学术论文与著作(*表示通讯作者,#表示共同作者):
学术论文(代表作,引用次数来自Google Scholar,更新日期2021年9月) 1. D. Yuan*, C.E. Grover, G. Hu, M. Pan, E. R. Miller, J.L. Conover, S.P. Hunt, J.A. Udall*, J. F. Wendel. Parallel and Intertwining Threads of Domestication in Allopolyploid Cotton. Advanced Science 2021, 2003634. https.//doi.org/10.1002/advs.202003634 (IF=15.840,Cited:3) 2. Wang M#, Tu L#, Yuan D#, Zhu D, Shen C, Li J, Liu F, Pei L, Wang P, Zhao G et al. Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense. Nature genetics 2019, 51(2).224–229. https.//www.nature.com/articles/s41588-018-0282-x (IF=27.603, Cited:229) 3. Yuan D#, Tang Z#, Wang M#, Gao W, Tu L, Jin X, Chen L, He Y, Zhang L, Zhu L et al. The genome sequence of Sea-Island cotton (Gossypium barbadense) provides insights into the allopolyploidization and development of superior spinnable fibres. Scientific reports 2015, 5.17662. https.//www.nature.com/articles/srep17662 (IF=5.578, Cited:182) 4. Wang M, Yuan D*, Gao W, Li Y, Tan J, Zhang X*. A comparative genome analysis of PME and PMEI families reveals the evolution of pectin metabolism in plant cell walls. PLoS One 2013, 8(8).e72082. https.//www.ncbi.nlm.nih.gov/pubmed/23951288 (IF=3.730,Cited:85) 5. Yuan D, Tu L, Zhang X. Generation, annotation and analysis of first large-scale expressed sequence tags from developing fiber of Gossypium barbadense L. PLoS One 2011, 6(7).e22758. https.//journals.plos.org/plosone/article?id=10.1371/journal.pone.0022758 (IF=4.411, Cited:29)
其它学术论文 1. Li J, Yuan D, Wang P, Wang Q, Sun M, Liu Z, Si H, Xu Z, Ma Y, Zhang B, Pei L, Tu L, Zhu L, Chen L-L, Lindsey K, Zhang X, Jin S, Wang M: Cotton pan-genome retrieves the lost sequences and genes during domestication and selection. Genome Biology 2021, 22(1):119. https://doi.org/10.1186/s13059-021-02351-w 2. Grover CE, Yuan D, Arick MA, II,, Miller ER, Hu G, Peterson DG, Wendel JF, Udall JA: The Gossypium stocksii genome as a novel resource for cotton improvement. G3 Genes|Genomes|Genetics 2021. https://doi.org/10.1093/g3journal/jkab125 3. Ding Y, Zhang R, Zhu L, Wang M, Ma Y, Yuan D, Liu N, Hu H, Min L, Zhang X: An enhanced photosynthesis and carbohydrate metabolic capability contributes to heterosis of the cotton (Gossypium hirsutum) hybrid ‘Huaza Mian H318’, as revealed by genome-wide gene expression analysis. BMC Genomics 2021, 22(1):277. https://doi.org/10.1186/s12864-021-07580-8 4. Li B, Liang S, Alariqi M, Wang F, Wang G, Wang Q, Xu Z, Yu L, Naeem Zafar M, Sun L, Si H, Yuan D, Guo W, Wang Y, Lindsey K, Zhang X, Jin S: The application of temperature sensitivity CRISPR/LbCpf1 (LbCas12a) mediated genome editing in allotetraploid cotton (G. hirsutum) and creation of nontransgenic, gossypol-free cotton. Plant Biotechnol J 2021, 19(2):221-223. https://www.ncbi.nlm.nih.gov/pubmed/32854160 5. Xiao S, Hu Q, Zhang X, Si H, Liu S, Chen L, Chen K, Berne S, Yuan D, Lindsey K, Zhang X, Zhu L: Orchestration of plant development and defense by indirect crosstalk of salicylic acid and brassinosteorid signaling via transcription factor GhTINY2. Journal of Experimental Botany 2021, 72(13):4721-4743. https://doi.org/10.1093/jxb/erab186 6. Zhou J, Zhang S, Wang J, Shen H, Ai B, Gao W, Zhang C, Fei Q, Yuan D, Wu Z, Tembrock LR, Li S, Gu C, Liao X: Chloroplast genomes in Populus (Salicaceae): comparisons from an intensively sampled genus reveal dynamic patterns of evolution. Scientific Reports 2021, 11(1):9471. https://doi.org/10.1038/s41598-021-88160-4 7. Grover CE, Pan M, Yuan D, Arick MA, Hu G, Brase L, Stelly DM, Lu Z, Schmitz RJ, Peterson DG, Wendel JF, Udall JA: The Gossypium longicalyx Genome as a Resource for Cotton Breeding and Evolution. G3 (Bethesda) 2020, 10(5):1457-1467. https://www.ncbi.nlm.nih.gov/pubmed/32122962 8. Grover CE, Yoo MJ, Lin M, Murphy MD, Harker DB, Byers RL, Lipka AE, Hu G, Yuan D, Conover JL, Udall JA, Paterson AH, Gore MA, Wendel JF: Genetic Analysis of the Transition from Wild to Domesticated Cotton (Gossypium hirsutum L.). G3 (Bethesda) 2020, 10(2):731-754. https://www.ncbi.nlm.nih.gov/pubmed/31843806 9. Bao Y, Hu G, Grover CE, Conover J, Yuan D, Wendel JF: Unraveling cis and trans regulatory evolution during cotton domestication. Nat Commun 2019, 10(1):5399. https://www.ncbi.nlm.nih.gov/pubmed/31776348 10. Hu L, Xu Z, Wang M, Fan R, Yuan D, Wu B, Wu H, Qin X, Yan L, Tan L, Sim S, Li W, Saski CA, Daniell H, Wendel JF, Lindsey K, Zhang X, Hao C, Jin S: The chromosome-scale reference genome of black pepper provides insight into piperine biosynthesis. Nat Commun 2019, 10(1):4702. https://www.ncbi.nlm.nih.gov/pubmed/31619678 11. Li B, Rui H, Li Y, Wang Q, Alariqi M, Qin L, Sun L, Ding X, Wang F, Zou J, Wang Y, Yuan D, Zhang X, Jin S: Robust CRISPR/Cpf1 (Cas12a)-mediated genome editing in allotetraploid cotton (Gossypium hirsutum). Plant Biotechnol J 2019, 17(10):1862-1864. https://www.ncbi.nlm.nih.gov/pubmed/31055869 12. Udall JA, Long E, Hanson C, Yuan D, Ramaraj T, Conover JL, Gong L, Arick MA, Grover CE, Peterson DG, Wendel JF: De Novo Genome Sequence Assemblies of Gossypium raimondii and Gossypium turneri. G3 (Bethesda) 2019, 9(10):3079-3085. https://www.ncbi.nlm.nih.gov/pubmed/31462444 13. Udall JA, Long E, Ramaraj T, Conover JL, Yuan D, Grover CE, Gong L, Arick MA, 2nd, Masonbrink RE, Peterson DG, Wendel JF: The Genome Sequence of Gossypioides kirkii Illustrates a Descending Dysploidy in Plants. Front Plant Sci 2019, 10:1541. https://www.ncbi.nlm.nih.gov/pubmed/31827481 14. Wang M, Tu L, Lin M, Lin Z, Wang P, Yang Q, Ye Z, Shen C, Li J, Zhang L, Zhou X, Nie X, Li Z, Guo K, Ma Y, Huang C, Jin S, Zhu L, Yang X, Min L, Yuan D, Zhang Q, Lindsey K, Zhang X: Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication. Nat Genet 2017, 49(4):579-587. https://www.ncbi.nlm.nih.gov/pubmed/28263319 15. Li Y, Tu L, Pettolino FA, Ji S, Hao J, Yuan D, Deng F, Tan J, Hu H, Wang Q: GbEXPATR, a species‐specific expansin, enhances cotton fibre elongation through cell wall restructuring. Plant biotechnology journal 2016, 14(3):951-963. https://onlinelibrary.wiley.com/doi/full/10.1111/pbi.12450 16. Wang M, Wang P, Tu L, Zhu S, Zhang L, Li Z, Zhang Q, Yuan D, Zhang X: Multi-omics maps of cotton fibre reveal epigenetic basis for staged single-cell differentiation. Nucleic Acids Res 2016, 44(9):4067-4079. https://www.ncbi.nlm.nih.gov/pubmed/27067544 17. Wang M, Yuan D, Tu L, Gao W, He Y, Hu H, Wang P, Liu N, Lindsey K, Zhang X: Long noncoding RNAs and their proposed functions in fibre development of cotton (Gossypium spp.). New Phytologist 2015, 207(4):1181-1197. https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.13429 18. Wu Y, Min L, Wu Z, Yang L, Zhu L, Yang X, Yuan D, Guo X, Zhang X: Defective pollen wall contributes to male sterility in the male sterile line 1355A of cotton. Scientific reports 2015, 5:9608. https://www.ncbi.nlm.nih.gov/pubmed/26043720 19. Jin F, Hu L, Yuan D, Xu J, Gao W, He L, Yang X, Zhang X: Comparative transcriptome analysis between somatic embryos (SE s) and zygotic embryos in cotton: evidence for stress response functions in SE development. Plant biotechnology journal 2014, 12(2):161-173. https://onlinelibrary.wiley.com/doi/full/10.1111/pbi.12123 20. Liu C, Yuan D, Lin Z: Construction of an EST-SSR-based interspecific transcriptome linkage map of fibre development in cotton. Journal of genetics 2014, 93(3):689-697. https://www.ncbi.nlm.nih.gov/pubmed/25572227 21. Sun L, Zhu L, Xu L, Yuan D, Min L, Zhang X: Cotton cytochrome P450 CYP82D regulates systemic cell death by modulating the octadecanoid pathway. Nature communications 2014, 5:5372. https://www.nature.com/articles/ncomms6372 22. Li X, Yuan D, Zhang J, Lin Z, Zhang X: Genetic mapping and characteristics of genes specifically or preferentially expressed during fiber development in cotton. PLoS One 2013, 8(1):e54444. https://www.ncbi.nlm.nih.gov/pubmed/23372723 23. Liu C, Yuan D, Zhang X, Lin Z: Isolation, characterization and mapping of genes differentially expressed during fibre development between Gossypium hirsutum and G. barbadense by cDNA-SRAP. Journal of genetics 2013, 92(2):175-181. https://pubmed.ncbi.nlm.nih.gov/23970073/ 24. Min L, Zhu L, Tu L, Deng F, Yuan D, Zhang X: Cotton GhCKI disrupts normal male reproduction by delaying tapetum programmed cell death via inactivating starch synthase. The Plant Journal 2013, 75(5):823-835. https://onlinelibrary.wiley.com/doi/full/10.1111/tpj.12245/ 25. Yang X, Wang L, Yuan D, Lindsey K, Zhang X: Small RNA and degradome sequencing reveal complex miRNA regulation during cotton somatic embryogenesis. Journal of experimental botany 2013, 64(6):1521-1536. https://www.ncbi.nlm.nih.gov/pubmed/23382553 26. Li X, Yuan D, Wang H, Chen X, Wang B, Lin Z, Zhang X: Increasing cotton genome coverage with polymorphic SSRs as revealed by SSCP. Genome 2012, 55(6):459-470. https://cdnsciencepub.com/doi/full/10.1139/g2012-032/ 27. Yang X, Zhang X, Yuan D, Jin F, Zhang Y, Xu J: Transcript profiling reveals complex auxin signalling pathway and transcription regulation involved in dedifferentiation and redifferentiation during somatic embryogenesis in cotton. BMC plant biology 2012, 12(1):110. https://bmcplantbiol.biomedcentral.com/articles/10.1186/1471-2229-12-110 28. Yuan D, Liang S, Lin Z, Zhang X: In silico comparative analysis of EST-SSRs in three cotton genomes. African Journal of Biotechnology 2012, 11(69):13269-13371. 29. Hu L, Yang X, Yuan D, Zeng F, Zhang X: GhHmgB3 deficiency deregulates proliferation and differentiation of cells during somatic embryogenesis in cotton. Plant biotechnology journal 2011, 9(9):1038-1048. https://onlinelibrary.wiley.com/doi/full/10.1111/j.1467-7652.2011.00617.x 30. Xu L, Zhu L, Tu L, Liu L, Yuan D, Jin L, Long L, Zhang X: Lignin metabolism has a central role in the resistance of cotton to the wilt fungus Verticillium dahliae as revealed by RNA-Seq-dependent transcriptional analysis and histochemistry. Journal of experimental botany 2011, 62(15):5607-5621. https://academic.oup.com/jxb/article/62/15/5607/561887 31. Yu Y, Yuan D, Liang S, Li X, Wang X, Lin Z, Zhang X: Genome structure of cotton revealed by a genome-wide SSR genetic map constructed from a BC 1 population between Gossypium hirsutum and G. barbadense. BMC genomics 2011, 12(1):15. https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-12-15 教材与著作 1. Hu G, Grover CE, Yuan D, Dong Y, Miller E, Conover JL, Wendel JF: Evolution and Diversity of the Cotton Genome. In: Cotton Precision Breeding. Edited by Rahman M-u, Zafar Y, Zhang T. Cham: Springer International Publishing; 2021: 25-78. 2. Maojun Wang, Daojun Yuan, Xianlong Zhang. Genome Sequencing, In. Cotton, 2nd edition, edited by David Fang and Richard G. Percy, published by American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, 2015, P289-302. 3. 《农学概论》参编,2009,中国矿业大学出版社.
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