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Tao D, Kalendar R, Paterson AH. Editorial: Interspecific hybridization in plant biology, volume II. FRONTIERS IN PLANT SCIENCE 2024; 15:1412622. [PMID: 38736442 PMCID: PMC11088942 DOI: 10.3389/fpls.2024.1412622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 04/22/2024] [Indexed: 05/14/2024]
Affiliation(s)
- Dayun Tao
- Yunnan Seed Laboratory/Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Ruslan Kalendar
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Andrew H. Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, United States
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2
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Zhang T, Huang W, Zhang L, Li DZ, Qi J, Ma H. Phylogenomic profiles of whole-genome duplications in Poaceae and landscape of differential duplicate retention and losses among major Poaceae lineages. Nat Commun 2024; 15:3305. [PMID: 38632270 PMCID: PMC11024178 DOI: 10.1038/s41467-024-47428-9] [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: 07/13/2023] [Accepted: 04/02/2024] [Indexed: 04/19/2024] Open
Abstract
Poaceae members shared a whole-genome duplication called rho. However, little is known about the evolutionary pattern of the rho-derived duplicates among Poaceae lineages and implications in adaptive evolution. Here we present phylogenomic/phylotranscriptomic analyses of 363 grasses covering all 12 subfamilies and report nine previously unknown whole-genome duplications. Furthermore, duplications from a single whole-genome duplication were mapped to multiple nodes on the species phylogeny; a whole-genome duplication was likely shared by woody bamboos with possible gene flow from herbaceous bamboos; and recent paralogues of a tetraploid Oryza are implicated in tolerance of seawater submergence. Moreover, rho duplicates showing differential retention among subfamilies include those with functions in environmental adaptations or morphogenesis, including ACOT for aquatic environments (Oryzoideae), CK2β for cold responses (Pooideae), SPIRAL1 for rapid cell elongation (Bambusoideae), and PAI1 for drought/cold responses (Panicoideae). This study presents a Poaceae whole-genome duplication profile with evidence for multiple evolutionary mechanisms that contribute to gene retention and losses.
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Affiliation(s)
- Taikui Zhang
- Department of Biology, the Eberly College of Science, and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, State College, PA, 16802, USA
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Weichen Huang
- Department of Biology, the Eberly College of Science, and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Lin Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Ji Qi
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China.
| | - Hong Ma
- Department of Biology, the Eberly College of Science, and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, State College, PA, 16802, USA.
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3
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Fang C, Jiang N, Teresi SJ, Platts AE, Agarwal G, Niederhuth C, Edger PP, Jiang J. Dynamics of accessible chromatin regions and subgenome dominance in octoploid strawberry. Nat Commun 2024; 15:2491. [PMID: 38509076 PMCID: PMC10954716 DOI: 10.1038/s41467-024-46861-0] [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: 08/07/2023] [Accepted: 03/12/2024] [Indexed: 03/22/2024] Open
Abstract
Subgenome dominance has been reported in diverse allopolyploid species, where genes from one subgenome are preferentially retained and are more highly expressed than those from other subgenome(s). However, the molecular mechanisms responsible for subgenome dominance remain poorly understood. Here, we develop genome-wide map of accessible chromatin regions (ACRs) in cultivated strawberry (2n = 8x = 56, with A, B, C, D subgenomes). Each ACR is identified as an MNase hypersensitive site (MHS). We discover that the dominant subgenome A contains a greater number of total MHSs and MHS per gene than the submissive B/C/D subgenomes. Subgenome A suffers fewer losses of MHS-related DNA sequences and fewer MHS fragmentations caused by insertions of transposable elements. We also discover that genes and MHSs related to stress response have been preferentially retained in subgenome A. We conclude that preservation of genes and their cognate ACRs, especially those related to stress responses, play a major role in the establishment of subgenome dominance in octoploid strawberry.
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Affiliation(s)
- Chao Fang
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Ning Jiang
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Michigan State University AgBioResearch, East Lansing, MI, 48824, USA
- Genetics and Genome Sciences Program, Michigan State University, East Lansing, MI, 48824, USA
| | - Scott J Teresi
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Genetics and Genome Sciences Program, Michigan State University, East Lansing, MI, 48824, USA
| | - Adrian E Platts
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Gaurav Agarwal
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Chad Niederhuth
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Michigan State University AgBioResearch, East Lansing, MI, 48824, USA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA.
- Michigan State University AgBioResearch, East Lansing, MI, 48824, USA.
- Genetics and Genome Sciences Program, Michigan State University, East Lansing, MI, 48824, USA.
| | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA.
- Michigan State University AgBioResearch, East Lansing, MI, 48824, USA.
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4
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Ou Y, Li H, Li J, Dai X, He J, Wang S, Liu Q, Yang C, Wang J, Zhao R, Yin Z, Shu Y, Liu S. Formation of Different Polyploids Through Disrupting Meiotic Crossover Frequencies Based on cntd1 Knockout in Zebrafish. Mol Biol Evol 2024; 41:msae047. [PMID: 38421617 PMCID: PMC10939445 DOI: 10.1093/molbev/msae047] [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: 08/11/2023] [Revised: 02/02/2024] [Accepted: 02/28/2024] [Indexed: 03/02/2024] Open
Abstract
Polyploidy, a significant catalyst for speciation and evolutionary processes in both plant and animal kingdoms, has been recognized for a long time. However, the exact molecular mechanism that leads to polyploid formation, especially in vertebrates, is not fully understood. Our study aimed to elucidate this phenomenon using the zebrafish model. We successfully achieved an effective knockout of the cyclin N-terminal domain containing 1 (cntd1) using CRISPR/Cas9 technology. This resulted in impaired formation of meiotic crossovers, leading to cell-cycle arrest during meiotic metaphase and triggering apoptosis of spermatocytes in the testes. Despite these defects, the mutant (cntd1-/-) males were still able to produce a limited amount of sperm with normal ploidy and function. Interestingly, in the mutant females, it was the ploidy not the capacity of egg production that was altered. This resulted in the production of haploid, aneuploid, and unreduced gametes. This alteration enabled us to successfully obtain triploid and tetraploid zebrafish from cntd1-/- and cntd1-/-/- females, respectively. Furthermore, the tetraploid-heterozygous zebrafish produced reduced-diploid gametes and yielded all-triploid or all-tetraploid offspring when crossed with wild-type (WT) or tetraploid zebrafish, respectively. Collectively, our findings provide direct evidence supporting the crucial role of meiotic crossover defects in the process of polyploidization. This is particularly evident in the generation of unreduced eggs in fish and, potentially, other vertebrate species.
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Affiliation(s)
- Yuan Ou
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
- College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Huilin Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
- College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Juan Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
- College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Xiangyan Dai
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Jiaxin He
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Sciences, Central South University, Changsha 410078, China
| | - Shi Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
- College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Qingfeng Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
- College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Conghui Yang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
- College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Jing Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
- College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Rurong Zhao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
- College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Zhan Yin
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
| | - Yuqin Shu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
- College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
- College of Life Sciences, Hunan Normal University, Changsha 410081, China
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5
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Mu W, Li K, Yang Y, Breiman A, Yang J, Wu Y, Zhu M, Wang S, Catalan P, Nevo E, Liu J. Subgenomic Stability of Progenitor Genomes During Repeated Allotetraploid Origins of the Same Grass Brachypodium hybridum. Mol Biol Evol 2023; 40:msad259. [PMID: 38000891 PMCID: PMC10708906 DOI: 10.1093/molbev/msad259] [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: 07/06/2023] [Revised: 10/17/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Both homeologous exchanges and homeologous expression bias are generally found in most allopolyploid species. Whether homeologous exchanges and homeologous expression bias differ between repeated allopolyploid speciation events from the same progenitor species remains unknown. Here, we detected a third independent and recent allotetraploid origin for the model grass Brachypodium hybridum. Our homeologous exchange with replacement analyses indicated the absence of significant homeologous exchanges in any of the three types of wild allotetraploids, supporting the integrity of their progenitor subgenomes and the immediate creation of the amphidiploids. Further homeologous expression bias tests did not uncover significant subgenomic dominance in different tissues and conditions of the allotetraploids. This suggests a balanced expression of homeologs under similar or dissimilar ecological conditions in their natural habitats. We observed that the density of transposons around genes was not associated with the initial establishment of subgenome dominance; rather, this feature is inherited from the progenitor genome. We found that drought response genes were highly induced in the two subgenomes, likely contributing to the local adaptation of this species to arid habitats in the third allotetraploid event. These findings provide evidence for the consistency of subgenomic stability of parental genomes across multiple allopolyploidization events that led to the same species at different periods. Our study emphasizes the importance of selecting closely related progenitor species genomes to accurately assess homeologous exchange with replacement in allopolyploids, thereby avoiding the detection of false homeologous exchanges when using less related progenitor species genomes.
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Affiliation(s)
- Wenjie Mu
- State Key Laboratory of Herbage Innovation and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Kexin Li
- State Key Laboratory of Herbage Innovation and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Yongzhi Yang
- State Key Laboratory of Herbage Innovation and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Adina Breiman
- Department of Evolutionary and Environmental Biology, University of Tel-Aviv, Tel-Aviv 6997801, Israel
| | - Jiao Yang
- State Key Laboratory of Herbage Innovation and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Ying Wu
- State Key Laboratory of Herbage Innovation and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Mingjia Zhu
- State Key Laboratory of Herbage Innovation and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Shuai Wang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Pilar Catalan
- Escuela Politecnica Superior de Huesca, Universidad de Zaragoza, Huesca 22071, Spain
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Haifa 3498838, Israel
| | - Jianquan Liu
- State Key Laboratory of Herbage Innovation and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
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6
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Zhang RG, Shang HY, Jia KH, Ma YP. Subgenome phasing for complex allopolyploidy: case-based benchmarking and recommendations. Brief Bioinform 2023; 25:bbad513. [PMID: 38189536 PMCID: PMC10772947 DOI: 10.1093/bib/bbad513] [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: 09/20/2023] [Revised: 11/27/2023] [Accepted: 12/13/2023] [Indexed: 01/09/2024] Open
Abstract
Accurate subgenome phasing is crucial for understanding the origin, evolution and adaptive potential of polyploid genomes. SubPhaser and WGDI software are two common methodologies for subgenome phasing in allopolyploids, particularly in scenarios lacking known diploid progenitors. Triggered by a recent debate over the subgenomic origins of the cultivated octoploid strawberry, we examined four well-documented complex allopolyploidy cases as benchmarks, to evaluate and compare the accuracy of the two software. Our analysis demonstrates that the subgenomic structure phased by both software is in line with prior research, effectively tracing complex allopolyploid evolutionary trajectories despite the limitations of each software. Furthermore, using these validated methodologies, we revisited the controversial issue regarding the progenitors of the octoploid strawberry. The results of both methodologies reaffirm Fragaria vesca and Fragaria iinumae as progenitors of the octoploid strawberry. Finally, we propose recommendations for enhancing the accuracy of subgenome phasing in future studies, recognizing the potential of integrated tools for advanced complex allopolyploidy research and offering a new roadmap for robust subgenome-based phylogenetic analysis.
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Affiliation(s)
- Ren-Gang Zhang
- State Key Laboratory of Plant Diversity and Specialty Crops/Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201 Yunnan, China
- University of Chinese Academy of Sciences, Beijing 101408 Beijing, China
| | - Hong-Yun Shang
- State Key Laboratory of Plant Diversity and Specialty Crops/Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201 Yunnan, China
| | - Kai-Hua Jia
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan 250100 Shandong, China
| | - Yong-Peng Ma
- State Key Laboratory of Plant Diversity and Specialty Crops/Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201 Yunnan, China
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7
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Lv R, Gou X, Li N, Zhang Z, Wang C, Wang R, Wang B, Yang C, Gong L, Zhang H, Liu B. Chromosome translocation affects multiple phenotypes, causes genome-wide dysregulation of gene expression, and remodels metabolome in hexaploid wheat. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1564-1582. [PMID: 37265000 DOI: 10.1111/tpj.16338] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/17/2023] [Accepted: 05/30/2023] [Indexed: 06/03/2023]
Abstract
Chromosomal rearrangements (CRs) may occur in newly formed polyploids due to compromised meiotic fidelity. Moreover, CRs can be more readily tolerated in polyploids allowing their longer-term retention and hence potential spreading/fixation within a lineage. The direct functional consequences of CRs in plant polyploids remain unexplored. Here, we identified a heterozygous individual from a synthetic allohexaploid wheat in which the terminal parts of the long-arms of chromosomes 2D (approximately 193 Mb) and 4A (approximately 167 Mb) were reciprocally translocated. Five homogeneous translocation lines including both unbalanced and balanced types were developed by selfing fertilization of the founder mutant (RT [2DL; 4AL]-ter/1, reciprocal translocation). We investigated impacts of these translocations on phenotype, genome-wide gene expression and metabolome. We find that, compared with sibling wild-type, CRs in the form of both unbalanced and balanced translocations induced substantial changes of gene expression primarily via trans-regulation in the nascent allopolyploid wheat. The CRs also manifested clear phenotypic and metabolic consequences. In particular, the genetically balanced, stable reciprocal translocations lines showed immediate enhanced reproductive fitness relative to wild type. Our results underscore the profound impact of CRs on gene expression in nascent allopolyploids with wide-ranging phenotypic and metabolic consequences, suggesting CRs are an important source of genetic variation that can be exploited for crop breeding.
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Affiliation(s)
- Ruili Lv
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Xiaowan Gou
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
- School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Zhibin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Changyi Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Ruisi Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Bin Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Chunwu Yang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Huakun Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
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Bird KA, Pires JC, VanBuren R, Xiong Z, Edger PP. Dosage-sensitivity shapes how genes transcriptionally respond to allopolyploidy and homoeologous exchange in resynthesized Brassica napus. Genetics 2023; 225:iyad114. [PMID: 37338008 PMCID: PMC10471226 DOI: 10.1093/genetics/iyad114] [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: 03/10/2023] [Revised: 03/10/2023] [Accepted: 06/12/2023] [Indexed: 06/21/2023] Open
Abstract
The gene balance hypothesis proposes that selection acts on the dosage (i.e. copy number) of genes within dosage-sensitive portions of networks, pathways, and protein complexes to maintain balanced stoichiometry of interacting proteins, because perturbations to stoichiometric balance can result in reduced fitness. This selection has been called dosage balance selection. Dosage balance selection is also hypothesized to constrain expression responses to dosage changes, making dosage-sensitive genes (those encoding members of interacting proteins) experience more similar expression changes. In allopolyploids, where whole-genome duplication involves hybridization of diverged lineages, organisms often experience homoeologous exchanges that recombine, duplicate, and delete homoeologous regions of the genome and alter the expression of homoeologous gene pairs. Although the gene balance hypothesis makes predictions about the expression response to homoeologous exchanges, they have not been empirically tested. We used genomic and transcriptomic data from 6 resynthesized, isogenic Brassica napus lines over 10 generations to identify homoeologous exchanges, analyzed expression responses, and tested for patterns of genomic imbalance. Groups of dosage-sensitive genes had less variable expression responses to homoeologous exchanges than dosage-insensitive genes, a sign that their relative dosage is constrained. This difference was absent for homoeologous pairs whose expression was biased toward the B. napus A subgenome. Finally, the expression response to homoeologous exchanges was more variable than the response to whole-genome duplication, suggesting homoeologous exchanges create genomic imbalance. These findings expand our knowledge of the impact of dosage balance selection on genome evolution and potentially connect patterns in polyploid genomes over time, from homoeolog expression bias to duplicate gene retention.
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Affiliation(s)
- Kevin A Bird
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI 48824, USA
| | - J Chris Pires
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Robert VanBuren
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA
| | - Zhiyong Xiong
- Key Laboratory of Herbage and Endemic Crop Biotechnology, Inner Mongolia University, Hohhot, Inner Mongolia 010070, China
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI 48824, USA
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9
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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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10
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Goeckeritz CZ, Rhoades KE, Childs KL, Iezzoni AF, VanBuren R, Hollender CA. Genome of tetraploid sour cherry (Prunus cerasus L.) 'Montmorency' identifies three distinct ancestral Prunus genomes. HORTICULTURE RESEARCH 2023; 10:uhad097. [PMID: 37426879 PMCID: PMC10323630 DOI: 10.1093/hr/uhad097] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 05/04/2023] [Indexed: 07/11/2023]
Abstract
Sour cherry (Prunus cerasus L.) is a valuable fruit crop in the Rosaceae family and a hybrid between progenitors closely related to extant Prunus fruticosa (ground cherry) and Prunus avium (sweet cherry). Here we report a chromosome-scale genome assembly for sour cherry cultivar Montmorency, the predominant cultivar grown in the USA. We also generated a draft assembly of P. fruticosa to use alongside a published P. avium sequence for syntelog-based subgenome assignments for 'Montmorency' and provide compelling evidence P. fruticosa is also an allotetraploid. Using hierarchal k-mer clustering and phylogenomics, we show 'Montmorency' is trigenomic, containing two distinct subgenomes inherited from a P. fruticosa-like ancestor (A and A') and two copies of the same subgenome inherited from a P. avium-like ancestor (BB). The genome composition of 'Montmorency' is AA'BB and little-to-no recombination has occurred between progenitor subgenomes (A/A' and B). In Prunus, two known classes of genes are important to breeding strategies: the self-incompatibility loci (S-alleles), which determine compatible crosses, successful fertilization, and fruit set, and the Dormancy Associated MADS-box genes (DAMs), which strongly affect dormancy transitions and flowering time. The S-alleles and DAMs in 'Montmorency' and P. fruticosa were manually annotated and support subgenome assignments. Lastly, the hybridization event 'Montmorency' is descended from was estimated to have occurred less than 1.61 million years ago, making sour cherry a relatively recent allotetraploid. The 'Montmorency' genome highlights the evolutionary complexity of the genus Prunus and will inform future breeding strategies for sour cherry, comparative genomics in the Rosaceae, and questions regarding neopolyploidy.
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Affiliation(s)
- Charity Z Goeckeritz
- Department of Horticulture, Michigan State University, 1066 Bogue St, East Lansing, MI 48824, USA
| | - Kathleen E Rhoades
- Department of Horticulture, Michigan State University, 1066 Bogue St, East Lansing, MI 48824, USA
| | - Kevin L Childs
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA
| | - Amy F Iezzoni
- Department of Horticulture, Michigan State University, 1066 Bogue St, East Lansing, MI 48824, USA
| | - Robert VanBuren
- Department of Horticulture, Michigan State University, 1066 Bogue St, East Lansing, MI 48824, USA
| | - Courtney A Hollender
- Department of Horticulture, Michigan State University, 1066 Bogue St, East Lansing, MI 48824, USA
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