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.

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.

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.

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

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-

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 new chimeric chiron genes evolved essential roles in zebrafish embryonic development by regulating NAD+ levels

The origination of new genes is important for generating genetic novelties for adaptive evolution and biological diversity.However, their potential roles in embryonic development, evolutionary processes into ancient networks, and contributions to adaptive evolution remain poorly investigated. Here, we identified a novel chimeric gene family, the chiron family, and explored its genetic basis and functional evolution underlying the adaptive evolution of Danioninae fishes. The ancestral chiron gene originated through retroposition of nampt in Danioninae 48–54 million years ago(Mya) and expanded into five duplicates(chiron1–5) in zebrafish 1–4 Mya. The chiron genes(chirons) likely originated in embryonic development and gradually extended their expression in the testis. Functional experiments showed that chirons were essential for zebrafish embryo development. By integrating into the NAD^(+) synthesis pathway, chirons could directly catalyze the NAD^(+) rate-limiting reaction and probably impact two energy metabolism genes(nmnat 1 and naprt) to be under positive selection in Danioninae fishes. Together,these results mainly demonstrated that the origin of new chimeric chiron genes may be involved in adaptive evolution by integrating and impacting the NAD^(+) biosynthetic pathway. This coevolution may contribute to the physiological adaptation of Danioninae fishes to widespread and varied biomes in Southeast Asian.

The power of“controllers”:Transposon-mediated duplicated genes evolve towards neofunctionalization

Since the discovery of the first transposon by Dr.Barbara McClintock,the prevalence and diversity of transposable elements(TEs)have been gradually recognized.As fundamental genetic components,TEs drive organismal evolution not only by contributing functional sequences(e.g.,regulatory elements or“controllers”as phrased by Dr.McClintock)but also by shuffling genomic sequences.In the latter respect,TE-mediated gene duplications have contributed to the origination of new genes and attracted extensive interest.In response to the development of this field,we herein attempt to provide an overview of TEmediated duplication by focusing on common rules emerging across duplications generated by different TE types.Specifically,despite the huge divergence of transposition machinery across TEs,we identify three common features of various TE-mediated duplication mechanisms,including end bypass,template switching,and recurrent transposition.These three features lead to one common functional outcome,namely,TE-mediated duplicates tend to be subjected to exon shuffling and neofunctionalization.Therefore,the intrinsic properties of the mutational mechanism constrain the evolutionary trajectories of these duplicates.We finally discuss the future of this field including an in-depth characterization of both the duplication mechanisms and functions of TE-mediated duplicates.

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.

Ruminant-specific genes identified using high-quality genome data and their roles in rumen evolution

Ruminants comprise a highly successful group of mammals with striking morphological innovations,including the presence of a rumen.Many studies have shown that species-specific or lineage-specific genes(referred to as new genes)play important roles in phenotypic evolution.In this study,we identified 1064 ruminant-specific genes based on the newly assembled high-quality genomes of representative members of two ruminant families and other publically available high-quality genomes.Ruminantspecific genes shared similar evolutionary and expression patterns with new genes found in other mammals,such as primates and rodents.Most new genes were derived from gene duplication and tended to be expressed in the testes or immune-related tissues,but were depleted in the adult brain.We also found that most genes expressed in the rumen were genes predating sheep–sperm whale split(referred to as old genes),but some new genes were also involved in the evolution of the rumen,and contributed more during rumen development than in the adult rumen.Notably,expression levels of members of the ruminant-specific PRD-SPRRII gene family,which are subject to positive selection,varied throughout rumen development and may thus play important roles in the development of the keratin-rich surface of the rumen.Overall,this study generated two novel ruminant genomes and also provided novel insights into the evolution of new mammalian organs.

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.

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。】