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| 1 | Origination and evolution of orphan genes and de novo genes in the genome of Caenorhabditis elegans显示文摘Orphan genes that lack detectable homologues in other lineages could contribute to a variety of biological functions. However,their origination and function mechanisms remain largely unknown. Herein, through a comprehensive and systematic computational pipeline, we identified 893 orphan genes in the lineage of C. elegans, of which only a low fraction(0.9%) were derived from transposon elements. Six new protein-coding genes that de novo originated from non-coding DNA sequences in the genome of C. elegans were also identified. The authenticity and functionality of these orphan genes and de novo genes are supported by three lines of evidences, consisting of transcriptional data, and in silico proteomic data, and the fixation status data in wild populations. Orphan genes and de novo genes exhibited simple gene structures, such as, short in protein length, of fewer exons,and are frequently X-linked. RNA-seq data analysis showed these orphan genes are enriched with expression in embryo development and gonad, and their potential function in early development was further supported by gene ontology enrichment analysis results. Meanwhile, de novo genes were found to be with significant expression in gonad, and functional enrichment analysis of the co-expression genes of these de novo genes suggested they may be functionally involved in signaling transduction pathway and metabolism process. Our results presented the first systematic evidence on the evolution of orphan genes and de novo origin of genes in nematodes and their impacts on the functional and phenotypic evolution, and thus could shed new light on our appreciation of the importance of these new genes. | Wenyu Zhang Yuanxiao Gao Manyuan Long Bairong Shen | 2019 | Science China(Life Sciences)2019，62，4： | 5 |
| 2 | Topological evolution of coexpression networks by new gene integration maintains the hierarchical and modular structures in human ancestors显示文摘We analyze the global structure and evolution of human gene coexpression networks driven by new gene integration. When the Pearson correlation coefficient is greater than or equal to 0.5, we find that the coexpression network consists of 334 small components and one 'giant' connected subnet comprising of 6317 interacting genes. This network shows the properties of power-law degree distribution and small-world. The average clustering coefficient of younger genes is larger than that of the elderly genes(0.6685 vs. 0.5762). Particularly, we find that the younger genes with a larger degree also show a property of hierarchical architecture. The younger genes play an important role in the overall pivotability of the network and this network contains few redundant duplicate genes. Moreover, we find that gene duplication and orphan genes are two dominant evolutionary forces in shaping this network. Both the duplicate genes and orphan genes develop new links through a 'rich-gets-richer'mechanism. With the gradual integration of new genes into the ancestral network, most of the topological structure features of the network would gradually increase. However, the exponent of degree distribution and modularity coefficient of the whole network do not change significantly, which implies that the evolution of coexpression networks maintains the hierarchical and modular structures in human ancestors. | Jian Zu Yuexi Gu Yu Li Chentong Li Wenyu Zhang Yong E.Zhang UnJin Lee Li Zhang Manyuan Long | 2019 | Science China(Life Sciences)2019，62，4： | 3 |
| 3 | Side effects of Tamiflu: clues from an Asian single nucleotide polymorphism显示文摘Tamiflu(Oseltamivir phosphate)seems to be a double-edged sword to some in Asia.While it is counted on againstinfluenza and a feared avian influenza pandemic[1],the drug is also associated with side effects,ranging from neu-ropsychiatric,gastrointestinal,to hyperthennia and skin problems.According to a document from US Food and DrugAdministration in 2005[2],1184 cases of side effects have been reported. Interestingly 69 out of the 75 pediatric caseswere from Japan,including two teen suicides.The situation seemed to have made a gloomier turn recently.It was reportedin February,2007 that two Japanese teenagers jumped from apartment buildings after taking Tamiflu and died,bringingthe total number of deaths after taking Tamiftu in Japan to 54[3,4].Although no direct causal relationship had been es-tablished yet,the Japan Health Ministry warned doctors about giving the drug to teenagers.In comparison,relatively fewcases of severe side effects were reported from America and European countries[5].What is wrong with this picture?Ithas concerned and bewildered many.The pages in this issue[6]offer one fascinating hypothesis that tries to explain themystery using an integrated approach combining structural bioinformatic analysis and enzyme assays. | Manyuan Long | 2007 | Cell Research2007，17，4： | 2 |
| 4 | Male non-coding RNA genes identified by comparative genomic analysis of the Drosophila genomes显示文摘这个问题由杨等出版了一篇研究文章。北京大学“在在果蝇的密切相关的种类之中的性相关的非编码的 RNA 表示模式的重要分叉”。在 D 的 genomic 分析。melanogaster 和它的近亲, D.simulans, D。yakuba 和另外的相关种类, D。pseudoobscura 和 D。virillis,杨 et al.identified 一打性腺 --( 主要睾丸 --) 表示非编码的 RNA (ncRNA ) 基因。这些 ncRNA 基因在这些显示出分叉的表示模式,这被揭示种类。在学习使用的简单方法能高效地从大量有机体在一组密切相关的种被用于 ncRNA 基因的察觉。这个评价不在这篇论文详细重申实验和解释。相反,我们将在生物学的理解和性复制的进化在相关结果的意义的讨论提出我们的强调。我们将在 ncRNA 基因的区域的开发和教育讨论这个工作的一般意义。 | LONG ManYuan ZHU ZuoYan | 2007 | Chinese Science Bulletin2007，52，6： | 1 |
| 5 | Significant divergence of sex-related non-coding RNA expression patterns among closely related species in Drosophila显示文摘Whether or not non-coding RNA genes play a significant role in reproductive biology and evolution of sex determination systems is an important problem. We report identification of sex-related non-coding RNA (ncRNA) genes and an analysis of ncRNAs expression patterns among Drosophila species. We detected 12 candidate ncRNAs that are expressed in the gonads of D. melanogaster by an integrative approach of RT-PCR and computational analysis of sequence conservation across species. We ex-perimentally analyzed these ncRNA gene transcripts in head, ovary and testis of closely related species D. simulans, D. yakuba,D. pseudoobscura and D. virilis. We observed that the occurrence and extent of expression of most ncRNA fragments among closely related species show significant divergence. | YANG YongFei LI Zheng FAN QiChang LONG ManYuan ZHANG WenXia | 2007 | Chinese Science Bulletin2007，52，6： | 1 |
| 6 | The Subtelomere of Oryza sativa Chromosome 3 Short Arm as a Hot Bed of New Gene Origination in Rice显示文摘尽管有新基因的非随机的 genomic 分发的一般观察,新基因是否优先地在相关分子的机制驾驶的某些 genomic 区域发生,是不清楚的。用 1.5 ? 从染色体 3 Oryza glaberrima 和 O 的短手臂的 genomic 序列的 Mb。punctata,我们与参考 O 进行了比较 genomic 分析。sativa ssp。装饰用的梨树染色体。我们识别了位于染色体 3 的 subtelomeric 区域的中间的一个 60-kb 片断,它对种类 O 唯一。sativa。这个区域包含了在 100 万年以前从亚洲、非洲的栽培米饭的祖先分叉的亚洲栽培米饭种类(MYA ) 发生了的基因副本。为 12 基因和在 O 在这个片断识别的一完全的 retrotransposon。sativa ssp。装饰用的梨树,我们寻找了他们的父母基因。复制 paralogs 的高类似进一步支持这些基因的最近的起源。我们发现这个片断最近通过多重独立基因再结合和 transposon 插入事件被产生。在 12 基因之中,我们发现五把妄想的基因结构从多重父母基因导出。九从 12 新基因似乎功能,由 Ka/Ks 分析和 cDNA 或 MPSS 数据的存在建议了。为八抄录基因,而且,至少二基因能作为防卫被分类或强调反应相关的基因。给 subtelomeres 与再结合和抄写的高率被联系的这些调查结果,和事实, subtelomeres 可以便于基因再结合和 transposon 插入并且在米饭染色体为新基因起源用作热点,是可能的。 | Chuanzhu Fana Yong Zhang Yeisoo Yu Steve Rounsley Manyuan Long Rod A. Wing | 2008 | Molecular Plant2008，1，5： | 1 |
| 7 | A zebrafish-specific chimeric gene evolved essential developmental functions:discussion of conceptual significance显示文摘Since the early 1990s,it has been known that new genes originate anytime in evolution in any organisms since the remote past billion years ago(BYA)(Long and Langley,1993;Long et al.,2013).It is also widely accepted that gene duplication is a main process in which new gene duplicate iscreated from a parental gene. | Manyuan Long | 2021 | Science China(Life Sciences)2021，64，5： | 0 |
| 8 | A Microarray Based Genomic Hybridization Method for Identification of New Genes in Plants:Case Analyses of Arabidopsis and Oryza显示文摘系统地在密切相关的种类估计基因复制事件,我们不得不使用比较 genomic 途径,通过 genomic 顺序比较的任何一个或比较 genomic 杂交(CGH ) 。给植物种类的完全的 genomic 序列的缺乏,在我们采用了的现在的学习一个数组基于 CGH 在类 Arabidopsis 调查基因复制。从四种的碎片 genomic 脱氧核糖核酸,也就是 Arabidopsis thaliana, A.lyrata subsp。lyrata,一。lyrata subsp。petraea,和 A。haller i,是到 Affymetrix 的 hybridized (SantaClara, CA,美国) 并列从 genomic 被设计的数组 A 定序。thaliana。信号紧张的 Pairwisecomparisons 被做沿着 eachphylo 基因的分支推断潜在的复制候选人。沿着类的基因复制的 94 个潜在的候选人被识别。在他们之中,多数(94 中的 69 个) 是 A。thaliana 系特定。这结果显示数组基于 CGH 途径可以被用来在包含密切相关的种类的另外的植物类识别复制的候选人,例如 Oryza,特别地为 AA 染色体种。我们通过在 O 之间的 retrotransposon 比较了基因复制的度。sativa 和 A。thaliana 并且发现怪物制动火箭的一个惊人地更高的数字在米饭提出了基因。通过制动火箭位置和另外的机制的基因复制的更高的率可以显示草种类能适应更多样的环境…… | Chuanzhu Fan Maria D. Vibranovski Ying Chen Manyuan Long | 2007 | Journal of Integrative Plant Biology2007，49，6： | 0 |
| 9 | Evolution of genes and genomes: an emerging paradigm in life science显示文摘Traditional molecular biology,defined in a broad sense to include most of life science research that focuses on single or a few genes to understand their functions and application values to medicine and agriculture,has generated interesting and important accomplishments. | Manyuan Long Bairong Shen | 2019 | Science China(Life Sciences)2019，62，4： | 0 |
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