Cited by 429Chromosomal and Genetic VariationsEvolution and Genetic DynamicsGenomics and Phylogenetic Studies

The DOI matches its Crossref record; 136 of the 137 references it cites were found in a registry or an index.

New genes as drivers of phenotypic evolution

Open access

Chen, Sidi, Krinsky, Benjamin H., Long, Manyuan·2013·Nature Reviews Genetics

Open this paper in CoChat — free account

Abstract

During the course of evolution, genomes acquire novel genetic elements as sources of functional and phenotypic diversity, including new genes that originated in recent evolution. In the past few years, substantial progress has been made in understanding the evolution and phenotypic effects of new genes. In particular, an emerging picture is that new genes, despite being present in the genomes of only a subset of species, can rapidly evolve indispensable roles in fundamental biological processes, including development, reproduction, brain function and behaviour. The molecular underpinnings of how new genes can develop these roles are starting to be characterized. These recent discoveries yield fresh insights into our broad understanding of biological diversity at refined resolution.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.1038/nrg3521

Cites

136 of 136 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Targeted gene expression as a means of altering cell fates and generating dominant phenotypes
Brand, A. H., & Perrimon, N. (1993) · Development · doi:10.1242/dev.118.2.401 · Cited by 9,510
Evolution by Gene Duplication
Ohno, S. (1970) · doi:10.1007/978-3-642-86659-3 · Cited by 7,833
Lethality and centrality in protein networks
Jeong, H., Mason, S., Barabási, A., & Oltvai, Z. (2001) · Nature · doi:10.1038/35075138 · Cited by 5,327
Untitled work
(1977) · Cited by 4,052
Post-embryonic cell lineages of the nematode, Caenorhabditis elegans
Sulston, J. E., & Horvitz, H. R. (1977) · Developmental Biology · doi:10.1016/0012-1606(77)90158-0 · Cited by 3,479
Emergence of a new antibiotic resistance mechanism in India, Pakistan, and the UK: a molecular, biological, and epidemiological study
Kumarasamy, K. K., Toleman, M. A., Walsh, T. R., Bagaria, J., Butt, F., Balakrishnan, R., Chaudhary, U., Doumith, M., Giske, C. G., Irfan, S., et al. (2010) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(10)70143-2 · Cited by 2,922
Evolution at Two Levels in Humans and Chimpanzees: Their macromolecules are so alike that regulatory mutations may account for their biological differences
King, M.-C., & Wilson, A. C. (1975) · Science · doi:10.1126/science.1090005 · Cited by 2,815
Ontogeny and Phylogeny.
Løvtrup, S., & Gould, S. J. (1978) · Systematic Zoology · doi:10.2307/2412825 · Cited by 2,359
The cytoplasmic body component TRIM5α restricts HIV-1 infection in Old World monkeys
Stremlau, M. H., Owens, C. M., Perron, M. J., Kießling, M. K., Autissier, P., & Sodroski, J. (2004) · Nature · doi:10.1038/nature02343 · Cited by 1,810
Syncytin is a captive retroviral envelope protein involved in human placental morphogenesis
Mi, S., Lee, X., Li, X., Veldman, G. M., Finnerty, H. F., Collins‐Racie, L. A., LaVallie, E. R., Tang, X.-Y., Edouard, P., Howes, S., et al. (2000) · Nature · doi:10.1038/35001608 · Cited by 1,711

Flagged first, then by citations

Show all 137 references

1 of the 137 references couldn’t be matched to a known paper.

Research works printed but not linked: 2

Coyne, J. A. & Orr, H. A. Speciation (Sinauer Associates Sunderland, 2004).
Strausfeld, N. J. & Li, Y. Representation of the calyces in the medial and vertical lobes of cockroach mushroom bodies. J. Comp. Neurol. 409, 626–646 (1999). · DOI

Sorted by citations

Items 101–200 of 429

Detection of orphan domains in Drosophila using “hydrophobic cluster analysis”
Bitard‐Feildel, T., Heberlein, M., Bornberg‐Bauer, E., & Callebaut, I. (2015) · Biochimie · doi:10.1016/j.biochi.2015.02.019 · Cited by 39
Evolutionary Fates and Dynamic Functionalization of Young Duplicate Genes in Arabidopsis Genomes
Wang, J., Tao, F., Marowsky, N. C., & Fan, C. (2016) · PLANT PHYSIOLOGY · doi:10.1104/pp.16.01177 · Cited by 36
Of mice, men and immunity: a case for evolutionary systems biology
Ernst, P. B., & Carvunis, A. (2018) · Nature Immunology · doi:10.1038/s41590-018-0084-4 · Cited by 38
Understanding the proteome encoded by “non-coding RNAs”: new insights into human genome
Lu, S., Wang, T., Zhang, G., & He, Q. (2020) · Science China Life Sciences · doi:10.1007/s11427-019-1677-8 · Cited by 35
Rosaceae phylogenomic studies provide insights into the evolution of new genes
Jiang, L., Li, X., Lyu, K., Wang, H., Li, Z., Qi, W., Zhang, L., & Cao, Y. (2024) · Horticultural Plant Journal · doi:10.1016/j.hpj.2024.02.002 · Cited by 34
Origination and evolution of orphan genes and de novo genes in the genome of Caenorhabditis elegans
Zhang, W., Gao, Y., Long, M., & Shen, B. (2019) · Science China Life Sciences · doi:10.1007/s11427-019-9482-0 · Cited by 33
Self-citation
Species-specific partial gene duplication in Arabidopsis thaliana evolved novel phenotypic effects on morphological traits under strong positive selection
Huang, Y., Chen, J., Dong, C., Sosa, D., Xia, S., Ouyang, Y., Fan, C., Li, D.-Z., Mortola, E., Long, M., et al. (2021) · The Plant Cell · doi:10.1093/plcell/koab291 · Cited by 33
“The origination of novel genes is an important process contributing to the evolution of organisms, as new genes have the potential to become genetic sources of evolutionary innovation (Chen et al., 2013; Long et al., 2013).”
BackgroundSelf-citation
DNA transposons mediate duplications via transposition-independent and -dependent mechanisms in metazoans
Tan, S., Ma, H., Wang, J., Wang, M., Wang, M., Yin, H., Zhang, Y., Zhang, X., Shen, J., Wang, D., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-24585-9 · Cited by 34
Single-cell analysis of the amphioxus hepatic caecum and vertebrate liver reveals genetic mechanisms of vertebrate liver evolution
Wu, B., Xu, W., Wu, K., Li, Y., Hu, M., Feng, C., Zhu, C., Zheng, J., Cui, X., Li, J., et al. (2024) · Nature Ecology & Evolution · doi:10.1038/s41559-024-02510-9 · Cited by 31
“Conversely, substantial gene structural mutations, such as new genes, have also been thought to be important for morphological evolution 5,6 .”
Bacterial contribution to genesis of the novel germ line determinant oskar
Blondel, L., Jones, T. E. M., & Extavour, C. G. M. (2020) · eLife · doi:10.7554/elife.45539 · Cited by 32
“However, it is clear that novel genes can evolve functional connections with existing networks, become essential (Chen et al., 2010), and in some cases lead to new functions (Cornelis et al., 2012) and contribute to phenotypic diversity (Chen et al., 2013).”
Background
Genome-wide investigation of proline transporter (ProT) gene family in tomato: Bioinformatics and expression analyses in response to drought stress.
Akbudak, M. A., & Filiz, E. (2020) · Plant physiology and biochemistry : PPB · doi:10.1016/j.plaphy.2020.10.004 · Cited by 25
Linkage mapping and genome annotation give novel insights into gene family expansions and regional recombination rate variation in the painted lady (Vanessa cardui) butterfly
Shipilina, D., Näsvall, K., Höök, L., Vila, R., Talavera, G., & Backström, N. (2022) · Genomics · doi:10.1016/j.ygeno.2022.110481 · Cited by 34
Deciphering the Genetic Basis of Silkworm Cocoon Colors Provides New Insights into Biological Coloration and Phenotypic Diversification
Lu, Y., Luo, J., An, E., Lu, B., Wei, Y., Chen, X., Lu, K., Liang, S., Hu, H., Han, M., et al. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad017 · Cited by 31
“source of new genetic functions, in acquiring genetic traits for environmental adaptation (Long et al. 2003, 2013; Chen et al. 2013).”
Background
Up-regulation of the human-specific CHRFAM7A gene in inflammatory bowel disease
Baird, A., Coimbra, R. S. M., Dang, X., Eliceiri, B. P., & Costantini, T. W. (2016) · BBA Clinical · doi:10.1016/j.bbacli.2015.12.003 · Cited by 30
“…at ScienceDirect BBA Clinical j ourna l homepage: www.e lsev ie r .com/ locate /bbac l in Up-regulation of the human-specific CHRFAM7A gene in inflammatory bowel disease Andrew Baird a,⁎, Raul Coimbra a, Xitong Dang a,b, Brian P. Eliceiri a, Todd W. Costantini a a Division of Trauma, Surgical…”
Background
De novo gene integration into regulatory networks via interaction with conserved genes in peach
Cao, Y., Hong, J., Zhao, Y., Li, X., Feng, X., Wang, H., Zhang, L., Lin, M., Cai, Y., & Han, Y. (2024) · Horticulture Research · doi:10.1093/hr/uhae252 · Cited by 30
Rapid Evolution of Gained Essential Developmental Functions of a Young Gene via Interactions with Other Essential Genes
Lee, Y. C. G., Ventura, I. M., Rice, G. R., Chen, D.-Y., Colmenares, S. U., & Long, M. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz137 · Cited by 28
Self-citation
Emergence of a Novel Chimeric Gene Underlying Grain Number in Rice
Chen, H., Tang, Y., Liu, J., Tan, L., Jiang, J., Wang, M., Zhu, Z., Sun, X., & Sun, C. (2016) · Genetics · doi:10.1534/genetics.116.188201 · Cited by 27
“Many newly emerged genes, which have evolved novel functions, are involved in development, reproduction, and stress responses in various organisms (Tautz and DomazetLoso 2011; Chen et al. 2013).”
Evolution of Gene Structural Complexity: An Alternative-Splicing-Based Model Accounts for Intron-Containing Retrogenes
Zhang, C., Gschwend, A. R., Ouyang, Y., & Long, M. (2014) · PLANT PHYSIOLOGY · doi:10.1104/pp.113.231696 · Cited by 27
“Gene structures can also change and evolve over time; changing a gene’s coding and noncoding structure can lead to the formation of new genes and neofunctionalization (Chen et al., 2013).”
BackgroundSelf-citation
Tracing the De Novo Origin of Protein-Coding Genes in Yeast
Wu, B., & Knudson, A. (2018) · mBio · doi:10.1128/mbio.01024-18 · Cited by 28
“The mechanisms giving rise to new genes can be placed into four categories (1): (i) gene duplication and rapid divergence, in which a new gene is derived from already existing genes in the same genome; (ii) horizontal gene transfer, in which a new gene is derived from already existing genes but from different genomes;…”
Background
Interrelationships Between Bones, Muscles, and Performance: Biting in the Lizard Tupinambis merianae
Fabre, A., Andrade, D. V., Huyghe, K., Cornette, R., & Herrel, A. (2014) · Evolutionary Biology · doi:10.1007/s11692-014-9286-3 · Cited by 27
“…of evolutionary processes, questions concerning the drivers and origins of phenotypic diversity remain central in evolutionary biology (e.g. Chen et al. 2013; Cox and Rabosky Electronic supplementary material The online version of this article (doi:10.1007/s11692-014-9286-3) contains…”
BackgroundInfluential
Social parasitism and the molecular basis of phenotypic evolution
Cini, A., Patalano, S., Segonds-Pichon, A., Busby, G., Cervo, R., & Sumner, S. (2015) · Frontiers in Genetics · doi:10.3389/fgene.2015.00032 · Cited by 26
“New genes may be important drivers of phenotypic evolution (Chen et al., 2013).”
Background
Expression of evolutionarily novel genes in tumors
Kozlov, A. P. (2016) · Infectious Agents and Cancer · doi:10.1186/s13027-016-0077-6 · Cited by 28
Transcriptional Landscapes of Divergent Sporophyte Development in Two Mosses, Physcomitrium (Physcomitrella) patens and Funaria hygrometrica
Kirbis, A., Waller, M., Ricca, M., Bont, Z., Neubauer, A., Goffinet, B., & Szövényi, P. (2020) · Frontiers in Plant Science · doi:10.3389/fpls.2020.00747 · Cited by 28
Erratum to: Behavioral and genetic mechanisms of social evolution: insights from incipiently and facultatively social bees
Shell, W. A., & Rehan, S. M. (2017) · Apidologie · doi:10.1007/s13592-017-0544-0 · Cited by 26
Adaptive evolution by spontaneous domain fusion and protein relocalization
Farr, A. D., Remigi, P., & Rainey, P. B. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0283-7 · Cited by 24
Origins, evolution, and physiological implications of de novo genes in yeast
Parikh, S. B., Houghton, C. J., Oss, S. B. V., Wacholder, A. C., & Carvunis, A. (2022) · Yeast · doi:10.1002/yea.3810 · Cited by 23
“…attention as a major potential source of genetic, structural, and phenotypic novelty (Abrusan, 2013; Bornberg‐Bauer et al., 2021; Capra et al., 2010; Chen et al., 2013; Knopp et al., 2019; Lee et al., 2019; McLysaght & Guerzoni, 2015; McLysaght & Hurst, 2016; Reinhardt et al., 2013; Schlotterer,…”
Background
Gene refashioning through innovative shifting of reading frames in mosses
Guan, Y., Liu, L., Qia, W., Zhao, J., Li, P., Hu, J., Yang, Z., Running, M., Sun, H., & Huang, J. (2018) · Nature Communications · doi:10.1038/s41467-018-04025-x · Cited by 24
Genes with spiralian-specific protein motifs are expressed in spiralian ciliary bands
Wu, L., Hiebert, L. S., Klann, M., Passamaneck, Y. J., Bastin, B. R., Schneider, S., Martindale, M. Q., Seaver, E. C., Maslakova, S. A., & Lambert, J. D. (2020) · Nature Communications · doi:10.1038/s41467-020-17780-7 · Cited by 21
GenOrigin: A comprehensive protein-coding gene origination database on the evolutionary timescale of life
Tong, Y., Shi, M., Qian, S. H., Chen, Y., Luo, Z.-H., Tu, Y., Xiong, Y.-L., Geng, Y.-J., Chen, C., & Chen, Z. (2021) · Journal of genetics and genomics/Journal of Genetics and Genomics · doi:10.1016/j.jgg.2021.03.018 · Cited by 24
Genome-wide identification of the HSP70 genes in Pacific oyster Magallana gigas and their response to heat stress
Lu, H., Liu, C., Yang, C., He, Z., Wang, L., & Song, L. (2024) · Cell Stress and Chaperones · doi:10.1016/j.cstres.2024.06.002 · Cited by 23
“26 After tandem duplication, dose-sensitive genes are lost through selective sweeps to ensure normal organism function, and environmental stress-related genes tend to be amplified and diversified.”
Background
Nuclear RNA Exosome and Pervasive Transcription: Dual Sculptors of Genome Function
Ogami, K., & Suzuki, H. I. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms222413401 · Cited by 24
“This evolutionary trajectory is in contrast to that of protein-coding genes that mostly originate from gene duplication [45,46].”
Result
Experimental Evolution and the Nature of Biodiversity
Kassen, R. (2024) · doi:10.1093/oso/9780192898661.001.0001 · Cited by 24
On the evolutionary origins of insect seminal fluid proteins
Sirot, L. K. (2019) · General and Comparative Endocrinology · doi:10.1016/j.ygcen.2019.01.011 · Cited by 21
Pseudogenes and their potential functions in hematopoiesis
Ma, Y., Chen, Z., & Yu, J. (2021) · Experimental Hematology · doi:10.1016/j.exphem.2021.09.001 · Cited by 22
Transcriptome characterization of three wild Chinese Vitis uncovers a large number of distinct disease related genes
Jiao, C., Gao, M., Wang, X., & Fei, Z. (2015) · BMC Genomics · doi:10.1186/s12864-015-1442-3 · Cited by 22
“The enrichment of stress-related processes in distinct genes is consistent with the hypotheses that wild plants, which are often exposed to an adverse environment, such as extreme temperatures, aberrant pH, toxic chemicals and pathogens, tend to have accelerated adaptive evolution of stress genes [52], while during do…”
Background
Nervous systems and scenarios for the invertebrate-to-vertebrate transition
Holland, N. D. (2015) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2015.0047 · Cited by 24
A comparative analysis of BCL-2 family
Choudhury, S. (2019) · Bioinformation · doi:10.6026/97320630015299 · Cited by 22
Expression Profile and Gene Age Jointly Shaped the Genome-Wide Distribution of Premature Termination Codons in a Drosophila melanogaster Population
Yang, H., He, B., Ma, H., Tsaur, S.-C., Ma, C., Wu, Y., Ting, C., & Zhang, Y. E. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu299 · Cited by 23
“2012)? Even shortly after their origins, speciesspecific or lineage-specific genes may play versatile functions and serve as drivers of phenotypic evolution (Chen et al. 2013).”
Background
Co‐option of a carotenoid cleavage dioxygenase gene (CCD4a) into the floral symmetry gene regulatory network contributes to the polymorphic floral shape–color combinations in Chrysanthemum sensu lato
Zhang, C., Rong, Y., Jiang, C., Guo, Y., & Rao, G. (2022) · New Phytologist · doi:10.1111/nph.18325 · Cited by 21
New genes helped acorn barnacles adapt to a sessile lifestyle
Han, Z., Wang, Z., Rittschof, D., Huang, Z., Chen, L., Hao, H., Yao, S., Su, P., Huang, M., Zhang, Y., et al. (2024) · Nature Genetics · doi:10.1038/s41588-024-01733-7 · Cited by 21
“Furthermore, a full-length transcriptome library was constructed with mixed tissues and sequenced using the PacBio Sequel platform, generating a total of 21.21 Gb long reads (Supplementary Table 11).”
Influential
Limnephilid taxa revised by speciation traits: Rhadicoleptus, Isogamus, Melampophylax genera, Chaetopteryx rugulosa, Psilopteryx psorosa species groups, Drusus bolivari, Annitella kosciuszkii species complexes (Trichoptera: Limnephilidae)
Oláh, J., Chvojka, P., Coppa, G., Godunko, R. J., Lodovici, O., Majecka, K., Majecki, J., Szczesny, B., Urbanič, G., & Valle, M. (2015) · Opuscula Zoologica · doi:10.18348/opzool.2015.1.3 · Cited by 21
“Recent studies have identified very rapidly evolving species-specific new genes with important phenotypic effects on sexual reproduction (Chen et al. 2013).”
Background
SinEx DB: a database for single exon coding sequences in mammalian genomes
Jorquera, R., Ortiz, R., Ossandon, F. J., Cárdenas, J. P., Sepúlveda, R., González, C., & Holmes, D. S. (2016) · Database · doi:10.1093/database/baw095 · Cited by 21
“Other molecular mechanisms for the origin of SEGs have been proposed such as de novo origin (13), DNA-based duplication from intron-containing genes (14), and intron loss, among others (15, 16).”
Background
Potential of Platinum Standard Reference Genomes to Exploit Natural Variation in the Wild Relatives of Rice
Mussurova, S., Al-Bader, N., Zuccolo, A., & Wing, R. A. (2020) · Frontiers in Plant Science · doi:10.3389/fpls.2020.579980 · Cited by 21
“De novo originated genes can provide novel biological functions and have previously been shown to play a key role in pathogen resistance in plants (Chen et al., 2013).”
Background
Deep analysis of wild Vitis flower transcriptome reveals unexplored genome regions associated with sex specification
Ramos, M. J. N., Coito, J. L., Fino, J., Cunha, J., Silva, H., de Almeida, P. G., Costa, M. M. R., Amâncio, S., Paulo, O. S., & Rocheta, M. (2016) · Plant Molecular Biology · doi:10.1007/s11103-016-0553-9 · Cited by 20
Genetic innovations: Transposable element recruitment and de novo formation lead to the birth of orphan genes in the rice genome
Jin, G., Zhou, Y., Yang, H. Y., Hu, Y., Shi, Y., Li, L., Siddique, A. N., Liu, C., Zhu, A., Zhang, C., et al. (2019) · Journal of Systematics and Evolution · doi:10.1111/jse.12548 · Cited by 20
“4B) (Nekrutenko & Li, 2001; Long et al., 2003, 2013; Shapiro, 2005; Chen et al., 2013).”
Regulation plays a multifaceted role in the retention of gene duplicates
Hallin, J., & Landry, C. R. (2019) · PLoS Biology · doi:10.1371/journal.pbio.3000519 · Cited by 20
“This dynamic gain and loss of genes and the associated changes to regulation and function contribute to phenotypic differences between species and among populations of the same species [1].”
Background
A P‐type pentatricopeptide repeat protein ZmRF5 promotes 5′ region partial cleavages of atp6c transcripts to restore the fertility of CMS‐C maize by recruiting a splicing factor
Lin, Y., Yang, H., Liu, H., Lu, X., Cao, H., Li, B., Chang, Y., Guo, Z., Ding, D., Hu, Y., et al. (2023) · Plant Biotechnology Journal · doi:10.1111/pbi.14263 · Cited by 20
“Two strategies are adopted by new mutated or evolved genes to gain new molecular or cell function, one is to integrate into the existing gene network, and the other is to rebuild a new interaction network (Chen et al ., 2013; Zhang et al ., 2015).”
Background
LINE-1-like retrotransposons contribute to RNA-based gene duplication in dicots
Zhu, Z., Tan, S., Zhang, Y., & Zhang, Y. E. (2016) · Scientific Reports · doi:10.1038/srep24755 · Cited by 20
Exaptation at the molecular genetic level
Brosius, J. (2018) · Science China Life Sciences · doi:10.1007/s11427-018-9447-8 · Cited by 21
Landscape of the Dark Transcriptome Revealed Through Re-mining Massive RNA-Seq Data
Li, J., Singh, U., Arendsee, Z. W., & Wurtele, E. S. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.722981 · Cited by 18
Evolutionary history of glucose-6-phosphatase encoding genes in vertebrate lineages: towards a better understanding of the functions of multiple duplicates
Marandel, L., Panserat, S., Plagnes‐Juan, E., Arbenoits, E., Soengas, J. L., & Bobe, J. (2017) · BMC Genomics · doi:10.1186/s12864-017-3727-1 · Cited by 21
“development of the human brain, behavioural control as well as the metabolic responses of organisms [8, 9].”
Background
Multiple Pristionchus pacificus genomes reveal distinct evolutionary dynamics between de novo candidates and duplicated genesPreprint
Prabh, N., & Rödelsperger, C. (2022) · Genome Research · doi:10.1101/gr.276431.121 · Cited by 22
“New genes can arise from gene duplication events or emerge de novo from previously noncoding sequences (Chen et al. 2013; Van Oss and Carvunis 2019).”
Background
Population-Specific Genetic and Expression Differentiation in Europeans
Jiang, X., & Assis, R. (2020) · Genome Biology and Evolution · doi:10.1093/gbe/evaa021 · Cited by 18
A de novo gene originating from the mitochondria controls floral transition in Arabidopsis thaliana
Takeda, T., Shirai, K., Kim, Y.-W., Higuchi‐Takeuchi, M., Shimizu, M., Kondo, T., Ushijima, T., Matsushita, T., Shinozaki, K., & Hanada, K. (2022) · Plant Molecular Biology · doi:10.1007/s11103-022-01320-6 · Cited by 20
“Phenotypic evolution has been accelerated by newly emerged genes (Chen et al. 2013; Arendsee et al. 2014; Kumar et al. 2015), most of which were likely derived from gene duplication events (Tautz and Domazet-Lošo 2011).”
Background
Genomics in neglected and underutilized fruit crops: A chromosome‐scale genome sequence of cherimoya ( Annona cherimola )
Talavera, A., Fernández‐Pozo, N., Matas, A. J., Hormaza, J. I., & Bombarely, A. (2023) · Plants People Planet · doi:10.1002/ppp3.10366 · Cited by 19
A novel gene REPTOR2 activates the autophagic degradation of wing disc in pea aphid
Yuan, E., Guo, H., Chen, W., Du, B., Mi, Y., Qi, Z., Yuan, Y., Zhu‐Salzman, K., Ge, F., & Sun, Y. (2023) · eLife · doi:10.7554/elife.83023 · Cited by 19
Gene duplications facilitate C4-CAM compatibility in common purslane
Wang, X., Ma, X., Yan, G., Hua, L., Liu, H., Huang, W., Liang, Z., Chao, Q., Hibberd, J. M., Jiao, Y., et al. (2023) · PLANT PHYSIOLOGY · doi:10.1093/plphys/kiad451 · Cited by 22
“The expansion and contraction of gene families have a profound influence in shaping stress resistance and driving phenotypic diversity and adaptive evolution in flowering plants (Jiao et al. 2011; Chen et al. 2013; Wu et al. 2020; Zhang et al. 2020; Wang et al. 2022).”
Background
Gene family information facilitates variant interpretation and identification of disease-associated genesPreprint
Lal, D., May, P., Samocha, K. E., Kosmicki, J. A., Robinson, E., Møller, R. S., Krause, R., Nüernberg, P., Weckhuysen, S., Jonghe, P. D., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/159780 · Cited by 19
“Evolutionary younger paralogs show higher functional redundancy 29 .”
Background
The nearly complete assembly of the Cercis chinensis genome and Fabaceae phylogenomic studies provide insights into new gene evolution
Li, J., Shen, J., Wang, R., Chen, Y., Zhang, T., Wang, H., Guo, C., & Qi, J. (2022) · Plant Communications · doi:10.1016/j.xplc.2022.100422 · Cited by 16
“1 (Long et al., 2003; Chen et al., 2013).”
Background
Genomic Insights into Mollusk Terrestrialization: Parallel and Convergent Gene Family Expansions as Key Facilitators in Out-of-the-Sea Transitions
Arístide, L., & Fernández, R. (2023) · Genome Biology and Evolution · doi:10.1093/gbe/evad176 · Cited by 23
“This is particularly relevant, as gene repertoire evolution has been shown to be an important mode of adaptive evolution (Demuth and Hahn 2009; Chen et al. 2013).”
Background
Convergent and divergent evolution of microRNA ‐mediated regulation in metazoans
Wang, Y., Tang, X., & Lü, J. (2023) · Biological reviews/Biological reviews of the Cambridge Philosophical Society · doi:10.1111/brv.13033 · Cited by 23
“On the other hand, changes in seed sequences can lead to distinct regulatory functions among duplicated miRNAs (Sun, Lin & Chen, 2013; Ninova, Ronshaugen & Grif ﬁ ths-Jones, 2014; Berezikov, 2011; Mohammed et al ., 2014 a ).”
Background
Studying the genetic basis of speciation in high gene flow marine invertebrates
Pogson, G. H. (2016) · Current Zoology · doi:10.1093/cz/zow093 · Cited by 18
“The importance of new genes in forming reproductive barriers between species is largely unknown, but they appear to diverge quickly and often acquire new functions (Chen et al. 2013; Long et al. 2013).”
Background
A two-level model for the role of complex and young genes in the formation of organism complexity and new insights into the relationship between evolution and development
Yang, D. C., Xu, A., Shen, P., Gao, C., Zang, J., Qiu, C., Ouyang, H., Jiang, Y., & He, F. (2018) · EvoDevo · doi:10.1186/s13227-018-0111-4 · Cited by 18
The Effects of Sequence Length and Composition of Random Sequence Peptides on the Growth of E. coli Cells
Castro, J. F., & Tautz, D. (2021) · Genes · doi:10.3390/genes12121913 · Cited by 17
Promoter evolution of mammalian gene duplicates
Fraimovitch, E., & Hagai, T. (2023) · BMC Biology · doi:10.1186/s12915-023-01590-6 · Cited by 17
“Background Gene duplication introduces new gene copies and, as such, plays a central role in genome evolution and organismal complexity [1, 2].”
Background
Evolution of root nodule symbiosis via paleopolyploidy and modular pathway rewiring
Liu, H., Hou, L., Lan, L., Zhang, R., Wang, D.-J., Feng, H., Chen, C., Ye, J.-J., Oyebanji, O. O., Chukwuma, E. C., et al. (2026) · Cell Host & Microbe · doi:10.1016/j.chom.2026.01.001 · Cited by 17
Self-citation
The genome of Magnolia hypoleuca provides a new insight into cold tolerance and the evolutionary position of magnoliids
Zhou, L., Hou, F.-X., Wang, L., Zhang, L., Wang, Y.-L., Yin, Y.-P., Pei, J., Peng, C., Qin, X.-B., & Gao, J.-H. (2023) · Frontiers in Plant Science · doi:10.3389/fpls.2023.1108701 · Cited by 16
Orphan genes are not a distinct biological entity
Pereira, A. B., Marano, M., Bathala, R., Zaragoza, R. A., Neira, A., Samano, A., Owoyemi, A. O., & Casola, C. (2024) · BioEssays · doi:10.1002/bies.202400146 · Cited by 15
Functional Divergence of Plant‐Derived Thaumatin‐Like Protein Genes in Two Closely Related Whitefly Species
Hu, Y., Cheng, G., Yang, Z., Han, H., Tian, T., Yang, X., Xie, W., Wang, S., Wu, Q., Zhou, X. J., et al. (2025) · Advanced Science · doi:10.1002/advs.202502193 · Cited by 17
Emergence and Evolution of Hominidae-Specific Coding and Noncoding Genomic Sequences
Saber, M. M., Babarinde, I. A., Hettiarachchi, N., & Saitou, N. (2016) · Genome Biology and Evolution · doi:10.1093/gbe/evw132 · Cited by 17
“Key words: Hominidae, conserved noncoding sequences, lineage-specific genes, DSCR4, accelerated evolution.”
Background
Human-specific gene CHRFAM7A mediates M2 macrophage polarization via the Notch pathway to ameliorate hypertrophic scar formation
Li, T., Chen, W., Zhang, Q., & Deng, C.-L. (2020) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2020.110611 · Cited by 17
Uniqueness of Entamoeba sulfur metabolism: sulfolipid metabolism that plays pleiotropic roles in the parasitic life cycle
Mi‐ichi, F., Miyamoto, T., & Yoshida, H. (2017) · Molecular Microbiology · doi:10.1111/mmi.13827 · Cited by 17
“LGT is a process that generates new genes, which can drive adaptive evolution (Chen et al., 2013).”
Background
Oryza-Specific Orphan Protein Triggers Enhanced Resistance to Xanthomonas oryzae pv. oryzae in Rice
Moon, H., Jeong, A.-R., Kwon, O., & Park, C. (2022) · Frontiers in Plant Science · doi:10.3389/fpls.2022.859375 · Cited by 16
“…Science | www.frontiersin.org 1 March 2022 | Volume 13 | Article 859375 functional study of the orphan genes is fundamentally important for understanding the origin of new species, species-specific morphological features, and evolution of immune systems (Khalturin et al., 2009; Chen et al., 2013).”
Background
Promoter recruitment drives the emergence of proto-genes in a long-term evolution experiment with Escherichia coli
uz‐Zaman, M. H., D’Alton, S., Barrick, J. E., & Ochman, H. (2024) · PLoS Biology · doi:10.1371/journal.pbio.3002418 · Cited by 16
Honeybees’ novel complementary sex-determining system: function and origin
Seiler, J., & Beye, M. (2024) · Trends in Genetics · doi:10.1016/j.tig.2024.08.001 · Cited by 14
ORFanFinder: automated identification of taxonomically restricted orphan genes
Ekstrom, A., & Yin, Y. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw122 · Cited by 15
DNA methylation changes facilitated evolution of genes derived from Mutator-like transposable elements
Wang, J., Yu, Y., Tao, F., Zhang, J., Copetti, D., Kudrna, D., Talag, J., Lee, S., Wing, R. A., & Fan, C. (2016) · Genome biology · doi:10.1186/s13059-016-0954-8 · Cited by 16
“New genes can be generated through various mechanisms [18, 19, 21, 22].”
Background
The Persistent Contributions of RNA to Eukaryotic Gen(om)e Architecture and Cellular FunctionPreprint
Brosius, J. (2014) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a016089 · Cited by 15
“Gradual change from a duplicated gene, via those encoding isoforms, up to the acquisition of novel functions including subfunctionalization (Lynch and Force 2000) is now well documented (Roth et al. 2007; Kaessmann 2010; Chen et al. 2013).”
Background
Improved ontology for eukaryotic single-exon coding sequences in biological databases
Jorquera, R., González, C., Clausen, P. T. L. C., Petersen, B., & Holmes, D. S. (2018) · Database · doi:10.1093/database/bay089 · Cited by 15
“Although many SEGs are thought to be RGs (14), molecular mechanisms distinct to retrotransposition have been proposed for the origin of SEGs, such as de novo origin (35), DNA-based duplication from intron-containing genes (36) and intron loss, among others (37, 38).”
Background
The molecular basis of phenotypic evolution: beyond the usual suspects
Lin, R., Ferreira, B. T., & Yuan, Y. (2024) · Trends in Genetics · doi:10.1016/j.tig.2024.04.010 · Cited by 15
Run or Die in the Evolution of New MicroRNAs—Testing the Red Queen Hypothesis on De Novo New Genes
Zhao, Y., Lu, G.-A., Yang, H., Lin, P., Liufu, Z., Tang, T., & Xu, J. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa317 · Cited by 15
“The majority of new genes belong to the former, comprising duplicated, (retro-)transposed, and chimeric genes (Chen et al. 2013).”
Rapid Functional and Sequence Differentiation of a Tandemly Repeated Species-Specific Multigene Family inDrosophila
Clifton, B. D., Librado, P., Yeh, S., Solares, E., Real, D. A., Jayasekera, S., Zhang, W., Shi, M., Park, R., Magie, R. D., et al. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw212 · Cited by 16
“…and fertility (Chen et al. 2010; Mayer et al. 2015), therefore their study is instrumental for determining how early mutational mechanisms and evolutionary forces refine the functional attributes of a gene and its organismal impact shortly after its formation (Hahn 2009; Chen et al. 2013).”
Background
Haploid selection drives new gene male germline expressionPreprint
Raíces, J. B., Otto, P. A., & Vibranovski, M. D. (2019) · Genome Research · doi:10.1101/gr.238824.118 · Cited by 15
“Newgeneoriginationisthoughttoplayamajorroleinphenotypic evolution (Kaessmann 2010; Chen et al. 2013).”
Marsdenia tenacissima genome reveals calcium adaptation and tenacissoside biosynthesis
Zhou, Y., Fan, W., Zhang, H., Zhang, J., Zhang, G., Wang, D., Xiang, G., Zhao, C., Li, L., He, S., et al. (2022) · The Plant Journal · doi:10.1111/tpj.16081 · Cited by 14
Neofunctionalization of tandem duplicate genes encoding putative β-L-arabinofuranosidases in Arabidopsis
Tao, F., Sollapura, V., Robert, L. S., & Fan, C. (2023) · PLANT PHYSIOLOGY · doi:10.1093/plphys/kiad169 · Cited by 14
A genome assembly of ginger (Zingiber officinale Roscoe) provides insights into genome evolution and 6-gingerol biosynthesis.
Chen, Z.-J., Zhang, L.-Y., Lv, Y., Qu, S., Liu, W.-J., Wang, K., Gao, S., Zhu, F., Cao, B., & Xu, K. (2024) · The Plant Journal · doi:10.1111/tpj.16625 · Cited by 18
Genomic insights into ecological adaptation of oaks revealed by phylogenomic analysis of multiple species
Wang, T., Ning, X., Zheng, S.-S., Li, Y., Lu, Z.-J., Meng, H., Ge, B., Kozlowski, G., Yan, M., & Song, Y. (2024) · Acta Botanica Yunnanica · doi:10.1016/j.pld.2024.07.008 · Cited by 15
“The expansion and contraction of gene families have been well-documented as crucial driving forces in lineage splitting and functional diversi ﬁ cation (Chen et al., 2013).”
Gene Duplication and Alternative Splicing as Evolutionary Drivers of Proteome Specialization
Mantica, F., & Irimia, M. (2025) · BioEssays · doi:10.1002/bies.202400202 · Cited by 13
Integrative analyses of RNA editing, alternative splicing, and expression of young genes in human brain transcriptome by deep RNA sequencing
Wu, D., Ye, L., Li, Y., Sun, Y., Shao, Y., Chen, C., Zhu, Z., Li, Z., Wang, L., Irwin, D. M., et al. (2015) · Journal of Molecular Cell Biology · doi:10.1093/jmcb/mjv043 · Cited by 14
“Contribution of young protein-coding genes to the evolution of the human brain New genes provide crucial material for the evolutionary innovation of phenotypes such as development, behavior, and reproduction (Chen et al., 2013; Long et al., 2013).”
Background
Clade-specific genes and the evolutionary origin of novelty; new tools in the toolkit
Wu, L., & Lambert, J. D. (2022) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2022.05.025 · Cited by 13
Genomic Characterization of Variable Surface Antigens Reveals a Telomere Position Effect as a Prerequisite for RNA Interference-Mediated Silencing in Paramecium tetraurelia
Baranas̆ić, D., Oppermann, T., Cheaib, M., Cullum, J., SCHMIDT, H. J., & Simon, M. C. (2014) · mBio · doi:10.1128/mbio.01328-14 · Cited by 14
“Across kingdoms, phenotypic evolution was described as resulting from the creation of new genes, predominantly originating from duplication events (50).”
Background
Evolution and meiotic organization of heteromorphic sex chromosomes
Daish, T., & Grützner, F. (2019) · Current topics in developmental biology/Current Topics in Developmental Biology · doi:10.1016/bs.ctdb.2019.01.009 · Cited by 14
Srag Regulates Autophagy via Integrating into a Preexisting Autophagy Pathway in Testis
Cheng, Y., Lai, F., Wang, X., Shang, D., Zou, J., Luo, M., Xia, X., Cheng, H., & Zhou, R. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa195 · Cited by 14
Exploring the Genomic Patterns in Human and Mouse Cerebellums Via Single-Cell Sequencing and Machine Learning Method
Li, Z., Wang, D., Liao, H., Zhang, S., Guo, W., Chen, L., Lü, L., Huang, T., & Cai, Y. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.857851 · Cited by 14
“Researchers reported that some new genes participated in lineage-or species-speci ﬁ c phenotypic evolution (Chen et al., 2013).”
Background
Facing lethal temperatures: Heat‐shock response in desert and temperate ants
Araujo, N. D. S., Perez, R., Willot, Q., Defrance, M., & Aron, S. (2023) · Ecology and Evolution · doi:10.1002/ece3.10438 · Cited by 13
“New genes are known to be particularly relevant to species' ad-aptative response to stress (Chen et al., 2013; Johnson, 2018; Kaessmann, 2010 ; Taylor & Raes, 2004 ).”
The haplotype‐resolved genome of diploid Chrysanthemum indicum unveils new acacetin synthases genes and their evolutionary history
Hou, Z., Yang, S. L., He, W., Lu, T., Feng, X., Zang, L., Bai, W., Chen, X., Nie, B., Li, C., et al. (2024) · The Plant Journal · doi:10.1111/tpj.16854 · Cited by 15
Topological evolution of coexpression networks by new gene integration maintains the hierarchical and modular structures in human ancestors
Zu, J., Gu, Y., Li, Y., Li, C., Zhang, W., Zhang, Y. E., Lee, U., Zhang, L., & Long, M. (2019) · Science China Life Sciences · doi:10.1007/s11427-019-9483-6 · Cited by 12
Self-citation
Integrative analysis of young genes, positively selected genes and lncRNAs in the development of Drosophila melanogaster
Liu, H., Li, Y., Irwin, D. M., Zhang, Y., & Wu, D. (2014) · BMC Evolutionary Biology · doi:10.1186/s12862-014-0241-9 · Cited by 13
Functional Evolution in Orthologous Cell-encoded RNA-dependent RNA Polymerases
Qian, X., Hamid, F., Sahili, A. E., Darwis, D., Wong, Y. H., Bhushan, S., Makeyev, E. V., & Lescar, J. (2016) · Journal of Biological Chemistry · doi:10.1074/jbc.m115.685933 · Cited by 13
“Gene duplication followed by paralog divergence is amajor driving force in protein evolution (41, 42), and it clearly contributed toRdRPdiversification.”
Background
On the Origin and Evolution of Drosophila New Genes during Spermatogenesis
Su, Q., He, H., & Zhou, Q. (2021) · Genes · doi:10.3390/genes12111796 · Cited by 12
“These patterns can be explained by the fact that retrogenes and de novo genes are much more likely to acquire novel cis-regulatory elements than DNA-based new gene duplications [1,2].”
Background

Authors: Chen, S., Krinsky, B. H., & Long, M.
Affiliations: University of Chicago (US)
Corresponding author: Long, Manyuan
ORCID: Chen, Sidi
Long, Manyuan
Venue: Nature Reviews Genetics
Publisher: Springer Science and Business Media LLC
Published: 2013-08-16
Volume: 14
Issue: 9
Pages: 645-660
ISSN: 1471-0056 (ISSN-L)
1471-0064
DOI: 10.1038/nrg3521
PMC: PMC4236023
OpenAlex: W2057844822
Cited by: 428
References: 137
Citations by year: 2026: 21 · 2025: 34 · 2024: 64 · 2023: 46 · 2022: 30 · 2021: 28 · 2020: 30 · 2019: 41 · 2018: 22 · 2017: 26 · 2016: 36 · 2015: 17 · 2014: 27 · 2013: 6
FWCI: 3.06
Type: journal article
Language: en
Update notices: erratum (2013-08-22)
Open access: green
www.ncbi.nlm.nih.gov
Licence: www.springer.com/tdm (tdm)
www.springer.com/tdm (vor)
Locations: Nature Reviews Genetics (publishedVersion)
PubMed (publishedVersion)
Europe PMC (PubMed Central) (acceptedVersion)
PubMed Central (acceptedVersion)
Funders: National Institutes of Health
U.S. Public Health Service (1R01100768‑01A1)
National Institute of General Medical Sciences (R01GM100768, T32GM007197)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords: neofunctionalization, novel genes, gene birth, phenotypic evolution, genome evolution, gene duplication, developmental processes, reproduction, brain function, behavior, biodiversity, functional redundancy
MeSH terms: Animals, Behavior, Animal, Brain, Biological Evolution, Gene Expression Regulation, Genes, Humans, Phenotype, Plants, Reproduction, Sex Characteristics, Species Specificity, Evolution, Molecular, Biodiversity

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

New genes as drivers of phenotypic evolution

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks