Dong-Dong Wu

Kunming Institute of Zoology CAS, Yün-nan, Yunnan, China

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Publications (33)162.34 Total impact

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    ABSTRACT: Next-generation RNA-sequencing has been successfully used for identification of transcript assembly, evaluation of gene expression levels, and detection of post-transcriptional modifications. Despite these large-scale studies, additional comprehensive RNA-seq data from different subregions of the human brain are required to fully evaluate the evolutionary patterns experienced by the human brain transcriptome. Here, we provide a total of 6.5 billion RNA-seq reads from different subregions of the human brain. A significant correlation was observed between the levels of alternative splicing and RNA-editing, which might be explained by a competition between the molecular machineries responsible for the splicing and editing of RNA. Young human protein-coding genes demonstrate biased expression to the neocortical and non-neocortical regions during evolution on the lineage leading to humans. We also found that a significantly greater number of young human protein-coding genes are expressed in the putamen, a tissue that was also observed to have the highest level of RNA-editing activity. The putamen, which previously received little attention, plays an important role in cognitive ability, and our data suggest a potential contribution of the putamen to human evolution. © The Author (2015). Published by Oxford University Press on behalf of Journal of Molecular Cell Biology, IBCB, SIBS, CAS. All rights reserved.
    Journal of Molecular Cell Biology 07/2015; DOI:10.1093/jmcb/mjv043 · 8.43 Impact Factor
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    ABSTRACT: Much like other indigenous domesticated animals, Tibetan chickens living at high altitudes (2,200~4,100 m) show specific physiological adaptations to the extreme environmental conditions of the Tibetan Plateau, but the genetic bases of these adaptations are not well characterized. Here, we assembled a de novo genome of a Tibetan chicken, and re-sequenced whole genomes of 32 additional chickens, including Tibetan chickens, village chickens, game fowl, and Red Junglefowl, and found that the Tibetan chickens could broadly be placed into two groups. Further analyses revealed that several candidate genes in the calcium-signaling pathway are possibly involved in adaptation to the hypoxia experienced by these chickens, as these genes appear to have experienced directional selection in the two Tibetan chicken populations, suggesting a potential genetic mechanism underlying high altitude adaptation in Tibetan chickens. The candidate selected genes identified in this study, and their variants, may be useful targets for clarifying our understanding of the domestication of chickens in Tibet, and might be useful in current breeding efforts to develop improved breeds for the highlands. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
    Molecular Biology and Evolution 03/2015; DOI:10.1093/molbev/msv071 · 14.31 Impact Factor
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    ABSTRACT: Dogs shared a much closer relationship with humans than any other domesticated animals, probably due to their unique social cognitive capabilities, which were hypothesized to be a by-product of selection for tameness toward humans. Here, we demonstrate that genes involved in glutamate metabolism, which account partially for fear response, indeed show the greatest population differentiation by whole genome comparison of dogs and wolves. However, the changing direction of their expression supports a role in increasing excitatory synaptic plasticity in dogs rather than reducing fear response. Since synaptic plasticity are widely believed to be cellular correlates of learning and memory, this change may alter the learning and memory abilities of ancient scavenging wolves, weaken the fear reaction toward humans, and prompt the initial interspecific contact.
    Genome Biology and Evolution 11/2014; 6(11). DOI:10.1093/gbe/evu245 · 4.53 Impact Factor
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    ABSTRACT: New genes, which provide material for evolutionary innovation, have been extensively studied for many years in animals where it is observed that they commonly show an expression bias for the testis. Thus the testis is a major source for the generation of new genes in animals. The source tissue for new genes in plants is unclear. Here, we find that new genes in plants show a bias in expression to mature pollen, and are also enriched in a gene co-expression module that correlates with mature pollen in Arabidopsis thaliana. Transposable elements are significantly enriched in the new genes, and the high activity of transposable elements in the vegetative nucleus, compared to the germ cells, suggests that new genes are most easily generated in the vegetative nucleus in the mature pollen. We propose an "out of pollen" hypothesis for the origin of new genes in flowing plants.
    Genome Biology and Evolution 09/2014; 6(10). DOI:10.1093/gbe/evu206 · 4.53 Impact Factor
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    ABSTRACT: With the assistance of their human companions, dogs have dispersed into new environments during the expansion of human civilization. Tibetan Mastiff (TM), a native of the Tibetan Plateau, was derived from the domesticated Chinese native dog and, like Tibetans, has adapted to the extreme environment of high altitude. Here, we genotyped genome wide SNPs from 32 Tibetan Mastiffs, and compared them with SNPs from 20 Chinese native dogs and 14 grey wolves (Canis lupus). We identified 16 genes with signals of positive selection in the Tibetan Mastiff, with 12 of these candidate genes associated with functions that have roles in adaptation to high altitude adaptation, such as EPAS1, SIRT7, PLXNA4, and MAFG that have roles in responses to hypoxia. This study provides important information on the genetic diversity of the Tibetan Mastiff and potential mechanisms for adaptation to hypoxia.
    Molecular Biology and Evolution 02/2014; DOI:10.1093/molbev/msu070 · 14.31 Impact Factor
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    ABSTRACT: Domesticated dogs have many unique behaviors not found in gray wolves that have augmented their interaction and communication with humans. The genetic basis of such unique behaviors in dogs remains poorly understood. We found that genes within regions highly differentiated between outbred Chinese native dogs and wolves show high bias for expression localized to brain tissues, particularly the prefrontal cortex, a specific region responsible for complex cognitive behaviors. In contrast, candidate genes showing high population differentiation between Chinese native dogs and German Shepherd dogs did not demonstrate significant expression bias. These observations indicate that these candidate genes highly expressed in the brain have rapidly evolved. This rapid evolution was probably driven by artificial selection during the primary transition from wolves to ancient dogs, and was consistent with the evolution of dog-specific characteristics, such as behavior transformation, for thousands of years.
    Molecular Biology and Evolution 05/2013; 30. DOI:10.1093/molbev/mst088 · 14.31 Impact Factor
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    ABSTRACT: Spirocyclic oxetanes were found to undergo versatile transformations under different acid-mediated conditions. Treatment of spirocyclopropyl oxetanes with excess amounts of hydrochloric or hydrobromic acid at room temperature resulted in the formation of spirocyclopropyl fused butenolides with good yields. The transformation of spirocyclopropyl oxetanes mediated by hydroiodic acid led to spirocyclopropyl fused γ-butyrolactones instead of butenolides. Transformation of spirocyclopropyl oxetanes catalyzed by Lewis acid was also explored and found to give distinct products such as spirobutyl indolinones. The reaction mechanisms involved in the acid-mediated transformations were proposed.
    RSC Advances 04/2013; 3(20):7529-7536. DOI:10.1039/C3RA00178D · 3.84 Impact Factor
  • Dong-Dong Wu, Ya-Ping Zhang
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    ABSTRACT: De novo origination has recently been appreciated to be an important mechanism contributing to the origin of genes. Evidence indicates that de novo originated genes can evolve important and even essential functions rapidly. We present an "adaptation following neutrality" process to explain the evolution of essential function of new genes. How new de novo originated genes become involved in pathways and interact with other old genes, and the exact functions of these new genes, however, remains largely undocumented. Examinations of the function of de novo origin and the function of noncoding RNA genes should become more frequent and appreciated in the future studies.
    Molecular Phylogenetics and Evolution 02/2013; 67(2). DOI:10.1016/j.ympev.2013.02.013 · 4.02 Impact Factor
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    ABSTRACT: GDF5 is a member of the bone morphogenetic protein (BMP) gene family, and plays an important role in the development of the skeletal system. Variants of the gene are associated with osteoarthritis and height in some human populations. Here, we resequenced the gene in individuals from four geographically separated human populations, and found that the evolution of the promoter region deviated from neutral expectations, with the sequence evolution driven by positive selection in the East Asian population, especially the haplotypes carrying the derived alleles of 5' UTR SNPs rs143384 and rs143383. The derived alleles of rs143384 and rs143383, which are associated with a risk of osteoarthritis and decreased height, have high frequencies in non-Africans and show strong extended haplotype homozygosity and high population differentiation in East Asian. It is concluded that positive selection has driven the rapid evolution of the two osteoarthritis osteoarthritis-risk and decreased height associated variants of the human GDF5 gene, and supports the suggestion that the reduction in body size during the terminal Pleistocene and Holocene period might have been an adaptive process influenced by genetic factors.
    PLoS ONE 08/2012; 7(8):e42553. DOI:10.1371/journal.pone.0042553 · 3.53 Impact Factor
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    ABSTRACT: Photoinduced reactions of isatin and N-methyl-1,3,4-isoquinolinetrione with bicycloalkylidenes such as bicyclopropylidene, cyclopropylidenecyclobutane, cyclopropylidenecyclohexane and bicyclohexylidene were investigated. The reactions gave spirooxetanes as the major products derived from the [2 + 2] photocycloaddition pathway via 1,4-biradical recombination. Unusual products including the [4 + 2 + 2] cycloadducts, the oxoisochroman derivatives and other ring-rearranged products were derived from competitive pathways via 1,6-biradical recombination. The presence of oxygen in the reaction solution was found to be relevant to the distribution of different types of products. Mechanisms were proposed to rationalize the chemo- and regioselectivity in the photoreactions and the origin of the different types of products.
    Organic & Biomolecular Chemistry 05/2012; 10(18):3626-35. DOI:10.1039/c2ob07158d · 3.49 Impact Factor
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    ABSTRACT: RNASEL is a 2-5A-dependent endoribonuclease that is a component of the interferon-induced 2-5A system, which plays a crucial role in the antiviral and apoptotic activities of interferons. In humans, many polymorphic sites within the RNASEL gene have been associated with an increased risk of developing prostate cancer. Here, we obtained coding sequences for the RNASEL gene from 11 primates and found evidence that positive selection has operated on the C-terminal endoribonuclease domain and the N-terminal ankyrin repeats domain of the protein, domains that directly interact with virus (i.e., ankyrin repeats are responsible for receiving environmental signals, and the endoribonuclease catalyses the destruction of the pathogenic viral RNA). To extend this finding, we studied variation within this gene in modern human populations by resequencing alleles from 144 individuals representing four separate populations. Interestingly, the frequency of the 541D allele shows a negative association with the incidence rate of prostate cancer in worldwide populations, and haplotypes containing the 541D polymorphisms demonstrate signatures of positive selection. RNASEL variants having the 541D haplotype likely have a greater ability to defend against infections by viruses, thus the loss of this activity may be associated with the development of prostate cancer. We provide evidence that positive selection has operated on the RNASEL gene, and its evolution is correlated with its function in pathogen defense and cancer association.
    Molecular Biology and Evolution 04/2012; 29(10):3161-8. DOI:10.1093/molbev/mss123 · 14.31 Impact Factor
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    ABSTRACT: In the cation of the title organic ion pair compound, C23H20ClN2O3 +·CH3O−, the cyclo­hexyl ring shows a half-boat conformation and the dihedral angles between two benzene rings and the pyran ring are 83.14 (7) and 73.18 (9)°. In the crystal, centrosymmetrically related cations are linked into a dimer by pairs of N—H⋯N hydrogen bonds, generating an R 2 2(12) ring motif. The anion inter­acts with the dimer through an N—H⋯O hydrogen bond. π–π inter­actions between pyran rings of adjacent dimers, with a centroid–centroid distance of 3.861 (2) Å, are also observed.
    Acta Crystallographica Section E Structure Reports Online 03/2012; 68(Pt 3):o824. DOI:10.1107/S1600536812007088 · 0.35 Impact Factor
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    ABSTRACT: The title compound, C24H22N2O4 center dot H2O, was obtained by the reaction of 3,4-dimethoxybenzaldehyde, malononitrile and 5-phenylcyclohexane-1,3-dione. The cyclohexyl and pyran rings show half-boat and V-shaped conformations, respectively. The dihedral angle between the phenyl and benzene ring planes is 30.67 (9)degrees. The organic molecules are packed in a two-dimensional network parallel to the bc plane stabilized by intermolecular N-H center dot center dot center dot N and N-H center dot center dot center dot O hydrogen bonds.
    Acta Crystallographica Section E Structure Reports Online 02/2012; 68(Pt 2):o409-10. DOI:10.1107/S1600536811056285 · 0.35 Impact Factor
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    ABSTRACT: CLEC4M is a C-type lectin gene serving as cell adhesion receptor and pathogen recognition receptor. It recognizes several pathogens of important public health concern. In particular, a highly polymorphic variable number tandem repeat (VNTR) at the neck-region of CLEC4M had been associated with genetic predisposition to some infectious diseases. To gain insight into the origin and evolution of this VNTR in CLEC4M, we studied 21 Africans, 20 Middle Easterns, 35 Europeans, 38 Asians, 13 Oceania, and 18 Americans (a total of 290 chromosomes) from the (Human Genome Diversity Panel) HGDP-CEPH panel; these samples covered most of alleles of this VNTR locus present in human populations. We identified a limited number of haplotypes among the basic repeat subunits that is 69 base pairs in length. Only 8 haplotypes were found. Their sequence identities were determined in the 290 chromosomes. VNTR alleles of different repeat length (from 4 to 9 repeats) were analyzed for composition and orientation of these subunits. Our results showed that the subunit configuration of the same repeat number of VNTR locus from different populations were, in fact, virtually identical. It implies that most of the VNTR alleles existed before dispersion of modern humans outside Africa. Further analyses indicate that the present diversity profile of this locus in worldwide populations is generated from the effect of migration of different tribes and neutral evolution. Our findings do not support the hypothesis that the origin of the VNTR alleles were arisen by independent (separate) mutation events and caused by differential allele advantage and natural selection as suggested by previous report based on SNP data.
    PLoS ONE 01/2012; 7(1):e30268. DOI:10.1371/journal.pone.0030268 · 3.53 Impact Factor
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    Dong-Dong Wu, David M Irwin, Ya-Ping Zhang
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    ABSTRACT: Author Summary The origin of genes can involve mechanisms such as gene duplication, exon shuffling, retroposition, mobile elements, lateral gene transfer, gene fusion/fission, and de novo origination. However, de novo origin, which means genes originate from a non-coding DNA region, is considered to be a very rare occurrence. Here we identify 60 new protein-coding genes that originated de novo on the human lineage since divergence from the chimpanzee, supported by both transcriptional and proteomic evidence. It is inconsistent with the traditional view that the de novo origin of new genes is rare. RNA–seq data indicate that these de novo originated genes have their highest expression in the cerebral cortex and testes, suggesting these genes may contribute to phenotypic traits that are unique to humans, such as development of cognitive ability. Therefore, the importance of de novo origination needs greater appreciation.
    PLoS Genetics 11/2011; 7(11):e1002379. DOI:10.1371/journal.pgen.1002379 · 8.17 Impact Factor
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    ABSTRACT: A major reduction of genetic diversity in mtDNA occurred during the domestication of East Asian pigs. However, the extent to which genetic diversity has been lost in the nuclear genome is uncertain. To reveal levels and patterns of nucleotide diversity and to elucidate the genetic relationships and demographic history of domestic pigs and their ancestors, wild boars, we investigated 14 nuclear markers (including 8 functional genes, 2 pseudogenes and 4 intergenic regions) from 11 different chromosomes in East Asia-wide samples and pooled them with previously obtained mtDNA data for a combined analysis. The results indicated that domestic pigs and wild boars possess comparable levels of nucleotide diversity across the nuclear genome, which is inconsistent with patterns that have been found in mitochondrial genome. This incongruence between the mtDNA and nuclear genomes is suggestive of a large-scale backcross between male wild boars and female domestic pigs in East Asia. Our data reveal the impacts of founder effects and backcross on the pig genome and help us better understand the complex demographic histories of East Asian pigs, which will be useful for future work on artificial selection.
    PLoS ONE 10/2011; 6(10):e26416. DOI:10.1371/journal.pone.0026416 · 3.53 Impact Factor
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    Dong-Dong Wu, Ya-Ping Zhang
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    ABSTRACT: Horizontal gene transfer, the movement of genetic materials across the normal mating barriers between organisms occurs frequently and contributes significantly to the evolution of both eukaryotic and prokaryotic genomes. However, few concurrent transfers of functionally related genes implemented in a pathway from eukaryotes to prokaryotes are observed. Here, we did phylogenetic analyses to support that the genes, i.e. dihydrofolate reductase, glycine hydroxymethyltransferase, and thymidylate synthase involved in thymidylate metabolism, in Hz-1 virus were obtained from insect genome recently by independent horizontal gene transfers. In addition, five other related genes in nucleotide metabolism show evidences of horizontal gene transfers. These genes demonstrate similar expression pattern, and they may have formatted a functionally related pathway (e.g. thymidylate synthesis, and DNA replication) in Hz-1 virus. In conclusion, we provide an example of horizontal gene transfer of functionally related genes in a pathway to prokaryote from eukaryote.
    Genomics 08/2011; 98(5):367-9. DOI:10.1016/j.ygeno.2011.08.006 · 2.79 Impact Factor
  • Dong‐Dong Wu, Ya‐Ping Zhang
    eLS, 01/2011; , ISBN: 9780470015902
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    Dong-Dong Wu, Ya-Ping Zhang
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    ABSTRACT: During the colonization of the world, after dispersal out of African, modern humans encountered changeable environments and substantial phenotypic variations that involve diverse behaviors, lifestyles and cultures, were generated among the different modern human populations. Here, we study the level of population differentiation among different populations of human genes. Intriguingly, genes involved in osteoblast development were identified as being enriched with higher FST SNPs, a result consistent with the proposed role of the skeletal system in accounting for variation among human populations. Genes involved in the development of hair follicles, where hair is produced, were also found to have higher levels of population differentiation, consistent with hair morphology being a distinctive trait among human populations. Other genes that showed higher levels of population differentiation include those involved in pigmentation, spermatid, nervous system and organ development, and some metabolic pathways, but few involved with the immune system. Disease-related genes demonstrate excessive SNPs with lower levels of population differentiation, probably due to purifying selection. Surprisingly, we find that Mendelian-disease genes appear to have a significant excessive of SNPs with high levels of population differentiation, possibly because the incidence and susceptibility of these diseases show differences among populations. As expected, microRNA regulated genes show lower levels of population differentiation due to purifying selection. Our analysis demonstrates different level of population differentiation among human populations for different gene groups.
    BMC Evolutionary Biology 01/2011; 11(1):16. DOI:10.1186/1471-2148-11-16 · 3.41 Impact Factor
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    Dong-Dong Wu, David M Irwin, Ya-Ping Zhang
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    ABSTRACT: Proteins involved in a pathway are likely to evolve in a correlated fashion, and coevolving gene families tend to undergo complementary gains and losses. Accordingly, gene copy numbers (i.e., repertoire size) tend to show parallel changes during the evolution of coevolving gene families. To test and verify this hypothesis, here we describe positive correlations among the repertoire sizes of six gene families, that is, trypsin-like serine protease, odorant-binding protein, odorant receptor, gustatory receptor, cytochrome P450, and glutathione S-transferase after excluding the possibility of phylogenetic constraint and random drift. The observed correlations are indicative of parallel changes in the repertoire sizes of the six gene families that are due to similar demands for the quantity of these different genes in different lineages of Drosophila. In conclusion, we propose that the correlated evolution among these six gene families in Drosophila is a signature of a parallel response to ecological adaptation.
    Genome Biology and Evolution 01/2011; 3:396-400. DOI:10.1093/gbe/evr034 · 4.53 Impact Factor

Publication Stats

239 Citations
162.34 Total Impact Points

Institutions

  • 2008–2014
    • Kunming Institute of Zoology CAS
      • State Key Laboratory of Genetic Resources and Evolution
      Yün-nan, Yunnan, China
    • Beijing University of Aeronautics and Astronautics (Beihang University)
      • State Key Laboratory for Environmental Software Development
      Beijing, Beijing Shi, China
  • 2012–2013
    • Nanjing University
      • Department of Chemical Engineering
      Nan-ching, Jiangsu Sheng, China
  • 2010–2012
    • Chinese Academy of Sciences
      Peping, Beijing, China
  • 2007–2009
    • Fujian Academy of Agricultural Sciences
      Fujiang, Heilongjiang Sheng, China
    • Jiangsu Academy of Agricultural Sciences
      Nan-ching-hsü, Jiangxi Sheng, China