China
| | - Kim Johnson
- Department of Animal, Plant and Soil Sciences, La Trobe Institute for Agriculture & Food, La Trobe University, Melbourne, VIC, Australia
- Sino-Australia Plant Cell Wall Research Centre, College of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Lin’an, Hangzhou, China
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11
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Johnson KL. From Fuzz to Fiber: Identification of Genes Involved in Cotton Fiber Elongation. PLANT PHYSIOLOGY 2020; 183:23-24. [PMID: 32385179 PMCID: PMC7210616 DOI: 10.1104/pp.20.00233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Affiliation(s)
- Kim L Johnson
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Victoria 3086, Australia
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12
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Zhu G, Gao W, Song X, Sun F, Hou S, Liu N, Huang Y, Zhang D, Ni Z, Chen Q, Guo W. Genome-wide association reveals genetic variation of lint yield components under salty field conditions in cotton (Gossypium hirsutum L.). BMC PLANT BIOLOGY 2020; 20:23. [PMID: 31937242 PMCID: PMC6961271 DOI: 10.1186/s12870-019-2187-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 12/05/2019] [Indexed: 05/02/2023]
Abstract
BACKGROUND Salinity is one of the most significant environmental factors limiting the productivity of cotton. However, the key genetic components responsible for the reduction in cotton yield in saline-alkali soils are still unclear. RESULTS Here, we evaluated three main components of lint yield, single boll weight (SBW), lint percentage (LP) and boll number per plant (BNPP), across 316 G. hirsutum accessions under four salt conditions over two years. Phenotypic analysis indicated that LP was unchanged under different salt conditions, however BNPP decreased significantly and SBW increased slightly under high salt conditions. Based on 57,413 high-quality single nucleotide polymorphisms (SNPs) and genome-wide association study (GWAS) analysis, a total of 42, 91 and 25 stable quantitative trait loci (QTLs) were identified for SBW, LP and BNPP, respectively. Phenotypic and QTL analysis suggested that there was little correlation among the three traits. For LP, 8 stable QTLs were detected simultaneously in four different salt conditions, while fewer repeated QTLs for SBW or BNPP were identified. Gene Ontology (GO) analysis indicated that their regulatory mechanisms were also quite different. Via transcriptome profile data, we detected that 10 genes from the 8 stable LP QTLs were predominantly expressed during fiber development. Further, haplotype analyses found that a MYB gene (GhMYB103), with the two SNP variations in cis-regulatory and coding regions, was significantly correlated with lint percentage, implying a crucial role in lint yield. We also identified that 40 candidate genes from BNPP QTLs were salt-inducible. Genes related to carbohydrate metabolism and cell structure maintenance were rich in plants grown in high salt conditions, while genes related to ion transport were active in plants grown in low salt conditions, implying different regulatory mechanisms for BNPP at high and low salt conditions. CONCLUSIONS This study provides a foundation for elucidating cotton salt tolerance mechanisms and contributes gene resources for developing upland cotton varieties with high yields and salt stress tolerance.
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Affiliation(s)
- Guozhong Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Engineering Research Center of Hybrid Cotton Development (the Ministry of Education), Nanjing Agricultural University, Nanjing, 210095 China
| | - Wenwei Gao
- Engineering Research Center for Cotton (the Ministry of Education), Xinjiang Agricultural University, Urumqi, 830052 China
| | - Xiaohui Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Engineering Research Center of Hybrid Cotton Development (the Ministry of Education), Nanjing Agricultural University, Nanjing, 210095 China
| | - Fenglei Sun
- Engineering Research Center for Cotton (the Ministry of Education), Xinjiang Agricultural University, Urumqi, 830052 China
| | - Sen Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Engineering Research Center of Hybrid Cotton Development (the Ministry of Education), Nanjing Agricultural University, Nanjing, 210095 China
| | - Na Liu
- Engineering Research Center for Cotton (the Ministry of Education), Xinjiang Agricultural University, Urumqi, 830052 China
| | - Yajie Huang
- Engineering Research Center for Cotton (the Ministry of Education), Xinjiang Agricultural University, Urumqi, 830052 China
| | - Dayong Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Engineering Research Center of Hybrid Cotton Development (the Ministry of Education), Nanjing Agricultural University, Nanjing, 210095 China
| | - Zhiyong Ni
- Engineering Research Center for Cotton (the Ministry of Education), Xinjiang Agricultural University, Urumqi, 830052 China
| | - Quanjia Chen
- Engineering Research Center for Cotton (the Ministry of Education), Xinjiang Agricultural University, Urumqi, 830052 China
| | - Wangzhen Guo
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Engineering Research Center of Hybrid Cotton Development (the Ministry of Education), Nanjing Agricultural University, Nanjing, 210095 China
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13
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Sun Q, Huang J, Guo Y, Yang M, Guo Y, Li J, Zhang J, Xu W. A cotton NAC domain transcription factor, GhFSN5, negatively regulates secondary cell wall biosynthesis and anther development in transgenic Arabidopsis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 146:303-314. [PMID: 31783206 DOI: 10.1016/j.plaphy.2019.11.030] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/29/2019] [Accepted: 11/18/2019] [Indexed: 06/10/2023]
Abstract
NAC domain transcription factors (TFs) are plant-specific transcriptional regulators, some of which play crucial roles in secondary cell wall (SCW) biosynthesis in plants. Cotton is one of the most important natural fiber producing crops, whose mature fiber SCW contains more than 90% cellulose with very small amounts of xylan and lignin, but little is known about the molecular mechanism underlying fiber SCW formation. We previously identified seven fiber preferentially expressed NAC members, GhFSN1-7. One, GhFSN1, was demonstrated to positively regulate fiber SCW thickening, but the functions of other GhFSN members remain unknown. In this study, roles of GhFSN5 were dissected. qRT-PCR analysis showed that GhFSN5 was predominantly transcribed during the fiber SCW thickening stage. In addition, a large number of fiber SCW biosynthetic genes and SCW-related TFs were co-expressed with GhFSN5. Heterologous expression of GhFSN5 in Arabidopsis resulted in plants with smaller siliques and severe sterility. Anther dehiscence in transgenic lines was not substantially affected, but most pollen was collapsed and nonviable. Furthermore, cellulose and lignin contents in inflorescence stems as well as roots were reduced in transgenic lines, compared with the wild type. Moreover, a set of SCW biosynthetic genes for cellulose, xylan and lignin and several transcription factors involved in regulation of SCW formation were down-regulated in transgenic plants. Our findings indicate that GhFSN5 acts as a negative regulator of SCW formation and anther development and expands our understanding of transcriptional regulation of SCW biosynthesis.
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Affiliation(s)
- Qianwen Sun
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Junfeng Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Yifan Guo
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Mingming Yang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Yanjun Guo
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Juan Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Jie Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Wenliang Xu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China.
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14
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Zhou S, Zhang J, Han H, Zhang J, Ma H, Zhang Z, Lu Y, Liu W, Yang X, Li X, Li L. Full-length transcriptome sequences of Agropyron cristatum facilitate the prediction of putative genes for thousand-grain weight in a wheat-A. cristatum translocation line. BMC Genomics 2019; 20:1025. [PMID: 31881839 PMCID: PMC6935218 DOI: 10.1186/s12864-019-6416-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 12/19/2019] [Indexed: 01/09/2023] Open
Abstract
Background Agropyron cristatum (L.) Gaertn. (2n = 4x = 28; genomes PPPP) is a wild relative of common wheat (Triticum aestivum L.) and provides many desirable genetic resources for wheat improvement. However, there is still a lack of reference genome and transcriptome information for A. cristatum, which severely impedes functional and molecular breeding studies. Results Single-molecule long-read sequencing technology from Pacific Biosciences (PacBio) was used to sequence full-length cDNA from a mixture of leaves, roots, stems and caryopses and constructed the first full-length transcriptome dataset of A. cristatum, which comprised 44,372 transcripts. As expected, the PacBio transcripts were generally longer and more complete than the transcripts assembled via the Illumina sequencing platform in previous studies. By analyzing RNA-Seq data, we identified tissue-enriched transcripts and assessed their GO term enrichment; the results indicated that tissue-enriched transcripts were enriched for particular molecular functions that varied by tissue. We identified 3398 novel and 1352 A. cristatum-specific transcripts compared with the wheat gene model set. To better apply this A. cristatum transcriptome, the A. cristatum transcripts were integrated with the wheat genome as a reference sequence to try to identify candidate A. cristatum transcripts associated with thousand-grain weight in a wheat-A. cristatum translocation line, Pubing 3035. Conclusions Full-length transcriptome sequences were used in our study. The present study not only provides comprehensive transcriptomic insights and information for A. cristatum but also proposes a new method for exploring the functional genes of wheat relatives under a wheat genetic background. The sequence data have been deposited in the NCBI under BioProject accession number PRJNA534411.
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Affiliation(s)
- Shenghui Zhou
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jinpeng Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Haiming Han
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jing Zhang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Huihui Ma
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhi Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yuqing Lu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Weihua Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xinming Yang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiuquan Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lihui Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Gao Z, Sun W, Wang J, Zhao C, Zuo K. GhbHLH18 negatively regulates fiber strength and length by enhancing lignin biosynthesis in cotton fibers. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 286:7-16. [PMID: 31300144 DOI: 10.1016/j.plantsci.2019.05.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 05/06/2019] [Accepted: 05/25/2019] [Indexed: 05/08/2023]
Abstract
Cotton fibers are developed epidermal cells of the seed coat and contain large amounts of cellulose and minor lignin-like components. Lignin in the cell walls of cotton fibers effectively provides mechanical strength and is also presumed to restrict fiber elongation and secondary cell wall synthesis. To analyze the effect of lignin and lignin-like phenolics on fiber quality and the transcriptional regulation of lignin synthesis in cotton fibers, we characterized the function of a bHLH transcription factor, GhbHLH18, during fiber elongation stage. GhbHLH18 knock-down plants have longer and stronger fibers, and accumulate less lignin-like phenolics in mature cotton fibers than control plants. By mining public transcriptomic data for developing fibers, we discovered that GhbHLH18 is coexpressed with most lignin synthesis pathway genes. Furthermore, we showed that GhbHLH18 strongly binds to the E-box in the promoter region of GhPER8 and activates its expression. Transient over expression of GhPER8 protein in tobacco leaves significantly decreased the content of coniferyl alcohol and sinapic alcohol-the substrate respectively for G-lignin and S-lignin biosynthesis. These results suggest that GhbHLH18 is negatively associated with fiber quality by activating peroxidase-mediated lignin metabolism, thus the paper represents an alternative strategy to improve fiber quality.
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Affiliation(s)
- Zhengyin Gao
- Plant Biotechnology Research Center, SJTU-Cornell Institute of Sustainable Agriculture and Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wenjie Sun
- Plant Biotechnology Research Center, SJTU-Cornell Institute of Sustainable Agriculture and Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jun Wang
- Plant Biotechnology Research Center, SJTU-Cornell Institute of Sustainable Agriculture and Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chunyan Zhao
- Plant Biotechnology Research Center, SJTU-Cornell Institute of Sustainable Agriculture and Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Kaijing Zuo
- Plant Biotechnology Research Center, SJTU-Cornell Institute of Sustainable Agriculture and Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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16
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Luan MW, Chen W, Xing JF, Xiao CL, Chen Y, Xie SQ. DNA N6-Methyladenosine modification role in transmitted variations from genomic DNA to RNA in Herrania umbratica. BMC Genomics 2019; 20:508. [PMID: 31215402 PMCID: PMC6582544 DOI: 10.1186/s12864-019-5776-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 05/07/2019] [Indexed: 11/16/2022] Open
Abstract
Background DNA methylation is an important epigenetic modification. Recently the developed single-molecule real-time (SMRT) sequencing technology provided an efficient way to detect DNA N6-methyladenine (6mA) modification that played an important role in epigenetic and positively regulated gene expression. In addition, the gene expression was also regulated by genetic variation. However, the relationship between DNA 6mA modification and variation is still unknown. Results We collected the SMRT long-reads DNA, Illumina short reads DNA and RNA datasets from the young leaves of Herrania umbratica, and used them to detect 35,654 6mA modification sites, 829,894 DNA variations and 60,672 RNA variations respectively, among which, there are 303 DNA variations and 19 RNA variations with 6mA modification, and 57,468 transmitted genetic variations from DNA to RNA. The results illustrated that the genes with 6mA modification were significant disadvantage to mutate than those genes without modification (p-value< 4.9e-08). And result from the linear regression model showed the 6mA densities of genes were associated with the transmitted variations type 0/1 to 1/1 (p-value < 0.001). Conclusions The variations of DNA and RNA in genes with 6mA modification were significant less than those in unmodified genes. Furthermore, the variations in 6mA modified genes were easily transmitted from DNA to RNA, especially the transmitted variation from DNA heterozygote to RNA homozygote. Electronic supplementary material The online version of this article (10.1186/s12864-019-5776-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mei-Wei Luan
- Research Center for Terrestrial Biodiversity of the South China Sea, Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Natural Rubber Cooperative Innovation Centre of Hainan Province & Ministry of Education of China, Hainan University, Haikou, 570228, China
| | - Wei Chen
- Research Center for Terrestrial Biodiversity of the South China Sea, Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Natural Rubber Cooperative Innovation Centre of Hainan Province & Ministry of Education of China, Hainan University, Haikou, 570228, China
| | - Jian-Feng Xing
- Research Center for Terrestrial Biodiversity of the South China Sea, Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Natural Rubber Cooperative Innovation Centre of Hainan Province & Ministry of Education of China, Hainan University, Haikou, 570228, China
| | - Chuan-Le Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Ying Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China.
| | - Shang-Qian Xie
- Research Center for Terrestrial Biodiversity of the South China Sea, Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Natural Rubber Cooperative Innovation Centre of Hainan Province & Ministry of Education of China, Hainan University, Haikou, 570228, China.
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17
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Guo X, Runavot JL, Bourot S, Meulewaeter F, Hernandez-Gomez M, Holland C, Harholt J, Willats WGT, Mravec J, Knox P, Ulvskov P. Metabolism of polysaccharides in dynamic middle lamellae during cotton fibre development. PLANTA 2019; 249:1565-1581. [PMID: 30737556 DOI: 10.1007/s00425-019-03107-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 02/04/2019] [Indexed: 06/09/2023]
Abstract
Evidence is presented that cotton fibre adhesion and middle lamella formation are preceded by cutin dilution and accompanied by rhamnogalacturonan-I metabolism. Cotton fibres are single cell structures that early in development adhere to one another via the cotton fibre middle lamella (CFML) to form a tissue-like structure. The CFML is disassembled around the time of initial secondary wall deposition, leading to fibre detachment. Observations of CFML in the light microscope have suggested that the development of the middle lamella is accompanied by substantial cell-wall metabolism, but it has remained an open question as to which processes mediate adherence and which lead to detachment. The mechanism of adherence and detachment were investigated here using glyco-microarrays probed with monoclonal antibodies, transcript profiling, and observations of fibre auto-digestion. The results suggest that adherence is brought about by cutin dilution, while the presence of relevant enzyme activities and the dynamics of rhamnogalacturonan-I side-chain accumulation and disappearance suggest that both attachment and detachment are accompanied by rhamnogalacturonan-I metabolism.
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Affiliation(s)
- Xiaoyuan Guo
- Department of Plant and Environmental Sciences, Copenhagen University, Frederiksberg, Denmark
| | - Jean-Luc Runavot
- Bayer CropScience NV, Innovation Center, Technologiepark 38, 9052, Ghent, Belgium
| | - Stéphane Bourot
- Bayer CropScience NV, Innovation Center, Technologiepark 38, 9052, Ghent, Belgium
| | - Frank Meulewaeter
- Bayer CropScience NV, Innovation Center, Technologiepark 38, 9052, Ghent, Belgium
| | - Mercedes Hernandez-Gomez
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Claire Holland
- Department of Plant and Environmental Sciences, Copenhagen University, Frederiksberg, Denmark
| | - Jesper Harholt
- Department of Plant and Environmental Sciences, Copenhagen University, Frederiksberg, Denmark
| | - William G T Willats
- School of Agriculture, Food and Rural Development, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Jozef Mravec
- Department of Plant and Environmental Sciences, Copenhagen University, Frederiksberg, Denmark
| | - Paul Knox
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Peter Ulvskov
- Department of Plant and Environmental Sciences, Copenhagen University, Frederiksberg, Denmark.
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18
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Jan S, Abbas N, Ashraf M, Ahmad P. Roles of potential plant hormones and transcription factors in controlling leaf senescence and drought tolerance. PROTOPLASMA 2019; 256:313-329. [PMID: 30311054 DOI: 10.1007/s00709-018-1310-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 09/18/2018] [Indexed: 06/08/2023]
Abstract
Plant leaves offer an exclusive windowpane to uncover the changes in organs, tissues, and cells as they advance towards the process of senescence and death. Drought-induced leaf senescence is an intricate process with remarkably coordinated phases of onset, progression, and completion implicated in an extensive reprogramming of gene expression. Advancing leaf senescence remobilizes nutrients to younger leaves thereby contributing to plant fitness. However, numerous mysteries remain unraveled concerning leaf senescence. We are not still able to correlate leaf senescence and drought stress to endogenous and exogenous environments. Furthermore, we need to decipher how molecular mechanisms of the leaf senescence and levels of drought tolerance are advanced and how is the involvement of SAGs in drought tolerance and plant fitness. This review provides the perspicacity indispensable for facilitating our coordinated point of view pertaining to leaf senescence together with inferences on progression of whole plant aging. The main segments discussed in the review include coordination between hormonal signaling, leaf senescence, drought tolerance, and crosstalk between hormones in leaf senescence regulation.
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Affiliation(s)
- Sumira Jan
- ICAR- Central Institute of Temperate Horticulture, Rangreth, Air Field, Srinagar, Jammu and Kashmir, India
| | - Nazia Abbas
- Indian Institute of Integrative Medicine, Sanatnagar, Srinagar, Jammu and Kashmir, India
| | | | - Parvaiz Ahmad
- Department of Botany and Microbiology, Faculty of Science, King Saud University, Riyadh, 11451, Saudi Arabia.
- Department of Botany, S.P. College, Srinagar, Jammu and Kashmir, 190001, India.
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19
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Huang J, Guo Y, Sun Q, Zeng W, Li J, Li X, Xu W. Genome-Wide Identification of R2R3-MYB Transcription Factors Regulating Secondary Cell Wall Thickening in Cotton Fiber Development. PLANT & CELL PHYSIOLOGY 2019; 60:687-701. [PMID: 30576529 DOI: 10.1093/pcp/pcy238] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 12/14/2018] [Indexed: 05/02/2023]
Abstract
MYB proteins represent one of the largest transcription factor (TF) families in plants, some of which act as key transcriptional regulators of secondary cell wall (SCW) biosynthesis. Cotton (Gossypium hirsutum) fiber is thought to be an ideal single-cell model to study cell elongation and SCW biosynthesis. However, little knowledge regarding the TFs controlling fiber SCW biosynthesis, particularly for R2R3-MYBs is known. By far, no comprehensive genome-wide analysis of the secondary wall-associated R2R3-MYBs has been reported in cultivated tetraploid upland cotton. In this study, we identified 419 R2R3-MYB genes by systematically examining the cotton genome. A combination of phylogenetic, RNA-seq and co-expression analyses indicated that 36 R2R3-MYBs were either preferentially or highly expressed in 20 day post anthesis (dpa) fibers and are putative SCW regulators. Among these MYB genes, 22 MYBs are homologs of known SCW MYB proteins and the other 14 MYBs are novel proteins without prior reported SCW biosynthesis-related functions. Finally, we highlighted on the roles of two MYBs named GhMYB46_D13 and GhMYB46_D9, both of which displayed the highest expression in 20 dpa fibers. Expression of GhMYB46_D13 or GhMYB46_D9 individually in Arabidopsis resulted in ectopic SCW deposition in transgenic plants. Furthermore, both GhMYB46_D13 and GhMYB46_D9 were able to activate the cotton fiber SCW cellulose synthase gene promoters. Thus, we have identified 36 R2R3-MYBs as potential SCW regulators in cotton fibers that represent strong candidates for further functional studies during fiber development and SCW thickening.
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Affiliation(s)
- Junfeng Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Yanjun Guo
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Qianwen Sun
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Wei Zeng
- Sino-Australia Plant Cell Wall Research Centre, State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Juan Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Xuebao Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Wenliang Xu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
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20
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Bahari MNA, Sakeh NM, Abdullah SNA, Ramli RR, Kadkhodaei S. Transciptome profiling at early infection of Elaeis guineensis by Ganoderma boninense provides novel insights on fungal transition from biotrophic to necrotrophic phase. BMC PLANT BIOLOGY 2018; 18:377. [PMID: 30594134 PMCID: PMC6310985 DOI: 10.1186/s12870-018-1594-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 12/06/2018] [Indexed: 05/27/2023]
Abstract
BACKGROUND Basal stem rot (BSR) caused by hemibiotroph Ganoderma boninense is a devastating disease resulting in a major loss to the oil palm industry. Since there is no physical symptom in oil palm at the early stage of G. boninense infection, characterisation of molecular defense responses in oil palm during early interaction with the fungus is of the utmost importance. Oil palm (Elaeis guineensis) seedlings were artificially infected with G. boninense inoculums and root samples were obtained following a time-course of 0, 3, 7, and 11 days-post-inoculation (d.p.i) for RNA sequencing (RNA-seq) and identification of differentially expressed genes (DEGs). RESULTS The host counter-attack was evidenced based on fungal hyphae and Ganoderma DNA observed at 3 d.p.i which became significantly reduced at 7 and 11 d.p.i. DEGs revealed upregulation of multifaceted defense related genes such as PR-protein (EgPR-1), protease inhibitor (EgBGIA), PRR protein (EgLYK3) chitinase (EgCht) and expansin (EgEXPB18) at 3 d.p.i and 7 d.p.i which dropped at 11 d.p.i. Later stage involved highly expressed transcription factors EgERF113 and EgMYC2 as potential regulators of necrotrophic defense at 11 d.p.i. The reactive oxygen species (ROS) elicitor: peroxidase (EgPER) and NADPH oxidase (EgRBOH) were upregulated and maintained throughout the treatment period. Growth and nutrient distribution were probably compromised through suppression of auxin signalling and iron uptake genes. CONCLUSIONS Based on the analysis of oil palm gene expression, it was deduced that the biotrophic phase of Ganoderma had possibly occurred at the early phase (3 until 7 d.p.i) before being challenged by the fungus via switching its lifestyle into the necrotrophic phase at later stage (11 d.p.i) and finally succumbed the host. Together, the findings suggest the dynamic defense process in oil palm and potential candidates that can serve as phase-specific biomarkers at the early stages of oil palm-G. boninense interaction.
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Affiliation(s)
| | - Nurshafika Mohd Sakeh
- Institute of Plantation Studies, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor Malaysia
| | - Siti Nor Akmar Abdullah
- Institute of Plantation Studies, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor Malaysia
- Faculty of Agriculture, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor Malaysia
| | - Redzyque Ramza Ramli
- Institute of Plantation Studies, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor Malaysia
| | - Saied Kadkhodaei
- Research Institute for Biotechnology and Bioengineering, Isfahan University of Technology, Isfahan, 84156-83111 Iran
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Feng H, Li X, Chen H, Deng J, Zhang C, Liu J, Wang T, Zhang X, Dong J. GhHUB2, a ubiquitin ligase, is involved in cotton fiber development via the ubiquitin-26S proteasome pathway. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:5059-5075. [PMID: 30053051 PMCID: PMC6184758 DOI: 10.1093/jxb/ery269] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 07/12/2018] [Indexed: 05/02/2023]
Abstract
Cotton fibers, which are extremely elongated single cells of epidermal seed trichomes and have highly thickened cell walls, constitute the most important natural textile material worldwide. However, the regulation of fiber development is not well understood. Here, we report that GhHUB2, a functional homolog of AtHUB2, controls fiber elongation and secondary cell wall (SCW) deposition. GhHUB2 is ubiquitously expressed, including within fibers. Overexpression of GhHUB2 in cotton increased fiber length and SCW thickness, while RNAi knockdown of GhHUB2 resulted in shortened fibers and thinner cell walls. We found that GhHUB2 interacted with GhKNL1, a transcriptional repressor predominantly expressed in developing fibers, and that GhHUB2 ubiquitinated and degraded GhKNL1 via the ubiquitin-26S proteasome pathway. GhHUB2 negatively regulated GhKNL1 protein levels and lead to the disinhibition of genes such as GhXTH1, Gh1,3-β-G, GhCesA4, GhAGP4, GhCTL1, and GhCOBL4, thus promoting fiber elongation and enhancing SCW biosynthesis. We found that GhREV-08, a transcription factor that participates in SCW deposition and auxin signaling pathway, was a direct target of GhKNL1. In conclusion, our study uncovers a novel function of HUB2 in plants in addition to its monoubiquitination of H2B. Moreover, we provide evidence for control of the fiber development by the ubiquitin-26S proteasome pathway.
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Affiliation(s)
- Hao Feng
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xin Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Hong Chen
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jie Deng
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Chaojun Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Ji Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Tao Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xueyan Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jiangli Dong
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
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Xiao G, He P, Zhao P, Liu H, Zhang L, Pang C, Yu J. Genome-wide identification of the GhARF gene family reveals that GhARF2 and GhARF18 are involved in cotton fibre cell initiation. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:4323-4337. [PMID: 29897556 PMCID: PMC6093391 DOI: 10.1093/jxb/ery219] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 06/06/2017] [Indexed: 05/12/2023]
Abstract
Auxin signalling plays an essential role in regulating plant development. Auxin response factors (ARFs), which are critical components of auxin signalling, modulate the expression of early auxin-responsive genes by binding to auxin response factor elements (AuxREs). However, there has been no comprehensive characterization of this gene family in cotton. Here, we identified 56 GhARF genes in the assembled Gossypium hirsutum genome. This gene family was divided into 17 subfamilies, and 44 members of them were distributed across 21 chromosomes. GhARF6 and GhARF11 subfamily genes were predominantly expressed in vegetative tissues, whereas GhARF2 and GhARF18 subfamily genes were highly expressed during seed fibre cell initiation. GhARF2-1 and GhARF18-1 were exclusively expressed in trichomes, organs similar to cotton seed fibre cells, and overexpression of these genes in Arabidopsis enhances trichome initiation. Comparative transcriptome analysis combined with AuxRE prediction revealed 11 transcription factors as potential target genes of GhARF2 and GhARF18. Six of these genes were significantly expressed during seed fibre cell initiation and were bound by GhARF2-1 and GhARF18-1 in yeast one-hybrid assays. Our results suggest that GhARF2 and GhARF18 genes may be key regulators of cotton seed fibre initiation by regulating the expression of several transcription factor genes. This study deepens our understanding of auxin-mediated initiation of cotton seed fibre cells and helps us in breeding better cotton varieties in the future.
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Affiliation(s)
- Guanghui Xiao
- Key Laboratory of the Ministry of Education for Medicinal Plant Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in the Northwest of China, College of Life Sciences, Shaanxi Normal University, Xi’an, China
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
- Correspondence: , , or
| | - Peng He
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Peng Zhao
- Key Laboratory of the Ministry of Education for Medicinal Plant Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in the Northwest of China, College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Hao Liu
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Li Zhang
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Chaoyou Pang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
- Correspondence: , , or
| | - Jianing Yu
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
- Correspondence: , , or
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MacMillan CP, Birke H, Chuah A, Brill E, Tsuji Y, Ralph J, Dennis ES, Llewellyn D, Pettolino FA. Correction to: Tissue and cell-specific transcriptomes in cotton reveal the subtleties of gene regulation underlying the diversity of plant secondary cell walls. BMC Genomics 2018; 19:261. [PMID: 29665776 PMCID: PMC5902885 DOI: 10.1186/s12864-018-4634-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 03/27/2018] [Indexed: 11/25/2022] Open
Affiliation(s)
| | - Hannah Birke
- CSIRO Agriculture and Food, PO Box 1700, Canberra, ACT 2601, Australia.,Present address: Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Aaron Chuah
- John Curtin School of Medical Research, The Australian National University, ACT, Canberra, 2601, Australia
| | - Elizabeth Brill
- CSIRO Agriculture and Food, PO Box 1700, Canberra, ACT 2601, Australia
| | - Yukiko Tsuji
- Department of Biochemistry and the Department of Energy's Great Lakes BioEnergy Research Center, The Wisconsin Energy Institute, 1552 University Avenue, Madison, WI, 53726-4084, USA
| | - John Ralph
- Department of Biochemistry and the Department of Energy's Great Lakes BioEnergy Research Center, The Wisconsin Energy Institute, 1552 University Avenue, Madison, WI, 53726-4084, USA
| | | | - Danny Llewellyn
- CSIRO Agriculture and Food, PO Box 1700, Canberra, ACT 2601, Australia
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