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Wang M, Li Z, Wang H, Zhao J, Zhang Y, Lin K, Zheng S, Feng Y, Zhang Y, Teng W, Tong Y, Zhang W, Xue Y, Mao H, Li H, Zhang B, Rasheed A, Bhavani S, Liu C, Ling HQ, Hu YQ, Zhang Y. A Quantitative Computational Framework for Allopolyploid Single-Cell Data Integration and Core Gene Ranking in Development. Mol Biol Evol 2024; 41:msae178. [PMID: 39213378 PMCID: PMC11421573 DOI: 10.1093/molbev/msae178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 07/20/2024] [Accepted: 08/13/2024] [Indexed: 09/04/2024] Open
Abstract
Polyploidization drives regulatory and phenotypic innovation. How the merger of different genomes contributes to polyploid development is a fundamental issue in evolutionary developmental biology and breeding research. Clarifying this issue is challenging because of genome complexity and the difficulty in tracking stochastic subgenome divergence during development. Recent single-cell sequencing techniques enabled probing subgenome-divergent regulation in the context of cellular differentiation. However, analyzing single-cell data suffers from high error rates due to high dimensionality, noise, and sparsity, and the errors stack up in polyploid analysis due to the increased dimensionality of comparisons between subgenomes of each cell, hindering deeper mechanistic understandings. In this study, we develop a quantitative computational framework, called "pseudo-genome divergence quantification" (pgDQ), for quantifying and tracking subgenome divergence directly at the cellular level. Further comparing with cellular differentiation trajectories derived from single-cell RNA sequencing data allows for an examination of the relationship between subgenome divergence and the progression of development. pgDQ produces robust results and is insensitive to data dropout and noise, avoiding high error rates due to multiple comparisons of genes, cells, and subgenomes. A statistical diagnostic approach is proposed to identify genes that are central to subgenome divergence during development, which facilitates the integration of different data modalities, enabling the identification of factors and pathways that mediate subgenome-divergent activity during development. Case studies have demonstrated that applying pgDQ to single-cell and bulk tissue transcriptomic data promotes a systematic and deeper understanding of how dynamic subgenome divergence contributes to developmental trajectories in polyploid evolution.
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Affiliation(s)
- Meiyue Wang
- Beijing Life Science Academy, Beijing, China
- State Key Laboratory of Genetic Engineering, Department of Biochemistry, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Institute of Plant Biology, Fudan University, Shanghai 200438, China
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences\Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China
| | - Zijuan Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Haoyu Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, College of Agriculture, Henan University, Kaifeng, Henan 457004, China
| | - Junwei Zhao
- Beijing Life Science Academy, Beijing, China
| | - Yuyun Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Kande Lin
- National Key Laboratory for Crop Genetics and Germplasm Enhancement and Utilization, CIC-MCP, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Shusong Zheng
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yilong Feng
- National Key Laboratory for Crop Genetics and Germplasm Enhancement and Utilization, CIC-MCP, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yu'e Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wan Teng
- Key Lab of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yiping Tong
- Key Lab of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenli Zhang
- National Key Laboratory for Crop Genetics and Germplasm Enhancement and Utilization, CIC-MCP, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yongbiao Xue
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hude Mao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hao Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, College of Agriculture, Henan University, Kaifeng, Henan 457004, China
| | - Bo Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 81008, China
| | - Awais Rasheed
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
- International Maize and Wheat Improvement Center (CIMMYT), China Office, c/o CAAS, Beijing, 100081, China
| | - Sridhar Bhavani
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45, Carretera, México-Veracruz, El Batán, Texcoco CP 56237E do. de México, Mexico
| | - Chenghong Liu
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences\Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China
| | - Hong-Qing Ling
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- Yazhouwan National Laboratory, Sanya, Hainan 572025, China
| | - Yue-Qing Hu
- State Key Laboratory of Genetic Engineering, Department of Biochemistry, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Institute of Plant Biology, Fudan University, Shanghai 200438, China
| | - Yijing Zhang
- State Key Laboratory of Genetic Engineering, Department of Biochemistry, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Institute of Plant Biology, Fudan University, Shanghai 200438, China
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Cohen CG, Levy Y, Toscano-Rivero D, Manasherova E, Agmon-Levin N, Kenett RS, Jean-Claude BJ, Mazer BD, Hovav R, Kidon MI. Peanut allergen characterization and allergenicity throughout development. FRONTIERS IN ALLERGY 2024; 5:1395834. [PMID: 39347505 PMCID: PMC11438479 DOI: 10.3389/falgy.2024.1395834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 07/02/2024] [Indexed: 10/01/2024] Open
Abstract
Introduction Peanut allergy (PA) in children is a major concern. There is a need for better biological material for both diagnosis and oral immunotherapy (OIT) treatments. The unique state of seeds at early reproductive stages may affect the allergenicity of storage proteins, and impact clinical diagnostic and OIT protocols. The objective of this study was to evaluate the major allergen content in sequential seed developmental stages and monitor allergenicity via specific IgE binding quantification and skin prick testing. Methods Seeds were collected from peanut plants and sorted into five developmental stages: initial (S1), developing (S2), full-size without coloration (S3), full-size with coloration (S4), and fully mature (S5) seeds. Samples were characterized by RNA-Seq, ELISA, and immunohistochemistry. Lyophilized, ground preparations were used for evaluation of skin test responses in sixty challenge-proven PA children. Results Gene expression, protein content, and specific IgE binding of allergenic proteins increased throughout seed maturation and development. An expression bias towards the less allergenic A-genome copy of the major allergen Ara h 2 was found in earlier stages, especially in stage S2. Immunohistochemical staining showed that Ara h 2 is more dispersed in the cell and less accumulated within organized bodies at stage S2 versus stage S4. Significant differences were found in mean wheal responses between the commercial peanut extract (equivalent to stage S5) and stages S1 and S2, but not with stage S4, upon skin prick testing in subjects with PA. Discussion The observed decrease in peanut-specific IgE binding of immature peanut seeds may be a result not only of decreased amounts of allergenic proteins, but also of profound changes in seed composition and conformation. This may be significant for developing a safer and more effective peanut OIT protocol.
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Affiliation(s)
- Casey G. Cohen
- Department of Pediatrics and Division of Experimental Medicine, McGill University and The Research Institute of The McGill University Health Centre (RI-MUHC), Montreal, Canada
| | - Yael Levy
- Plant Sciences Institute, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Diana Toscano-Rivero
- Department of Pediatrics and Division of Experimental Medicine, McGill University and The Research Institute of The McGill University Health Centre (RI-MUHC), Montreal, Canada
| | - Ekaterina Manasherova
- Plant Sciences Institute, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Nancy Agmon-Levin
- Clinical Immunology, Angioedema and Allergy Unit, Center for Autoimmune Diseases, Sheba Medical Center, Tel Hashomer, Israel
- Safra Children's Hospital, Sheba Medical Centre, Tel Hashomer, Israel
| | | | - Bertrand J. Jean-Claude
- Department of Medicine and Division of Experimental Medicine, McGill University and Research Institute of The McGill University Health Centre (RI-MUHC), Montreal, Canada
| | - Bruce D. Mazer
- Department of Pediatrics and Division of Experimental Medicine, McGill University and The Research Institute of The McGill University Health Centre (RI-MUHC), Montreal, Canada
| | - Ran Hovav
- Plant Sciences Institute, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Mona I. Kidon
- Clinical Immunology, Angioedema and Allergy Unit, Center for Autoimmune Diseases, Sheba Medical Center, Tel Hashomer, Israel
- Safra Children's Hospital, Sheba Medical Centre, Tel Hashomer, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
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Liu X, Wang T, Ruan Y, Xie X, Tan C, Guo Y, Li B, Qu L, Deng L, Li M, Liu C. Comparative Metabolome and Transcriptome Analysis of Rapeseed ( Brassica napus L.) Cotyledons in Response to Cold Stress. PLANTS (BASEL, SWITZERLAND) 2024; 13:2212. [PMID: 39204648 PMCID: PMC11360269 DOI: 10.3390/plants13162212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Revised: 08/01/2024] [Accepted: 08/06/2024] [Indexed: 09/04/2024]
Abstract
Cold stress affects the seed germination and early growth of winter rapeseed, leading to yield losses. We employed transmission electron microscopy, physiological analyses, metabolome profiling, and transcriptome sequencing to understand the effect of cold stress (0 °C, LW) on the cotyledons of cold-tolerant (GX74) and -sensitive (XY15) rapeseeds. The mesophyll cells in cold-treated XY15 were severely damaged compared to slightly damaged cells in GX74. The fructose, glucose, malondialdehyde, and proline contents increased after cold stress in both genotypes; however, GX74 had significantly higher content than XY15. The pyruvic acid content increased after cold stress in GX74, but decreased in XY15. Metabolome analysis detected 590 compounds, of which 32 and 74 were differentially accumulated in GX74 (CK vs. cold stress) and XY15 (CK vs. cold stressed). Arachidonic acid and magnoflorine were the most up-accumulated metabolites in GX74 subjected to cold stress compared to CK. There were 461 and 1481 differentially expressed genes (DEGs) specific to XY15 and GX74 rapeseeds, respectively. Generally, the commonly expressed genes had higher expressions in GX74 compared to XY15 in CK and cold stress conditions. The expression changes in DEGs related to photosynthesis-antenna proteins, chlorophyll biosynthesis, and sugar biosynthesis-related pathways were consistent with the fructose and glucose levels in cotyledons. Compared to XY15, GX74 showed upregulation of a higher number of genes/transcripts related to arachidonic acid, pyruvic acid, arginine and proline biosynthesis, cell wall changes, reactive oxygen species scavenging, cold-responsive pathways, and phytohormone-related pathways. Taken together, our results provide a detailed overview of the cold stress responses in rapeseed cotyledons.
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Affiliation(s)
- Xinhong Liu
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China; (X.L.); (Y.G.)
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha 410128, China; (Y.R.); (X.X.); (C.T.)
- Yuelushan Laboratory, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Tonghua Wang
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China; (X.L.); (Y.G.)
- Yuelushan Laboratory, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Ying Ruan
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha 410128, China; (Y.R.); (X.X.); (C.T.)
| | - Xiang Xie
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha 410128, China; (Y.R.); (X.X.); (C.T.)
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Chengfang Tan
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha 410128, China; (Y.R.); (X.X.); (C.T.)
| | - Yiming Guo
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China; (X.L.); (Y.G.)
- Yuelushan Laboratory, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Bao Li
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China; (X.L.); (Y.G.)
- Yuelushan Laboratory, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Liang Qu
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China; (X.L.); (Y.G.)
- Yuelushan Laboratory, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Lichao Deng
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China; (X.L.); (Y.G.)
- Yuelushan Laboratory, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Mei Li
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China; (X.L.); (Y.G.)
- Yuelushan Laboratory, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Chunlin Liu
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha 410128, China; (Y.R.); (X.X.); (C.T.)
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
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Han B, Chang Y, Tan RR, Han C. Evaluating deep learning techniques for identifying tongue features in subthreshold depression: a prospective observational study. Front Psychiatry 2024; 15:1361177. [PMID: 39176227 PMCID: PMC11338782 DOI: 10.3389/fpsyt.2024.1361177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 07/15/2024] [Indexed: 08/24/2024] Open
Abstract
Objective This study aims to evaluate the potential of using tongue image features as non-invasive biomarkers for diagnosing subthreshold depression and to assess the correlation between these features and acupuncture treatment outcomes using advanced deep learning models. Methods We employed five advanced deep learning models-DenseNet169, MobileNetV3Small, SEResNet101, SqueezeNet, and VGG19_bn-to analyze tongue image features in individuals with subthreshold depression. These models were assessed based on accuracy, precision, recall, and F1 score. Additionally, we investigated the relationship between the best-performing model's predictions and the success of acupuncture treatment using Pearson's correlation coefficient. Results Among the models, SEResNet101 emerged as the most effective, achieving an impressive 98.5% accuracy and an F1 score of 0.97. A significant positive correlation was found between its predictions and the alleviation of depressive symptoms following acupuncture (Pearson's correlation coefficient = 0.72, p<0.001). Conclusion The findings suggest that the SEResNet101 model is highly accurate and reliable for identifying tongue image features in subthreshold depression. It also appears promising for assessing the impact of acupuncture treatment. This study contributes novel insights and approaches to the auxiliary diagnosis and treatment evaluation of subthreshold depression.
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Affiliation(s)
- Bo Han
- Department of Rehabilitation, Daqing Longnan Hospital, Daqing, China
| | - Yue Chang
- Department of Pharmacy, Baoan Central Hospital of Shenzhen, Shenzhen, China
| | - Rui-rui Tan
- Changchun University of Chinese Medicine, Changchun, China
| | - Chao Han
- Department of Acupuncture, Shenzhen Bao’an Authentic Traditional Chinese Medicine (TCM) Therapy Hospital, Shenzhen, China
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Aufiero G, Fruggiero C, D’Angelo D, D’Agostino N. Homoeologs in Allopolyploids: Navigating Redundancy as Both an Evolutionary Opportunity and a Technical Challenge-A Transcriptomics Perspective. Genes (Basel) 2024; 15:977. [PMID: 39202338 PMCID: PMC11353593 DOI: 10.3390/genes15080977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 07/22/2024] [Accepted: 07/23/2024] [Indexed: 09/03/2024] Open
Abstract
Allopolyploidy in plants involves the merging of two or more distinct parental genomes into a single nucleus, a significant evolutionary process in the plant kingdom. Transcriptomic analysis provides invaluable insights into allopolyploid plants by elucidating the fate of duplicated genes, revealing evolutionary novelties and uncovering their environmental adaptations. By examining gene expression profiles, scientists can discern how duplicated genes have evolved to acquire new functions or regulatory roles. This process often leads to the development of novel traits and adaptive strategies that allopolyploid plants leverage to thrive in diverse ecological niches. Understanding these molecular mechanisms not only enhances our appreciation of the genetic complexity underlying allopolyploidy but also underscores their importance in agriculture and ecosystem resilience. However, transcriptome profiling is challenging due to genomic redundancy, which is further complicated by the presence of multiple chromosomes sets and the variations among homoeologs and allelic genes. Prior to transcriptome analysis, sub-genome phasing and homoeology inference are essential for obtaining a comprehensive view of gene expression. This review aims to clarify the terminology in this field, identify the most challenging aspects of transcriptome analysis, explain their inherent difficulties, and suggest reliable analytic strategies. Furthermore, bulk RNA-seq is highlighted as a primary method for studying allopolyploid gene expression, focusing on critical steps like read mapping and normalization in differential gene expression analysis. This approach effectively captures gene expression from both parental genomes, facilitating a comprehensive analysis of their combined profiles. Its sensitivity in detecting low-abundance transcripts allows for subtle differences between parental genomes to be identified, crucial for understanding regulatory dynamics and gene expression balance in allopolyploids.
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Affiliation(s)
| | | | | | - Nunzio D’Agostino
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy; (G.A.); (C.F.); (D.D.)
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You J, Liu Z, Qi Z, Ma Y, Sun M, Su L, Niu H, Peng Y, Luo X, Zhu M, Huang Y, Chang X, Hu X, Zhang Y, Pi R, Liu Y, Meng Q, Li J, Zhang Q, Zhu L, Lin Z, Min L, Yuan D, Grover CE, Fang DD, Lindsey K, Wendel JF, Tu L, Zhang X, Wang M. Regulatory controls of duplicated gene expression during fiber development in allotetraploid cotton. Nat Genet 2023; 55:1987-1997. [PMID: 37845354 PMCID: PMC10632151 DOI: 10.1038/s41588-023-01530-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 09/14/2023] [Indexed: 10/18/2023]
Abstract
Polyploidy complicates transcriptional regulation and increases phenotypic diversity in organisms. The dynamics of genetic regulation of gene expression between coresident subgenomes in polyploids remains to be understood. Here we document the genetic regulation of fiber development in allotetraploid cotton Gossypium hirsutum by sequencing 376 genomes and 2,215 time-series transcriptomes. We characterize 1,258 genes comprising 36 genetic modules that control staged fiber development and uncover genetic components governing their partitioned expression relative to subgenomic duplicated genes (homoeologs). Only about 30% of fiber quality-related homoeologs show phenotypically favorable allele aggregation in cultivars, highlighting the potential for subgenome additivity in fiber improvement. We envision a genome-enabled breeding strategy, with particular attention to 48 favorable alleles related to fiber phenotypes that have been subjected to purifying selection during domestication. Our work delineates the dynamics of gene regulation during fiber development and highlights the potential of subgenomic coordination underpinning phenotypes in polyploid plants.
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Affiliation(s)
- Jiaqi You
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Zhenping Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Zhengyang Qi
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yizan Ma
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Mengling Sun
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Ling Su
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Hao Niu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yabing Peng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xuanxuan Luo
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Mengmeng Zhu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yuefan Huang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xing Chang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xiubao Hu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yuqi Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Ruizhen Pi
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yuqi Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Qingying Meng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Jianying Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Qinghua Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Longfu Zhu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Ling Min
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Daojun Yuan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Corrinne E Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - David D Fang
- Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA, USA
| | - Keith Lindsey
- Department of Biosciences, Durham University, Durham, UK
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Lili Tu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
| | - Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
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Sun J, Okada M, Tameshige T, Shimizu-Inatsugi R, Akiyama R, Nagano A, Sese J, Shimizu K. A low-coverage 3' RNA-seq to detect homeolog expression in polyploid wheat. NAR Genom Bioinform 2023; 5:lqad067. [PMID: 37448590 PMCID: PMC10336777 DOI: 10.1093/nargab/lqad067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 06/12/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
Although allopolyploid species are common among natural and crop species, it is not easy to distinguish duplicated genes, known as homeologs, during their genomic analysis. Yet, cost-efficient RNA sequencing (RNA-seq) is to be developed for large-scale transcriptomic studies such as time-series analysis and genome-wide association studies in allopolyploids. In this study, we employed a 3' RNA-seq utilizing 3' untranslated regions (UTRs) containing frequent mutations among homeologous genes, compared to coding sequence. Among the 3' RNA-seq protocols, we examined a low-cost method Lasy-Seq using an allohexaploid bread wheat, Triticum aestivum. HISAT2 showed the best performance for 3' RNA-seq with the least mapping errors and quick computational time. The number of detected homeologs was further improved by extending 1 kb of the 3' UTR annotation. Differentially expressed genes in response to mild cold treatment detected by the 3' RNA-seq were verified with high-coverage conventional RNA-seq, although the latter detected more differentially expressed genes. Finally, downsampling showed that even a 2 million sequencing depth can still detect more than half of expressed homeologs identifiable by the conventional 32 million reads. These data demonstrate that this low-cost 3' RNA-seq facilitates large-scale transcriptomic studies of allohexaploid wheat and indicate the potential application to other allopolyploid species.
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Affiliation(s)
- Jianqiang Sun
- Research Center for Agricultural Information Technology, National Agriculture and Food Research Organization, 3-1-1 Kannondai, Tsukuba, Ibaraki 305-8517, Japan
| | - Moeko Okada
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, Totsuka-ward, Yokohama, Kanagawa 244-0813, Japan
| | - Toshiaki Tameshige
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, Totsuka-ward, Yokohama, Kanagawa 244-0813, Japan
- Division of Biological Sciences, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Reiko Akiyama
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Yokotani 1-5, Seta Ohe-cho, Otsu, Shiga 520-2194, Japan
- Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Daihouji, Tsuruoka, Yamagata 997-0017, Japan
| | - Jun Sese
- Humanome Lab, Inc., 2-4-10, Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
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Benson CW, Sheltra MR, Maughan PJ, Jellen EN, Robbins MD, Bushman BS, Patterson EL, Hall ND, Huff DR. Homoeologous evolution of the allotetraploid genome of Poa annua L. BMC Genomics 2023; 24:350. [PMID: 37365554 DOI: 10.1186/s12864-023-09456-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 06/15/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND Poa annua (annual bluegrass) is an allotetraploid turfgrass, an agronomically significant weed, and one of the most widely dispersed plant species on earth. Here, we report the chromosome-scale genome assemblies of P. annua's diploid progenitors, P. infirma and P. supina, and use multi-omic analyses spanning all three species to better understand P. annua's evolutionary novelty. RESULTS We find that the diploids diverged from their common ancestor 5.5 - 6.3 million years ago and hybridized to form P. annua ≤ 50,000 years ago. The diploid genomes are similar in chromosome structure and most notably distinguished by the divergent evolutionary histories of their transposable elements, leading to a 1.7 × difference in genome size. In allotetraploid P. annua, we find biased movement of retrotransposons from the larger (A) subgenome to the smaller (B) subgenome. We show that P. annua's B subgenome is preferentially accumulating genes and that its genes are more highly expressed. Whole-genome resequencing of several additional P. annua accessions revealed large-scale chromosomal rearrangements characterized by extensive TE-downsizing and evidence to support the Genome Balance Hypothesis. CONCLUSIONS The divergent evolutions of the diploid progenitors played a central role in conferring onto P. annua its remarkable phenotypic plasticity. We find that plant genes (guided by selection and drift) and transposable elements (mostly guided by host immunity) each respond to polyploidy in unique ways and that P. annua uses whole-genome duplication to purge highly parasitized heterochromatic sequences. The findings and genomic resources presented here will enable the development of homoeolog-specific markers for accelerated weed science and turfgrass breeding.
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Affiliation(s)
- Christopher W Benson
- Department of Plant Science, Pennsylvania State University, University Park, PA, USA.
- Intercollegiate Graduate Degree Program in Plant Biology, Pennsylvania State University, University Park, PA, USA.
| | - Matthew R Sheltra
- Department of Plant Science, Pennsylvania State University, University Park, PA, USA
- Intercollegiate Graduate Degree Program in Plant Biology, Pennsylvania State University, University Park, PA, USA
| | - Peter J Maughan
- Department of Plant and Wildlife Sciences, Brigham Young University, Logan, UT, USA
| | - Eric N Jellen
- Department of Plant and Wildlife Sciences, Brigham Young University, Logan, UT, USA
| | | | | | - Eric L Patterson
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Nathan D Hall
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - David R Huff
- Department of Plant Science, Pennsylvania State University, University Park, PA, USA.
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He L, He W, Luo J, Xu M. Upregulated ENC1 predicts unfavorable prognosis and correlates with immune infiltration in endometrial cancer. Front Cell Dev Biol 2022; 10:919637. [PMID: 36531950 PMCID: PMC9751423 DOI: 10.3389/fcell.2022.919637] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 11/17/2022] [Indexed: 07/30/2023] Open
Abstract
A better knowledge of the molecular process behind uterine corpus endometrial carcinoma (UCEC) is important for prognosis prediction and the development of innovative targeted gene therapies. The purpose of this research is to discover critical genes associated with UCEC. We analyzed the gene expression profiles of TCGA-UCEC and GSE17025, respectively, using Weighted Gene Co-expression Network Analysis (WGCNA) and differential gene expression analysis. From four sets of findings, a total of 95 overlapping genes were retrieved. On the 95 overlapping genes, KEGG pathway and GO enrichment analysis were conducted. Then, we mapped the PPI network of 95 overlapping genes using the STRING database. Twenty hub genes were evaluated using the Cytohubba plugin, including NR3C1, ATF3, KLF15, THRA, NR4A1, FOSB, PER3, HLF, NTRK3, EGR3, MAPK13, ARNTL2, PKM2, SCD, EIF5A, ADHFE1, RERGL, TUB, and ENC1. The expression levels of NR3C1, PKM2, and ENC1 were shown to be adversely linked with the survival time of UCEC patients using univariate Cox regression analysis and Kaplan-Meier survival calculation. ENC1 were also overexpressed in UCEC tumor tissues or cell lines, as shown by quantitative real-time PCR and Western blotting. Then we looked into it further and discovered that ENC1 expression was linked to tumor microenvironment and predicted various immunological checkpoints. In conclusion, our data indicate that ENC1 may be required for the development of UCEC and may serve as a future biomarker for diagnosis and therapy.
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Affiliation(s)
- Lingling He
- Department of Obstetrics and Gynecology, Ganzhou People's Hospital, Ganzhou, China
- Department of Obstetrics and Gynecology, Ganzhou Hospital-Nanfang Hospital, Southern Medical University, Ganzhou, China
- Department of Obstetrics and Gynecology, The Affiliated Ganzhou Hospital of Nanchang University, Ganzhou, China
| | - Wenjing He
- Department of Endocrinology, Baoji Gaoxin Hospital, Baoji, China
| | - Ji Luo
- Department of Obstetrics and Gynecology, Ganzhou People's Hospital, Ganzhou, China
- Department of Obstetrics and Gynecology, Ganzhou Hospital-Nanfang Hospital, Southern Medical University, Ganzhou, China
- Department of Obstetrics and Gynecology, The Affiliated Ganzhou Hospital of Nanchang University, Ganzhou, China
| | - Minjuan Xu
- Department of Obstetrics and Gynecology, Ganzhou People's Hospital, Ganzhou, China
- Department of Obstetrics and Gynecology, Ganzhou Hospital-Nanfang Hospital, Southern Medical University, Ganzhou, China
- Department of Obstetrics and Gynecology, The Affiliated Ganzhou Hospital of Nanchang University, Ganzhou, China
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Coexpression Network Analysis-Based Identification of Critical Genes Differentiating between Latent and Active Tuberculosis. DISEASE MARKERS 2022; 2022:2090560. [PMID: 36411825 PMCID: PMC9674975 DOI: 10.1155/2022/2090560] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 10/25/2022] [Indexed: 11/13/2022]
Abstract
Methods Three Gene Expression Omnibus (GEO) microarray datasets (GSE19491, GSE98461, and GSE152532) were downloaded, with GSE19491 and GSE98461 then being merged to form a training dataset. Hub genes capable of differentiating between ATB and LTBI were then identified through differential expression analyses and a WGCNA analysis of this training dataset. Receiver operating characteristic (ROC) curves were then used to gauge to the diagnostic accuracy of these hub genes in the test dataset (GSE152532). Gene expression-based immune cell infiltration and the relationship between such infiltration and hub gene expression were further assessed via a single-sample gene set enrichment analysis (ssGSEA). Results In total, 485 differentially expressed genes were analyzed, with the WGCNA approach yielding 8 coexpression models. Of these, the black module was the most closely correlated with ATB. In total, five hub genes (FBXO6, ATF3, GBP1, GBP4, and GBP5) were identified as potential biomarkers associated with LTBI progression to ATB based on a combination of differential expression and LASSO analyses. The area under the ROC curve values for these five genes ranged from 0.8 to 0.9 in the test dataset, and ssGSEA revealed the expression of these genes to be negatively correlated with lymphocyte activity but positively correlated with myeloid and inflammatory cell activity. Conclusion The five hub genes identified in this study may play a novel role in tuberculosis-related immunopathology and offer value as novel biomarkers differentiating LTBI from ATB.
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11
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Zhang K, Li J, Li G, Zhao Y, Dong Y, Zhang Y, Sun W, Wang J, Yao J, Ma Y, Wang H, Zhang Z, Wang T, Xie K, Wendel JF, Liu B, Gong L. Compensatory Genetic and Transcriptional Cytonuclear Coordination in Allopolyploid Lager Yeast (Saccharomyces pastorianus). Mol Biol Evol 2022; 39:msac228. [PMID: 36260528 PMCID: PMC9665066 DOI: 10.1093/molbev/msac228] [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] [Indexed: 12/04/2022] Open
Abstract
Cytonuclear coordination between biparental-nuclear genomes and uniparental-cytoplasmic organellar genomes in plants is often resolved by genetic and transcriptional cytonuclear responses. Whether this mechanism also acts in allopolyploid members of other kingdoms is not clear. Additionally, cytonuclear coordination of interleaved allopolyploid cells/individuals within the same population is underexplored. The yeast Saccharomyces pastorianus provides the opportunity to explore cytonuclear coevolution during different growth stages and from novel dimensions. Using S. pastorianus cells from multiple growth stages in the same environment, we show that nuclear mitochondria-targeted genes have undergone both asymmetric gene conversion and growth stage-specific biased expression favoring genes from the mitochondrial genome donor (Saccharomyces eubayanus). Our results suggest that cytonuclear coordination in allopolyploid lager yeast species entails an orchestrated and compensatory genetic and transcriptional evolutionary regulatory shift. The common as well as unique properties of cytonuclear coordination underlying allopolyploidy between unicellular yeasts and higher plants offers novel insights into mechanisms of cytonuclear evolution associated with allopolyploid speciation.
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Affiliation(s)
- Keren Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin 130024, China
| | - Juzuo Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin 130024, China
| | - Guo Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin 130024, China
| | - Yue Zhao
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin 130024, China
| | - Yuefan Dong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin 130024, China
| | - Ying Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin 130024, China
| | - Wenqing Sun
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin 130024, China
| | - Junsheng Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin 130024, China
| | - Jinyang Yao
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin 130024, China
| | - Yiqiao Ma
- Jilin Academy of Vegetable and Flower Science, Changchun, Jilin 130033, China
| | - Hongyan Wang
- Laboratory of Plant Epigenetics and Evolution, School of Life Science, Liaoning University, Shenyang, Liaoning 110036, China
| | - Zhibin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin 130024, China
| | - Tianya Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin 130024, China
| | - Kun Xie
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin 130024, China
| | - Jonathan F Wendel
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50010, USA
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin 130024, China
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin 130024, China
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Chen L, Hua J, He X. Co-expression network analysis identifies potential candidate hub genes in severe influenza patients needing invasive mechanical ventilation. BMC Genomics 2022; 23:703. [PMID: 36243706 PMCID: PMC9569050 DOI: 10.1186/s12864-022-08915-9] [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: 06/21/2022] [Accepted: 09/26/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Influenza is a contagious disease that affects people of all ages and is linked to considerable mortality during epidemics and occasional outbreaks. Moreover, effective immunological biomarkers are needed for elucidating aetiology and preventing and treating severe influenza. Herein, we aimed to evaluate the key genes linked with the disease severity in influenza patients needing invasive mechanical ventilation (IMV). Three gene microarray data sets (GSE101702, GSE21802, and GSE111368) from blood samples of influenza patients were made available by the Gene Expression Omnibus (GEO) database. The GSE101702 and GSE21802 data sets were combined to create the training set. Hub indicators for IMV patients with severe influenza were determined using differential expression analysis and Weighted correlation network analysis (WGCNA) from the training set. The receiver operating characteristic curve (ROC) was also used to evaluate the hub genes from the test set's diagnostic accuracy. Different immune cells' infiltration levels in the expression profile and their correlation with hub gene markers were examined using single-sample gene set enrichment analysis (ssGSEA). RESULTS In the present study, we evaluated a total of 447 differential genes. WGCNA identified eight co-expression modules, with the red module having the strongest correlation with IMV patients. Differential genes were combined to obtain 3 hub genes (HLA-DPA1, HLA-DRB3, and CECR1). The identified genes were investigated as potential indicators for patients with severe influenza who required IMV using the least absolute shrinkage and selection operator (LASSO) approach. The ROC showed the diagnostic value of the three hub genes in determining the severity of influenza. Using ssGSEA, it has been revealed that the expression of key genes was negatively correlated with neutrophil activation and positively associated with adaptive cellular immune response. CONCLUSION We evaluated three novel hub genes that could be linked to the immunopathological mechanism of severe influenza patients who require IMV treatment and could be used as potential biomarkers for severe influenza prevention and treatment.
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Affiliation(s)
- Liang Chen
- Department of Infectious Diseases, Nanjing Lishui People's Hospital, Zhongda Hospital Lishui Branch, Southeast University, Nanjing, China
| | - Jie Hua
- Department of Gastroenterology, Liyang People's Hospital, Liyang Branch Hospital of Jiangsu Province Hospital, Nanjing, China
| | - Xiaopu He
- Department of Geriatric Gastroenterology, The First Affiliated Hospital With Nanjing Medical University, No.300 Guangzhou Road, Nanjing city, 210029, Jiangsu Province, China.
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Akagi T, Jung K, Masuda K, Shimizu KK. Polyploidy before and after domestication of crop species. CURRENT OPINION IN PLANT BIOLOGY 2022; 69:102255. [PMID: 35870416 DOI: 10.1016/j.pbi.2022.102255] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/01/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
Recent advances in the genomics of polyploid species answer some of the long-standing questions about the role of polyploidy in crop species. Here, we summarize the current literature to reexamine scenarios in which polyploidy played a role both before and after domestication. The prevalence of polyploidy can help to explain environmental robustness in agroecosystems. This review also clarifies the molecular basis of some agriculturally advantageous traits of polyploid crops, including yield increments in polyploid cotton via subfunctionalization, modification of a separated sexuality to selfing in polyploid persimmon via neofunctionalization, and transition to a selfing system via nonfunctionalization combined with epistatic interaction between duplicated S-loci. The rapid progress in genomics and genetics is discussed along with how this will facilitate functional studies of understudied polyploid crop species.
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Affiliation(s)
- Takashi Akagi
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan.
| | - Katharina Jung
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zürich, Switzerland
| | - Kanae Masuda
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zürich, Switzerland; Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, 244-0813 Totsuka-ward, Yokohama, Japan.
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14
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Shimizu KK. Robustness and the generalist niche of polyploid species: Genome shock or gradual evolution? CURRENT OPINION IN PLANT BIOLOGY 2022; 69:102292. [PMID: 36063635 DOI: 10.1016/j.pbi.2022.102292] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 07/01/2022] [Accepted: 07/27/2022] [Indexed: 05/26/2023]
Abstract
The prevalence of polyploidy in wild and crop species has stimulated debate over its evolutionary advantages and disadvantages. Previous studies have focused on changes occurring at the polyploidization events, including genome-wide changes termed "genome shock," as well as ancient polyploidy. Recent bioinformatics advances and empirical studies of Arabidopsis and wheat relatives are filling a research gap: the functional evolutionary study of polyploid species using RNA-seq, DNA polymorphism, and epigenomics. Polyploid species can become generalists in natura through environmental robustness by inheriting and merging parental stress responses. Their evolvability is enhanced by mutational robustness working on inherited standing variation. The identification of key genes responsible for gradual adaptive evolution will encourage synthetic biological approaches to transfer polyploid advantages to other species.
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Affiliation(s)
- Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zürich, Switzerland; Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, 244-0813 Totsuka-ward, Yokohama, Japan.
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Perez LM, Mauleon R, Arick MA, Magbanua ZV, Peterson DG, Dean JFD, Tseng TM. Transcriptome analysis of the 2,4-dichlorophenoxyacetic acid (2,4-D)-tolerant cotton chromosome substitution line CS-B15sh and its susceptible parental lines G. hirsutum L. cv. Texas Marker-1 and G. barbadense L. cv. Pima 379. FRONTIERS IN PLANT SCIENCE 2022; 13:910369. [PMID: 36072333 PMCID: PMC9441920 DOI: 10.3389/fpls.2022.910369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
The cotton chromosome substitution line, CS-B15sh, exhibits 41% lower injury from 2,4-D when applied at the field recommended rate of 1.12 kg ae ha-1 (1×) than does Texas Marker-1 (TM-1). CS-B15sh was developed in the genetic background of Gossypium hirsutum L. cv TM-1 and has chromosome introgression on the short arm of chromosome 15 from Gossypium barbadense L. cv. Pima 379. In a previous experiment, we observed reduced translocation of [14C]2,4-D outside the treated leaf tissue in CS-B15sh, which contrasted with an increased translocation of the herbicide in the tissues above and below the treated leaf in TM-1. Our results indicate a potential 2,4-D tolerance mechanism in CS-B15sh involving altered movement of 2,4-D. Here, we used RNA sequencing (RNA-seq) to determine the differential expression of genes between 2,4-D-challenged and control plants of the tolerant (CS-B15sh) and susceptible lines (TM-1 and Pima 379). Several components of the 2,4-D/auxin-response pathway-including ubiquitin E3 ligase, PB1|AUX/IAA, ARF transcription factors, and F-box proteins of the SCFTIR1/AFB complex-were upregulated with at least threefold higher expression in TM-1 compared with CS-B15sh, while both Pima 379 and TM-1 showed the same fold change expression for PB1|AUX/IAA mRNA. Some genes associated with herbicide metabolism, including flavin monooxygenase (Gohir.A01G174100) and FAD-linked oxidase (Gohir.D06G002600), exhibited at least a twofold increase in CS-B15sh than in TM-1 (the gene was not expressed in Pima 379), suggesting a potential relationship between the gene's expression and 2,4-D tolerance. It is interesting to note that glutathione S-transferase was differentially expressed in both CS-B15sh and Pima 379 but not in TM-1, while cytochrome P450 and other genes involved in the oxidation-reduction process were significantly expressed only in CS-B15sh in response to 2,4-D. Gene set enrichment analysis on the union DEGs of the three cotton genotypes revealed the depletion of transcripts involved in photosynthesis and enrichment of transcripts involved in ABA response and signaling.
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Affiliation(s)
- Loida M. Perez
- Department of Biochemistry, Molecular Biology, Entomology & Plant Pathology, Mississippi State University, Starkville, MS, United States
| | - Ramil Mauleon
- Faculty of Science and Engineering, Southern Cross University, East Lismore, NSW, Australia
| | - Mark A. Arick
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, MS, United States
| | - Zenaida V. Magbanua
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, MS, United States
| | - Daniel G. Peterson
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, MS, United States
| | - Jeffrey F. D. Dean
- Department of Biochemistry, Molecular Biology, Entomology & Plant Pathology, Mississippi State University, Starkville, MS, United States
| | - Te Ming Tseng
- Department of Plant and Soil Sciences, Mississippi State University, Starkville, MS, United States
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Chen L, Shen E, Zhao Y, Wang H, Wilson I, Zhu QH. The Conservation of Long Intergenic Non-Coding RNAs and Their Response to Verticillium dahliae Infection in Cotton. Int J Mol Sci 2022; 23:ijms23158594. [PMID: 35955726 PMCID: PMC9368808 DOI: 10.3390/ijms23158594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 07/28/2022] [Accepted: 07/30/2022] [Indexed: 02/04/2023] Open
Abstract
Long intergenic non-coding RNAs (lincRNAs) have been demonstrated to be vital regulators of diverse biological processes in both animals and plants. While many lincRNAs have been identified in cotton, we still know little about the repositories and conservativeness of lincRNAs in different cotton species or about their role in responding to biotic stresses. Here, by using publicly available RNA-seq datasets from diverse sources, including experiments of Verticillium dahliae (Vd) infection, we identified 24,425 and 17,713 lincRNAs, respectively, in Gossypium hirsutum (Ghr) and G. barbadense (Gba), the two cultivated allotetraploid cotton species, and 6933 and 5911 lincRNAs, respectively, in G. arboreum (Gar) and G. raimondii (Gra), the two extant diploid progenitors of the allotetraploid cotton. While closely related subgenomes, such as Ghr_At and Gba_At, tend to have more conserved lincRNAs, most lincRNAs are species-specific. The majority of the synthetic and transcribed lincRNAs (78.2%) have a one-to-one orthologous relationship between different (sub)genomes, although a few of them (0.7%) are retained in all (sub)genomes of the four species. The Vd responsiveness of lincRNAs seems to be positively associated with their conservation level. The major functionalities of the Vd-responsive lincRNAs seem to be largely conserved amongst Gra, Ghr, and Gba. Many Vd-responsive Ghr-lincRNAs overlap with Vd-responsive QTL, and several lincRNAs were predicted to be endogenous target mimicries of miR482/2118, with a pair being highly conserved between Ghr and Gba. On top of the confirmation of the feature characteristics of the lincRNAs previously reported in cotton and other species, our study provided new insights into the conservativeness and divergence of lincRNAs during cotton evolution and into the relationship between the conservativeness and Vd responsiveness of lincRNAs. The study also identified candidate lincRNAs with a potential role in disease response for functional characterization.
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Affiliation(s)
- Li Chen
- School of Life Sciences, Westlake University, Hangzhou 310024, China;
| | - Enhui Shen
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China;
| | - Yunlei Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (Y.Z.); (H.W.)
| | - Hongmei Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (Y.Z.); (H.W.)
| | - Iain Wilson
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia;
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia;
- Correspondence:
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17
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Dong Y, Hu G, Grover CE, Miller ER, Zhu S, Wendel JF. Parental legacy versus regulatory innovation in salt stress responsiveness of allopolyploid cotton (Gossypium) species. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:872-887. [PMID: 35686631 PMCID: PMC9540634 DOI: 10.1111/tpj.15863] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
Polyploidy provides an opportunity for evolutionary innovation and species diversification, especially under stressful conditions. In allopolyploids, the conditional dynamics of homoeologous gene expression can be either inherited from ancestral states pre-existing in the parental diploids or novel upon polyploidization, the latter potentially permitting a wider range of phenotypic responses to stresses. To gain insight into regulatory mechanisms underlying the diversity of salt resistance in Gossypium species, we compared global transcriptomic responses to modest salinity stress in two allotetraploid (AD-genome) cotton species, Gossypium hirsutum and G. mustelinum, relative to their model diploid progenitors (A-genome and D-genome). Multivariate and pairwise analyses of salt-responsive changes revealed a profound alteration of gene expression for about one third of the transcriptome. Transcriptional responses and associated functional implications of salt acclimation varied across species, as did species-specific coexpression modules among species and ploidy levels. Salt responsiveness in both allopolyploids was strongly biased toward the D-genome progenitor. A much lower level of transgressive downregulation was observed in the more salt-tolerant G. mustelinum than in the less tolerant G. hirsutum. By disentangling inherited effects from evolved responses, we show that expression biases that are not conditional upon salt stress approximately equally reflect parental legacy and regulatory novelty upon allopolyploidization, whereas stress-responsive biases are predominantly novel, or evolved, in allopolyploids. Overall, our work suggests that allopolyploid cottons acquired a wide range of stress response flexibility relative to their diploid ancestors, most likely mediated by complex suites of duplicated genes and regulatory factors.
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Affiliation(s)
- Yating Dong
- Department of AgronomyZhejiang UniversityHangzhouZhejiang310 053China
- Department of Ecology, Evolution, and Organismal Biology (EEOB), Bessey HallIowa State UniversityAmesIA50011USA
| | - Guanjing Hu
- State Key Laboratory of Cotton BiologyInstitute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang455 000China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhen518 120China
| | - Corrinne E. Grover
- Department of Ecology, Evolution, and Organismal Biology (EEOB), Bessey HallIowa State UniversityAmesIA50011USA
| | - Emma R. Miller
- Department of Ecology, Evolution, and Organismal Biology (EEOB), Bessey HallIowa State UniversityAmesIA50011USA
| | - Shuijin Zhu
- Department of AgronomyZhejiang UniversityHangzhouZhejiang310 053China
| | - Jonathan F. Wendel
- Department of Ecology, Evolution, and Organismal Biology (EEOB), Bessey HallIowa State UniversityAmesIA50011USA
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Behling AH, Winter DJ, Ganley ARD, Cox MP. Cross-kingdom transcriptomic trends in the evolution of hybrid gene expression. J Evol Biol 2022; 35:1126-1137. [PMID: 35830478 PMCID: PMC9546207 DOI: 10.1111/jeb.14059] [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: 11/11/2021] [Accepted: 06/13/2022] [Indexed: 11/29/2022]
Abstract
Hybridization is a route to speciation that occurs widely across the eukaryote tree of life. The success of allopolyploids (hybrid species with increased ploidy) and homoploid hybrids (with unchanged ploidy) is well documented. However, their formation and establishment is not straightforward, with a suite of near‐instantaneous and longer term biological repercussions faced by the new species. Central to these challenges is the rewiring of gene regulatory networks following the merger of distinct genomes inherited from both parental species. Research on the evolution of hybrid gene expression has largely involved studies on a single hybrid species or a few gene families. Here, we present the first standardized transcriptome‐wide study exploring the fates of genes following hybridization across three kingdoms: animals, plants and fungi. Within each kingdom, we pair an allopolyploid system with a closely related homoploid hybrid to decouple the influence of increased ploidy from genome merger. Genome merger, not changes in ploidy, has the greatest effect on posthybridization expression patterns across all study systems. Strikingly, we find that differentially expressed genes in parent species preferentially switch to more similar expression in hybrids across all kingdoms, likely as a consequence of regulatory trans‐acting cross‐talk within the hybrid nucleus. We also highlight the prevalence of gene loss or silencing among extremely differentially expressed genes in hybrid species across all kingdoms. These shared patterns suggest that the evolutionary process of hybridization leads to common high‐level expression outcomes, regardless of the particular species or kingdom.
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Affiliation(s)
- Anna H Behling
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - David J Winter
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Austen R D Ganley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Murray P Cox
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
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19
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Wei J, Fang Y, Jiang H, Wu XT, Zuo JH, Xia XC, Li JQ, Stich B, Cao H, Liu YX. Combining QTL mapping and gene co-expression network analysis for prediction of candidate genes and molecular network related to yield in wheat. BMC PLANT BIOLOGY 2022; 22:288. [PMID: 35698038 PMCID: PMC9190149 DOI: 10.1186/s12870-022-03677-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 05/27/2022] [Indexed: 05/21/2023]
Abstract
BACKGROUND Wheat (Triticum aestivum L.) is an important cereal crop. Increasing grain yield for wheat is always a priority. Due to the complex genome of hexaploid wheat with 21 chromosomes, it is difficult to identify underlying genes by traditional genetic approach. The combination of genetics and omics analysis has displayed the powerful capability to identify candidate genes for major quantitative trait loci (QTLs), but such studies have rarely been carried out in wheat. In this study, candidate genes related to yield were predicted by a combined use of linkage mapping and weighted gene co-expression network analysis (WGCNA) in a recombinant inbred line population. RESULTS QTL mapping was performed for plant height (PH), spike length (SL) and seed traits. A total of 68 QTLs were identified for them, among which, 12 QTLs were stably identified across different environments. Using RNA sequencing, we scanned the 99,168 genes expression patterns of the whole spike for the recombinant inbred line population. By the combined use of QTL mapping and WGCNA, 29, 47, 20, 26, 54, 46 and 22 candidate genes were predicted for PH, SL, kernel length (KL), kernel width, thousand kernel weight, seed dormancy, and seed vigor, respectively. Candidate genes for different traits had distinct preferences. The known PH regulation genes Rht-B and Rht-D, and the known seed dormancy regulation genes TaMFT can be selected as candidate gene. Moreover, further experiment revealed that there was a SL regulatory QTL located in an interval of about 7 Mbp on chromosome 7A, named TaSL1, which also involved in the regulation of KL. CONCLUSIONS A combination of QTL mapping and WGCNA was applied to predicted wheat candidate genes for PH, SL and seed traits. This strategy will facilitate the identification of candidate genes for related QTLs in wheat. In addition, the QTL TaSL1 that had multi-effect regulation of KL and SL was identified, which can be used for wheat improvement. These results provided valuable molecular marker and gene information for fine mapping and cloning of the yield-related trait loci in the future.
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Affiliation(s)
- Jun Wei
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Fang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hao Jiang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xing-Ting Wu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing-Hong Zuo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xian-Chun Xia
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jin-Quan Li
- Strube Research GmbH & Co., KG, 38387, S ̈ollingen, Germany
| | - Benjamin Stich
- Institute of Quantitative Genetics and Genomics of Plants, Heinrich Heine University, D ̈usseldorf, Germany
| | - Hong Cao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yong-Xiu Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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20
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Shearman JR, Naktang C, Sonthirod C, Kongkachana W, U-Thoomporn S, Jomchai N, Maknual C, Yamprasai S, Promchoo W, Ruang-Areerate P, Pootakham W, Tangphatsornruang S. Assembly of a hybrid mangrove, Bruguiera hainesii, and its two ancestral contributors, Bruguiera cylindrica and Bruguiera gymnorhiza. Genomics 2022; 114:110382. [PMID: 35526741 DOI: 10.1016/j.ygeno.2022.110382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 04/19/2022] [Accepted: 05/02/2022] [Indexed: 01/14/2023]
Abstract
Mangroves are plants that live in tropical and subtropical coastal regions of the world, they are adapted to high salt environments and cyclic tidal flooding. Mangroves play important ecological roles, including acting as breeding grounds for many fish species and to prevent coastal erosion. The genomes of three mangrove species, Bruguiera gymnorhiza, Bruguiera cylindrica, and a hybrid of the two, Bruguiera hainesii were sequenced, assembled and annotated. The two progenitor species, B. gymnorhiza and B. cylindrica, were found to be highly similar to each other and sufficiently similar to B. parviflora to allow it to be used for reference based scaffolding to generate chromosome level scaffolds. The two subgenomes of B. hainesii were independently assembled and scaffolded. Analysis of B. hainesii confirms that it is a hybrid and the hybridisation event was estimated at 2.4 to 3.5 million years ago using a Bayesian Relaxed Molecular Clock approach.
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Affiliation(s)
- Jeremy R Shearman
- National Omics Center, National Science and Technology Development Agency, 111 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani 12120, Thailand
| | - Chaiwat Naktang
- National Omics Center, National Science and Technology Development Agency, 111 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani 12120, Thailand
| | - Chutima Sonthirod
- National Omics Center, National Science and Technology Development Agency, 111 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani 12120, Thailand
| | - Wasitthee Kongkachana
- National Omics Center, National Science and Technology Development Agency, 111 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani 12120, Thailand
| | - Sonicha U-Thoomporn
- National Omics Center, National Science and Technology Development Agency, 111 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani 12120, Thailand
| | - Nukoon Jomchai
- National Omics Center, National Science and Technology Development Agency, 111 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani 12120, Thailand
| | - Chatree Maknual
- Department of Marine and Coastal Resources, 120 The Government Complex, Chaengwatthana Rd., Thung Song Hong, Bangkok 10210, Thailand
| | - Suchart Yamprasai
- Department of Marine and Coastal Resources, 120 The Government Complex, Chaengwatthana Rd., Thung Song Hong, Bangkok 10210, Thailand
| | - Waratthaya Promchoo
- Department of Marine and Coastal Resources, 120 The Government Complex, Chaengwatthana Rd., Thung Song Hong, Bangkok 10210, Thailand
| | - Panthita Ruang-Areerate
- National Omics Center, National Science and Technology Development Agency, 111 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani 12120, Thailand
| | - Wirulda Pootakham
- National Omics Center, National Science and Technology Development Agency, 111 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani 12120, Thailand
| | - Sithichoke Tangphatsornruang
- National Omics Center, National Science and Technology Development Agency, 111 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani 12120, Thailand.
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21
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Zhang L, He J, He H, Wu J, Li M. Genome-wide unbalanced expression bias and expression level dominance toward Brassica oleracea in artificially synthesized intergeneric hybrids of Raphanobrassica. HORTICULTURE RESEARCH 2021; 8:246. [PMID: 34848691 PMCID: PMC8633066 DOI: 10.1038/s41438-021-00672-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/27/2021] [Accepted: 07/30/2021] [Indexed: 05/04/2023]
Abstract
Raphanobrassica (RrRrCrCr, 2n = 4x = 36), which is generated by distant hybridization between the maternal parent Raphanus sativus (RsRs, 2n = 2x = 18) and the paternal parent Brassica oleracea (C°C°, 2n = 2x = 18), displays intermediate silique phenotypes compared to diploid progenitors. However, the hybrid shares much more similarities in silique phenotypes with those of B. oleracea than those of R. sativus. Strikingly, the silique of Raphanobrassica is obviously split into two parts. To investigate the gene expression patterns behind these phenomena, transcriptome analysis was performed on the upper, middle, and lower sections of pods (RCsiu, RCsim, and RCsil), seeds in the upper and lower sections of siliques (RCseu and RCsel) from Raphanobrassica, whole pods (Rsi and Csi) and all seeds in the siliques (Rse and Cse) from R. sativus and B. oleracea. Transcriptome shock was observed in all five aforementioned tissues of Raphanobrassica. Genome-wide unbalanced biased expression and expression level dominance were also discovered, and both of them were toward B. oleracea in Raphanobrassica, which is consistent with the observed phenotypes. The present results reveal the global gene expression patterns of different sections of siliques of Raphanobrassica, pods, and seeds of B. oleracea and R. sativus, unraveling the tight correlation between global gene expression patterns and phenotypes of the hybrid and its parents.
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Affiliation(s)
- Libin Zhang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Jianjie He
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Hongsheng He
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Jiangsheng Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Maoteng Li
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
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22
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Milosavljevic S, Kuo T, Decarli S, Mohn L, Sese J, Shimizu KK, Shimizu-Inatsugi R, Robinson MD. ARPEGGIO: Automated Reproducible Polyploid EpiGenetic GuIdance workflOw. BMC Genomics 2021; 22:547. [PMID: 34273949 PMCID: PMC8285871 DOI: 10.1186/s12864-021-07845-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 06/23/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Whole genome duplication (WGD) events are common in the evolutionary history of many living organisms. For decades, researchers have been trying to understand the genetic and epigenetic impact of WGD and its underlying molecular mechanisms. Particular attention was given to allopolyploid study systems, species resulting from an hybridization event accompanied by WGD. Investigating the mechanisms behind the survival of a newly formed allopolyploid highlighted the key role of DNA methylation. With the improvement of high-throughput methods, such as whole genome bisulfite sequencing (WGBS), an opportunity opened to further understand the role of DNA methylation at a larger scale and higher resolution. However, only a few studies have applied WGBS to allopolyploids, which might be due to lack of genomic resources combined with a burdensome data analysis process. To overcome these problems, we developed the Automated Reproducible Polyploid EpiGenetic GuIdance workflOw (ARPEGGIO): the first workflow for the analysis of epigenetic data in polyploids. This workflow analyzes WGBS data from allopolyploid species via the genome assemblies of the allopolyploid's parent species. ARPEGGIO utilizes an updated read classification algorithm (EAGLE-RC), to tackle the challenge of sequence similarity amongst parental genomes. ARPEGGIO offers automation, but more importantly, a complete set of analyses including spot checks starting from raw WGBS data: quality checks, trimming, alignment, methylation extraction, statistical analyses and downstream analyses. A full run of ARPEGGIO outputs a list of genes showing differential methylation. ARPEGGIO was made simple to set up, run and interpret, and its implementation ensures reproducibility by including both package management and containerization. RESULTS We evaluated ARPEGGIO in two ways. First, we tested EAGLE-RC's performance with publicly available datasets given a ground truth, and we show that EAGLE-RC decreases the error rate by 3 to 4 times compared to standard approaches. Second, using the same initial dataset, we show agreement between ARPEGGIO's output and published results. Compared to other similar workflows, ARPEGGIO is the only one supporting polyploid data. CONCLUSIONS The goal of ARPEGGIO is to promote, support and improve polyploid research with a reproducible and automated set of analyses in a convenient implementation. ARPEGGIO is available at https://github.com/supermaxiste/ARPEGGIO .
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Affiliation(s)
- Stefan Milosavljevic
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Tony Kuo
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Canada
| | - Samuele Decarli
- Department of Computer Science, ETH Zurich, Zurich, Switzerland
| | - Lucas Mohn
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Jun Sese
- AIST Artificial Intelligence Research Center, Tokyo, Japan
- Humanome Lab Inc., Chuo-ku, Tokyo, Japan
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Mark D Robinson
- SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland.
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.
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23
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Yuan D, Grover CE, Hu G, Pan M, Miller ER, Conover JL, Hunt SP, Udall JA, Wendel JF. Parallel and Intertwining Threads of Domestication in Allopolyploid Cotton. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2003634. [PMID: 34026441 PMCID: PMC8132148 DOI: 10.1002/advs.202003634] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 02/02/2021] [Indexed: 05/09/2023]
Abstract
The two cultivated allopolyploid cottons, Gossypium hirsutum and Gossypium barbadense, represent a remarkable example of parallel independent domestication, both involving dramatic morphological transformations under selection from wild perennial plants to annualized row crops. Deep resequencing of 643 newly sampled accessions spanning the wild-to-domesticated continuum of both species, and their allopolyploid relatives, are combined with existing data to resolve species relationships and elucidate multiple aspects of their parallel domestication. It is confirmed that wild G. hirsutum and G. barbadense were initially domesticated in the Yucatan Peninsula and NW South America, respectively, and subsequently spread under domestication over 4000-8000 years to encompass most of the American tropics. A robust phylogenomic analysis of infraspecific relationships in each species is presented, quantify genetic diversity in both, and describe genetic bottlenecks associated with domestication and subsequent diffusion. As these species became sympatric over the last several millennia, pervasive genome-wide bidirectional introgression occurred, often with striking asymmetries involving the two co-resident genomes of these allopolyploids. Diversity scans revealed genomic regions and genes unknowingly targeted during domestication and additional subgenomic asymmetries. These analyses provide a comprehensive depiction of the origin, divergence, and adaptation of cotton, and serve as a rich resource for cotton improvement.
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Affiliation(s)
- Daojun Yuan
- Department of EcologyEvolution, and Organismal Biology (EEOB)Bessey HallIowa State UniversityAmesIA50011USA
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubei430070China
| | - Corrinne E. Grover
- Department of EcologyEvolution, and Organismal Biology (EEOB)Bessey HallIowa State UniversityAmesIA50011USA
| | - Guanjing Hu
- Department of EcologyEvolution, and Organismal Biology (EEOB)Bessey HallIowa State UniversityAmesIA50011USA
| | - Mengqiao Pan
- State Key Laboratory of Crop Genetics and Germplasm EnhancementCotton Hybrid R & D Engineering CenterNanjing Agricultural UniversityNanjing210095China
| | - Emma R. Miller
- Department of EcologyEvolution, and Organismal Biology (EEOB)Bessey HallIowa State UniversityAmesIA50011USA
| | - Justin L. Conover
- Department of EcologyEvolution, and Organismal Biology (EEOB)Bessey HallIowa State UniversityAmesIA50011USA
| | | | - Joshua A. Udall
- Crop Germplasm Research UnitUSDA‐ARSCollege StationTX77845USA
| | - Jonathan F. Wendel
- Department of EcologyEvolution, and Organismal Biology (EEOB)Bessey HallIowa State UniversityAmesIA50011USA
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24
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Shimizu KK, Copetti D, Okada M, Wicker T, Tameshige T, Hatakeyama M, Shimizu-Inatsugi R, Aquino C, Nishimura K, Kobayashi F, Murata K, Kuo T, Delorean E, Poland J, Haberer G, Spannagl M, Mayer KFX, Gutierrez-Gonzalez J, Muehlbauer GJ, Monat C, Himmelbach A, Padmarasu S, Mascher M, Walkowiak S, Nakazaki T, Ban T, Kawaura K, Tsuji H, Pozniak C, Stein N, Sese J, Nasuda S, Handa H. De Novo Genome Assembly of the Japanese Wheat Cultivar Norin 61 Highlights Functional Variation in Flowering Time and Fusarium-Resistant Genes in East Asian Genotypes. PLANT & CELL PHYSIOLOGY 2021; 62:8-27. [PMID: 33244607 PMCID: PMC7991897 DOI: 10.1093/pcp/pcaa152] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 11/22/2020] [Indexed: 05/08/2023]
Abstract
Bread wheat is a major crop that has long been the focus of basic and breeding research. Assembly of its genome has been difficult because of its large size and allohexaploid nature (AABBDD genome). Following the first reported assembly of the genome of the experimental strain Chinese Spring (CS), the 10+ Wheat Genomes Project was launched to produce multiple assemblies of worldwide modern cultivars. The only Asian cultivar in the project is Norin 61, a representative Japanese cultivar adapted to grow across a broad latitudinal range, mostly characterized by a wet climate and a short growing season. Here, we characterize the key aspects of its chromosome-scale genome assembly spanning 15 Gb with a raw scaffold N50 of 22 Mb. Analysis of the repetitive elements identified chromosomal regions unique to Norin 61 that encompass a tandem array of the pathogenesis-related 13 family. We report novel copy-number variations in the B homeolog of the florigen gene FT1/VRN3, pseudogenization of its D homeolog and the association of its A homeologous alleles with the spring/winter growth habit. Furthermore, the Norin 61 genome carries typical East Asian functional variants different from CS, ranging from a single nucleotide to multi-Mb scale. Examples of such variation are the Fhb1 locus, which confers Fusarium head-blight resistance, Ppd-D1a, which confers early flowering, Glu-D1f for Asian noodle quality and Rht-D1b, which introduced semi-dwarfism during the green revolution. The adoption of Norin 61 as a reference assembly for functional and evolutionary studies will enable comprehensive characterization of the underexploited Asian bread wheat diversity.
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Affiliation(s)
- Kentaro K Shimizu
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Dario Copetti
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Department of Environmental Systems Science, Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Moeko Okada
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Toshiaki Tameshige
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
- Department of Biology, Faculty of Science, Niigata University, Niigata, Japan
| | - Masaomi Hatakeyama
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Functional Genomics Center Zurich, Zurich, Switzerland
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | | | - Kazusa Nishimura
- Graduate School of Agriculture, Kyoto University, Kizugawa, Japan
| | - Fuminori Kobayashi
- Division of Basic Research, Institute of Crop Science, NARO, Tsukuba, Japan
| | - Kazuki Murata
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Tony Kuo
- National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
- University of Guelph, Centre for Biodiversity Genomics, Guelph, ON, Canada
| | - Emily Delorean
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Jesse Poland
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Georg Haberer
- Helmholtz Zentrum München—Research Center for Environmental Health, Neuherberg, Germany
| | - Manuel Spannagl
- Helmholtz Zentrum München—Research Center for Environmental Health, Neuherberg, Germany
| | - Klaus F X Mayer
- Helmholtz Zentrum München—Research Center for Environmental Health, Neuherberg, Germany
- School of Life Sciences, Technical University Munich, Weihenstephan, Germany
| | | | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, USA
| | - Cecile Monat
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Sudharsan Padmarasu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Sean Walkowiak
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
- Canadian Grain Commission, Grain Research Laboratory, Winnipeg, MB, Canada
| | - Tetsuya Nakazaki
- Graduate School of Agriculture, Kyoto University, Kizugawa, Japan
| | - Tomohiro Ban
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Kanako Kawaura
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Hiroyuki Tsuji
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Curtis Pozniak
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
- Department of Crop Science, Center of Integrated Breeding Research (CiBreed), Georg-August-University, Göttingen, Germany
| | - Jun Sese
- National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
- Humanome Lab, Inc, Tokyo, Japan
| | - Shuhei Nasuda
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Hirokazu Handa
- Division of Basic Research, Institute of Crop Science, NARO, Tsukuba, Japan
- Laboratoty of Plant Breeding, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan
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25
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Chen P, Jian H, Wei F, Gu L, Hu T, Lv X, Guo X, Lu J, Ma L, Wang H, Wu A, Mao G, Yu S, Wei H. Phylogenetic Analysis of the Membrane Attack Complex/Perforin Domain-Containing Proteins in Gossypium and the Role of GhMACPF26 in Cotton Under Cold Stress. FRONTIERS IN PLANT SCIENCE 2021; 12:684227. [PMID: 34868097 PMCID: PMC8641546 DOI: 10.3389/fpls.2021.684227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 10/04/2021] [Indexed: 05/03/2023]
Abstract
The membrane attack complex/perforin (MACPF) domain-containing proteins are involved in the various developmental processes and in responding to diverse abiotic stress. The function and regulatory network of the MACPF genes are rarely reported in Gossypium spp. We study the detailed identification and partial functional verification of the members of the MACPF family. Totally, 100 putative MACPF proteins containing complete MACPF domain were identified from the four cotton species. They were classified into three phylogenetic groups and underwent multifold pressure indicating that selection produced new functional differentiation. Cotton MACPF gene family members expanded mainly through the whole-genome duplication (WGD)/segmental followed by the dispersed. Expression and cis-acting elements analysis revealed that MACPFs play a role in resistance to abiotic stresses, and some selected GhMACPFs were able to respond to the PEG and cold stresses. Co-expression analysis showed that GhMACPFs might interact with valine-glutamine (VQ), WRKY, and Apetala 2 (AP2)/ethylene responsive factor (ERF) domain-containing genes under cold stress. In addition, silencing endogenous GhMACPF26 in cotton by the virus-induced gene silencing (VIGS) method indicated that GhMACPF26 negatively regulates cold tolerance. Our data provided a comprehensive phylogenetic evolutionary view of Gossypium MACPFs. The MACPFs may work together with multiple transcriptional factors and play roles in acclimation to abiotic stress, especially cold stress in cotton.
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Affiliation(s)
- Pengyun Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Hongliang Jian
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Fei Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Lijiao Gu
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China
| | - Tingli Hu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiaoyan Lv
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiaohao Guo
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jianhua Lu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Liang Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Hantao Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Aimin Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Guangzhi Mao
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
- *Correspondence: Shuxun Yu,
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
- Hengling Wei,
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