Dr. YU Jun is currently a professor of Beijing Institute of Genomics, Chinese Academy of Sciences (CAS). He is also the director of Beijing Key Laboratory of Genome and Precision Medicine Technologies. Dr. YU obtained his B.S. degree in biochemistry from Jilin University in 1983 and Ph.D. degree in biomedical sciences from New York University Medical School in 1990. He had served as a Research Assistant Professor at NYU since 1990 until he joined University of Washington Genome Center in 1993. Dr. YU is one of the founders of Beijing Institute of Genomics and has been the deputy director until 2012. Dr. YU participated in and presided many important projects including The International Human Genome Project (Chinese part), Super Hybrid Rice Genome Project, The Silkworm Genome Project, The Date Palm Genome Project etc.
Dr. YU has been engaged in genomics, bioinformatics and human genetics, and put forward many new concepts and important theories of genome research. Firstly, he presented “nucleotide composition change dynamics of genome”, which emphasis the determinative role of key molecular mechanisms and cellular processes in genome structure; Secondly, he believe in “key enzymes (and their mechanism) determinism”, which points out the significance of bacteria dnaE in genome component and evolution. This theory implies the existence and importance of eukaryotes non-Darwinian evolution genome variation. Recently, Dr. YU raises “The 5-Track Genome Biology” (Operational Track; Homeostatic Track; Compartmental Track; Informational Track and Plasticity Track) and “Life’s Three Dilemmas at Molecular Levels” (Replication-transcription dilemma; Replication-repair dilemma; Genetic and non-genetic dilemma). His research achievements have been published on many international first-class magazines such as Nature Communications, Nature, Science, PLoS Biology, PNAS, and Genome Research etc.
Research interests along the direction of systematic studies of genomes are focused on applications of fast-accumulating genome information and new concepts on several basic biological systems, including (1) comparative genomics (including pangenomics and metagenomics), epigenomics, and ribogenomics; (2) domestication of plants and animals as well as recent mutations in humans; (3) hybrid vigor, sex determination, and fruiting of crop plants; (4) medicinal plant genomics and metablomics; (5) origins of genetic code, molecular mechanisms, and origin of cellular processes; (6) new model organisms and molecular mechanisms of phenotypic plasticity in microbes, plants, arthropods, worms, and vertebrates; (7) instrumentation and methodology for DNA sequencing and analysis.
Genome sequence and genetic diversity of the common carp, Cyprinus carpio
The common carp, Cyprinus carpio, is one of the most important cyprinid species and globally accounts for 14% of aquaculture production worldwide. Here we present a draft genome of domesticated C. carpio (strain Songpu), whose current assembly contains 52,610 protein-coding genes and an approximate 92.3% coverage of its paleotetraploidized genome (2n = 100). The latest round of whole genome duplication has been estimated that occurred approximately 8.2 million years ago. Genome resequencing of 33 representative individuals from worldwide populations demonstrates a single origin for C. carpio in two subspecies (C. carpio subsp. Haematopterus and C. carpio subsp. carpio). Integrative genomic and transcriptomic analyses unveiled potential trait-related loci and genes associated with scaling patterns and skin color. In combination with the high-resolution genetic map, the draft genome paves the way for better molecular studies and improved genome-assisted breeding of C. carpio and other closely related species.
Comparative analyses of the C. carpio genome.
Awards and Honors
TWAS Prize in Agricultural Sciences for 2012.
Outstanding Science and Technology Achievements (Group, 2003), Chinese Academy of Sciences.
National Natural Science Award (Second Place, Group, 2002). The State Department of China.
Scientific Leader of the Year, 2002. The first “SA50” Award by Scientific American.
“Qiushi” Annual Award for Scientific Achievement (Group, 2002), QiuShi Science and Technology Foundation (Hong Kong).
100-Person Plan, Chinese Academy of Sciences (2002–2005).
Outstanding Young Investigator Award (B Class), the Natural Science Foundation of P. R. China (1999–2002)
Selected Publications and Books
1. As one of the corresponding authors: Al-Mssallem et al. (2013) A Draft Genome Sequence of Date Palm (Phoenix dactylifera L.). Nature Communication. Publishing online August 6.
2. Dapeng Wang, Yan Xia, Xinna Li, Lixia Hou and Jun Yu. (2012). The Rice Genome Knowledgebase (RGKbase): an annotation database for rice comparative genomics and evolutionary biology. Nucleic Acids Res 41(D1): D1199–D1205.
3. Zhang Zhang, Jun Li, Peng Cui, Feng Ding, Ang Li, Jeffrey P. Townsend, Jun Yu. (2012). Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance. BMC Bioinformatics 13:43.
4. Jun Yu as a listed author of the Schistosoma japonicum Genome Sequencing and Functional Analysis Consortium. (2009) The Schistosoma japonicum genome reveals features of host–parasite interplay. Nature 460: 345–351.
5. Liang Yang and Jun Yu. (2009) A Comparative Analysis of Divergently-Paired Genes (DPGs) of Drosophila and Vertebrate Genomes. BMC Evolutionary Biology 9:55.
6. Kaifu Chen, Qingshu Meng, Lina Ma, Qingyou Liu, Petrus Tang, Chungshung Chiu, Songnian Hu, Jun Yu.(2008). A novel DNA sequence periodicity decodes nucleosome positioning. Nucleic Acids Res. 36:6228–36.
7. Jun Yu co-authored in Muzny et al (2006). The DNA sequence, annotation and analysis of human chromosome 3. Nature 440(7088):1194-8.
8. Jun Yu as one of the listed authors of the International HapMap Consortium. (2005) A haplotype map of the human genome. Nature 437:1299-1320.
9. Jun Yu, Wang J, Lin W, Li S, Li H, et al. (2005) The Genomes of Oryza sativa: A History of Duplications Rice genomes. PLoS Biol 3:e38.
10. Jun Yu co-first authored in International Chicken Polymorphism Map Consortium. (2004) A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature 431:717–722.
11. Jun Yu co-authored in International Chicken Genome Sequencing Consortium. (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 431:695–716.
12. Jun Yu co-first authored in Xia et al. (2004) A draft sequence of the genome of the domesticated silkworm Bombyx mori). Science 310:1938–1940.
13. Jun Yu as one of the listed authors and co-PI of the Chinese effort, International Human Genome Sequencing Consortium. (2004) Finishing the euchromatic sequence of the human genome. Nature 431:931–945.
14. Wong, Gane Ka-Shu, Jun Wang, Douglas A. Passey, and Jun Yu. (2002) Codon-Usage Gradients in Gramineae Genomes. Genome Res 12:851–856.
15. Jun Yu et al. (2002) A draft sequence assembly of the rice (Oryza sativa ssp. indica) genome. Science 296:79–93.
16. Wong, G.K.-S., D.A. Passey, and J. Yu. (2001) Most of the human genome is transcribed. Genome Res 11:1975–1977.
17. Yang, Z., G. K-S. Wong, M.A. Eberle, M. Kibukawa, D.A. Passey, W.R. Hughes, L. Kruglyak, and J. Yu. (2000) Sampling SNPs. Nature Genetics 26:13–14.
18. Jun Yu co-first authored Wong et al. (1997) Multiple-complete-digest restriction fragment mapping: Generating sequence-ready maps for large-scale DNA sequencing. Proc Natl Acad Sci USA 94:5225–5230.
19. Jun Yu co-first authored Lin et al. (1994) Uroplakin Ia and Ib, two major differentiation products of bladder epithelium, belong to a family of four transmembrane domain (4TM) proteins. J Cell Biol 125:171–182.
20. Jun Yu, M. Manabe, X.-R. Wu, C. Xu, B. Surya and T.-T. Sun (1990) Uroplakin I: a 27-kD protein associated with the asymmetric unit membrane of mammalian urothelium J Cell Biol 111:1207–1216.