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Xu Y, Bush SJ, Yang X, Xu L, Wang B, Ye K. Evolutionary analysis of conserved non-coding elements subsequent to whole-genome duplication in opium poppy. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1804-1824. [PMID: 37706612 DOI: 10.1111/tpj.16466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 08/28/2023] [Accepted: 09/05/2023] [Indexed: 09/15/2023]
Abstract
Whole-genome duplication (WGD) leads to the duplication of both coding and non-coding sequences within an organism's genome, providing an abundant supply of genetic material that can drive evolution, ultimately contributing to plant adaptation and speciation. Although non-coding sequences contain numerous regulatory elements, they have been understudied compared to coding sequences. In order to address this gap, we explored the evolutionary patterns of regulatory sequences, coding sequences and transcriptomes using conserved non-coding elements (CNEs) as regulatory element proxies following the recent WGD event in opium poppy (Papaver somniferum). Our results showed similar evolutionary patterns in subgenomes of regulatory and coding sequences. Specifically, the biased or unbiased retention of coding sequences reflected the same pattern as retention levels in regulatory sequences. Further, the divergence of gene expression patterns mediated by regulatory element variations occurred at a more rapid pace than that of gene coding sequences. However, gene losses were purportedly dependent on relaxed selection pressure in coding sequences. Specifically, the rapid evolution of tissue-specific benzylisoquinoline alkaloid production in P. somniferum was associated with regulatory element changes. The origin of a novel stem-specific ACR, which utilized ancestral cis-elements as templates, is likely to be linked to the evolutionary trajectory behind the transition of the PSMT1-CYP719A21 cluster from high levels of expression solely in P. rhoeas root tissue to its elevated expression in P. somniferum stem tissue. Our findings demonstrate that rapid regulatory element evolution can contribute to the emergence of new phenotypes and provide valuable insights into the high evolvability of regulatory elements.
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Affiliation(s)
- Yu Xu
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Stephen J Bush
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xinyi Yang
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Linfeng Xu
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Bo Wang
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Kai Ye
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Genome Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
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2
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Iohannes SD, Jackson D. Tackling redundancy: genetic mechanisms underlying paralog compensation in plants. THE NEW PHYTOLOGIST 2023; 240:1381-1389. [PMID: 37724752 DOI: 10.1111/nph.19267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/29/2023] [Indexed: 09/21/2023]
Abstract
Gene duplication is a powerful source of biological innovation giving rise to paralogous genes that undergo diverse fates. Redundancy between paralogous genes is an intriguing outcome of duplicate gene evolution, and its maintenance over evolutionary time has long been considered a paradox. Redundancy can also be dubbed 'a geneticist's nightmare': It hinders the predictability of genome editing outcomes and limits our ability to link genotypes to phenotypes. Genetic studies in yeast and plants have suggested that the ability of ancient redundant duplicates to compensate for dosage perturbations resulting from a loss of function depends on the reprogramming of gene expression, a phenomenon known as active compensation. Starting from considerations on the stoichiometric constraints that drive the evolutionary stability of redundancy, this review aims to provide insights into the mechanisms of active compensation between duplicates that could be targeted for breaking paralog dependencies - the next frontier in plant functional studies.
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Affiliation(s)
- Sessen Daniel Iohannes
- School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, 11724, NY, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, 11724, NY, USA
| | - David Jackson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, 11724, NY, USA
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3
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Jia Y, Xu M, Hu H, Chapman B, Watt C, Buerte B, Han N, Zhu M, Bian H, Li C, Zeng Z. Comparative gene retention analysis in barley, wild emmer, and bread wheat pangenome lines reveals factors affecting gene retention following gene duplication. BMC Biol 2023; 21:25. [PMID: 36747211 PMCID: PMC9903521 DOI: 10.1186/s12915-022-01503-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 12/16/2022] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Gene duplication is a prevalent phenomenon and a major driving force underlying genome evolution. The process leading to the fixation of gene duplicates following duplication is critical to understand how genome evolves but remains fragmentally understood. Most previous studies on gene retention are based on gene duplicate analyses in single reference genome. No population-based comparative gene retention analysis has been performed to date. RESULTS Taking advantage of recently published genomic data in Triticeae, we dissected a divergent homogentisate phytyltransferase (HPT2) lineage caught in the middle stage of gene fixation following duplication. The presence/absence of HPT2 in barley (diploid), wild emmer (tetraploid), and bread wheat (hexaploid) pangenome lines appears to be associated with gene dosage constraint and environmental adaption. Based on these observations, we adopted a phylogeny-based orthology inference approach and performed comparative gene retention analyses across barley, wild emmer, and bread wheat. This led to the identification of 326 HPT2-pattern-like genes at whole genome scale, representing a pool of gene duplicates in the middle stage of gene fixation. Majority of these HPT2-pattern-like genes were identified as small-scale duplicates, such as dispersed, tandem, and proximal duplications. Natural selection analyses showed that HPT2-pattern-like genes have experienced relaxed selection pressure, which is generally accompanied with partial positive selection and transcriptional divergence. Functional enrichment analyses showed that HPT2-pattern-like genes are over-represented with molecular-binding and defense response functions, supporting the potential role of environmental adaption during gene retention. We also observed that gene duplicates from larger gene family are more likely to be lost, implying a gene dosage constraint effect. Further comparative gene retention analysis in barley and bread wheat pangenome lines revealed combined effects of species-specific selection and gene dosage constraint. CONCLUSIONS Comparative gene retention analyses at the population level support gene dosage constraint, environmental adaption, and species-specific selection as three factors that may affect gene retention following gene duplication. Our findings shed light on the evolutionary process leading to the retention of newly formed gene duplicates and will greatly improve our understanding on genome evolution via duplication.
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Affiliation(s)
- Yong Jia
- grid.1025.60000 0004 0436 6763Western Crop Genetic Alliance, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia ,grid.1025.60000 0004 0436 6763Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia
| | - Mingrui Xu
- grid.410595.c0000 0001 2230 9154College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121 China
| | - Haifei Hu
- grid.1025.60000 0004 0436 6763Western Crop Genetic Alliance, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia ,grid.1025.60000 0004 0436 6763Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia
| | - Brett Chapman
- grid.1025.60000 0004 0436 6763Western Crop Genetic Alliance, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia ,grid.1025.60000 0004 0436 6763Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia
| | - Calum Watt
- grid.1025.60000 0004 0436 6763Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia ,grid.516230.30000 0005 0233 6218Intergrain Pty Ltd, Bibra Lake, WA 6163 Australia
| | - B. Buerte
- grid.13402.340000 0004 1759 700XInstitute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Ning Han
- grid.13402.340000 0004 1759 700XInstitute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Muyuan Zhu
- grid.13402.340000 0004 1759 700XInstitute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Hongwu Bian
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Chengdao Li
- Western Crop Genetic Alliance, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia. .,Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia. .,Department of Primary Industries and Regional Development, 3-Baron-Hay Court, South Perth, WA, 6151, Australia.
| | - Zhanghui Zeng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China. .,Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China. .,Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou, 311121, China.
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4
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Sharbrough J, Conover JL, Gyorfy MF, Grover CE, Miller ER, Wendel JF, Sloan DB. Global Patterns of subgenome evolution in organelle-targeted genes of six allotetraploid angiosperms. Mol Biol Evol 2022; 39:6564157. [PMID: 35383845 PMCID: PMC9040051 DOI: 10.1093/molbev/msac074] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Whole-genome duplications (WGDs) are a prominent process of diversification in eukaryotes. The genetic and evolutionary forces that WGD imposes on cytoplasmic genomes are not well understood, despite the central role that cytonuclear interactions play in eukaryotic function and fitness. Cellular respiration and photosynthesis depend on successful interaction between the 3,000+ nuclear-encoded proteins destined for the mitochondria or plastids and the gene products of cytoplasmic genomes in multi-subunit complexes such as OXPHOS, organellar ribosomes, Photosystems I and II, and Rubisco. Allopolyploids are thus faced with the critical task of coordinating interactions between the nuclear and cytoplasmic genes that were inherited from different species. Because the cytoplasmic genomes share a more recent history of common descent with the maternal nuclear subgenome than the paternal subgenome, evolutionary “mismatches” between the paternal subgenome and the cytoplasmic genomes in allopolyploids might lead to the accelerated rates of evolution in the paternal homoeologs of allopolyploids, either through relaxed purifying selection or strong directional selection to rectify these mismatches. We report evidence from six independently formed allotetraploids that the subgenomes exhibit unequal rates of protein-sequence evolution, but we found no evidence that cytonuclear incompatibilities result in altered evolutionary trajectories of the paternal homoeologs of organelle-targeted genes. The analyses of gene content revealed mixed evidence for whether the organelle-targeted genes are lost more rapidly than the non-organelle-targeted genes. Together, these global analyses provide insights into the complex evolutionary dynamics of allopolyploids, showing that the allopolyploid subgenomes have separate evolutionary trajectories despite sharing the same nucleus, generation time, and ecological context.
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Affiliation(s)
- Joel Sharbrough
- Biology Department, Colorado State University, Fort Collins, CO, USA.,Biology Department, New Mexico Institute of Mining and Technology, Socorro, NM, USA
| | - Justin L Conover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | | | - Corrinne E Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Emma R Miller
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Daniel B Sloan
- Biology Department, Colorado State University, Fort Collins, CO, USA
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5
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Jones DM, Vandepoele K. Identification and evolution of gene regulatory networks: insights from comparative studies in plants. CURRENT OPINION IN PLANT BIOLOGY 2020; 54:42-48. [PMID: 32062128 DOI: 10.1016/j.pbi.2019.12.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 12/10/2019] [Accepted: 12/18/2019] [Indexed: 05/04/2023]
Abstract
The availability of genome sequences, genome-wide assays of transcription factor binding, and accessible chromatin maps have unveiled gene regulatory landscapes in plants. This understanding has ushered in comparative gene regulatory network studies that assess network rewiring between species, across time, and between biological tissues. Comparisons of cis-regulatory elements across the plant kingdom have uncovered examples of conserved sequences, but also of divergence, indicating that selective pressures can vary in different plant families. Transcription factor duplication, followed by spatiotemporal expression divergence of the duplicates, also appears to be a key mechanism of network evolution. Here, we review recent literature describing the regulation of gene expression in plants, and how comparative studies provide insights into how these regulatory interactions change and lead to gene regulatory network rewiring.
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Affiliation(s)
- D Marc Jones
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium; Bioinformatics Institute Ghent, Ghent University, 9052 Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium; Bioinformatics Institute Ghent, Ghent University, 9052 Ghent, Belgium.
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6
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Fan K, Yuan S, Chen J, Chen Y, Li Z, Lin W, Zhang Y, Liu J, Lin W. Molecular evolution and lineage-specific expansion of the PP2C family in Zea mays. PLANTA 2019; 250:1521-1538. [PMID: 31346803 DOI: 10.1007/s00425-019-03243-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 07/16/2019] [Indexed: 05/19/2023]
Abstract
97 ZmPP2Cs were clustered into 10 subfamilies with biased subfamily evolution and lineage-specific expansion. Segmental duplication after the divergence of maize and sorghum might have led to primary expansion of ZmPP2Cs. The protein phosphatase 2C (PP2C) enzymes control many stress responses and developmental processes in plants. In Zea mays, a comprehensive understanding of the evolution and expansion of the PP2C family is still lacking. In the current study, 97 ZmPP2Cs were identified and clustered into 10 subfamilies. Through the analysis of the PP2C family in monocots, the ZmPP2C subfamilies displayed biased subfamily molecular evolution and lineage-specific expansion, as evidenced by their differing numbers of member genes, expansion and evolutionary rates, conserved subdomains, chromosomal distributions, expression levels, responsive-regulatory elements and regulatory networks. Moreover, while segmental duplication events have caused the primary expansion of the ZmPP2Cs, the majority of their diversification occurred following the additional whole-genome duplication that took place after the divergence of maize and sorghum (Sorghum bicolor). After this event, the PP2C subfamilies showed asymmetric evolutionary rates, with the D, F2 and H subfamily likely the most closely to resemble its ancestral subfamily's genes. These findings could provide novel insights into the molecular evolution and expansion of the PP2C family in maize, and lay the foundation for the functional analysis of these enzymes in maize and related monocots.
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Affiliation(s)
- Kai Fan
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 35002, China
| | - Shuna Yuan
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences/Danzhou Investigation and Experiment Station of Tropical Crops, Ministry of Agriculture, Danzhou, 571737, China
| | - Jie Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 35002, China
| | - Yunrui Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 35002, China
| | - Zhaowei Li
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 35002, China
| | - Weiwei Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 35002, China
| | - Yongqiang Zhang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 35002, China
| | - Jianping Liu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 35002, China
| | - Wenxiong Lin
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 35002, China.
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7
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Dong Z, Yu J, Li H, Huang W, Xu L, Zhao Y, Zhang T, Xu W, Jiang J, Su Z, Jin W. Transcriptional and epigenetic adaptation of maize chromosomes in Oat-Maize addition lines. Nucleic Acids Res 2019; 46:5012-5028. [PMID: 29579310 PMCID: PMC6007749 DOI: 10.1093/nar/gky209] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 03/13/2018] [Indexed: 01/16/2023] Open
Abstract
By putting heterologous genomic regulatory systems into contact, chromosome addition lines derived from interspecific or intergeneric crosses allow the investigation of transcriptional regulation in new genomic environments. Here, we report the transcriptional and epigenetic adaptation of stably inherited alien maize chromosomes in two oat–maize addition (OMA) lines. We found that the majority of maize genes displayed maize-specific transcription in the oat genomic environment. Nevertheless, a quarter of the expressed genes encoded by the two maize chromosomes were differentially expressed genes (DEGs). Notably, highly conserved orthologs were more severely differentially expressed in OMAs than less conserved orthologs. Additionally, syntenic genes and highly abundant genes were over-represented among DEGs. Gene suppression was more common than activation among the DEGs; however, the genes in the former maize pericentromere, which expanded to become the new centromere in OMAs, were activated. Histone modifications (H3K4me3, H3K9ac and H3K27me3) were consistent with these transcriptome results. We expect that cis regulation is responsible for unchanged expression in OMA versus maize; and trans regulation is the predominant mechanism behind DEGs. The genome interaction identified here reveals the important consequences of interspecific/intergeneric crosses and potential mechanisms of plant evolution when genomic environments interact.
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Affiliation(s)
- Zhaobin Dong
- National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education, Key Laboratory of Crop Genetic Improvement, Beijing Municipality, Center for Crop Functional Genomics and Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing 10093, P. R. China.,Plant Gene Expression Center, U.S. Department of Agriculture-Agricultural Research Service, Plant and Microbial Biology Department, University of California at Berkeley, CA 94710, USA
| | - Juan Yu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 10093, P. R. China
| | - Hui Li
- National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education, Key Laboratory of Crop Genetic Improvement, Beijing Municipality, Center for Crop Functional Genomics and Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing 10093, P. R. China
| | - Wei Huang
- National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education, Key Laboratory of Crop Genetic Improvement, Beijing Municipality, Center for Crop Functional Genomics and Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing 10093, P. R. China
| | - Ling Xu
- National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education, Key Laboratory of Crop Genetic Improvement, Beijing Municipality, Center for Crop Functional Genomics and Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing 10093, P. R. China.,Plant Gene Expression Center, U.S. Department of Agriculture-Agricultural Research Service, Plant and Microbial Biology Department, University of California at Berkeley, CA 94710, USA
| | - Yue Zhao
- National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education, Key Laboratory of Crop Genetic Improvement, Beijing Municipality, Center for Crop Functional Genomics and Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing 10093, P. R. China
| | - Tao Zhang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Wenying Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 10093, P. R. China
| | - Jiming Jiang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA.,Department of Plant Biology, Department of Horticulture, Michigan State University, East Lansing, MI 48824 USA
| | - Zhen Su
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 10093, P. R. China
| | - Weiwei Jin
- National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education, Key Laboratory of Crop Genetic Improvement, Beijing Municipality, Center for Crop Functional Genomics and Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing 10093, P. R. China
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8
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Li Q, Qiao X, Yin H, Zhou Y, Dong H, Qi K, Li L, Zhang S. Unbiased subgenome evolution following a recent whole-genome duplication in pear ( Pyrus bretschneideri Rehd.). HORTICULTURE RESEARCH 2019; 6:34. [PMID: 30854211 PMCID: PMC6395616 DOI: 10.1038/s41438-018-0110-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 11/09/2018] [Accepted: 11/23/2018] [Indexed: 05/06/2023]
Abstract
Genome fractionation (also known as diploidization) frequently occurs following paleopolyploidization events. Biased fractionation between subgenomes has been found in some paleo-allopolyploids, while this phenomenon is absent in paleo-autopolyploids. Pear (Pyrus bretschneideri Rehd.) experienced a recent whole-genome duplication (WGD, ~30 million years ago); however, the evolutionary fate of the two subgenomes derived from this WGD event is not clear. In this study, we identified the two paleo-subgenomes in pear using peach (Prunus persica) as an outgroup and investigated differences in the gene loss rate, evolutionary rate, gene expression level, and DNA methylation level between these two subgenomes. Fractionation bias was not found between the two pear subgenomes, which evolved at similar evolutionary rates. The DNA methylation level of the two subgenomes showed little bias, and we found no expression dominance between the subgenomes. However, we found that singleton genes and homeologous genes within each subgenome showed divergent evolutionary patterns of selective constraints, expression and epigenetic modification. These results provide insights into subgenome evolution following paleopolyploidization in pear.
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Affiliation(s)
- Qionghou Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, 210095 Nanjing, China
| | - Xin Qiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, 210095 Nanjing, China
| | - Hao Yin
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, 210095 Nanjing, China
| | - Yuhang Zhou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, 210095 Nanjing, China
| | - Huizhen Dong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, 210095 Nanjing, China
| | - Kaijie Qi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, 210095 Nanjing, China
| | - Leiting Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, 210095 Nanjing, China
| | - Shaoling Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, 210095 Nanjing, China
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9
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Christensen KA, Rondeau EB, Minkley DR, Leong JS, Nugent CM, Danzmann RG, Ferguson MM, Stadnik A, Devlin RH, Muzzerall R, Edwards M, Davidson WS, Koop BF. The Arctic charr (Salvelinus alpinus) genome and transcriptome assembly. PLoS One 2018; 13:e0204076. [PMID: 30212580 PMCID: PMC6136826 DOI: 10.1371/journal.pone.0204076] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 08/31/2018] [Indexed: 01/17/2023] Open
Abstract
Arctic charr have a circumpolar distribution, persevere under extreme environmental conditions, and reach ages unknown to most other salmonids. The Salvelinus genus is primarily composed of species with genomes that are structured more like the ancestral salmonid genome than most Oncorhynchus and Salmo species of sister genera. It is thought that this aspect of the genome may be important for local adaptation (due to increased recombination) and anadromy (the migration of fish from saltwater to freshwater). In this study, we describe the generation of a new genetic map, the sequencing and assembly of the Arctic charr genome (GenBank accession: GCF_002910315.2) using the newly created genetic map and a previous genetic map, and present several analyses of the Arctic charr genes and genome assembly. The newly generated genetic map consists of 8,574 unique genetic markers and is similar to previous genetic maps with the exception of three major structural differences. The N50, identified BUSCOs, repetitive DNA content, and total size of the Arctic charr assembled genome are all comparable to other assembled salmonid genomes. An analysis to identify orthologous genes revealed that a large number of orthologs could be identified between salmonids and many appear to have highly conserved gene expression profiles between species. Comparing orthologous gene expression profiles may give us a better insight into which genes are more likely to influence species specific phenotypes.
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Affiliation(s)
- Kris A. Christensen
- Fisheries and Oceans Canada, Centre for Aquaculture and Environmental Research, West Vancouver, British Columbia, Canada
- University of Victoria, Department of Biology, Victoria, British Columbia, Canada
- Simon Fraser University, Molecular Biology and Biochemistry, Burnaby, British Columbia, Canada
| | - Eric B. Rondeau
- Fisheries and Oceans Canada, Centre for Aquaculture and Environmental Research, West Vancouver, British Columbia, Canada
- University of Victoria, Department of Biology, Victoria, British Columbia, Canada
| | - David R. Minkley
- University of Victoria, Department of Biology, Victoria, British Columbia, Canada
| | - Jong S. Leong
- University of Victoria, Department of Biology, Victoria, British Columbia, Canada
| | - Cameron M. Nugent
- University of Guelph, Department of Integrative Biology, Guelph, Ontario, Canada
| | - Roy G. Danzmann
- University of Guelph, Department of Integrative Biology, Guelph, Ontario, Canada
| | - Moira M. Ferguson
- University of Guelph, Department of Integrative Biology, Guelph, Ontario, Canada
| | - Agnieszka Stadnik
- Simon Fraser University, Molecular Biology and Biochemistry, Burnaby, British Columbia, Canada
| | - Robert H. Devlin
- Fisheries and Oceans Canada, Centre for Aquaculture and Environmental Research, West Vancouver, British Columbia, Canada
| | | | | | - William S. Davidson
- Simon Fraser University, Molecular Biology and Biochemistry, Burnaby, British Columbia, Canada
| | - Ben F. Koop
- University of Victoria, Department of Biology, Victoria, British Columbia, Canada
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10
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Liang Z, Schnable JC. Functional Divergence between Subgenomes and Gene Pairs after Whole Genome Duplications. MOLECULAR PLANT 2018; 11:388-397. [PMID: 29275166 DOI: 10.1016/j.molp.2017.12.010] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 11/28/2017] [Accepted: 12/12/2017] [Indexed: 05/20/2023]
Abstract
Gene loss following whole genome duplication (WGD) is often biased, with one subgenome retaining more ancestral genes and the other sustaining more gene deletions. While bias toward the greater expression of gene copies on one subgenome can explain bias in gene loss, this raises the question to what drives differences in gene expression levels between subgenomes. Differences in chromatin modifications and epigenetic markers between subgenomes in several model species are now being identified, providing an explanation for bias in gene expression between subgenomes. WGDs can be classified into duplications with higher, biased gene loss and bias in gene expression between subgenomes versus those with lower, unbiased rates of gene loss and an absence of detectable bias between subgenomes; however, the originally proposed link between these two classes and whether WGD results from an allo- or autopolyploid event is inconsistent with recent data from the allopolyploid Capsella bursa-pastoris. The gene balance hypothesis can explain bias in the functional categories of genes retained following WGD, the difference in gene loss rates between unbiased and biased WGDs, and how plant genomes have avoided being overrun with genes encoding dose-sensitive subunits of multiprotein complexes. Comparisons of gene expression patterns between retained transcription factor pairs in maize suggest the high degree of retention for WGD-derived pairs of transcription factors may instead be explained by the older duplication-degeneration-complementation model.
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Affiliation(s)
- Zhikai Liang
- Plant Science Innovation & Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68503, USA
| | - James C Schnable
- Plant Science Innovation & Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68503, USA.
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11
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Lehti-Shiu MD, Panchy N, Wang P, Uygun S, Shiu SH. Diversity, expansion, and evolutionary novelty of plant DNA-binding transcription factor families. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:3-20. [PMID: 27522016 DOI: 10.1016/j.bbagrm.2016.08.005] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 07/21/2016] [Accepted: 08/06/2016] [Indexed: 12/19/2022]
Abstract
Plant transcription factors (TFs) that interact with specific sequences via DNA-binding domains are crucial for regulating transcriptional initiation and are fundamental to plant development and environmental response. In addition, expansion of TF families has allowed functional divergence of duplicate copies, which has contributed to novel, and in some cases adaptive, traits in plants. Thus, TFs are central to the generation of the diverse plant species that we see today. Major plant agronomic traits, including those relevant to domestication, have also frequently arisen through changes in TF coding sequence or expression patterns. Here our goal is to provide an overview of plant TF evolution by first comparing the diversity of DNA-binding domains and the sizes of these domain families in plants and other eukaryotes. Because TFs are among the most highly expanded gene families in plants, the birth and death process of TFs as well as the mechanisms contributing to their retention are discussed. We also provide recent examples of how TFs have contributed to novel traits that are important in plant evolution and in agriculture.This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
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Affiliation(s)
| | - Nicholas Panchy
- The Genetics Graduate Program, Michigan State University, East Lansing, MI 48824, USA
| | - Peipei Wang
- Department of Plant Biology, East Lansing, MI 48824, USA
| | - Sahra Uygun
- The Genetics Graduate Program, Michigan State University, East Lansing, MI 48824, USA
| | - Shin-Han Shiu
- Department of Plant Biology, East Lansing, MI 48824, USA; The Genetics Graduate Program, Michigan State University, East Lansing, MI 48824, USA.
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12
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The Atlantic salmon genome provides insights into rediploidization. Nature 2016; 533:200-5. [PMID: 27088604 PMCID: PMC8127823 DOI: 10.1038/nature17164] [Citation(s) in RCA: 619] [Impact Index Per Article: 77.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 01/26/2016] [Indexed: 01/24/2023]
Abstract
The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about the evolutionary fate of a duplicated vertebrate genome in 70 extant lineages. Here we present a high-quality genome assembly for Atlantic salmon (Salmo salar), and show that large genomic reorganizations, coinciding with bursts of transposon-mediated repeat expansions, were crucial for the post-Ss4R rediploidization process. Comparisons of duplicate gene expression patterns across a wide range of tissues with orthologous genes from a pre-Ss4R outgroup unexpectedly demonstrate far more instances of neofunctionalization than subfunctionalization. Surprisingly, we find that genes that were retained as duplicates after the teleost-specific whole-genome duplication 320 million years ago were not more likely to be retained after the Ss4R, and that the duplicate retention was not influenced to a great extent by the nature of the predicted protein interactions of the gene products. Finally, we demonstrate that the Atlantic salmon assembly can serve as a reference sequence for the study of other salmonids for a range of purposes. The genome sequence is presented for the Atlantic salmon (Salmo salar), providing information about a rediploidization following a salmonid-specific whole-genome duplication event that resulted in an autotetraploidization. William Davidson and colleagues report sequencing and assembly of the Atlantic salmon genome, which they demonstrate as a useful reference to also improve the genome assembly of other salmanoids. Their analyses provide insights into duplicate retention patterns across two rounds of whole-genome duplication that have occurred in this lineage.
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13
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Tine M. Evolutionary significance and diversification of the phosphoglucose isomerase genes in vertebrates. BMC Res Notes 2015; 8:799. [PMID: 26682538 PMCID: PMC4684624 DOI: 10.1186/s13104-015-1683-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 11/09/2015] [Indexed: 01/20/2024] Open
Abstract
Background Phosphoglucose isomerase (PGI) genes are important multifunctional proteins whose evolution has, until now, not been well elucidated because of the limited number of completely sequenced genomes. Although the multifunctionality of this gene family has been considered as an original and innate characteristic, PGI genes may have acquired novel functions through changes in coding sequences and exon/intron structure, which are known to lead to functional divergence after gene duplication. A whole-genome comparative approach was used to estimate the rates of molecular evolution of this protein family. Results The results confirm the presence of two isoforms in teleost fishes and only one variant in all other vertebrates. Phylogenetic reconstructions grouped the PGI genes into five main groups: lungfishes/coelacanth/cartilaginous fishes, teleost fishes, amphibians, reptiles/birds and mammals, with the teleost group being subdivided into two subclades comprising PGI1 and PGI2. This PGI partitioning into groups is consistent with the synteny and molecular evolution results based on the estimation of the ratios of nonsynonymous to synonymous changes (Ka/Ks) and divergence rates between both PGI paralogs and orthologs. Teleost PGI2 shares more similarity with the variant found in all other vertebrates, suggesting that it has less evolved than PGI1 relative to the PGI of common vertebrate ancestor. Conclusions The diversification of PGI genes into PGI1 and PGI2 is consistent with a teleost-specific duplication before the radiation of this lineage, and after its split from the other infraclasses of ray-finned fishes. The low average Ka/Ks ratios within teleost and mammalian lineages suggest that both PGI1 and PGI2 are functionally constrained by purifying selection and may, therefore, have the same functions. By contrast, the high average Ka/Ks ratios and divergence rates within reptiles and birds indicate that PGI may be involved in different functions. The synteny analyses show that the genomic region harbouring PGI genes has independently undergone genomic rearrangements in mammals versus the reptile/bird lineage in particular, which may have contributed to the actual functional diversification of this gene family. Electronic supplementary material The online version of this article (doi:10.1186/s13104-015-1683-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mbaye Tine
- Molecular Zoology Laboratory, Department of Zoology, University of Johannesburg, Auckland Park, 2006, South Africa. .,Genome Centre Cologne at MPI for Plant Breeding Research, 22 Carl-von-Linné-Weg 10, 50829, Cologne, Germany.
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14
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Freeling M, Scanlon MJ, Fowler JE. Fractionation and subfunctionalization following genome duplications: mechanisms that drive gene content and their consequences. Curr Opin Genet Dev 2015; 35:110-8. [PMID: 26657818 DOI: 10.1016/j.gde.2015.11.002] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 11/09/2015] [Accepted: 11/09/2015] [Indexed: 12/11/2022]
Abstract
A gene's duplication relaxes selection. Loss of duplicate, low-function DNA (fractionation) sometimes follows, mostly by deletion in plants, but mostly via the pseudogene pathway in fish and other clades with smaller population sizes. Subfunctionalization--the founding term of the Xfunctionalization lexicon--while not the general cause of differences in duplicate gene retention, becomes primary as the number of a gene's cis-regulatory sites increases. Balanced gene drive explains retention for the average gene. Both maintenance-of-balance and subfunctionalization drive gene content nonrandomly, and currently fall outside of our accepted Theory of Evolution. The 'typical' mutation encountered by a gene duplicate is not a neutral loss-of-function; dominant mutations (Muller's lexicon; these are not neutral) abound, and confound X functionalization terms like 'neofunctionalization'. Confusion of words may cause confusion of thought. As with many plants, fish tetraploidies provide a higher throughput surrogate-genetic method to infer function from human and other vertebrate ENCODE-like regulatory sites.
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Affiliation(s)
- Michael Freeling
- Department of Plant and Microbial Biology, Univ. California, Berkeley, CA 94720, United States.
| | - Michael J Scanlon
- Section of Plant Biology, Cornell University, Ithaca, NY 14853, United States
| | - John E Fowler
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, United States
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15
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Abstract
BACKGROUND Previous work on whole genome doubling in plants established the importance of gene functional category in provoking or suppressing duplicate gene loss, or fractionation. Other studies, particularly in Paramecium have correlated levels of gene expression with vulnerability or resistance to duplicate loss. RESULTS Here we analyze the simultaneous effect of function category and expression in two plant data sets, rosids and asterids. CONCLUSION We demonstrate function category and expression level have independent effects, though expression does not play the dominant role it does in Paramecium.
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16
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Jourda C, Cardi C, Mbéguié-A-Mbéguié D, Bocs S, Garsmeur O, D'Hont A, Yahiaoui N. Expansion of banana (Musa acuminata) gene families involved in ethylene biosynthesis and signalling after lineage-specific whole-genome duplications. THE NEW PHYTOLOGIST 2014; 202:986-1000. [PMID: 24716518 DOI: 10.1111/nph.12710] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 12/25/2013] [Indexed: 05/26/2023]
Abstract
Whole-genome duplications (WGDs) are widespread in plants, and three lineage-specific WGDs occurred in the banana (Musa acuminata) genome. Here, we analysed the impact of WGDs on the evolution of banana gene families involved in ethylene biosynthesis and signalling, a key pathway for banana fruit ripening. Banana ethylene pathway genes were identified using comparative genomics approaches and their duplication modes and expression profiles were analysed. Seven out of 10 banana ethylene gene families evolved through WGD and four of them (1-aminocyclopropane-1-carboxylate synthase (ACS), ethylene-insensitive 3-like (EIL), ethylene-insensitive 3-binding F-box (EBF) and ethylene response factor (ERF)) were preferentially retained. Banana orthologues of AtEIN3 and AtEIL1, two major genes for ethylene signalling in Arabidopsis, were particularly expanded. This expansion was paralleled by that of EBF genes which are responsible for control of EIL protein levels. Gene expression profiles in banana fruits suggested functional redundancy for several MaEBF and MaEIL genes derived from WGD and subfunctionalization for some of them. We propose that EIL and EBF genes were co-retained after WGD in banana to maintain balanced control of EIL protein levels and thus avoid detrimental effects of constitutive ethylene signalling. In the course of evolution, subfunctionalization was favoured to promote finer control of ethylene signalling.
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Affiliation(s)
| | | | - Didier Mbéguié-A-Mbéguié
- CIRAD, UMR QUALISUD, F-97130, Capesterre-Belle-Eau, Guadeloupe, France
- CIRAD, UMR QUALISUD, F-34398, Montpellier, France
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17
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Todeschini AL, Georges A, Veitia RA. Transcription factors: specific DNA binding and specific gene regulation. Trends Genet 2014; 30:211-9. [PMID: 24774859 DOI: 10.1016/j.tig.2014.04.002] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 03/26/2014] [Accepted: 04/01/2014] [Indexed: 12/15/2022]
Abstract
Specific recognition of cis-regulatory regions is essential for correct gene regulation in response to developmental and environmental signals. Such DNA sequences are recognized by transcription factors (TFs) that recruit the transcriptional machinery. Achievement of specific sequence recognition is not a trivial problem; many TFs recognize similar consensus DNA-binding sites and a genome can harbor thousands of consensus or near-consensus sequences, both functional and nonfunctional. Although genomic technologies have provided large-scale snapshots of TF binding, a full understanding of the mechanistic and quantitative details of specific recognition in the context of gene regulation is lacking. Here, we explore the various ways in which TFs recognizing similar consensus sites distinguish their own targets from a large number of other sequences to ensure specific cellular responses.
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Affiliation(s)
| | - Adrien Georges
- Institut Jacques Monod, Paris, France; Université Paris Diderot, Paris, France
| | - Reiner A Veitia
- Institut Jacques Monod, Paris, France; Université Paris Diderot, Paris, France.
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18
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Subramaniam S, Wang X, Freeling M, Pires JC. The fate of Arabidopsis thaliana homeologous CNSs and their motifs in the Paleohexaploid Brassica rapa. Genome Biol Evol 2013; 5:646-60. [PMID: 23493633 PMCID: PMC3641636 DOI: 10.1093/gbe/evt035] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Following polyploidy, duplicate genes are often deleted, and if they are not, then duplicate regulatory regions are sometimes lost. By what mechanism is this loss and what is the chance that such a loss removes function? To explore these questions, we followed individual Arabidopsis thaliana–A. thaliana conserved noncoding sequences (CNSs) into the Brassica ancestor, through a paleohexaploidy and into Brassica rapa. Thus, a single Brassicaceae CNS has six potential orthologous positions in B. rapa; a single Arabidopsis CNS has three potential homeologous positions. We reasoned that a CNS, if present on a singlet Brassica gene, would be unlikely to lose function compared with a more redundant CNS, and this is the case. Redundant CNSs go nondetectable often. Using this logic, each mechanism of CNS loss was assigned a metric of functionality. By definition, proved deletions do not function as sequence. Our results indicated that CNSs that go nondetectable by base substitution or large insertion are almost certainly still functional (redundancy does not matter much to their detectability frequency), whereas those lost by inferred deletion or indels are approximately 75% likely to be nonfunctional. Overall, an average nondetectable, once-redundant CNS more than 30 bp in length has a 72% chance of being nonfunctional, and that makes sense because 97% of them sort to a molecular mechanism with “deletion” in its description, but base substitutions do cause loss. Similarly, proved-functional G-boxes go undetectable by deletion 82% of the time. Fractionation mutagenesis is a procedure that uses polyploidy as a mutagenic agent to genetically alter RNA expression profiles, and then to construct testable hypotheses as to the function of the lost regulatory site. We show fractionation mutagenesis to be a “deletion machine” in the Brassica lineage.
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19
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Gene dosage effects: nonlinearities, genetic interactions, and dosage compensation. Trends Genet 2013; 29:385-93. [PMID: 23684842 DOI: 10.1016/j.tig.2013.04.004] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 03/23/2013] [Accepted: 04/15/2013] [Indexed: 11/20/2022]
Abstract
High-throughput genomic analyses have shown that many mutations, including loss-of-function (LOF) mutations, are present in diseased as well as in healthy individuals. Gene dosage effects due to deletions, duplications, and LOF mutations provide avenues to explore oligo- and multigenic inheritance. Here, we focus on several mechanisms that mediate gene dosage effects and analyze biochemical interactions among multiple gene products that are sources of nonlinear relations connecting genotypes and phenotypes. We also explore potential mechanisms that compensate for gene dosage effects. Understanding these issues is critical to understanding why an individual bearing a few damaging mutations can be severely diseased, whereas others harboring tens of potentially deleterious mutations can appear quite healthy.
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20
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Spangler JB, Feltus FA. Conserved Non-Coding Sequences are Associated with Rates of mRNA Decay in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2013; 4:129. [PMID: 23675377 PMCID: PMC3650315 DOI: 10.3389/fpls.2013.00129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 04/19/2013] [Indexed: 06/02/2023]
Abstract
Steady-state mRNA levels are tightly regulated through a combination of transcriptional and post-transcriptional control mechanisms. The discovery of cis-acting DNA elements that encode these control mechanisms is of high importance. We have investigated the influence of conserved non-coding sequences (CNSs), DNA patterns retained after an ancient whole genome duplication event, on the breadth of gene expression and the rates of mRNA decay in Arabidopsis thaliana. The absence of CNSs near α duplicate genes was associated with a decrease in breadth of gene expression and slower mRNA decay rates while the presence CNSs near α duplicates was associated with an increase in breadth of gene expression and faster mRNA decay rates. The observed difference in mRNA decay rate was fastest in genes with CNSs in both non-transcribed and transcribed regions, albeit through an unknown mechanism. This study supports the notion that some Arabidopsis CNSs regulate the steady-state mRNA levels through post-transcriptional control mechanisms and that CNSs also play a role in controlling the breadth of gene expression.
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Affiliation(s)
- Jacob B. Spangler
- Department of Genetics and Biochemistry, Clemson UniversityClemson, SC, USA
| | - Frank Alex Feltus
- Department of Genetics and Biochemistry, Clemson UniversityClemson, SC, USA
- Plant and Environmental Sciences, Clemson UniversityClemson, SC, USA
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21
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Liu W, Sun L, Zhong M, Zhou Q, Gong Z, Li P, Tai P, Li X. Cadmium-induced DNA damage and mutations in Arabidopsis plantlet shoots identified by DNA fingerprinting. CHEMOSPHERE 2012; 89:1048-55. [PMID: 22717160 DOI: 10.1016/j.chemosphere.2012.05.068] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Revised: 05/11/2012] [Accepted: 05/16/2012] [Indexed: 05/03/2023]
Abstract
Random amplified polymorphic DNA (RAPD) test is a feasible method to evaluate the toxicity of environmental pollutants on vegetal organisms. Herein, Arabidopsis thaliana (Arabidopsis) plantlets following Cadmium (Cd) treatment for 26 d were screened for DNA genetic alterations by DNA fingerprinting. Four primers amplified 20-23 mutated RAPD fragments in 0.125-3.0 mg L(-1) Cd-treated Arabidopsis plantlets, respectively. Cloning and sequencing analysis of eight randomly selected mutated fragments revealed 99-100% homology with the genes of VARICOSE-Related, SLEEPY1 F-box, 40S ribosomal protein S3, phosphoglucomutase, and noncoding regions in Arabidopsis genome correspondingly. The results show the ability of RAPD analysis to detect significant genetic alterations in Cd-exposed seedlings. Although the exact functional importance of the other mutated bands is unknown, the presence of mutated loci in Cd-treated seedlings, prior to the onset of significant physiological effects, suggests that these altered loci are the early events in Cd-treated Arabidopsis seedlings and would greatly improve environmental risk assessment.
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Affiliation(s)
- Wan Liu
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China.
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22
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Dickinson H, Costa L, Gutierrez-Marcos J. Epigenetic neofunctionalisation and regulatory gene evolution in grasses. TRENDS IN PLANT SCIENCE 2012; 17:389-394. [PMID: 22575341 DOI: 10.1016/j.tplants.2012.04.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Revised: 04/06/2012] [Accepted: 04/11/2012] [Indexed: 05/31/2023]
Abstract
During plant evolution, genome duplication and subsequent selection acting on new gene pairs has frequently resulted in partition of gene functions, or acquisition of new functions. This 'sub- and neofunctionalisation' (subF and neoF) is held to have driven the expansion of key gene classes. One such gene class in maize (Zea mays) includes a pair of Polycomb group (PcG) protein genes that, unlike their single Arabidopsis (Arabidopsis thaliana) counterpart, are both parentally imprinted with only the maternal alleles being expressed in the seed endosperm. Surprisingly, this imprinting is regulated by different mechanisms in the two genes, resulting in different phasing of parent-specific expression. In this opinion article we propose that recruitment of different imprinting systems constitutes 'epigenetic neoF', and has enhanced maternal control over seed development, with a potential impact on the evolution of the large and persistent endosperms of cereal grains.
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Affiliation(s)
- Hugh Dickinson
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.
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23
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Schnable JC, Freeling M, Lyons E. Genome-wide analysis of syntenic gene deletion in the grasses. Genome Biol Evol 2012; 4:265-77. [PMID: 22275519 PMCID: PMC3318446 DOI: 10.1093/gbe/evs009] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The grasses, Poaceae, are one of the largest and most successful angiosperm families. Like many radiations of flowering plants, the divergence of the major grass lineages was preceded by a whole-genome duplication (WGD), although these events are not rare for flowering plants. By combining identification of syntenic gene blocks with measures of gene pair divergence and different frequencies of ancient gene loss, we have separated the two subgenomes present in modern grasses. Reciprocal loss of duplicated genes or genomic regions has been hypothesized to reproductively isolate populations and, thus, speciation. However, in contrast to previous studies in yeast and teleost fishes, we found very little evidence of reciprocal loss of homeologous genes between the grasses, suggesting that post-WGD gene loss may not be the cause of the grass radiation. The sets of homeologous and orthologous genes and predicted locations of deleted genes identified in this study, as well as links to the CoGe comparative genomics web platform for analyzing pan-grass syntenic regions, are provided along with this paper as a resource for the grass genetics community.
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Affiliation(s)
- James C Schnable
- Department of Plant and Microbial Biology, University of California-Berkeley, CA, USA
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24
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Schnable JC, Wang X, Pires JC, Freeling M. Escape from preferential retention following repeated whole genome duplications in plants. FRONTIERS IN PLANT SCIENCE 2012; 3:94. [PMID: 22639677 PMCID: PMC3355610 DOI: 10.3389/fpls.2012.00094] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Accepted: 04/24/2012] [Indexed: 05/21/2023]
Abstract
The well supported gene dosage hypothesis predicts that genes encoding proteins engaged in dose-sensitive interactions cannot be reduced back to single copies once all interacting partners are simultaneously duplicated in a whole genome duplication. The genomes of extant flowering plants are the result of many sequential rounds of whole genome duplication, yet the fraction of genomes devoted to encoding complex molecular machines does not increase as fast as expected through multiple rounds of whole genome duplications. Using parallel interspecies genomic comparisons in the grasses and crucifers, we demonstrate that genes retained as duplicates following a whole genome duplication have only a 50% chance of being retained as duplicates in a second whole genome duplication. Genes which fractionated to a single copy following a second whole genome duplication tend to be the member of a gene pair with less complex promoters, lower levels of expression, and to be under lower levels of purifying selection. We suggest the copy with lower levels of expression and less purifying selection contributes less to effective gene-product dosage and therefore is under less dosage constraint in future whole genome duplications, providing an explanation for why flowering plant genomes are not overrun with subunits of large dose-sensitive protein complexes.
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Affiliation(s)
- James C. Schnable
- Freeling Lab, Plant and Microbial Biology, University of California – BerkeleyBerkeley, CA, USA
| | - Xiaowu Wang
- Molecular Genetics Lab, Biotechnology Department, Institute of vegetables and flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - J. Chris Pires
- Biological Sciences, Bond Life Sciences Center, University of MissouriColombia, MO, USA
| | - Michael Freeling
- Freeling Lab, Plant and Microbial Biology, University of California – BerkeleyBerkeley, CA, USA
- *Correspondence: Michael Freeling, Freeling Lab, Plant and Microbial Biology, University of California – Berkeley, 111 Koshland Hall, PMB, Berkeley, CA 94720, USA. e-mail:
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25
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Zhang W, Wu Y, Schnable JC, Zeng Z, Freeling M, Crawford GE, Jiang J. High-resolution mapping of open chromatin in the rice genome. Genome Res 2011; 22:151-62. [PMID: 22110044 DOI: 10.1101/gr.131342.111] [Citation(s) in RCA: 175] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Gene expression is controlled by the complex interaction of transcription factors binding to promoters and other regulatory DNA elements. One common characteristic of the genomic regions associated with regulatory proteins is a pronounced sensitivity to DNase I digestion. We generated genome-wide high-resolution maps of DNase I hypersensitive (DH) sites from both seedling and callus tissues of rice (Oryza sativa). Approximately 25% of the DH sites from both tissues were found in putative promoters, indicating that the vast majority of the gene regulatory elements in rice are not located in promoter regions. We found 58% more DH sites in the callus than in the seedling. For DH sites detected in both the seedling and callus, 31% displayed significantly different levels of DNase I sensitivity within the two tissues. Genes that are differentially expressed in the seedling and callus were frequently associated with DH sites in both tissues. The DNA sequences contained within the DH sites were hypomethylated, consistent with what is known about active gene regulatory elements. Interestingly, tissue-specific DH sites located in the promoters showed a higher level of DNA methylation than the average DNA methylation level of all the DH sites located in the promoters. A distinct elevation of H3K27me3 was associated with intergenic DH sites. These results suggest that epigenetic modifications play a role in the dynamic changes of the numbers and DNase I sensitivity of DH sites during development.
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Affiliation(s)
- Wenli Zhang
- Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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Hudson CM, Puckett EE, Bekaert M, Pires JC, Conant GC. Selection for higher gene copy number after different types of plant gene duplications. Genome Biol Evol 2011; 3:1369-80. [PMID: 22056313 PMCID: PMC3240960 DOI: 10.1093/gbe/evr115] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2011] [Indexed: 01/03/2023] Open
Abstract
The evolutionary origins of the multitude of duplicate genes in the plant genomes are still incompletely understood. To gain an appreciation of the potential selective forces acting on these duplicates, we phylogenetically inferred the set of metabolic gene families from 10 flowering plant (angiosperm) genomes. We then compared the metabolic fluxes for these families, predicted using the Arabidopsis thaliana and Sorghum bicolor metabolic networks, with the families' duplication propensities. For duplications produced by both small scale (small-scale duplications) and genome duplication (whole-genome duplications), there is a significant association between the flux and the tendency to duplicate. Following this global analysis, we made a more fine-scale study of the selective constraints observed on plant sodium and phosphate transporters. We find that the different duplication mechanisms give rise to differing selective constraints. However, the exact nature of this pattern varies between the gene families, and we argue that the duplication mechanism alone does not define a duplicated gene's subsequent evolutionary trajectory. Collectively, our results argue for the interplay of history, function, and selection in shaping the duplicate gene evolution in plants.
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27
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Birchler JA, Veitia RA. Protein-Protein and Protein-DNA Dosage Balance and Differential Paralog Transcription Factor Retention in Polyploids. FRONTIERS IN PLANT SCIENCE 2011; 2:64. [PMID: 22645545 PMCID: PMC3355771 DOI: 10.3389/fpls.2011.00064] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Accepted: 09/22/2011] [Indexed: 05/08/2023]
Affiliation(s)
- James A. Birchler
- Division of Biological Sciences, University of MissouriColumbia, MO, USA
| | - Reiner A. Veitia
- CNRS UMR7592, Institut Jacques MonodParis, France
- Université Paris DiderotParis, France
- *Correspondence to:
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