14 results on '"Qian, Hao"'
Search Results
2. The dissection of R genes and locus Pc5.1 in Phytophthora capsici infection provides a novel view of disease resistance in peppers
- Author
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Jin-Song Du, Lin-Feng Hang, Qian Hao, Hai-Tao Yang, Siyad Ali, Radwa Salah Ezaat Badawy, Xiao-Yu Xu, Hua-Qiang Tan, Li-Hong Su, Huan-Xiu Li, Kai-Xi Zou, Yu Li, Bo Sun, Li-Jin Lin, and Yun-Song Lai
- Subjects
Root rot ,Disease resistance ,R gene ,NBS-ARC domain ,RNA-seq ,Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Phytophthora capsici root rot (PRR) is a disastrous disease in peppers (Capsicum spp.) caused by soilborne oomycete with typical symptoms of necrosis and constriction at the basal stem and consequent plant wilting. Most studies on the QTL mapping of P. capsici resistance suggested a consensus broad-spectrum QTL on chromosome 5 named Pc.5.1 regardless of P. capsici isolates and resistant resources. In addition, all these reports proposed NBS-ARC domain genes as candidate genes controlling resistance. Results We screened out 10 PRR-resistant resources from 160 Capsicum germplasm and inspected the response of locus Pc.5.1 and NBS-ARC genes during P. capsici infection by comparing the root transcriptomes of resistant pepper 305R and susceptible pepper 372S. To dissect the structure of Pc.5.1, we anchored genetic markers onto pepper genomic sequence and made an extended Pc5.1 (Ext-Pc5.1) located at 8.35 Mb–38.13 Mb on chromosome 5 which covered all Pc5.1 reported in publications. A total of 571 NBS-ARC genes were mined from the genome of pepper CM334 and 34 genes were significantly affected by P. capsici infection in either 305R or 372S. Only 5 inducible NBS-ARC genes had LRR domains and none of them was positioned at Ext-Pc5.1. Ext-Pc5.1 did show strong response to P. capsici infection and there were a total of 44 differentially expressed genes (DEGs), but no candidate genes proposed by previous publications was included. Snakin-1 (SN1), a well-known antimicrobial peptide gene located at Pc5.1, was significantly decreased in 372S but not in 305R. Moreover, there was an impressive upregulation of sugar pathway genes in 305R, which was confirmed by metabolite analysis of roots. The biological processes of histone methylation, histone phosphorylation, DNA methylation, and nucleosome assembly were strongly activated in 305R but not in 372S, indicating an epigenetic-related defense mechanism. Conclusions Those NBS-ARC genes that were suggested to contribute to Pc5.1 in previous publications did not show any significant response in P. capsici infection and there were no significant differences of these genes in transcription levels between 305R and 372S. Other pathogen defense-related genes like SN1 might account for Pc5.1. Our study also proposed the important role of sugar and epigenetic regulation in the defense against P. capsici.
- Published
- 2021
- Full Text
- View/download PDF
3. A transcriptomic profile of topping responsive non-coding RNAs in tobacco roots (Nicotiana tabacum)
- Author
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Xi Chen, Shuo Sun, Fangjie Liu, Enhui Shen, Lu Liu, Chuyu Ye, Bingguang Xiao, Michael P. Timko, Qian-Hao Zhu, Longjiang Fan, and Peijian Cao
- Subjects
Co-expression network ,Circular RNA ,Long non-coding RNA ,microRNA ,Nicotiana tabacum ,Topping ,Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long ncRNAs (lncRNAs) and circular RNAs (circRNAs), accomplish remarkable variety of biological functions. However, the composition of ncRNAs and their interactions with coding RNAs in modulating and controlling of cellular process in plants is largely unknown. Using a diverse group of high-throughput sequencing strategies, the mRNA, miRNA, lncRNA and circRNA compositions of tobacco (Nicotiana tabacum) roots determined and their alteration and potential biological functions in response to topping treatment analyzed. Results A total of 688 miRNAs, 7423 non-redundant lncRNAs and 12,414 circRNAs were identified, among which, some selected differentially expressed RNAs were verified by quantitative real-time PCR. Using the differentially expressed RNAs, a co-expression network was established that included all four types of RNAs. The number of circRNAs identified were higher than that of miRNAs and lncRNAs, but only two circRNAs were present in the co-expression network. LncRNAs appear to be the most active ncRNAs based on their numbers presented in the co-expression network, but none of them seems to be an eTM (endogenous Target Mimicry) of miRNAs. Integrated with analyses of sequence interaction, several mRNA-circRNA-miRNA interaction networks with a potential role in the regulation of nicotine biosynthesis were uncovered, including a QS-circQS-miR6024 interaction network. In this network miR6024 was significantly down-regulated, while the expression levels of its two targets, circQS and its host gene QS, were sharply increased following the topping treatment. Conclusions These results illustrated the transcriptomic profiles of tobacco roots, the organ responsible for nicotine biosynthesis. mRNAs always play the most important roles, while ncRNAs are also expressed extensively for topping treatment response, especially circRNAs are the most activated in the ncRNA pool. These studies also provided insights on the coordinated regulation module of coding and non-coding RNAs in a single plant biological sample. The findings reported here indicate that ncRNAs appear to form interaction complex for the regulation of stress response forming regulation networks with transcripts involved in nicotine biosynthesis in tobacco.
- Published
- 2019
- Full Text
- View/download PDF
4. Genome-wide identification of oil biosynthesis-related long non-coding RNAs in allopolyploid Brassica napus
- Author
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Enhui Shen, Xintian Zhu, Shuijin Hua, Hongyu Chen, Chuyu Ye, Longhua Zhou, Qing Liu, Qian-Hao Zhu, Longjiang Fan, and Xi Chen
- Subjects
Brassica napus ,lncRNA ,Coexpression ,Oil biosynthesis ,Conservation ,Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Long noncoding RNAs (lncRNAs) are transcripts longer than 200 bp that do not encode proteins but nonetheless have been shown to play important roles in various biological processes in plants. Brassica napus is an important seed oil crop worldwide and the target of many genetic improvement activities. To understand better the function of lncRNAs in regulating plant metabolic activities, we carried out a genome-wide lncRNA identification of lncRNAs in Brassica napus with a focus on lncRNAs involved in lipid metabolism. Twenty ribosomal RNA depleted strand specific RNA-seq (ssRNA-seq) datasets were generatred using RNAs isolated from B. napus seeds at four developmental stages. For comparison we also included 30 publically available RNA-seq datasets generated from poly(A) enriched mRNAs isolated from from various Brassica napus tissues in our analysis. Results A total of 8905 lncRNA loci were identified, including 7100 long intergenic noncoding RNA (lincRNA) loci and 1805 loci generating long noncoding natural antisense transcript (lncNAT). Many lncRNAs were identified only in the ssRNA-seq and poly(A) RNA-seq dataset, suggesting that B. napus has a large lncRNA repertoire and it is necessary to use libraries prepared from different tissues and developmental stages as well as different library preparation approaches to capture the whole spectrum of lncRNAs. Analysis of coexpression networks revealed that among the regulatory modules are networks containing lncRNAs and protein-coding genes related to oil biosynthesis indicating a possible role of lncRNAs in the control of lipid metabolism. One such example is that several lncRNAs are potential regulators of BnaC08g11970D that encodes oleosin1, a protein found in oil bodies and involved in seed lipid accumulation. We also observed that the expression levels of B. napus lncRNAs is positively correlated with their conservation levels. Conclusions We demonstrated that the B. napus genome has a large number of lncRNA and that these lncRNAs are expressed broadly across many developmental times and in different tissue types. We also provide evidence indicating that specific lncRNAs appear to be important regulators of lipid biosynthesis forming regulatory networks with transcripts involved in lipid biosynthesis. We also provide evidence that these lncRNAs are conserved in other species of the Brassicaceae family.
- Published
- 2018
- Full Text
- View/download PDF
5. A transcriptomic profile of topping responsive non-coding RNAs in tobacco roots (Nicotiana tabacum)
- Author
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Chen, Xi, Sun, Shuo, Liu, Fangjie, Shen, Enhui, Liu, Lu, Ye, Chuyu, Xiao, Bingguang, Timko, Michael P., Zhu, Qian-Hao, Fan, Longjiang, and Cao, Peijian
- Published
- 2019
- Full Text
- View/download PDF
6. The dissection of R genes and locus Pc5.1 in Phytophthora capsici infection provides a novel view of disease resistance in peppers
- Author
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Tan Huaqiang, Lijin Lin, Hang Linfeng, Qian Hao, Xiao-Yu Xu, Yunsong Lai, Li Yu, Jin-Song Du, Su Lihong, Kai-Xi Zou, Bo Sun, Huanxiu Li, Siyad Ali, Hai-Tao Yang, and Radwa Salah Ezaat Badawy
- Subjects
0106 biological sciences ,Phytophthora ,Root rot ,Candidate gene ,Nucleosome assembly ,Genes, vpr ,Locus (genetics) ,Plant disease resistance ,Quantitative trait locus ,QH426-470 ,01 natural sciences ,Epigenesis, Genetic ,03 medical and health sciences ,Genetics ,R gene ,NBS-ARC domain ,030304 developmental biology ,Plant Diseases ,0303 health sciences ,Disease resistance ,biology ,Dissection ,Research ,food and beverages ,biology.organism_classification ,Phytophthora capsici ,Histone phosphorylation ,RNA-seq ,Capsicum ,TP248.13-248.65 ,010606 plant biology & botany ,Biotechnology - Abstract
Background Phytophthora capsici root rot (PRR) is a disastrous disease in peppers (Capsicum spp.) caused by soilborne oomycete with typical symptoms of necrosis and constriction at the basal stem and consequent plant wilting. Most studies on the QTL mapping of P. capsici resistance suggested a consensus broad-spectrum QTL on chromosome 5 named Pc.5.1 regardless of P. capsici isolates and resistant resources. In addition, all these reports proposed NBS-ARC domain genes as candidate genes controlling resistance. Results We screened out 10 PRR-resistant resources from 160 Capsicum germplasm and inspected the response of locus Pc.5.1 and NBS-ARC genes during P. capsici infection by comparing the root transcriptomes of resistant pepper 305R and susceptible pepper 372S. To dissect the structure of Pc.5.1, we anchored genetic markers onto pepper genomic sequence and made an extended Pc5.1 (Ext-Pc5.1) located at 8.35 Mb–38.13 Mb on chromosome 5 which covered all Pc5.1 reported in publications. A total of 571 NBS-ARC genes were mined from the genome of pepper CM334 and 34 genes were significantly affected by P. capsici infection in either 305R or 372S. Only 5 inducible NBS-ARC genes had LRR domains and none of them was positioned at Ext-Pc5.1. Ext-Pc5.1 did show strong response to P. capsici infection and there were a total of 44 differentially expressed genes (DEGs), but no candidate genes proposed by previous publications was included. Snakin-1 (SN1), a well-known antimicrobial peptide gene located at Pc5.1, was significantly decreased in 372S but not in 305R. Moreover, there was an impressive upregulation of sugar pathway genes in 305R, which was confirmed by metabolite analysis of roots. The biological processes of histone methylation, histone phosphorylation, DNA methylation, and nucleosome assembly were strongly activated in 305R but not in 372S, indicating an epigenetic-related defense mechanism. Conclusions Those NBS-ARC genes that were suggested to contribute to Pc5.1 in previous publications did not show any significant response in P. capsici infection and there were no significant differences of these genes in transcription levels between 305R and 372S. Other pathogen defense-related genes like SN1 might account for Pc5.1. Our study also proposed the important role of sugar and epigenetic regulation in the defense against P. capsici.
- Published
- 2021
7. Genome-wide identification of oil biosynthesis-related long non-coding RNAs in allopolyploid Brassica napus
- Author
-
Shuijin Hua, Xi Chen, Longhua Zhou, Hongyu Chen, Qian-Hao Zhu, Qing Liu, Longjiang Fan, Chu-Yu Ye, Xintian Zhu, and Enhui Shen
- Subjects
0106 biological sciences ,0301 basic medicine ,lcsh:QH426-470 ,lcsh:Biotechnology ,Computational biology ,Conservation ,Biology ,Proteomics ,01 natural sciences ,Genome ,Polyploidy ,03 medical and health sciences ,lncRNA ,Lipid biosynthesis ,lcsh:TP248.13-248.65 ,Genetics ,Plant Oils ,Coexpression ,Gene ,Conserved Sequence ,Brassica napus ,Oil biosynthesis ,food and beverages ,Genomics ,Non-coding RNA ,Antisense RNA ,lcsh:Genetics ,030104 developmental biology ,RNA, Long Noncoding ,DNA microarray ,Genome, Plant ,Function (biology) ,Research Article ,010606 plant biology & botany ,Biotechnology - Abstract
Background Long noncoding RNAs (lncRNAs) are transcripts longer than 200 bp that do not encode proteins but nonetheless have been shown to play important roles in various biological processes in plants. Brassica napus is an important seed oil crop worldwide and the target of many genetic improvement activities. To understand better the function of lncRNAs in regulating plant metabolic activities, we carried out a genome-wide lncRNA identification of lncRNAs in Brassica napus with a focus on lncRNAs involved in lipid metabolism. Twenty ribosomal RNA depleted strand specific RNA-seq (ssRNA-seq) datasets were generatred using RNAs isolated from B. napus seeds at four developmental stages. For comparison we also included 30 publically available RNA-seq datasets generated from poly(A) enriched mRNAs isolated from from various Brassica napus tissues in our analysis. Results A total of 8905 lncRNA loci were identified, including 7100 long intergenic noncoding RNA (lincRNA) loci and 1805 loci generating long noncoding natural antisense transcript (lncNAT). Many lncRNAs were identified only in the ssRNA-seq and poly(A) RNA-seq dataset, suggesting that B. napus has a large lncRNA repertoire and it is necessary to use libraries prepared from different tissues and developmental stages as well as different library preparation approaches to capture the whole spectrum of lncRNAs. Analysis of coexpression networks revealed that among the regulatory modules are networks containing lncRNAs and protein-coding genes related to oil biosynthesis indicating a possible role of lncRNAs in the control of lipid metabolism. One such example is that several lncRNAs are potential regulators of BnaC08g11970D that encodes oleosin1, a protein found in oil bodies and involved in seed lipid accumulation. We also observed that the expression levels of B. napus lncRNAs is positively correlated with their conservation levels. Conclusions We demonstrated that the B. napus genome has a large number of lncRNA and that these lncRNAs are expressed broadly across many developmental times and in different tissue types. We also provide evidence indicating that specific lncRNAs appear to be important regulators of lipid biosynthesis forming regulatory networks with transcripts involved in lipid biosynthesis. We also provide evidence that these lncRNAs are conserved in other species of the Brassicaceae family. Electronic supplementary material The online version of this article (10.1186/s12864-018-5117-8) contains supplementary material, which is available to authorized users.
- Published
- 2018
8. Transcriptomic analysis of gene expression of Verticillium dahliae upon treatment of the cotton root exudates
- Author
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Jie Sun, Yanjun Li, Wen-Han Cheng, Yuqiang Sun, Qian-Hao Zhu, Xin-Yu Zhang, and Zhidi Feng
- Subjects
lcsh:QH426-470 ,lcsh:Biotechnology ,Verticillium ,Root exudates ,Plant Roots ,lcsh:TP248.13-248.65 ,Botany ,Genetics ,Coenzyme binding ,Verticillium dahliae ,Cultivar ,Gene ,Plant Proteins ,Wilt disease ,Gossypium ,Cofactor binding ,biology ,Gene Expression Profiling ,food and beverages ,Computational Biology ,Molecular Sequence Annotation ,biology.organism_classification ,Flavin adenine dinucleotide binding ,lcsh:Genetics ,Gene Ontology ,Phenotype ,Verticillium wilt ,Transcriptome ,Hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase ,Research Article ,Biotechnology - Abstract
Background Cotton Verticillium wilt is one of the most devastating diseases for cotton production in the world. Although this diseases have been widely studied at the molecular level from pathogens, the molecular basis of V. dahliae interacted with cotton has not been well examined. Results In this study, RNA-seq analysis was carried out on V. dahliae samples cultured by different root exudates from three cotton cultivars (a susceptible upland cotton cultivar, a tolerant upland cotton cultivar and a resistant island cotton cultivar) and water for 0 h, 6 h, 12 h, 24 h and 48 h. Statistical analysis of differentially expressed genes revealed that V. dahliae responded to all kinds of root exudates but more strongly to susceptible cultivar than to tolerant and resistant cultivars. Go analysis indicated that ‘hydrolase activity, hydrolyzing O-glycosyl compounds’ related genes were highly enriched in V. dahliae cultured by root exudates from susceptible cotton at early stage of interaction, suggesting genes related to this term were closely related to the pathogenicity of V. dahliae. Additionally, ‘transmembrane transport’, ‘coenzyme binding’, ‘NADP binding’, ‘cofactor binding’, ‘oxidoreductase activity’, ‘flavin adenine dinucleotide binding’, ‘extracellular region’ were commonly enriched in V. dahliae cultured by all kinds of root exudates at early stage of interaction (6 h and 12 h), suggesting that genes related to these terms were required for the initial steps of the roots infections. Conclusions Based on the GO analysis results, the early stage of interaction (6 h and 12 h) were considered as the critical stage of V. dahliae-cotton interaction. Comparative transcriptomic analysis detected that 31 candidate genes response to root exudates from cotton cultivars with different level of V. dahliae resistance, 68 response to only susceptible cotton cultivar, and 26 genes required for development of V. dahliae. Collectively, these expression data have advanced our understanding of key molecular events in the V. dahliae interacted with cotton, and provided a framework for further functional studies of candidate genes to develop better control strategies for the cotton wilt disease.
- Published
- 2020
9. A transcriptomic profile of topping responsive non-coding RNAs in tobacco roots (Nicotiana tabacum)
- Author
-
Enhui Shen, Lu Liu, Chu-Yu Ye, Michael P. Timko, Longjiang Fan, Qian-Hao Zhu, Fangjie Liu, Xi Chen, Shuo Sun, Peijian Cao, and Bingguang Xiao
- Subjects
0106 biological sciences ,Nicotine ,Transcriptomic profile ,lcsh:QH426-470 ,lcsh:Biotechnology ,Nicotiana tabacum ,Computational biology ,Proteomics ,Plant Roots ,01 natural sciences ,Transcriptome ,03 medical and health sciences ,Circular RNA ,lcsh:TP248.13-248.65 ,Tobacco ,microRNA ,Genetics ,Topping ,Gene Regulatory Networks ,030304 developmental biology ,Co-expression network ,0303 health sciences ,biology ,Gene Expression Profiling ,Computational Biology ,High-Throughput Nucleotide Sequencing ,biology.organism_classification ,Non-coding RNA ,Long non-coding RNA ,Biosynthetic Pathways ,lcsh:Genetics ,Gene Ontology ,RNA, Plant ,RNA, Long Noncoding ,DNA microarray ,Research Article ,010606 plant biology & botany ,Biotechnology - Abstract
Background Non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long ncRNAs (lncRNAs) and circular RNAs (circRNAs), accomplish remarkable variety of biological functions. However, the composition of ncRNAs and their interactions with coding RNAs in modulating and controlling of cellular process in plants is largely unknown. Using a diverse group of high-throughput sequencing strategies, the mRNA, miRNA, lncRNA and circRNA compositions of tobacco (Nicotiana tabacum) roots determined and their alteration and potential biological functions in response to topping treatment analyzed. Results A total of 688 miRNAs, 7423 non-redundant lncRNAs and 12,414 circRNAs were identified, among which, some selected differentially expressed RNAs were verified by quantitative real-time PCR. Using the differentially expressed RNAs, a co-expression network was established that included all four types of RNAs. The number of circRNAs identified were higher than that of miRNAs and lncRNAs, but only two circRNAs were present in the co-expression network. LncRNAs appear to be the most active ncRNAs based on their numbers presented in the co-expression network, but none of them seems to be an eTM (endogenous Target Mimicry) of miRNAs. Integrated with analyses of sequence interaction, several mRNA-circRNA-miRNA interaction networks with a potential role in the regulation of nicotine biosynthesis were uncovered, including a QS-circQS-miR6024 interaction network. In this network miR6024 was significantly down-regulated, while the expression levels of its two targets, circQS and its host gene QS, were sharply increased following the topping treatment. Conclusions These results illustrated the transcriptomic profiles of tobacco roots, the organ responsible for nicotine biosynthesis. mRNAs always play the most important roles, while ncRNAs are also expressed extensively for topping treatment response, especially circRNAs are the most activated in the ncRNA pool. These studies also provided insights on the coordinated regulation module of coding and non-coding RNAs in a single plant biological sample. The findings reported here indicate that ncRNAs appear to form interaction complex for the regulation of stress response forming regulation networks with transcripts involved in nicotine biosynthesis in tobacco.
- Published
- 2019
10. Genome-wide identification of oil biosynthesis-related long non-coding RNAs in allopolyploid Brassica napus
- Author
-
Shen, Enhui, primary, Zhu, Xintian, additional, Hua, Shuijin, additional, Chen, Hongyu, additional, Ye, Chuyu, additional, Zhou, Longhua, additional, Liu, Qing, additional, Zhu, Qian-Hao, additional, Fan, Longjiang, additional, and Chen, Xi, additional
- Published
- 2018
- Full Text
- View/download PDF
11. Selection and mutation on microRNA target sequences during rice evolution
- Author
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Helliwell Chris, Zhu Qian-Hao, Wang Yu, Gui Yijie, Guo Xingyi, and Fan Longjiang
- Subjects
Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background MicroRNAs (miRNAs) posttranscriptionally down-regulate gene expression by binding target mRNAs. Analysis of the evolution of miRNA binding sites is helpful in understanding the co-evolution between miRNAs and their targets. To understand this process in plants a comparative analysis of miRNA-targeted duplicated gene pairs derived from a well-documented whole genome duplication (WGD) event in combination with a population genetics study of six experimentally validated miRNA binding sites in rice (O. sativa) was carried out. Results Of the 1,331 pairs of duplicate genes from the WGD, 41 genes (29 pairs) were computationally predicted to be miRNA targets. Sequence substitution analysis indicated that the synonymous substitution rate was significantly lower in the miRNA binding sites than their 5' and 3' flanking regions. Of the 29 duplicated gene pairs, 17 have only one paralog been targeted by a miRNA. This could be due to either gain of a miRNA binding site after the WGD or because one of the duplicated genes has escaped from being a miRNA target after the WGD (loss of miRNA binding site). These possibilities were distinguished by separating miRNAs conserved in both dicots and monocot plants from rice-specific miRNAs and by phylogenetic analysis of miRNA target gene families. The gain/loss rate of miRNA binding sites was estimated to be 3.0 × 10-9 gain/loss per year. Most (70.6%) of the gains/losses were due to nucleotide mutation. By analysis of cultivated (O. sativa; n = 30) and wild (O. rufipogon; n = 15) rice populations, no segregating site was observed in six miRNA binding sites whereas 0.12–0.20 SNPs per 21-nt or 1.53–1.80 × 10-3 of the average pairwise nucleotide diversity (π) were found in their flanking regions. Conclusion Both molecular evolution and population genetics support the hypothesis that conservation of miRNA binding sites is maintained by purifying selection through elimination of deleterious alleles. Nucleotide mutations play a major role in the gain/loss of miRNA binding sites during evolution.
- Published
- 2008
- Full Text
- View/download PDF
12. Selection and mutation on microRNA target sequences during rice evolution
- Author
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Guo, Xingyi, primary, Gui, Yijie, additional, Wang, Yu, additional, Zhu, Qian-Hao, additional, Helliwell, Chris, additional, and Fan, Longjiang, additional
- Published
- 2008
- Full Text
- View/download PDF
13. Selection and mutation on microRNA target sequences during rice evolution.
- Author
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Xingyi Guo, Yijie Gui, Yu Wang, Qian-Hao Zhu, Helliwell, Chris, and Longjiang Fan
- Subjects
GENETIC mutation ,RNA ,NUCLEOTIDE sequence ,PLANT evolution ,RICE genetics ,GENE expression in plants ,BINDING sites ,PLANT chromosome numbers - Abstract
Background: MicroRNAs (miRNAs) posttranscriptionally down-regulate gene expression by binding target mRNAs. Analysis of the evolution of miRNA binding sites is helpful in understanding the co-evolution between miRNAs and their targets. To understand this process in plants a comparative analysis of miRNA-targeted duplicated gene pairs derived from a well-documented whole genome duplication (WGD) event in combination with a population genetics study of six experimentally validated miRNA binding sites in rice (O. sativa) was carried out. Results: Of the 1,331 pairs of duplicate genes from the WGD, 41 genes (29 pairs) were computationally predicted to be miRNA targets. Sequence substitution analysis indicated that the synonymous substitution rate was significantly lower in the miRNA binding sites than their 5' and 3' flanking regions. Of the 29 duplicated gene pairs, 17 have only one paralog been targeted by a miRNA. This could be due to either gain of a miRNA binding site after the WGD or because one of the duplicated genes has escaped from being a miRNA target after the WGD (loss of miRNA binding site). These possibilities were distinguished by separating miRNAs conserved in both dicots and monocot plants from rice-specific miRNAs and by phylogenetic analysis of miRNA target gene families. The gain/loss rate of miRNA binding sites was estimated to be 3.0 x 10
-9 gain/loss per year. Most (70.6%) of the gains/losses were due to nucleotide mutation. By analysis of cultivated (O. sativa; n = 30) and wild (O. rufipogon; n = 15) rice populations, no segregating site was observed in six miRNA binding sites whereas 0.12-0.20 SNPs per 21-nt or 1.53-1.80 x 10-3 of the average pairwise nucleotide diversity (π) were found in their flanking regions. Conclusion: Both molecular evolution and population genetics support the hypothesis that conservation of miRNA binding sites is maintained by purifying selection through elimination of deleterious alleles. Nucleotide mutations play a major role in the gain/loss of miRNA binding sites during evolution. [ABSTRACT FROM AUTHOR]- Published
- 2008
- Full Text
- View/download PDF
14. Selection and mutation on microRNA target sequences during rice evolution
- Author
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Yijie Gui, Qian-Hao Zhu, Longjiang Fan, Chris A. Helliwell, Xingyi Guo, and Yu Wang
- Subjects
lcsh:QH426-470 ,lcsh:Biotechnology ,MiRNA binding ,Biology ,Genes, Plant ,medicine.disease_cause ,Nucleotide diversity ,Evolution, Molecular ,Negative selection ,Genes, Duplicate ,Sequence Analysis, Protein ,Molecular evolution ,lcsh:TP248.13-248.65 ,medicine ,Genetics ,Selection, Genetic ,Gene ,Phylogeny ,Mutation ,Binding Sites ,Sequence Analysis, RNA ,Oryza ,MicroRNAs ,lcsh:Genetics ,Genetics, Population ,RNA, Plant ,DNA microarray ,Synonymous substitution ,Sequence Alignment ,Genome, Plant ,Research Article ,Biotechnology - Abstract
Background MicroRNAs (miRNAs) posttranscriptionally down-regulate gene expression by binding target mRNAs. Analysis of the evolution of miRNA binding sites is helpful in understanding the co-evolution between miRNAs and their targets. To understand this process in plants a comparative analysis of miRNA-targeted duplicated gene pairs derived from a well-documented whole genome duplication (WGD) event in combination with a population genetics study of six experimentally validated miRNA binding sites in rice (O. sativa) was carried out. Results Of the 1,331 pairs of duplicate genes from the WGD, 41 genes (29 pairs) were computationally predicted to be miRNA targets. Sequence substitution analysis indicated that the synonymous substitution rate was significantly lower in the miRNA binding sites than their 5' and 3' flanking regions. Of the 29 duplicated gene pairs, 17 have only one paralog been targeted by a miRNA. This could be due to either gain of a miRNA binding site after the WGD or because one of the duplicated genes has escaped from being a miRNA target after the WGD (loss of miRNA binding site). These possibilities were distinguished by separating miRNAs conserved in both dicots and monocot plants from rice-specific miRNAs and by phylogenetic analysis of miRNA target gene families. The gain/loss rate of miRNA binding sites was estimated to be 3.0 × 10-9 gain/loss per year. Most (70.6%) of the gains/losses were due to nucleotide mutation. By analysis of cultivated (O. sativa; n = 30) and wild (O. rufipogon; n = 15) rice populations, no segregating site was observed in six miRNA binding sites whereas 0.12–0.20 SNPs per 21-nt or 1.53–1.80 × 10-3 of the average pairwise nucleotide diversity (π) were found in their flanking regions. Conclusion Both molecular evolution and population genetics support the hypothesis that conservation of miRNA binding sites is maintained by purifying selection through elimination of deleterious alleles. Nucleotide mutations play a major role in the gain/loss of miRNA binding sites during evolution.
- Full Text
- View/download PDF
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