The Dof (DNA binding with One Finger) family encoding single zinc finger proteins has been known as a family of plant-specific transcription factors. These transcription factors are involved in a variety of function...The Dof (DNA binding with One Finger) family encoding single zinc finger proteins has been known as a family of plant-specific transcription factors. These transcription factors are involved in a variety of functions of importance for different biological processes in plants. In the current study, we identified 34 Dof family genes in tomato (Solanum lycopersicum L.), distributed on 11 chromosomes. A complete overview of SlDof genes in tomato is presented, including the gene structures, chromosome locations, phylogeny, protein motifs and evolution pattern. Phylogenetic analysis of 34 SlDof proteins resulted in four classes constituting six clusters. In addition, a comparative analysis between these genes in tomato, Arabidopsis (Arabidopsis thaliana L.) and rice (Oryza sativa L.) was also performed. The tomato Dof family expansion has been dated to recent duplication events, and segmental duplication is predominant for the SlDof genes. Furthermore, the SlDof genes displayed differential expression either in their transcript abundance or in their expression patterns under normal growth conditions. This is the first step towards genome-wide analyses of the Dof genes in tomato. Our study provides a very useful reference for cloning and functional analysis of the members of this gene family in tomato and other species.展开更多
癫痫(epilepsy)是一种世界范围内常见的神经系统疾病。据世界卫生组织(World Health Organiza—tion,WHO)的报告显示,癫痫的患病率在5.0‰~11.2%0,即大约全球有5000万的活动性癫痫患者(经常有癫痫发作并需要抗癫痫药物维持...癫痫(epilepsy)是一种世界范围内常见的神经系统疾病。据世界卫生组织(World Health Organiza—tion,WHO)的报告显示,癫痫的患病率在5.0‰~11.2%0,即大约全球有5000万的活动性癫痫患者(经常有癫痫发作并需要抗癫痫药物维持治疗者)。展开更多
Zinc finger-homeodomain proteins (ZHD) are present in many plants; however, the evolutionary history of the ZHD gene family remains largely unknown. We show here that ZHD genes are plant-specific, nearly all intronl...Zinc finger-homeodomain proteins (ZHD) are present in many plants; however, the evolutionary history of the ZHD gene family remains largely unknown. We show here that ZHD genes are plant-specific, nearly all intronless, and related to MINI ZINC FINGER (MIF) genes that possess only the zinc finger. Phylogenetic analyses of ZHD genes from representative land plants suggest that non.seed plant ZHD genes occupy basal positions and angiosperm homologs form seven distinct clades. Several clades contain genes from two or more major angiosperm groups, including eudicots, monocots, magnoliids, and other basal angiosperms, indicating that several duplications occurred before the diversification of flowering plants. In addition, specific lineages have experienced more recent duplications. Unlike the ZHD genes, MIFs are found only from seed plants, possibly derived from ZHDs by loss of the homeodomain before the divergence of seed plants. Moreover, the MIF genes have also undergone relatively recent gene duplications. Finally, genome duplication might have contributed substantially to the expansion of family size in angiosperms and caused a high level of functional redundancy/overlap in these genes.展开更多
Since the first MADS-box transcription factor genes were implicated in the establishment of floral organ identity in a couple of model plants, the size and scope of this gene family has begun to be appreciated in a mu...Since the first MADS-box transcription factor genes were implicated in the establishment of floral organ identity in a couple of model plants, the size and scope of this gene family has begun to be appreciated in a much wider range of species. Over the course of millions of years the number of MADS-box genes in plants has increased to the point that the Arabidopsis genome contains more than 100. The understanding gained from studying the evolution, regulation and function of multiple MADS-box genes in an increasing set of species, makes this large plant transcription factor gene family an ideal subject to study the processes that lead to an increase in gene number and the selective birth, death and repurposing of its component members. Here we will use examples taken from the MADS-box gene family to review what is known about the factors that influence the loss and retention of genes duplicated in different ways and examine the varied fates of the retained genes and their associated biological outcomes.展开更多
MicroRNAs (miRNAs) are 20-22 nucleotide non-coding RNAs that play important roles in plant and animal development. They are usually processed from larger precursors that can form stem-loop structures. Among 20 miRNA f...MicroRNAs (miRNAs) are 20-22 nucleotide non-coding RNAs that play important roles in plant and animal development. They are usually processed from larger precursors that can form stem-loop structures. Among 20 miRNA families that are conserved between Arabidopsis and rice, the rice miR395 gene family was unique because it was organized into compact clusters that could be transcribed as one single transcript. We show here that in fact this family had four clusters of total 24 genes. Three of these clusters were segmental duplications. They contained miR395 genes of both 120 bp and 66 bp long. However, only the latter was repeatedly duplicated. The fourth cluster contained miR395 genes of two different sizes that could be the consequences of intergenic recombination of genes from the first three clusters. On each cluster, both 1-duplication and 2-duplication histories were observed based on the sequence similarity between miR395 genes, some of which were nearly identical suggesting a recent origin. This was supported by a miR395 locus survey among several species of the genus Oryza, where two clusters were only found in species with an AA genome, the genome of the cultivated rice. A comparative study of the genomic organization of Medicago truncatula miR395 gene family showed significant expansion of intergenic spaces indicating that the originally clustered genes were drifting away from each other. The diverse genomic organizations of a conserved microRNA gene family in different plant genomes indicated that this important negative gene regulation system has undergone dramatic tune-ups in plant genomes.展开更多
The process of flowering is controlled by a hierarchy of floral genes that act as flowering time genes, inflorescence/floral meristem Identity genes, and/or floral organ-identity genes. The most important and well-cha...The process of flowering is controlled by a hierarchy of floral genes that act as flowering time genes, inflorescence/floral meristem Identity genes, and/or floral organ-identity genes. The most important and well-characterized floral genes are those that belong to the MADS-box family of transcription factors. Compelling evidence suggests that floral MADS-box genes have experienced a few large-scale duplication events. In particular, the precore eudicot duplication events have been considered to correlate with the emergence and diversification of core eudicots. Duplication of floral MADS-box genes has also been documented in monocots, particularly In grasses, although a systematic study is lacking. In the present study, by conducting extensive phylogenetlc analyses, we identified pre-Poaceae gene duplication events in each of the AP1, P1, AG, AGL11, AGL2/3/4, and AGL9gene lineages. Comparative genomic studies further indicated that some of these duplications actually resulted from the genome doubling event that occurred 66-70 million years ago (MYA). In addition, we found that after gene duplication, exonization (of intron sequences) and pseudoexonization (of exon sequences) have contributed to the divergence of duplicate genes in sequence structure and, possibly, gene function.展开更多
Nuclear factor Y(NF-Y) is a ubiquitous transcription factor that regulates important physiological and developmental processes. In this study, we identified 34 Os NF-Y genes in rice, including 6 newly identified genes...Nuclear factor Y(NF-Y) is a ubiquitous transcription factor that regulates important physiological and developmental processes. In this study, we identified 34 Os NF-Y genes in rice, including 6 newly identified genes. Expression profile analysis covering the whole life cycle revealed that transcripts of Os NF-Y differentially accumulated in a tissue-specific,preferential or constitutive manner. In addition, gene duplication studies and expression analyses were performed to determine the evolutionary origins of the Os NF-Y gene family.Nine Os NF-Y genes were differentially expressed after treatment of seedlings with one or more abiotic stresses such as drought, salt and cold. Analysis of expression correlation and Gene Ontology annotation suggested that Os NF-Y genes were co-expressed with genes that participated in stress, accumulation of seed storage reserves, and plant development.Co-expression analysis also revealed that Os NF-Y genes might interact with each other,suggesting that NF-Y subunits formed complexes that take part in transcriptional regulation. These results provide useful information for further elucidating the function of the NF-Y family and their regulatory pathways.展开更多
The enzymes of the CHS-superfamily are responsible for biosynthesis of a wide range of natural products in plants. They are important for flower pigmentation, protection against UV light and defense against phytopatho...The enzymes of the CHS-superfamily are responsible for biosynthesis of a wide range of natural products in plants. They are important for flower pigmentation, protection against UV light and defense against phytopathogens. Many plants were found to contain multiple copies of CHS genes. This review summarizes the recent progress in the studies of the CHS-superfamily, focusing on the duplication and divergent evolution of the CHS and CHS-like genes. Comparative analyses of gene structure, ex- pression patterns and catalytic properties revealed extensive differentiation in both regulation and func- tion among duplicate CHS genes. It is also proposed that the CHS-like enzymes in the CHS-superfamily evolved from CHS at different times in various or- ganisms. The CHS-superfamily thus offers a valuable model to study the rates and patterns of sequence divergence between duplicate genes.展开更多
基金supported by the State Major Basic Research Development Program (2011CB100600)the National Natural Science Foundation of China (31171974 and 30800755)
文摘The Dof (DNA binding with One Finger) family encoding single zinc finger proteins has been known as a family of plant-specific transcription factors. These transcription factors are involved in a variety of functions of importance for different biological processes in plants. In the current study, we identified 34 Dof family genes in tomato (Solanum lycopersicum L.), distributed on 11 chromosomes. A complete overview of SlDof genes in tomato is presented, including the gene structures, chromosome locations, phylogeny, protein motifs and evolution pattern. Phylogenetic analysis of 34 SlDof proteins resulted in four classes constituting six clusters. In addition, a comparative analysis between these genes in tomato, Arabidopsis (Arabidopsis thaliana L.) and rice (Oryza sativa L.) was also performed. The tomato Dof family expansion has been dated to recent duplication events, and segmental duplication is predominant for the SlDof genes. Furthermore, the SlDof genes displayed differential expression either in their transcript abundance or in their expression patterns under normal growth conditions. This is the first step towards genome-wide analyses of the Dof genes in tomato. Our study provides a very useful reference for cloning and functional analysis of the members of this gene family in tomato and other species.
基金a National Science Foundation Plant Genome Grant for theFloral Genome Project (DBI-0115684)the Biology Department and the Huck Institutes of the Life Sciences, Pennsylvania State UniversityThisstudy was conducted using material generated in part with support from theNational Science Foundation (No. 0215923)
文摘Zinc finger-homeodomain proteins (ZHD) are present in many plants; however, the evolutionary history of the ZHD gene family remains largely unknown. We show here that ZHD genes are plant-specific, nearly all intronless, and related to MINI ZINC FINGER (MIF) genes that possess only the zinc finger. Phylogenetic analyses of ZHD genes from representative land plants suggest that non.seed plant ZHD genes occupy basal positions and angiosperm homologs form seven distinct clades. Several clades contain genes from two or more major angiosperm groups, including eudicots, monocots, magnoliids, and other basal angiosperms, indicating that several duplications occurred before the diversification of flowering plants. In addition, specific lineages have experienced more recent duplications. Unlike the ZHD genes, MIFs are found only from seed plants, possibly derived from ZHDs by loss of the homeodomain before the divergence of seed plants. Moreover, the MIF genes have also undergone relatively recent gene duplications. Finally, genome duplication might have contributed substantially to the expansion of family size in angiosperms and caused a high level of functional redundancy/overlap in these genes.
基金funded by the Biotechnology and Biological Sciences Research Council(BBSRC) ERA-NET BB/G024995/1
文摘Since the first MADS-box transcription factor genes were implicated in the establishment of floral organ identity in a couple of model plants, the size and scope of this gene family has begun to be appreciated in a much wider range of species. Over the course of millions of years the number of MADS-box genes in plants has increased to the point that the Arabidopsis genome contains more than 100. The understanding gained from studying the evolution, regulation and function of multiple MADS-box genes in an increasing set of species, makes this large plant transcription factor gene family an ideal subject to study the processes that lead to an increase in gene number and the selective birth, death and repurposing of its component members. Here we will use examples taken from the MADS-box gene family to review what is known about the factors that influence the loss and retention of genes duplicated in different ways and examine the varied fates of the retained genes and their associated biological outcomes.
基金supported in part by a grant from Northern Illinois University Foundation to Long MAONational Institutes of Health(NIH)grant to Mitrick JOHNS and Long MAO(No.44-G1A62164)a grant from the National Natural Science Foundation of China for oversea young scholars to Long MAO(No.30228022).
文摘MicroRNAs (miRNAs) are 20-22 nucleotide non-coding RNAs that play important roles in plant and animal development. They are usually processed from larger precursors that can form stem-loop structures. Among 20 miRNA families that are conserved between Arabidopsis and rice, the rice miR395 gene family was unique because it was organized into compact clusters that could be transcribed as one single transcript. We show here that in fact this family had four clusters of total 24 genes. Three of these clusters were segmental duplications. They contained miR395 genes of both 120 bp and 66 bp long. However, only the latter was repeatedly duplicated. The fourth cluster contained miR395 genes of two different sizes that could be the consequences of intergenic recombination of genes from the first three clusters. On each cluster, both 1-duplication and 2-duplication histories were observed based on the sequence similarity between miR395 genes, some of which were nearly identical suggesting a recent origin. This was supported by a miR395 locus survey among several species of the genus Oryza, where two clusters were only found in species with an AA genome, the genome of the cultivated rice. A comparative study of the genomic organization of Medicago truncatula miR395 gene family showed significant expansion of intergenic spaces indicating that the originally clustered genes were drifting away from each other. The diverse genomic organizations of a conserved microRNA gene family in different plant genomes indicated that this important negative gene regulation system has undergone dramatic tune-ups in plant genomes.
基金Supported by the National Natural Science Foundation of China (30530090, 30470116 and 30121003) and Institute of Botany, the Chinese Academy of Sciences. Publication of this paper is supported by the National Natural Science Foundation of China (30624808).Acknowledgements The authors thank Drs Hong Ma (Department of Biology and the Huck Institute of Life Sciences, Pennsylvania State University, USA) and Hongyan Shan (Institute of Botany, the Chinese Acad- emy of Sciences, Beijing, China), and Yang Liu, Jian Zhang, and Jin Hu (Institute of Botany, the Chinese Academy of Sciences, Beijing, China) for their critical reading of the manuscript and their valuable comments. The authors also thank Dr Yang Zhong (School of Life Sciences, Fudan University) for helpful suggestions.
文摘The process of flowering is controlled by a hierarchy of floral genes that act as flowering time genes, inflorescence/floral meristem Identity genes, and/or floral organ-identity genes. The most important and well-characterized floral genes are those that belong to the MADS-box family of transcription factors. Compelling evidence suggests that floral MADS-box genes have experienced a few large-scale duplication events. In particular, the precore eudicot duplication events have been considered to correlate with the emergence and diversification of core eudicots. Duplication of floral MADS-box genes has also been documented in monocots, particularly In grasses, although a systematic study is lacking. In the present study, by conducting extensive phylogenetlc analyses, we identified pre-Poaceae gene duplication events in each of the AP1, P1, AG, AGL11, AGL2/3/4, and AGL9gene lineages. Comparative genomic studies further indicated that some of these duplications actually resulted from the genome doubling event that occurred 66-70 million years ago (MYA). In addition, we found that after gene duplication, exonization (of intron sequences) and pseudoexonization (of exon sequences) have contributed to the divergence of duplicate genes in sequence structure and, possibly, gene function.
基金supported by the National Natural Science Foundation of China(Nos.31570321,30971551)
文摘Nuclear factor Y(NF-Y) is a ubiquitous transcription factor that regulates important physiological and developmental processes. In this study, we identified 34 Os NF-Y genes in rice, including 6 newly identified genes. Expression profile analysis covering the whole life cycle revealed that transcripts of Os NF-Y differentially accumulated in a tissue-specific,preferential or constitutive manner. In addition, gene duplication studies and expression analyses were performed to determine the evolutionary origins of the Os NF-Y gene family.Nine Os NF-Y genes were differentially expressed after treatment of seedlings with one or more abiotic stresses such as drought, salt and cold. Analysis of expression correlation and Gene Ontology annotation suggested that Os NF-Y genes were co-expressed with genes that participated in stress, accumulation of seed storage reserves, and plant development.Co-expression analysis also revealed that Os NF-Y genes might interact with each other,suggesting that NF-Y subunits formed complexes that take part in transcriptional regulation. These results provide useful information for further elucidating the function of the NF-Y family and their regulatory pathways.
基金supported by the National Key Project for Basic Research(973)(Grant No.2003CB715904)the National Natural Science Foundation of China(Grant No.39830020).
文摘The enzymes of the CHS-superfamily are responsible for biosynthesis of a wide range of natural products in plants. They are important for flower pigmentation, protection against UV light and defense against phytopathogens. Many plants were found to contain multiple copies of CHS genes. This review summarizes the recent progress in the studies of the CHS-superfamily, focusing on the duplication and divergent evolution of the CHS and CHS-like genes. Comparative analyses of gene structure, ex- pression patterns and catalytic properties revealed extensive differentiation in both regulation and func- tion among duplicate CHS genes. It is also proposed that the CHS-like enzymes in the CHS-superfamily evolved from CHS at different times in various or- ganisms. The CHS-superfamily thus offers a valuable model to study the rates and patterns of sequence divergence between duplicate genes.