The inherent interest on the origin of genetic novelties can be traced back to Darwin. But it was not until recently that we were allowed to investigate the fundamental process of origin of new genes by the studies on...The inherent interest on the origin of genetic novelties can be traced back to Darwin. But it was not until recently that we were allowed to investigate the fundamental process of origin of new genes by the studies on newly evolved young genes. Two indispensible steps are involved in this process： origin of new gene copies through various mutational mechanisms and evolution of novel functions, which fur- ther more leads to fixation of the new copies within populations. The theoretical framework for the former step formed in 1970s. Ohno proposed gene duplication as the most important mechanism producing new gene copies. He also believed that the most common fate for new gene copies is to become pseudogenes. This classical view was validated and was also challenged by the characterization of the first functional young gene jingwei in Drosophila. Recent genome-wide comparison on young genes of Drosophila has elucidated a compre- hensive picture addressing remarkable roles of various mechanisms besides gene duplication during origin of new genes. Case surveys revealed it is not rare that new genes would evolve novel structures and functions to contribute to the adaptive evolution of organisms. Here, we review recent advances in understanding how new genes originated and evolved on the basis of genome-wide results and ex- perimental efforts on cases. We would finally discuss the future directions of this fast-growing research field in the context of functional genomics era.展开更多
Whitebacked planthopper (WBPH,Sogatella furcifera Horvath) is one ofthe most destructive insects for rice.The utilization of WBPH resistancegenes is always an efficient solution tothis problem. Besides five WBPHresist...Whitebacked planthopper (WBPH,Sogatella furcifera Horvath) is one ofthe most destructive insects for rice.The utilization of WBPH resistancegenes is always an efficient solution tothis problem. Besides five WBPHresistance genes registered, Wbph1,Wbph 2 , Wbph 3 , wbph 4 , andWbphS, classical segregation analysis展开更多
Fabaceae is a large family of angiosperms with high biodiversity that contains a variety of economically important crops and model plants for the study of biological nitrogen fixation.Polyploidization events have been...Fabaceae is a large family of angiosperms with high biodiversity that contains a variety of economically important crops and model plants for the study of biological nitrogen fixation.Polyploidization events have been extensively studied in some Fabaceae plants,but the occurrence of new genes is still concealed,owing to a lack of genomic information on certain species of the basal clade of Fabaceae.Cercis chinensis(Cercidoideae)is one such species;it diverged earliest from Fabaceae and is essential for phylogenomic studies and new gene predictions in Fabaceae.To facilitate genomic studies on Fabaceae,we performed genome sequencing of C.chinensis and obtained a 352.84 Mb genome,which was further assembled into seven pseudochromosomes with 30612 predicted protein-coding genes.Compared with other legume genomes,that of C.chinensis exhibits no lineage-specific polyploidization event.Further phylogenomic analyses of 22 legumes and 11 other angiosperms revealed that many gene families are lineage specific before and after the diversification of Fabaceae.Among them,dozens of genes are candidates for new genes that have evolved from intergenic regions and are thus regarded as de novo-originated genes.They differ significantly from established genes in coding sequence length,exon number,guanine–cytosine content,and expression patterns among tissues.Functional analysis revealed that many new genes are related to asparagine metabolism.This study represents an important advance in understanding the evolutionary pattern of new genes in legumes and provides a valuable resource for plant phylogenomic studies.展开更多
Despite general observations of non-random genomic distribution of new genes, it is unclear whether or not new genes preferentially occur in certain genomic regions driven by related molecular mechanisms. Using 1.5 Mb...Despite general observations of non-random genomic distribution of new genes, it is unclear whether or not new genes preferentially occur in certain genomic regions driven by related molecular mechanisms. Using 1.5 Mb of genomic sequences from short arms of chromosome 3 of Oryza glaberrima and O. punctata, we conducted a comparative genomic analysis with the reference O. sativa ssp. japonica genome. We identified a 60-kb segment located in the middle of the subtelomeric region of chromosome 3, which is unique to the species O. sativa. The region contained gene duplicates that occurred in Asian cultivated rice species that diverged from the ancestor of Asian and African cultivated rice one million years ago （MYA）. For the 12 genes and one complete retrotransposon identified in this segment in O. sativa ssp. japonica, we searched for their parental genes. The high similarity between duplicated paralogs further supports the recent origination of these genes. We found that this segment was recently generated through multiple independent gene recombination and transposon insertion events. Among the 12 genes, we found that five had chimeric gene structures derived from multiple parental genes. Nine out of the 12 new genes seem to be functional, as suggested by Ka/Ks analysis and the presence of cDNA and/or MPSS data. Furthermore, for the eight transcribed genes, at least two genes could be classified as defense or stress response-related genes. Given these findings, and the fact that subtelomeres are associated with high rates of recombination and transcription, it is likely that subtelomeres may facilitate gene recombination and transposon insertions and serve as hot spots for new gene origination in rice genomes.展开更多
Polydnaviruses(PDVs)are obligatory symbionts of parasitoid wasps and play an important role in suppressing host immune defenses.Although PDV genes that inhibit host melanization are known in Microplitis bracovirus,the...Polydnaviruses(PDVs)are obligatory symbionts of parasitoid wasps and play an important role in suppressing host immune defenses.Although PDV genes that inhibit host melanization are known in Microplitis bracovirus,the functional homologs in Cotesia bracoviruses remain unknown.Here,we find that Cotesia vestalis bracovirus(CvBV)can inhibit hemolymph melanization of its host,Plutella xylostella larvae,during the early stages of parasitization,and that overexpression of highly expressed CvBV genes reduced host phenoloxidase activity.Furthermore,CvBV-7-I in particular reduced host phenolox-idase activity within 12 h,and the injection of anti-CvBV-7-1 antibody increased the melanization of parasitized host larvae.Further analyses showed that CvBV-7-1 and three homologs from other Cotesia bracoviruses possessed a C-terminal leucine/isoleucine-rich region and had a similar flinction in inhibiting melanization.Therefore,a new family of bracovirus genes was proposed and named as C-terminal Leucine/isoleucine-rich Protein(CLP).Ectopic expression of CvBV-7-1 in Drosophila hemocytes increased susceptibility to bacterial repression of melanization and reduced the melanotic encapsulation of par-asitized D.melanogaster by the parasitoid Leptopilina boulardi.The formation rate of wasp pupae and the eclosion rate of C.vestalis were affected when the function of CvBV-7-1 was blocked.Our findings suggest that CLP genes from Cotesia bracoviruses encoded proteins that contain a C-terminal leucine/isoleucine-rich region and function as melanization inhibitors during the early stage of parasitization,which is important for successful parasitization.展开更多
To systematically estimate the gene duplication events In closely related species, we have to use comparative genomlc approaches, either through genomlc sequence comparison or comparative genomlc hybridization （CGH）...To systematically estimate the gene duplication events In closely related species, we have to use comparative genomlc approaches, either through genomlc sequence comparison or comparative genomlc hybridization （CGH）. Given the scarcity of complete genomlc sequences of plant species, in the present study we adopted an array based CGH to Investigate gene duplications In the genus Arabldopsls. Fragment genomlc DNA from four species, namely Arabidopsls thallana, A. lyrata subsp, lyrata, A. lyrata subsp, petraea, and A. halleri, was hybridized to Affymetrlx （Santa Clara, CA, USA） tiling arrays that are designed from the genomlc sequences of A. thallana. Pairwlse comparisons of signal intensity were made to infer the potential duplicated candidates along each phylogenetic branch. Ninety-four potential candidates of gene duplication along the genus were Identified. Among them, the majority （69 of 94） were A. thallana lineage specific. This result indicates that the array based CGH approach may be used to Identify candidates of duplication In other plant genera containing closely related species, such as Oryza, particularly for the AA genome species. We compared the degree of gene duplication through retrotransposon between O. satlva and A. thallana and found a strikingly higher number of chimera retroposed genes In rice. The higher rate of gene duplication through retroposltlon and other mechanisms may Indicate that the grass species Is able to adapt to more diverse environments.展开更多
我是一个退休教师,步入老境后,因体质原本较弱,加上深居简出,双腿的肌肉开始萎缩。行动不便,苦不堪言。随着老境的到来,哺乳动物的一个显著变化是:During the aging process,mammals lose up to a third of their skeletalmuscle mass a...我是一个退休教师,步入老境后,因体质原本较弱,加上深居简出,双腿的肌肉开始萎缩。行动不便,苦不堪言。随着老境的到来,哺乳动物的一个显著变化是:During the aging process,mammals lose up to a third of their skeletalmuscle mass and strength.今天,我从因特网上读到一篇文章,非常兴奋。一种基 因疗法(gene therapy)在老鼠身上的实验已经获得成功,这种疗法能减缓衰老:itmay be possible to preserve muscle size and strength in old age using thisapproach.将这种基因注入人体的方法耐人寻味。基因疗法的前景非常诱人:Thebeneficial effects of this gene therapy could easily be used by humans for athleticor even cosmetic enhancements.到了下世纪的中叶,也许,人的外貌将具有极大的迷惑性,人之外貌将很难成为人的年龄的“凭证”！虽然,我活不到那个时候,但是,想到未来科学的进展,我的心头仍洋溢着快慰和欣喜。】展开更多
Organisms have variable genome sizes and contain different numbers of genes. This difference demon-strates that new gene origination is a fundamental process in evolutionary biology. Though the study of the originatio...Organisms have variable genome sizes and contain different numbers of genes. This difference demon-strates that new gene origination is a fundamental process in evolutionary biology. Though the study of the origination of new genes dated back more than half a century ago, it is not until the 1990s when the first young gene jingwei was found that empirical investigation of the molecular mechanisms of origination of new genes became possible. In the recent years, several young genes were identified and the studies on these genes have greatly enriched the knowledge of this field. Yet more details in a general picture of new genes origination are to be clarified. We have developed a systematic approach to searching for young genes at the genomic level, in the hope to summarize a general pattern of the origination and evolution of new genes, such as the rate of new gene appearance, im-pact of new genes on their host genomes, etc.展开更多
Much progress has been made in the research of breeding new rice line through gene engineering by Life Science College of Fudan Univ, Shanghai, and the Plant Science Res Inst of Shanghai Acad of Agri. It was the first...Much progress has been made in the research of breeding new rice line through gene engineering by Life Science College of Fudan Univ, Shanghai, and the Plant Science Res Inst of Shanghai Acad of Agri. It was the first time internationally that the research adopted a man-combined gene, taking agrobacterium as car-展开更多
目的分析血红蛋白(Hb)New York在不同年龄段的携带人群中的表达差异。方法收集2017-10~2020-03在该院体检、就诊的103351例外周血和脐带血,55909例新生儿末梢血,对筛查结果为Hb New York的样本进行血液学分析和基因型检测。结果携带Hb N...目的分析血红蛋白(Hb)New York在不同年龄段的携带人群中的表达差异。方法收集2017-10~2020-03在该院体检、就诊的103351例外周血和脐带血,55909例新生儿末梢血,对筛查结果为Hb New York的样本进行血液学分析和基因型检测。结果携带Hb New York的样本共185例,其中脐带血4例,新生儿58例,成人123例。胎儿脐带血中Hb New York的含量为(1.30±0.94)%,新生儿含量为(7.87±6.21)%,成人含量为(43.30±2.83)%。携带Hb New York的成人血液学参数均处于正常参考值范围,除红细胞平均血红蛋白浓度(MCHC)外,其他参数与正常成人对照组比较差异均有统计学意义。基因检测显示,Hb New York杂合子167例,Hb New York复合静止型α-地贫7例,Hb New York复合轻型α-地贫11例。结论Hb New York在不同年龄人群的含量不同,与β珠蛋白基因的表达水平正相关。携带者血液学表型正常,合并地贫易表现为贫血,在地贫筛查与婚检、孕检的遗传咨询中值得关注。展开更多
基金a CAS-Max Planck Society Fellowship, an award （No. 30325016）；the National Science Foundation of China （NSFC）,two NSFC key grants （No. 30430400 and 30623007）the National Basic Research Program of China （973 Program）（No. 2007CB815703-5）W.W., and a NSFC grant(No.30500283）for junior researchers to S.Y.
文摘The inherent interest on the origin of genetic novelties can be traced back to Darwin. But it was not until recently that we were allowed to investigate the fundamental process of origin of new genes by the studies on newly evolved young genes. Two indispensible steps are involved in this process： origin of new gene copies through various mutational mechanisms and evolution of novel functions, which fur- ther more leads to fixation of the new copies within populations. The theoretical framework for the former step formed in 1970s. Ohno proposed gene duplication as the most important mechanism producing new gene copies. He also believed that the most common fate for new gene copies is to become pseudogenes. This classical view was validated and was also challenged by the characterization of the first functional young gene jingwei in Drosophila. Recent genome-wide comparison on young genes of Drosophila has elucidated a compre- hensive picture addressing remarkable roles of various mechanisms besides gene duplication during origin of new genes. Case surveys revealed it is not rare that new genes would evolve novel structures and functions to contribute to the adaptive evolution of organisms. Here, we review recent advances in understanding how new genes originated and evolved on the basis of genome-wide results and ex- perimental efforts on cases. We would finally discuss the future directions of this fast-growing research field in the context of functional genomics era.
基金supported by grants from the National Natural Science Foundation of China(grant number 32070247 to J.Q.)funds from the State Key Laboratory of Genetic Engineering at Fudan University,China.
文摘Fabaceae is a large family of angiosperms with high biodiversity that contains a variety of economically important crops and model plants for the study of biological nitrogen fixation.Polyploidization events have been extensively studied in some Fabaceae plants,but the occurrence of new genes is still concealed,owing to a lack of genomic information on certain species of the basal clade of Fabaceae.Cercis chinensis(Cercidoideae)is one such species;it diverged earliest from Fabaceae and is essential for phylogenomic studies and new gene predictions in Fabaceae.To facilitate genomic studies on Fabaceae,we performed genome sequencing of C.chinensis and obtained a 352.84 Mb genome,which was further assembled into seven pseudochromosomes with 30612 predicted protein-coding genes.Compared with other legume genomes,that of C.chinensis exhibits no lineage-specific polyploidization event.Further phylogenomic analyses of 22 legumes and 11 other angiosperms revealed that many gene families are lineage specific before and after the diversification of Fabaceae.Among them,dozens of genes are candidates for new genes that have evolved from intergenic regions and are thus regarded as de novo-originated genes.They differ significantly from established genes in coding sequence length,exon number,guanine–cytosine content,and expression patterns among tissues.Functional analysis revealed that many new genes are related to asparagine metabolism.This study represents an important advance in understanding the evolutionary pattern of new genes in legumes and provides a valuable resource for plant phylogenomic studies.
文摘Despite general observations of non-random genomic distribution of new genes, it is unclear whether or not new genes preferentially occur in certain genomic regions driven by related molecular mechanisms. Using 1.5 Mb of genomic sequences from short arms of chromosome 3 of Oryza glaberrima and O. punctata, we conducted a comparative genomic analysis with the reference O. sativa ssp. japonica genome. We identified a 60-kb segment located in the middle of the subtelomeric region of chromosome 3, which is unique to the species O. sativa. The region contained gene duplicates that occurred in Asian cultivated rice species that diverged from the ancestor of Asian and African cultivated rice one million years ago （MYA）. For the 12 genes and one complete retrotransposon identified in this segment in O. sativa ssp. japonica, we searched for their parental genes. The high similarity between duplicated paralogs further supports the recent origination of these genes. We found that this segment was recently generated through multiple independent gene recombination and transposon insertion events. Among the 12 genes, we found that five had chimeric gene structures derived from multiple parental genes. Nine out of the 12 new genes seem to be functional, as suggested by Ka/Ks analysis and the presence of cDNA and/or MPSS data. Furthermore, for the eight transcribed genes, at least two genes could be classified as defense or stress response-related genes. Given these findings, and the fact that subtelomeres are associated with high rates of recombination and transcription, it is likely that subtelomeres may facilitate gene recombination and transposon insertions and serve as hot spots for new gene origination in rice genomes.
基金supported by the Key Program of National Natural Science Foundation of China(31630060)National Key Research and Development Program of China(2019YFD0300104)to XXC+5 种基金the National Key Research and Development Program of China(2017YFD0200400)the National Science Fund for Excellent Young Scholars(31622048)the National Science Foundation of China(31772522)to JHHthe National Science Foundation of China(31672079)Zhejiang Provincial Natural Science Foundation of China(LR18C140001)to MSthe National Science Foundation of China(31901942)to ZHW.
文摘Polydnaviruses(PDVs)are obligatory symbionts of parasitoid wasps and play an important role in suppressing host immune defenses.Although PDV genes that inhibit host melanization are known in Microplitis bracovirus,the functional homologs in Cotesia bracoviruses remain unknown.Here,we find that Cotesia vestalis bracovirus(CvBV)can inhibit hemolymph melanization of its host,Plutella xylostella larvae,during the early stages of parasitization,and that overexpression of highly expressed CvBV genes reduced host phenoloxidase activity.Furthermore,CvBV-7-I in particular reduced host phenolox-idase activity within 12 h,and the injection of anti-CvBV-7-1 antibody increased the melanization of parasitized host larvae.Further analyses showed that CvBV-7-1 and three homologs from other Cotesia bracoviruses possessed a C-terminal leucine/isoleucine-rich region and had a similar flinction in inhibiting melanization.Therefore,a new family of bracovirus genes was proposed and named as C-terminal Leucine/isoleucine-rich Protein(CLP).Ectopic expression of CvBV-7-1 in Drosophila hemocytes increased susceptibility to bacterial repression of melanization and reduced the melanotic encapsulation of par-asitized D.melanogaster by the parasitoid Leptopilina boulardi.The formation rate of wasp pupae and the eclosion rate of C.vestalis were affected when the function of CvBV-7-1 was blocked.Our findings suggest that CLP genes from Cotesia bracoviruses encoded proteins that contain a C-terminal leucine/isoleucine-rich region and function as melanization inhibitors during the early stage of parasitization,which is important for successful parasitization.
基金Supported by Fellowships from the Pew Latin American Fellows Program and Conselho Nacional de Desenvolvimento Cientfico e Tecnologico （to MDV）, the USA National Science Foundation CAREER award （MCB0238168） and USA National Institutes of Health R01 grants （R01GM065429-01A1 and GM078070-01A1） to ML at the University of Chicago. Publication of this paper is supported by the National Natural Science Foundation of China （30624808）.Acknowledgements The authors thank Dr Hedibert F. Lopes （University of Chicago, Graduate School of Business, Chicago, USA） for his discussions regarding the statistical methods, Noboru Jo Sakabe （IQ- USP/LICR-Sao Paulo Branch, Sao Paulo, Brazil） for critical reading of the manuscript. The authors also thank those people who provided seed samples of Arabidopsis： ABRC Stock Center （The 0hio State University, Columbus, 0H 43210, USA）, Justin Borevitz （Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois 60637, USA）, Daphne Preuss （Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois 60637, USA）, Joy Bergelson （Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois 60637, USA）, and Mark MacNair （Department of Biological Sciences, University of Exeter, Exeter, EX4 6EZ, UK）.
文摘To systematically estimate the gene duplication events In closely related species, we have to use comparative genomlc approaches, either through genomlc sequence comparison or comparative genomlc hybridization （CGH）. Given the scarcity of complete genomlc sequences of plant species, in the present study we adopted an array based CGH to Investigate gene duplications In the genus Arabldopsls. Fragment genomlc DNA from four species, namely Arabidopsls thallana, A. lyrata subsp, lyrata, A. lyrata subsp, petraea, and A. halleri, was hybridized to Affymetrlx （Santa Clara, CA, USA） tiling arrays that are designed from the genomlc sequences of A. thallana. Pairwlse comparisons of signal intensity were made to infer the potential duplicated candidates along each phylogenetic branch. Ninety-four potential candidates of gene duplication along the genus were Identified. Among them, the majority （69 of 94） were A. thallana lineage specific. This result indicates that the array based CGH approach may be used to Identify candidates of duplication In other plant genera containing closely related species, such as Oryza, particularly for the AA genome species. We compared the degree of gene duplication through retrotransposon between O. satlva and A. thallana and found a strikingly higher number of chimera retroposed genes In rice. The higher rate of gene duplication through retroposltlon and other mechanisms may Indicate that the grass species Is able to adapt to more diverse environments.
文摘我是一个退休教师,步入老境后,因体质原本较弱,加上深居简出,双腿的肌肉开始萎缩。行动不便,苦不堪言。随着老境的到来,哺乳动物的一个显著变化是:During the aging process,mammals lose up to a third of their skeletalmuscle mass and strength.今天,我从因特网上读到一篇文章,非常兴奋。一种基 因疗法(gene therapy)在老鼠身上的实验已经获得成功,这种疗法能减缓衰老:itmay be possible to preserve muscle size and strength in old age using thisapproach.将这种基因注入人体的方法耐人寻味。基因疗法的前景非常诱人:Thebeneficial effects of this gene therapy could easily be used by humans for athleticor even cosmetic enhancements.到了下世纪的中叶,也许,人的外貌将具有极大的迷惑性,人之外貌将很难成为人的年龄的“凭证”！虽然,我活不到那个时候,但是,想到未来科学的进展,我的心头仍洋溢着快慰和欣喜。】
基金This work was supported by the National Natural Science Foundation of China （31671325 and 31271339）. N.O.O. thanks the CAS-TWAS President＇s Fellowship Program for Doctoral Candidates for support.
文摘Organisms have variable genome sizes and contain different numbers of genes. This difference demon-strates that new gene origination is a fundamental process in evolutionary biology. Though the study of the origination of new genes dated back more than half a century ago, it is not until the 1990s when the first young gene jingwei was found that empirical investigation of the molecular mechanisms of origination of new genes became possible. In the recent years, several young genes were identified and the studies on these genes have greatly enriched the knowledge of this field. Yet more details in a general picture of new genes origination are to be clarified. We have developed a systematic approach to searching for young genes at the genomic level, in the hope to summarize a general pattern of the origination and evolution of new genes, such as the rate of new gene appearance, im-pact of new genes on their host genomes, etc.
文摘Much progress has been made in the research of breeding new rice line through gene engineering by Life Science College of Fudan Univ, Shanghai, and the Plant Science Res Inst of Shanghai Acad of Agri. It was the first time internationally that the research adopted a man-combined gene, taking agrobacterium as car-
文摘目的分析血红蛋白(Hb)New York在不同年龄段的携带人群中的表达差异。方法收集2017-10~2020-03在该院体检、就诊的103351例外周血和脐带血,55909例新生儿末梢血,对筛查结果为Hb New York的样本进行血液学分析和基因型检测。结果携带Hb New York的样本共185例,其中脐带血4例,新生儿58例,成人123例。胎儿脐带血中Hb New York的含量为(1.30±0.94)%,新生儿含量为(7.87±6.21)%,成人含量为(43.30±2.83)%。携带Hb New York的成人血液学参数均处于正常参考值范围,除红细胞平均血红蛋白浓度(MCHC)外,其他参数与正常成人对照组比较差异均有统计学意义。基因检测显示,Hb New York杂合子167例,Hb New York复合静止型α-地贫7例,Hb New York复合轻型α-地贫11例。结论Hb New York在不同年龄人群的含量不同,与β珠蛋白基因的表达水平正相关。携带者血液学表型正常,合并地贫易表现为贫血,在地贫筛查与婚检、孕检的遗传咨询中值得关注。
