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  1. Yan Xue*...Rui Xia*..., Epigenetics in the modern era of crop improvements, Science China Life Sciences, 2025 Jan 08, publish online.

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  2. Zhengting Yang*# ... Yingxiao Mai# ... and Rui Xia*.A near-complete assembly of the Houttuynia cordata genome provides insights into the regulatory mechanism of flavonoid biosynthesis in Yuxingcao. Plant Communications, 2024 Oct 14, 5(10):101075.

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  3. Fengqi Wu, Yingxiao Mai, Chengjie Chen*, and Rui Xia*.SynGAP: a synteny-based toolkit for gene structure annotation polishing. Genome Biology ,2024 Aug 14. 25:218.

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  4. Xingling Su, Jiakun Zheng, Yanwei Hao,Rui Xia*, Jing Xu*. A high-efficiency method for simultaneous quantitation of bioactive gibberellins in Litchi chinensis using UHPLC-QQQ-MS/MS. Scientia Horticulturae, 2024. June 14; 336.

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  5. Xing Huang, Hongsen Liu, Fengqi Wu,..., Rui Xia*, Yuanlong Liu*. Diversification of FT-like genes in the PEBP family contributes to the variation of flowering traits in Sapindaceae species.Mol Horticulture. 2024 July 16; 4(1):28.

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  6. Qiuping Wu, Rui Xia, Jie Yang, Rong Chen, Zaohai Zeng*, Chao Fan*. Identification and comprehensive analysis of OFP genes for fruit shape influence in mango. Genes. 2024 Jun 21;15(7):823.

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  7. Jiawei Li# , Chengjie Chen# ... Rui Xia*.SapBase: A central portal for functional and comparative genomics of Sapindaceae species. Journal of Integrative Plant Biology. 2024 May 28; 00: 1–10.

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  8. Yujia Liu#, Boting Liu#... Rui Xia, Jing Xu*, and Yuanlong Liu*. Genomic identification and expression analysis of acid invertase (AINV) gene family in Dendrobium officinale Kimura et Migo. BMC Plant Biol. 2024 May 14;24(1):396.

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  9. Shuai Wu, Jinxia Shi, Qi Zheng, Yuqin Ma, Wenjun Zhou, Chengjie Mao, Chengjie Chen, Zhengwu Fang, Rui Xia, Yongli Qiao. Phytophthora sojae Effector PsAvh113 Targets Transcription Factors in Nicotiana benthamiana. Journal of Fungi, 2024 Apr 27, 10(5).

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  10. Hai Wang, Mengjiao Chen, Xin Wei, Rui Xia, Dong Pei, Xuehui Huang, Bin Han. Computational tools for plant genomics and breeding. Science China Life Sciences, 2024 Apr 23,67(8):1579-1590.

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  11. Yuan Yuan#... Rui Xia, and Muqing Zhang*. Small RNA and degradome deep sequencing reveal regulatory roles of miRNAs in response to Sugarcane mosaic virus infection on two contrasting sugarcane cultivars. Mol Plant Microbe Interact. 2024 Apr 10.

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  12. Guanliang Li#, Chengjie Chen#*, Peike Chen, Blake C. Meyers, Rui Xia*. sRNAminer: A multifunctional toolkit for next-generation sequencing small RNA data mining in plants. Science Bulletin (Beijing). 2024 Mar 30;69(6):784-791.

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  13. Yanqing Zhang... Rui Xia*.MicroRNA482/2118 is lineage-specifically involved in gibberellin signalling via the regulation of GID1 expression by targeting noncoding PHAS genes ... Plant Biotechnology Journal. 2024 Apr;22(4):819-832.

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  14. Chengjie Chen ... Zaohai Zeng, Jing Xu, Yuanlong Liu ... Rui Xia* . TBtools-II: A" One for All, All for One" Bioinformatics Platform for Biological Big-data Mining. Molecular Plant.(2023),16(11):1733-1742

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  15. Mei Liang*, Wenjie Chen , Amy M. LaFountain , Yuanlong Liu , Foen Peng, Rui Xia , H. D. Bradshaw4 , Yaowu Yuan*. Taxon-specific, phased siRNAs underlie a speciation locus in monkeyflowers. Science. 2023, 379(6632):576-582

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  16. 陈程杰*,夏瑞*. TBtools—大数据时代下的国产生物软件. 科学观察. 2022, 17(6): 33-35

  17. Xiaoqi Yue, Yue Zhang, ... ,Rui Xia,...,Wuqiang Ma* & Kaibing Zhou*. Genome-wide identification and expression analysis of carotenoid cleavageoxygenase genes in Litchi (Litchi chinensis Sonn.). BMC Plant Biology. 2022, 22(1):394.

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  18. Bo Liu, Guanliang Li, ..., Rui Xia,... Species-specific regulatory pathways of small RNAs play sophisticated roles in flower development in Dimocarpus longan Lour.Horticultural Plant Journal(2022),doi:org/10.1016/j.hpj.2022.12.004

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  19. Jiakun Zheng, Chengjie Chen, Guanliang Li, Peike Chen, Yuanlong Liu, Rui Xia*. Biogenesis of reproductive PhasiRNAs: exceptions to the rules. Plant Biotechnology Journal. 2022, 21(2):241-243.

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  20. Jiakun Zheng and Rui Xia*. Flower development and sex determination in horticultural crops. Fruit Research. 2022, 2(1): 1-9.

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  21. Chengjie Chen, Ya Wu, Rui Xia*. A painless way to customize Circos plot: From data preparation to visualization using TBtools. iMeta. 2022, 1(3): e35.

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  22. Shan Yang, Petr Cápal,...,Rui Xia, Muqing Zhang*, Zuhu Deng*. Sequence analysis of Erianthus arundinaceus chromosome 1 isolated by flow sorting after genomic in situ hybridization in suspension. The Crop Journal. 2022, 10(6): 1746-1754.

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  23. Xing Huang, Rui Xia*, Yuanlong Liu*. microRNA-mediated regulation in fruit quality. Current Opinion in Food Science. 2022, 46: 100837.

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  24. Guibing Hu#, Junting Feng#, Xu Xiang#,... , Rui Xia*  & Jianguo Li*. Two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars. Nature Genetics. 2022,54:73-83.

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  25. Yanqing Zhang#, Muhammad Waseem#, Zaohai Zeng,Jing Xu, Chengjie Chen, Yuanlong Liu,...,Rui Xia*. MicroRNA482/2118, a miRNA superfamily essential for both disease resistance and plant development. New Phytologist Foundation. 2021, 233(5):2047-2057

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  26. Jingwen Chen#, Qian Yan#,... Rui Xia*, Zaohai Zeng* and Yuanlong Liu*. The GRAS gene family and its roles in seed development in litchi (Litchi chinensis Sonn). BMS Plant Biology. 2021, 21(1):423.

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  27. Wenping Zhang#, Jishan Lin#, Jianguo Li#,Shaoquan Zheng#,... Rui Xia, Jisen Zhang, Ray Ming*. Rambutan genome revealed gene networks for spine formation and aril development. The Plant Journal. 2021, 108(4):1037-1052.

  28. Yanmin Zhu*#,Guanliang Li#,Jugpreet Singh#,..., Rui Xia*. Laccase directed lignification is one of the major processes associated with the defense response against pythium ultimum infection in Apple Roots.Plant Science.2021,12:629776.

  29. Daoheng Hu#,Yiming Yu#,Chun Wang#, ...,Rui Xia,...,Kejian Wang*& Jixian Zhai*.Multiplex CRISPR-Cas9 editing of DNA methyltransferases in rice uncovers a class of non-CG methylation specific for GC-rich regions.Plant Biologists.2021,33(9):2950-2964.

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  30. Kaili Wang, Yuanyuan Zhang, ..., Rui Xia, Lili Song*, Ai-Min Wu*. MicroRNAs play important roles in regulating rapid growth of the Phyllostachys edulis culm internode.New phytologist. 2021, 231(6):2215-2230.

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  31. Yongli Qiao∗, Rui Xia, ..., Wenbo Ma∗. Small RNAs in Plant Immunity and Virulence of Filamentous Pathogens. ANNUAL REVIEWS. 2021, 59:265-288.

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  32. Wenbing Su,..., Rui Xia, ... ,Shunquan Lin*,and Zhenhua Liu*. Polyploidy underlies co-option and diversification of biosynthetic triterpene pathways in the apple tribe. PNAS. 2021, 118(20):e2101767118.

  33. Chengjie Chen#, Jiawei Li#, ..., Rui Xia*. sRNAanno—a database repository of uniformly annotated small RNAs in plants.Horticulture research. 2021, 8(1):45.

  34. Muhammad Waseem, Yuanlong Liu, Rui Xia*. Long Non-Coding RNAs, the Dark Matter: An Emerging Regulatory Component in Plants. International Journal of Molecular Sciences. 2021, 22(1):86.

  35. Dongna Ma, Shanshan Dong, … Rui Xia*, Xingtan Zhang*. Chromosome‐level reference genome assembly provides insights into aroma biosynthesis in passion fruit (Passiflora edulis). Molecular Ecology Resources. 2020, 21(3):955-968.

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  36. Peng Tian, Xuemei Zhang, Rui Xia,... Blake C. Meyers*, Mingsheng Chen *. Evolution and diversification of reproductive phased small interfering RNAs in Oryza species. New Phytologist. 2020, 229(5):2970-2983.

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  37. Jinbu Jia#, Ronghuan Ji#, ..., Rui Xia, Bin Liu*, and Jixian Zhai*. Soybean Dicer-Like 2 Regulates Seed Coat Color via Production of Primary 22-nt Small Interfering RNAs from Long Inverted Repeats. 40. The Plant Cell. 2020, 32(12):3662-3673.

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  38. Baoqing Ding*, Rui Xia, ..., Blake C. Meyers, Yao-Wu Yuan*. Developmental genetics of corolla tube formation: role of the tasiRNA-ARF pathway and a conceptual model. The Plant Cell. 2020, 32(11):3452-3468.

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  39. Yuanlong Liu, Chong Teng, Rui Xia*, Blake Meyers*. Phased Secondary Small Interfering RNAs (phasiRNAs) in Plants: Their Biogenesis, Genic Sources, and Roles in Stress Responses, Development, and Reproduction. The Plant Cell. 2020, 32(10):3059-3080.

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  40. Chengjie Chen, ..., Margaret H. Frank, Yehua He, Rui Xia*. TBtools - an integrative toolkit developed for interactive analyses of big biological data. Molecular Plant(2020), 13(8):1194-1202.

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  41. Jinbu Jia#, Yanping Long#, Hong Zhang,..., Rui Xia , Xiaofeng Cao and Jixian Zhai*. Post-transcriptional splicing of nascent RNA contributes to widespread intron retention in plants.Nature Plants. 2020, 6(7):780-788. 

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  42. Minglei Zhao# , Caiqin Li#, Xingshuai Ma, Rui Xia,..., Chun-Lin Shi* and Jianguo Li*. KNOX protein KNAT1 regulates fruitlet abscission in litchi byrepressing ethylene biosynthetic genes. Journal of Experimental Botany. 2020, 71(14):4069-4082.

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  43. Mei Liang, Zonghong Cao, Andan Zhu, Yuanlong Liu,..., Rui Xia..., and Lijun Chai*. Evolution of self-compatibility by a mutant Sm-RNase in citrus. Nature Plants. 2020, 6(2):131-142.

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  44. Honghao Bi#, Qili Fei#, Riqing Li, Bo Liu, Rui Xia, Si Nian Char, Blake C. Meyers and Bing Yang*.Disruption of miRNAs equences by TALENs and CRISPR/Cas9 induces varied lengths of miRNA production.Plant Biotechnology Journal, 2019. 18(7):1526-1536.

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  45. Lei Feng , Rui Xia* , Yuanlong Liu* , Comprehensive Characterization of miRNA and PHAS Loci in the Diploid Strawberry (Fragaria vesca) Genome. Horticultural Plant Journal, 2019, 5(6):255-267

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  46. Hong Zhu#, Chengjie Chen#...,Yueming Jiang*, Xuewu Duan*,Rui Xia*. MicroRNA528, a hub regulator modulating ROS homeostasis via targeting of a diverse set of genes encoding copper‐containing proteins in monocots. New Phytologist, 2020, 225(1):385-399.

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  47. Chengjie Chen#, Yuanlong Liu#, Rui Xia*. Jack of many trades:The multifaceted role of miR528 in monocots. Molecular Plant, 2019, 12(8):1044-1046.

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  48. Caiqin Li#,Minglei Zhao#,Xingshuai Ma#, ...,Rui Xia,Hong Wu*,Jianguo Li*.The HD-Zip transcription factor LcHB2 regulates litchi fruit abscission through the activation of two cellulase genes.Journal of Experimental Botany,2019, 70(19):5189-5203.

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  49. Yanqing Zhang,...,Rui Xia*,....Genome-wide characterization of the auxin response factor(ARF) gene family of litchi (Litchi chinensis Sonn.): phylogenetic analysis, miRNA regulation and expression changes during fruitabscission.PeerJ,2019,7:e6677

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  50. Dongdong Li#, Wangshu Mou#, Rui Xia, ...,Zhongchi Liu* and Zisheng Luo*. Integrated analysis of high-throughput sequencing data shows abscisic acidresponsive genes and miRNAs in strawberry receptacle fruit ripening. Horticulture Research (2019) 6:26

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  51. Rui Xia*, Chengjie Chen, Suresh Pokhre, Wuqiang Ma, … Jianguo Li & Blake C. Meyers*. 24-nt reproductive phasiRNAs are broadly present in angiosperms. Nature Communications (2019) 10:627

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  52. Shaopeng Zhao, ..., Chengjie Chen,..., Rui Xia, and Xiurong Wang*. Transcriptomic analysis reveals the possible roles of sugar metabolism and export for positive mycorrhizal growth responses in soybean. Physiol Plant. 2019, 166(3):712-728.

  53. Chengjie Chen#, Zaohai Zeng#, Zongrang Liu, Rui Xia*. Small RNAs, emerging regulators critical for thedevelopment of horticultural traits. HorticultureResearch, 2018, 5:63.

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  54. Guanghui Guo#, Xinye Liu#, ..., Rui Xia,..., Qixin Sun*, Yingyin Yao*. Wheat miR9678 Affects Seed Germination byGenerating Phased siRNA and Modulating Abscisic Acid/Gibberellin Signaling. The Plant Cell, 2018, 30(4):796-814.

  55. Wuqiang Ma, Chengjie Chen, Yuanlong Liu,…, Jianguo Li*, and Rui Xia*. Coupling of microRNA-directed phasiRNA generation … polyadenylation in small RNA-mediated gene silencing. New Phytologist 2017, 217(4):1535-1550.

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  56. Yuanlong Liu, Lili Ke, Guizhi Wu, Yuantao Xu, Xiaomeng Wu, Rui Xia, Xiuxing Deng, Qiang Xu*. miR3954 is a trigger of phasiRNAs that affects flowering time in citrus. Plant Journal, 2017, 92(2):263-275.

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  57. Rui Xia, Jing Xu, Blake C. Meyers*. The Emergence, Evolution, and Diversification of the miR390-TAS3-ARF Pathway in Land Plants. The Plant Cell, 2017, 29 (6) 1232-1247.

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  58. Manjun Peng, Peiyuan Ying, Xuncheng Liu, Caiqin Li, Rui Xia, Jianguo Li*, Minglei Zhao*. Genome-wide identification of histone modifiers and their expression patternsduring fruit abscission in litchi. Frontiersin Plant Science, 2017, 8, 639.

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  59. Sebastian Reyes-Chin-Wo#, Zhiwen Wang#, Xinhua Yang#, …, Rui Xia, …, Richard W Michelmore*. Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce. Nature Communications, 2017, 8:14953.

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  60. Peiyuan Ying, …, Rui Xia, Minglei Zhao, Jianguo Li*. Identification and molecular characterization of an IDA-like gene from litchi, LcIDL1, whose ectopic expression promotes floral organ abscission in Arabidopsis. Scientific Reports, 2016, 6:37135.

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  61. Yu Zhang, Rui Xia, Hanhui Kuang and Blake C. Meyers*. The diversification of plant NBS-LRR defense genes directs the evolution of microRNAs thattarget them. Molecular Biology andEvolution, 2016, 33(10):2692-705.

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  62. Qili Fei, YuZhang, Rui Xia, Blake .C. Meyers*. SmallRNAs add zing to the zig-zag-zig model of plant defenses. Molecular Plant-Microbe Interactions, 2016, 29(3):165-9.

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  63. Behnam Khatabi, …, Rui Xia, …, Blake C. Meyers and Vincent N. Fondong*. High-resolution identification and abundance profiling of cassava (Manihot esculenta Crantz) microRNAs. BMC Genomics, 2016, 17:85.

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  64. Rui Xia, Jing Xu,Siwaret Arikit, Blake Meyers*. Extensive families of miRNAs and PHAS Loci in Norway spruce demonstratethe origins of complex phasiRNA networks in seed plants. Molecular Biology and Evolution,2015, 32(11):2905-18.

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  65. Han Zhang*, Rui Xia, Blake C. Meyers, Virginia Walbot. Evolution, functions andmysteries of plant ARGONAUTE proteins. Current Opinion in Plant Biology, 2015, 27:84-90.

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  66. Rui Xia#, Songqing Ye#, Zongrang Liu, Blake C.Meyers, Zhongchi Liu*. Novel and recently evolved miRNA clustersregulate expansive F-box genenetworks through phasiRNAs in wild diploid strawberry. Plant Physiology, 2015, 169(1):594-610.

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  67. Siwaret Arikit, Rui Xia, …, Blake C. Meyers*. An atlas of soybean small RNAs identifies phased siRNAs from hundreds of coding genes. The Plant Cell, 2014, 26(12):4584-601.

  68. Qili Fei, Rui Xia,Blake C. Meyers*. Phased, secondary siRNAs in post-transcriptional regulatorynetworks. The Plant Cell, 2013, 25: 2400-2415.

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  69. Rui Xia, Blake C. Meyers, Zhongchi Liu, Eric P. Beers, Songqing Ye, Zongrang Liu*. MicroRNA superfamilies descended from miR390 and their roles in secondary small interfering RNA biogenesis in eudicots. The Plant Cell 2013, 25:1555-1572.

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  70. Rui Xia, Hong Zhu, Yongqiang An, Eric P Beers and Zongrang Liu*. Apple miRNAs and tasiRNAs with novel regulatory networks. Genome Biology 2012, 13:R47.

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  71. Hong Zhu, Rui Xia,…Zongrang Liu*. Unique expression, processing regulation, and regulatory network of peach (Prunus persica) miRNAs. BMC Plant Biology, 2012, 12:149.

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  72. Rui Xia#, … Jianguo Li*. 3-Hydroxy-3-methylglutaryl coenzyme A reductase 1 (HMG1) is highly associated with the cell division during the early stage of fruit development … in Litchi chinensis. Gene, 2012, 498(1):28-35.

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  73. Hong Zhu, …, Rui Xia and Rongcai Yuan*. Transcriptomics of shading-induced and NAA-induced abscission in apple (Malus domestica) reveals a shared pathway involving reduced photosynthesis, … hormone crosstalk. BMC Plant Biology, 2011, 11:138.

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  74. Rui Xia, … Jianguo Li*. Cloning and characterisation of two genes for 3-hydroxy-3- methylglutaryl coenzyme … fruit development in Dimocarpus longan. Journal of Horticultural Science & Biotechnology, 2011, 86(1): 25-30.

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  75. 夏瑞,陆旺金, 李建国*. 一种改良的扩增cDNA 5' 末端的方法. 园艺学报, 2008, 35: 1533-1538.

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  76. 夏瑞,陆旺金, 李建国*, 杜娟. 简并引物的程序化设计与荔枝HMGR基因片段的克隆. 果树学报（2006）, 23(6):903-906. 

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