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Kumar A, Kumar S, Venkatesh K, Singh NK, Mandal PK, Sinha SK. Physio-molecular traits of contrasting bread wheat genotypes associated with 15N influx exhibiting homeolog expression bias in nitrate transporter genes under different external nitrate concentrations. PLANTA 2022; 255:104. [PMID: 35416522 DOI: 10.1007/s00425-022-03890-7] [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: 12/20/2021] [Accepted: 03/31/2022] [Indexed: 06/14/2023]
Abstract
The high affinity nitrate transport system is a potential target for improving nitrogen use efficiency of bread wheat growing either under optimal or limiting nitrate concentration. Nitrate uptake is one of the most important traits to take into account to improve nitrogen use efficiency in wheat (Triticum aestivum L.). In this study, we aimed to gain an insight into the regulation of NO3- -uptake and translocation systems in two contrasting wheat genotypes [K9107(K9) vs. Choti Lerma (CL)]. Different conditions, such as NO3--uptake rates, soil-types, N-free solid external media, and external NO3- levels at the seedling stage, were considered. We also studied the contribution of homeolog expression of five genes encoding two nitrate transporters in the root tissue, along with their overall transcript expression levels relative to specific external nitrate availability. We observed that K9107 had a higher 15N influx than Choti Lerma under both limiting as well as optimum external N conditions in vermiculite-perlite (i.e., N-free solid) medium, with the improved translocation efficiency in Choti Lerma. However, in different soil types, different levels of 15N-enrichment in both the genotypes were found. Our results also demonstrated that the partitioning of dry matter in root and shoot was different under these growing conditions. Moreover, K9107 showed significantly higher relative expression of TaNRT2.1 at the lowest and TaNPF6.1 and TaNPF6.2 at the highest external nitrate concentrations. We also observed genotype-specific and nitrate starvation-dependent homeolog expression bias in all five nitrate transporter genes. Our data suggest that K9107 had a higher NO3- influx capacity, involving different nitrate transporters, than Choti Lerma at the seedling stage.
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Affiliation(s)
- Amresh Kumar
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Sarvendra Kumar
- Department of Soil Science and Agricultural Chemistry, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India
| | - Karnam Venkatesh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India
| | - Nagendra Kumar Singh
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Pranab Kumar Mandal
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Subodh Kumar Sinha
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India.
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2
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Kuo TCY, Hatakeyama M, Tameshige T, Shimizu KK, Sese J. Homeolog expression quantification methods for allopolyploids. Brief Bioinform 2021; 21:395-407. [PMID: 30590436 PMCID: PMC7299288 DOI: 10.1093/bib/bby121] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/06/2018] [Accepted: 11/21/2018] [Indexed: 12/19/2022] Open
Abstract
Genome duplication with hybridization, or allopolyploidization, occurs in animals, fungi and plants, and is especially common in crop plants. There is an increasing interest in the study of allopolyploids because of advances in polyploid genome assembly; however, the high level of sequence similarity in duplicated gene copies (homeologs) poses many challenges. Here we compared standard RNA-seq expression quantification approaches used currently for diploid species against subgenome-classification approaches which maps reads to each subgenome separately. We examined mapping error using our previous and new RNA-seq data in which a subgenome is experimentally added (synthetic allotetraploid Arabidopsis kamchatica) or reduced (allohexaploid wheat Triticum aestivum versus extracted allotetraploid) as ground truth. The error rates in the two species were very similar. The standard approaches showed higher error rates (>10% using pseudo-alignment with Kallisto) while subgenome-classification approaches showed much lower error rates (<1% using EAGLE-RC, <2% using HomeoRoq). Although downstream analysis may partly mitigate mapping errors, the difference in methods was substantial in hexaploid wheat, where Kallisto appeared to have systematic differences relative to other methods. Only approximately half of the differentially expressed homeologs detected using Kallisto overlapped with those by any other method in wheat. In general, disagreement in low-expression genes was responsible for most of the discordance between methods, which is consistent with known biases in Kallisto. We also observed that there exist uncertainties in genome sequences and annotation which can affect each method differently. Overall, subgenome-classification approaches tend to perform better than standard approaches with EAGLE-RC having the highest precision.
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Affiliation(s)
- Tony C Y Kuo
- Artificial Intelligence Research Center, AIST, 2-3-26 Aomi, Koto-ku, Tokyo 135-0064, Japan.,AIST-Tokyo Tech RWBC-OIL, 2-12-1 Okayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Masaomi Hatakeyama
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland.,Functional Genomics Center Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge - Batiment Genopode, Lausanne 1015, Switzerland
| | - Toshiaki Tameshige
- Kihara Institute for Biological Research, Yokohama City University, 641-12, Maioka, Totsuka-ku, Yokohama 244-0813, Japan
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland.,Kihara Institute for Biological Research, Yokohama City University, 641-12, Maioka, Totsuka-ku, Yokohama 244-0813, Japan
| | - Jun Sese
- Artificial Intelligence Research Center, AIST, 2-3-26 Aomi, Koto-ku, Tokyo 135-0064, Japan.,AIST-Tokyo Tech RWBC-OIL, 2-12-1 Okayama, Meguro-ku, Tokyo 152-8550, Japan
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3
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Peng Z, Cheng H, Sun G, Pan Z, Wang X, Geng X, He S, Du X. Expression patterns and functional divergence of homologous genes accompanied by polyploidization in cotton (Gossypium hirsutum L.). SCIENCE CHINA-LIFE SCIENCES 2020; 63:1565-1579. [PMID: 32112269 DOI: 10.1007/s11427-019-1618-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 01/07/2020] [Indexed: 12/22/2022]
Abstract
Naturally allotetraploid cotton has been widely used as an ideal model to investigate gene expression remodeling as a consequence of polyploidization. However, the global gene pattern variation during early fiber development was unknown. In this study, through RNA-seq technology, we comprehensively investigated the expression patterns of homologous genes between allotetraploid cotton (G. hirsutum) and its diploid progenitors (G. arboreum and G. raimondii) at the fiber early development stage. In tetraploid cotton, genes showed expression level dominance (ELD) bias toward the A genome. This phenomenon was explained by the up-/downregulation of the homologs from the nondominant progenitor (D genome). Gene ontology (GO) enrichment results indicated that the ELD-A genes might be a prominent cause responsible for fiber property change through regulating the fatty acid biosynthesis/metabolism and microtubule procession, and the ELD-D genes might be involved in transcription regulation and stress inducement. In addition, the number and proportion of completely A- and D-subfunctionalized gene were similar at different fiber development stages. However, for neofunctionalization, the number and proportion of reactivated D-derived genes were greater than those of A at 3 and 5 DPA. Eventually, we found that some homologous genes belonging to several specific pathways might create novel asymmetric transcripts between two subgenomes during polyploidization and domestication process, further making the fiber property meet the human demands. Our study identified determinate pathways and their involved genes between allotetraploid cotton and their progenitors at early fiber development stages, providing new insights into the mechanism of cotton fiber evolution.
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Affiliation(s)
- Zhen Peng
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, 455000, China.,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Hua Cheng
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, 455000, China.,Anyang Institute of Technology, Anyang, 455000, China
| | - Gaofei Sun
- Anyang Institute of Technology, Anyang, 455000, China
| | - Zhaoe Pan
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, 455000, China
| | - Xiao Wang
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, 455000, China
| | - Xiaoli Geng
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, 455000, China
| | - Shoupu He
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, 455000, China. .,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China.
| | - Xiongming Du
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, 455000, China. .,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China.
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4
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Conserved noncoding sequences conserve biological networks and influence genome evolution. Heredity (Edinb) 2018; 120:437-451. [PMID: 29396421 DOI: 10.1038/s41437-018-0055-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 12/14/2017] [Accepted: 01/08/2018] [Indexed: 01/24/2023] Open
Abstract
Comparative genomics approaches have identified numerous conserved cis-regulatory sequences near genes in plant genomes. Despite the identification of these conserved noncoding sequences (CNSs), our knowledge of their functional importance and selection remains limited. Here, we used a combination of DNA methylome analysis, microarray expression analyses, and functional annotation to study these sequences in the model tree Populus trichocarpa. Methylation in CG contexts and non-CG contexts was lower in CNSs, particularly CNSs in the 5'-upstream regions of genes, compared with other sites in the genome. We observed that CNSs are enriched in genes with transcription and binding functions, and this also associated with syntenic genes and those from whole-genome duplications, suggesting that cis-regulatory sequences play a key role in genome evolution. We detected a significant positive correlation between CNS number and protein interactions, suggesting that CNSs may have roles in the evolution and maintenance of biological networks. The divergence of CNSs indicates that duplication-degeneration-complementation drives the subfunctionalization of a proportion of duplicated genes from whole-genome duplication. Furthermore, population genomics confirmed that most CNSs are under strong purifying selection and only a small subset of CNSs shows evidence of adaptive evolution. These findings provide a foundation for future studies exploring these key genomic features in the maintenance of biological networks, local adaptation, and transcription.
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Sun Y, Wu Y, Yang C, Sun S, Lin X, Liu L, Xu C, Wendel JF, Gong L, Liu B. Segmental allotetraploidy generates extensive homoeologous expression rewiring and phenotypic diversity at the population level in rice. Mol Ecol 2017; 26:5451-5466. [PMID: 28802080 DOI: 10.1111/mec.14297] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 06/04/2017] [Accepted: 07/24/2017] [Indexed: 02/03/2023]
Abstract
Allopolyploidization, that is, concomitant merging and doubling of two or more divergent genomes in a common nucleus/cytoplasm, is known to instantly alter genomewide transcriptome dynamics, a phenomenon referred to as "transcriptomic shock." However, the immediate effects of transcriptomic alteration in generating phenotypic diversity at the population level remain underinvestigated. Here, we employed the MassARRAY-based Sequenom platform to assess and compare orthologous, allelic and homoeologous gene expression status in two tissues (leaf and root) of a set of randomly chosen individuals from populations of parental rice subspecies (indica and japonica), in vitro "hybrids" (parental mixes), reciprocal F1 hybrids and reciprocal tetraploids at the 5th-selfed generation (S5). We show that hybridization and whole genome duplication (WGD) have opposing effects on allelic and homoeologous expression in the F1 hybrids and tetraploids, respectively. Whereas hybridization exerts strong attenuating effects on allelic expression differences in diploid hybrids, WGD augments the intrinsic parental differences and generates extensive and variable homoeolog content which triggers diversification in expression patterning among the tetraploid plants. Coupled with the vast phenotypic diversity observed among the tetraploid individuals, our results provide experimental evidence in support of the notion that allopolyploidy catalyses rapid phenotypic diversification in higher plants. Our data further suggest that largely stochastic homoeolog content reshuffling rather than alteration in total expression level may be an important feature of evolution in young segmental allopolyploids, which underlies rapid expression diversity at the population level.
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Affiliation(s)
- Yue Sun
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Ying Wu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Chunwu Yang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Shuai Sun
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Xiuyun Lin
- Jilin Academy of Agriculture, Changchun, China
| | - Lixia Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Chunming Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China.,Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
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6
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Xu Y, Wu H, Zhao M, Wu W, Xu Y, Gu D. Overexpression of the Transcription Factors GmSHN1 and GmSHN9 Differentially Regulates Wax and Cutin Biosynthesis, Alters Cuticle Properties, and Changes Leaf Phenotypes in Arabidopsis. Int J Mol Sci 2016; 17:E587. [PMID: 27110768 PMCID: PMC4849042 DOI: 10.3390/ijms17040587] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Revised: 03/29/2016] [Accepted: 04/12/2016] [Indexed: 11/16/2022] Open
Abstract
SHINE (SHN/WIN) clade proteins, transcription factors of the plant-specific APETALA 2/ethylene-responsive element binding factor (AP2/ERF) family, have been proven to be involved in wax and cutin biosynthesis. Glycine max is an important economic crop, but its molecular mechanism of wax biosynthesis is rarely characterized. In this study, 10 homologs of Arabidopsis SHN genes were identified from soybean. These homologs were different in gene structures and organ expression patterns. Constitutive expression of each of the soybean SHN genes in Arabidopsis led to different leaf phenotypes, as well as different levels of glossiness on leaf surfaces. Overexpression of GmSHN1 and GmSHN9 in Arabidopsis exhibited 7.8-fold and 9.9-fold up-regulation of leaf cuticle wax productions, respectively. C31 and C29 alkanes contributed most to the increased wax contents. Total cutin contents of leaves were increased 11.4-fold in GmSHN1 overexpressors and 5.7-fold in GmSHN9 overexpressors, mainly through increasing C16:0 di-OH and dioic acids. GmSHN1 and GmSHN9 also altered leaf cuticle membrane ultrastructure and increased water loss rate in transgenic Arabidopsis plants. Transcript levels of many wax and cutin biosynthesis and leaf development related genes were altered in GmSHN1 and GmSHN9 overexpressors. Overall, these results suggest that GmSHN1 and GmSHN9 may differentially regulate the leaf development process as well as wax and cutin biosynthesis.
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Affiliation(s)
- Yangyang Xu
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Hanying Wu
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Mingming Zhao
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Wang Wu
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yinong Xu
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Dan Gu
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
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7
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Kake-Guena SA, Touisse K, Vergilino R, Dufresne F, Blier PU, Lemieux H. Assessment of mitochondrial functions inDaphnia pulexclones using high-resolution respirometry. ACTA ACUST UNITED AC 2015; 323:292-300. [DOI: 10.1002/jez.1913] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 12/12/2014] [Accepted: 12/15/2014] [Indexed: 12/25/2022]
Affiliation(s)
| | - Kamal Touisse
- Campus Saint-Jean; University of Alberta; Edmonton Alberta Canada
| | - Roland Vergilino
- Département de biologie; Laboratoire de Physiologie Animale Intégrative; Université du Québec à Rimouski; Rimouski Québec Canada
| | - France Dufresne
- Département de biologie; Laboratoire de Physiologie Animale Intégrative; Université du Québec à Rimouski; Rimouski Québec Canada
| | - Pierre U. Blier
- Département de biologie; Laboratoire de Physiologie Animale Intégrative; Université du Québec à Rimouski; Rimouski Québec Canada
| | - Hélène Lemieux
- Campus Saint-Jean; University of Alberta; Edmonton Alberta Canada
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8
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Buggs RJA, Wendel JF, Doyle JJ, Soltis DE, Soltis PS, Coate JE. The legacy of diploid progenitors in allopolyploid gene expression patterns. Philos Trans R Soc Lond B Biol Sci 2015; 369:rstb.2013.0354. [PMID: 24958927 DOI: 10.1098/rstb.2013.0354] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Allopolyploidization (hybridization and whole-genome duplication) is a common phenomenon in plant evolution with immediate saltational effects on genome structure and gene expression. New technologies have allowed rapid progress over the past decade in our understanding of the consequences of allopolyploidy. A major question, raised by early pioneer of this field Leslie Gottlieb, concerned the extent to which gene expression differences among duplicate genes present in an allopolyploid are a legacy of expression differences that were already present in the progenitor diploid species. Addressing this question necessitates phylogenetically well-understood natural study systems, appropriate technology, availability of genomic resources and a suitable analytical framework, including a sufficiently detailed and generally accepted terminology. Here, we review these requirements and illustrate their application to a natural study system that Gottlieb worked on and recommended for this purpose: recent allopolyploids of Tragopogon (Asteraceae). We reanalyse recent data from this system within the conceptual framework of parental legacies on duplicate gene expression in allopolyploids. On a broader level, we highlight the intellectual connection between Gottlieb's phrasing of this issue and the more contemporary framework of cis- versus trans-regulation of duplicate gene expression in allopolyploid plants.
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Affiliation(s)
- Richard J A Buggs
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames IA 50011, USA
| | - Jeffrey J Doyle
- L. H. Bailey Hortorium, Department of Plant Biology, Cornell University, Ithaca, NY 14853, USA
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL 32611, USA Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Jeremy E Coate
- Department of Biology, Reed College, Portland, OR 97202, USA
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9
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Abstract
Allopolyploidization in plants entails the merger of two divergent nuclear genomes, typically with only one set (usually maternal) of parental plastidial and mitochondrial genomes and with an altered cytonuclear stoichiometry. Thus, we might expect cytonuclear coevolution to be an important dimension of allopolyploid evolution. Here, we investigate cytonuclear coordination for the key chloroplast protein rubisco (ribulose 1,5-bisphosphate carboxylase/oxygenase), which is composed of nuclear-encoded, small subunits (SSUs) and plastid-encoded, large subunits. By studying gene composition and diversity as well as gene expression in four model allopolyploid lineages, Arabidopsis, Arachis, Brassica, and Nicotiana, we demonstrate that paralogous nuclear-encoded rbcS genes within diploids are subject to homogenization via gene conversion and that such concerted evolution via gene conversion characterizes duplicated genes (homoeologs) at the polyploid level. Many gene conversions in the polyploids are intergenomic with respect to the diploid progenitor genomes, occur in functional domains of the homoeologous SSUs, and are directionally biased, such that the maternal amino acid states are favored. This consistent preferential maternal-to-paternal gene conversion is mirrored at the transcriptional level, with a uniform transcriptional bias of the maternal-like rbcS homoeologs. These data, repeated among multiple diverse angiosperm genera for an important photosynthetic enzyme, suggest that cytonuclear coevolution may be mediated by intergenomic gene conversion and altered transcription of duplicated, now homoeologous nuclear genes.
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Affiliation(s)
- Lei Gong
- Department of Ecology, Evolution and Organismal Biology, Iowa State University
| | - Mischa Olson
- Department of Ecology, Evolution and Organismal Biology, Iowa State University Department of Plant Biology, Cornell University
| | - Jonathan F Wendel
- Department of Ecology, Evolution and Organismal Biology, Iowa State University
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10
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Akama S, Shimizu-Inatsugi R, Shimizu KK, Sese J. Genome-wide quantification of homeolog expression ratio revealed nonstochastic gene regulation in synthetic allopolyploid Arabidopsis. Nucleic Acids Res 2014; 42:e46. [PMID: 24423873 PMCID: PMC3973336 DOI: 10.1093/nar/gkt1376] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 11/26/2013] [Accepted: 12/14/2013] [Indexed: 12/31/2022] Open
Abstract
Genome duplication with hybridization, or allopolyploidization, occurs commonly in plants, and is considered to be a strong force for generating new species. However, genome-wide quantification of homeolog expression ratios was technically hindered because of the high homology between homeologous gene pairs. To quantify the homeolog expression ratio using RNA-seq obtained from polyploids, a new method named HomeoRoq was developed, in which the genomic origin of sequencing reads was estimated using mismatches between the read and each parental genome. To verify this method, we first assembled the two diploid parental genomes of Arabidopsis halleri subsp. gemmifera and Arabidopsis lyrata subsp. petraea (Arabidopsis petraea subsp. umbrosa), then generated a synthetic allotetraploid, mimicking the natural allopolyploid Arabidopsis kamchatica. The quantified ratios corresponded well to those obtained by Pyrosequencing. We found that the ratios of homeologs before and after cold stress treatment were highly correlated (r = 0.870). This highlights the presence of nonstochastic polyploid gene regulation despite previous research identifying stochastic variation in expression. Moreover, our new statistical test incorporating overdispersion identified 226 homeologs (1.11% of 20 369 expressed homeologs) with significant ratio changes, many of which were related to stress responses. HomeoRoq would contribute to the study of the genes responsible for polyploid-specific environmental responses.
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Affiliation(s)
- Satoru Akama
- Department of Computer Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan and Institute of Evolutionary Biology and Environmental Studies and Institute of Plant Biology, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Rie Shimizu-Inatsugi
- Department of Computer Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan and Institute of Evolutionary Biology and Environmental Studies and Institute of Plant Biology, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Kentaro K. Shimizu
- Department of Computer Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan and Institute of Evolutionary Biology and Environmental Studies and Institute of Plant Biology, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Jun Sese
- Department of Computer Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan and Institute of Evolutionary Biology and Environmental Studies and Institute of Plant Biology, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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11
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Xu C, Bai Y, Lin X, Zhao N, Hu L, Gong Z, Wendel JF, Liu B. Genome-wide disruption of gene expression in allopolyploids but not hybrids of rice subspecies. Mol Biol Evol 2014; 31:1066-76. [PMID: 24577842 PMCID: PMC3995341 DOI: 10.1093/molbev/msu085] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Hybridization and polyploidization are prominent processes in plant evolution. Hybrids and allopolyploids typically exhibit radically altered gene expression patterns relative to their parents, a phenomenon termed “transcriptomic shock.” To distinguish the effects of hybridization from polyploidization on coregulation of divergent alleles, we analyzed expression of parental copies (homoeologs) of 11,608 genes using RNA-seq-based transcriptome profiling in reciprocal hybrids and tetraploids constructed from subspecies japonica and indica of Asian rice (Oryza sativa L.). The diploid hybrids and their derived allopolyploids differ dramatically in morphology, despite having the same suite of genes and genic proportions. Allelic and homoeolog-specific transcripts were unequivocally diagnosed in the hybrids and tetraploids based on parent-specific SNPs. Compared with the in silico hybrid (parental mix), the range of progenitor expression divergence was significantly reduced in both reciprocally generated F1 hybrids, presumably due to the ameliorating effects of a common trans environment on divergent cis-factors. In contrast, parental expression differences were greatly elaborated at the polyploid level, which we propose is a consequence of stoichiometric disruptions associated with the numerous chromosomal packaging and volumetric changes accompanying nascent polyploidy. We speculate that the emergent property of “whole genome doubling” has repercussions that reverberate throughout the transcriptome and downstream, ultimately generating altered phenotypes. This perspective may yield insight into the nature of adaptation and the origin of evolutionary novelty accompanying polyploidy.
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Affiliation(s)
- Chunming Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
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12
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Dufresne F, Stift M, Vergilino R, Mable BK. Recent progress and challenges in population genetics of polyploid organisms: an overview of current state-of-the-art molecular and statistical tools. Mol Ecol 2013; 23:40-69. [DOI: 10.1111/mec.12581] [Citation(s) in RCA: 248] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 10/29/2013] [Accepted: 10/30/2013] [Indexed: 12/19/2022]
Affiliation(s)
- France Dufresne
- Département de Biologie; Université du Québec à Rimouski; Québec QC Canada G5L 3A1
| | - Marc Stift
- Department of Biology; University of Konstanz; Konstanz D 78457 Germany
| | - Roland Vergilino
- Department of Integrative Biology; University of Guelph; Guelph ON Canada N1G 2W1
| | - Barbara K. Mable
- Institute of Biodiversity; Animal Health and Comparative Medicine; College of Medical, Veterinary and Life Sciences; University of Glasgow; Glasgow UK
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Polyploids and hybrids in changing environments: winners or losers in the struggle for adaptation? Heredity (Edinb) 2013; 110:95-6. [PMID: 23321773 DOI: 10.1038/hdy.2012.105] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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