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Li C, Ma J, Wang G, Li H, Wang H, Wang G, Jiang Y, Liu Y, Liu G, Liu G, Cheng R, Wang H, Wei J, Yao L. Exploring the SiCCT Gene Family and Its Role in Heading Date in Foxtail Millet. Front Plant Sci 2022; 13:863298. [PMID: 35755676 PMCID: PMC9218912 DOI: 10.3389/fpls.2022.863298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
CCT transcription factors are involved in the regulation of photoperiod and abiotic stress in Arabidopsis and rice. It is not clear that how CCT gene family expand and regulate heading date in foxtail millet. In this study, we conducted a systematic analysis of the CCT gene family in foxtail millet. Thirty-nine CCT genes were identified and divided into four subfamilies based on functional motifs. Analysis showed that dispersed duplication played a predominant role in the expansion of CCT genes during evolution. Nucleotide diversity analysis suggested that genes in CONSTANS (COL)-like, CCT MOTIF FAMILY (CMF)-like, and pseudoresponse response regulator (PRR)-like subfamilies were subjected to selection. Fifteen CCT genes were colocalized with previous heading date quantitative trait loci (QTL) and genome-wide association analysis (GWAS) signals. Transgenic plants were then employed to confirm that overexpression of the CCT gene SiPRR37 delayed the heading date and increased plant height. Our study first investigated the characterization and expansion of the CCT family in foxtail millet and demonstrated the role of SiPRR37. These results lay a significant foundation for further research on the function of CCT genes and provide a cue for the regulation of heading date.
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Affiliation(s)
- Congcong Li
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Biotechnology Research, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, China
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jian Ma
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Vegetable Research, Beijing Key Laboratory of Vegetable Germplasm Improvement, National Engineering Research Center for Vegetables, Beijing, China
| | - Genping Wang
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Haiquan Li
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Hailong Wang
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Biotechnology Research, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, China
| | - Guoliang Wang
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Biotechnology Research, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, China
| | - Yanmiao Jiang
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Yanan Liu
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Guiming Liu
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Biotechnology Research, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, China
| | - Guoqing Liu
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Ruhong Cheng
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Huan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianhua Wei
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Biotechnology Research, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, China
| | - Lei Yao
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Biotechnology Research, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, China
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Chang AYF, Liao BY. Recruitment of histone modifications to assist mRNA dosage maintenance after degeneration of cytosine DNA methylation during animal evolution. Genome Res 2017; 27:1513-1524. [PMID: 28720579 PMCID: PMC5580711 DOI: 10.1101/gr.221739.117] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 07/05/2017] [Indexed: 12/24/2022]
Abstract
Following gene duplication, mRNA expression of the duplicated gene is reduced to maintain mRNA dosage. In mammals, this process is achieved with increased cytosine DNA methylation of the promoters of duplicated genes to suppress transcriptional initiation. However, not all animal species possess a full apparatus for cytosine DNA methylation. For such species, such as the roundworm (Caenorhabditis elegans, "worm" hereafter) or fruit fly (Drosophila melanogaster, "fly" hereafter), it is unclear how reduced expression of duplicated genes has been achieved evolutionarily. Here, we hypothesize that in the absence of a classical cytosine DNA methylation pathway, histone modifications play an increasing role in maintaining mRNA dosage following gene duplication. We initially verified that reduced gene expression of duplicated genes had occurred in the worm, fly, and mouse (Mus musculus). Next, several histone marks, with the capacity to control mRNA abundance in the models studied, were examined. In the worm and fly, but not in the mouse, multiple histone modifications were found to assist mRNA dosage maintenance following gene duplication events and the possible involvement of adenine DNA methylation in this process was excluded. Furthermore, the histone marks and acting regions that mediated the reduction in duplicated gene expression were found to be largely organism specific. Thus, it appears that many of the histone marks that maintain mRNA dosage were independently recruited during the evolution of worms and flies to compensate for the loss of cytosine DNA methylation machinery from their genomes.
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Affiliation(s)
- Andrew Ying-Fei Chang
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli County 350, Taiwan, Republic of China
| | - Ben-Yang Liao
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli County 350, Taiwan, Republic of China
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Wang J, Tao F, Marowsky NC, Fan C. Evolutionary Fates and Dynamic Functionalization of Young Duplicate Genes in Arabidopsis Genomes. Plant Physiol 2016; 172:427-40. [PMID: 27485883 PMCID: PMC5074645 DOI: 10.1104/pp.16.01177] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 08/01/2016] [Indexed: 05/02/2023]
Abstract
Gene duplication is a primary means to generate genomic novelties, playing an essential role in speciation and adaptation. Particularly in plants, a high abundance of duplicate genes has been maintained for significantly long periods of evolutionary time. To address the manner in which young duplicate genes were derived primarily from small-scale gene duplication and preserved in plant genomes and to determine the underlying driving mechanisms, we generated transcriptomes to produce the expression profiles of five tissues in Arabidopsis thaliana and the closely related species Arabidopsis lyrata and Capsella rubella Based on the quantitative analysis metrics, we investigated the evolutionary processes of young duplicate genes in Arabidopsis. We determined that conservation, neofunctionalization, and specialization are three main evolutionary processes for Arabidopsis young duplicate genes. We explicitly demonstrated the dynamic functionalization of duplicate genes along the evolutionary time scale. Upon origination, duplicates tend to maintain their ancestral functions; but as they survive longer, they might be likely to develop distinct and novel functions. The temporal evolutionary processes and functionalization of plant duplicate genes are associated with their ancestral functions, dynamic DNA methylation levels, and histone modification abundances. Furthermore, duplicate genes tend to be initially expressed in pollen and then to gain more interaction partners over time. Altogether, our study provides novel insights into the dynamic retention processes of young duplicate genes in plant genomes.
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Affiliation(s)
- Jun Wang
- Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202
| | - Feng Tao
- Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202
| | - Nicholas C Marowsky
- Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202
| | - Chuanzhu Fan
- Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202
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Abstract
Eukaryotic genomes have large numbers of duplicated genes that can evolve new functions or expression patterns by changes in coding and regulatory sequences, referred to as neofunctionalization. In flowering plants, some duplicated genes are imprinted in the endosperm, where only one allele is expressed depending on its parental origin. We found that 125 imprinted genes in Arabidopsis arose from gene duplication events during the evolution of the Brassicales. Analyses of 46 gene pairs duplicated by an ancient whole-genome duplication (alpha WGD) indicated that many imprinted genes show an accelerated rate of amino acid changes compared with their paralogs. Analyses of microarray expression data from 63 organ types and developmental stages indicated that many imprinted genes have expression patterns restricted to flowers and/or seeds in contrast to their broadly expressed paralogs. Assays of expression in orthologs from outgroup species revealed that some imprinted genes have acquired an organ-specific expression pattern restricted to flowers and/or seeds. The changes in expression pattern and the accelerated sequence evolution in the imprinted genes suggest that some of them may have undergone neofunctionalization. The imprinted genes MPC, HOMEODOMAIN GLABROUS6 (HDG6), and HDG3 are particularly interesting cases that have different functions from their paralogs. This study indicates that a large number of imprinted genes in Arabidopsis are evolutionarily recent duplicates and that many of them show changes in expression profiles and accelerated sequence evolution. Acquisition of imprinting is a mode of duplicate gene divergence in plants that is more common than previously thought.
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Affiliation(s)
- Yichun Qiu
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Shao-Lun Liu
- Department of Life Science, Tunghai University, Taichung, Taiwan
| | - Keith L. Adams
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- *Corresponding author: E-mail:
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Abstract
Gene duplications during eukaroytic evolution, by successive rounds of polyploidy and by smaller scale duplications, have provided an enormous reservoir of new genes for the evolution of new functions. Preservation of many duplicated genes can be ascribed to changes in sequences, expression patterns, and functions. Protein subcellular relocalization (protein targeting to a new location within the cell) is another way that duplicated genes can diverge. We studied subcellular relocalization of gene pairs duplicated during the evolution of the Brassicaceae including gene pairs from the alpha whole genome duplication that occurred at the base of the family. We analyzed experimental localization data from green fluorescent protein experiments for 128 duplicate pairs in Arabidopsis thaliana, revealing 19 pairs with subcellular relocalization. Many more of the duplicate pairs with relocalization than with the same localization showed an accelerated rate of amino acid sequence evolution in one duplicate, and one gene showed evidence for positive selection. We studied six duplicate gene pairs in more detail. We used gene family analysis with several pairs to infer which gene shows relocalization. We identified potential sequence mutations through comparative analysis that likely result in relocalization of two duplicated gene products. We show that four cases of relocalization have new expression patterns, compared with orthologs in outgroup species, including two with novel expression in pollen. This study provides insights into subcellular relocalization of evolutionarily recent gene duplicates and features of genes whose products have been relocalized.
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Affiliation(s)
- Shao-Lun Liu
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada Present address: Department of Life Science, Tunghai University, Taichung, Taiwan
| | - An Qi Pan
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada Present address: Mintec Inc., Vancouver, BC, Canada
| | - Keith L Adams
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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