On the origin and evolution of new genes——a genomic and experimental perspective

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.

Mapping of Wbph6(t)-a new gene resistant to white-backed planthopper

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

The nearly complete assembly of the Cercis chinensis genome and Fabaceae phylogenomic studies provide insights into new gene evolution

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.

The Subtelomere of Oryza sativa Chromosome 3 Short Arm as a Hot Bed of New Gene Origination in Rice

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.

CLP gene family,a new gene family of Cotesia vestalis bracovirus inhibits melanization of Plutella xylostella hemolymph

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.

Origin of new genes after zygotic genome activation in vertebrate

New genes are drivers of evolutionary innovation and phenotypic evolution. Expression of new genes in early development raises the possibility that new genes could originate and be recruited for functions in embryonic development, but this remains undocu- mented. Here, based on temporal gene expression at different developmental stages in Xenopus tropicolis, we found that young protein-coding genes were significantly enriched for expression in developmental stages occurring after the midblastula trans- ition （MBT）, and displayed a decreasing trend in abundance in the subsequent stages after MBT. To complement the finding, we demonstrate essential functional attributes of a young orphan gene, named as Fog2, in morphological development. Our data indicate that new genes could originate after MBT and be recruited for functions in embryonic development, and thus provide insights for better understanding of the origin, evolution, and function of new genes.

A Microarray Based Genomic Hybridization Method for Identification of New Genes in Plants：Case Analyses of Arabidopsis and Oryza

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.

New Gene Therapy Treatment Keeps Mice Young

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。】

Origin and evolution of new genes

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.

A remarkable progress in breeding new rice line through gene engineering

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-

B亚型新等位基因803delC的分子生物学研究

目的分析研究1例新的B亚型等位基因血清学特点和分子生物学机制。方法应用血清学方法检测患者ABO血型。应用序列特异性引物-聚合酶链反应(PCR-SSP)检测ABO血型基因。应用Sanger基因序列分析检测ABO基因1~7外显子编码区域,确定基因突变位点。结果血清学鉴定患者正定型为O型,反定型为B型。PCR-SSP基因分型结果为A/O型,存在A基因,与血清学结果不符。进一步Sanger双链测序结果显示该标本在ABO^(*)B.01/ABO^(*)O.01.01的基础上,第7外显子803位置缺失C碱基。该突变最终导致多肽链上发生p.Ala268Gly和p.Phe269Ser的氨基酸替换,并且从269位置开始产生新的开放阅读框,新的开放阅读框第20号氨基酸为终止密码子,导致B基因表达终止。进一步ABO基因克隆测序证明该突变点位于ABO*B.01基因上,该突变已提交NCBI数据库,收录编号为OR343908。结论在中国人群中发现1种新的导致B变异型的ABO等位基因,基因检测方法可辅助鉴定血清学正、反定型不符的疑难血型。

小麦耐盐基因TaHKT1的新单倍型及其耐盐性评价

本研究利用0.5%盐胁迫对275份小麦品种(系)进行芽期耐盐性鉴定,测定发芽率、芽长、根长、根数、芽鲜质量、根鲜质量及根冠比等指标。利用主成分分析法将7个指标转化为3个主成分,累积贡献率为74.35%。通过主成分贡献率和隶属函数分析进一步将3个主成分简化为综合评价值(D)。根据D值的大小,利用聚类分析法将275份小麦品种(系)划分为高耐盐、中耐盐、耐盐、盐敏感和盐高敏感共5个等级,筛选出高耐盐种质11份、中耐盐107份、耐盐60份,累计占比64.7%。通过对13个小麦品种(系)进行TaHKT1基因序列分析,发现T∶T新单倍型与耐盐性相关。利用KASP标记对275份小麦品种(系)进行检测,有98份小麦品种(系)为新单倍型,占35.64%;新单倍型小麦品种(系)在各省份中所占比例不同。将小麦品种(系)的TaHKT1基因T∶T单倍型与耐盐性D值进行关联分析,结果表明,TaHKT1基因T∶T单倍型与小麦芽期耐盐性差异达极显著水平(p<0.01)。

文化基因视域下中国年画的海外收藏与影响力研究

中国年画在海外的收藏与展示表明国外对中国民间美术的热衷早于中国本土。流传海外的年画内容、图示、传播路径与存在样态,既阐释了传统民艺的精髓,又深化了中国民间美术跨境传播的认同理论。分析以年画为代表的中国民艺自发地与各地区文明之间进行的有机联系与互动,剖析海外对中国年画持续收藏与影响力研究,有利于提升中国传统民间艺术的对外传播力,使以年画为代表的国家级“非遗”在充满活力的传承中不断发扬光大。

新农科背景下基础化学实验课程红色基因挖掘与探索——以甘肃农业大学为例

新农科背景下开展课程思政对农林院校人才培养提出了新的挑战,课程中红色基因的挖掘是落实立德树人任务的重要环节.甘肃农业大学省级基础化学实验教学示范中心全面贯彻习近平新时代中国特色社会主义思想,落实立德树人根本任务,充分提炼基础化学实验课程的红色基因,全面构建了人物、时间和空间“三维一体”的基础化学实验红色基因课程思政体系.结果表明:通过红色基因课程思政体系的实施,有效提高了学生的学习兴趣,促使学生在实践中将红色基因内化成理想信念,实现学做结合与知行合一.

新时代视域下红色基因与思想政治教育融合研究

红色基因与高校思想政治教育的深度融合,阐述了新时代红色基因的概念及其功能,分析了红色基因作为高校思想政治教育的“助推器”“孵化器”“加速器”,进一步研究了新时代视域下红色基因融入思想政治教育的机制,最后从“红色基因+课堂教育教学”式融合、“红色基因+校园文化建设”式融合、“红色基因+社会实践活动”式融合、“红色基因+地方文化资源”式融合四个方面构建了新时代视域下红色基因与思想政治教育深度融合的有效途径。

新时代视域“大思政”背景下大学生传承红色基因新风貌

新时代视域“大思政”背景下大学生传承红色基因具有系统性,兼具时代特性。本文首先对新时代视域“大思政”背景下大学生传承红色基因的现状及特征进行考察,认为其目前存在大学生传承红色基因的态度参差不齐、传承方式单一、运行机制不完善等等特征。新时代视域“大思政”背景下大学生传承红色基因所面临的包括未形成系统性的架构、大学生认识程度存在差异、运行机制不完善等问题。基于此,新时代视域“大思政”背景下,将红色基因的元素纳入校园文化中,拓宽思想政治教育的途径;将红色基因的精神渗入课堂教学,丰富思想政治教育的内容;将红色基因的内涵并入社会实践,创新思想政治教育的方法;将红色基因的价值融入地方资源,凝聚思想政治教育的特色。

表达SFTSV Gn基因的重组5型腺病毒的构建与鉴定

为了构建出表达新布尼亚病毒(SFTSV)Gn基因的重组5型腺病毒,试验根据GenBank上发表的SFTSV Gn基因序列(登录号为ADZ04482.1)设计合成引物,采用特异性PCR方法在Gn基因前添加了KOZAK序列和tPA信号肽序列;然后通过酶切、连接等方法构建重组穿梭质粒PGA-KOZAK-tPA-Gn,与腺病毒骨架质粒pAd5-ΔE1ΔE3-5E4在BJ5183感受态细胞中进行同源重组,得到重组腺病毒质粒rAd5-KOZAK-tPA-Gn,用PacⅠ酶酶切重组腺病毒质粒,并将线性化的质粒转染至HEK 293细胞中进行病毒包装、扩繁和纯化;采用PCR扩增、Western-blot等技术检测病毒基因的表达情况,并测定重组腺病毒效价。结果表明:通过PCR扩增获得了1 546 bp的KOZAK-tPA-Gn基因,并成功构建了重组穿梭质粒;SFTSV Gn基因在重组腺病毒传代过程中稳定存在;重组腺病毒在HEK 293细胞中表达出分子量约为61 ku的SFTSV Gn蛋白;测得重组腺病毒效价为1×10^(-7.63)/0.1 mL TCID_(50)。说明试验成功构建出表达SFTSV Gn基因的重组5型腺病毒。

基因检测在新型口服抗凝药物个体化治疗中的应用

新型口服抗凝药物(New oral anticoagulants,NOACs)已广泛应用于血栓栓塞性疾病的预防和治疗,个体差异、基因因素等是影响其临床合理使用的关键。因此,有必要对患者进行基因检测,从而指导NOACs的个体化用药。本文主要概述了NOACs的个体化治疗,并介绍了基因多态性对NOACs治疗效果的影响,以及在药物基因组学模型中借助基因检测指导临床NOACs个体化治疗的应用。

两个中国视网膜色素变性家系EYS新突变位点的临床表型分析

目的 应用目标区域捕获技术检测两个中国视网膜色素变性(RP)家系的EYS新突变位点,并分析其类型与临床表型特征的关系。方法 采集2018年10月在沈阳何氏眼科医院门诊确诊为视网膜色素变性的两个家系共6人纳入研究,采集所有受检者外周血5 ml,提取DNA后,采用目标区域捕获测序和Sanger验证来鉴定基因变异位点,并进一步分析该基因变异的特殊临床表型。结果 在两个家系中,门诊确诊2例患者, 4例正常表型家庭成员。基因检测发现, 1例视网膜色素变性家族中发现了EYS基因的两个错义杂合突变c.3489T>A和c.5852C>T。在另一例视网膜色素变性家族中发现了EYS基因的两个基因突变,分别是c.6557G>A和c.8153C>A,经家系共分离确认为复合杂合突变。两个家系的夜盲发病年龄提前,视力极差。结论 本研究报告了2例中国常染色体隐性遗传视网膜色素变性(ARRP)家系中EYS的两个新发突变位点c.8153C>A和c.5852C>T,扩充了视网膜色素变性的基因谱和新的临床表型。光学相干断层扫描血管成像(OCT-A)检查有助于评估黄斑中心凹下脉络膜毛细血管萎缩程度,间接评估病情发展。

基于文化基因的杨家埠木版年画文创产品设计

目的探索杨家埠木版年画的保护与传承,构建杨家埠木版年画文化基因图谱,并进行文化创意产品设计,助力我国非物质文化遗产的现代化转化、助推社会经济和文化创意产业的发展。方法首先,通过文献研究、实地调查等研究手段对杨家埠木版年画资料进行分类、整理、归纳;其次,基于文化基因对杨家埠木版年画进行形态因子、色彩因子、纹样因子及语义因子的再提取并绘制基因图谱。结果生成杨家埠木版年画文化基因的延展IP形象盲盒、日历等文创产品实践案例,印证了文化基因理论指导杨家埠木版年画文创产品设计的可行性。结论文化基因图谱梳理了杨家埠年画的文化要素,有效地指导了杨家埠木版年画的文化创意设计,同时对其他非物质文化遗产传承与发展具有借鉴意义。