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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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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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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Yanqing Zhang... Rui Xia*.MicroRNA482/2118 is lineage-specifically involved in gibberellin signalling via the regulation of GID1 expression by targeting noncoding PHAS genes and subsequently instigated phasiRNAs. PBJ. 2024 Apr;22(4):819-832.
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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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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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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
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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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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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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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Jiakun Zheng and Rui Xia*. Flower development and sex determination in horticultural crops. Fruit Research. 2022, 2(1): 1-9.
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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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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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Xing Huang, Rui Xia*, Yuanlong Liu*. microRNA-mediated regulation in fruit quality. Current Opinion in Food Science. 2022, 46: 100837.
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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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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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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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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.
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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.
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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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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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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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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.
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Chengjie Chen#, Jiawei Li#, ..., Rui Xia*. sRNAanno—a database repository of uniformly annotated small RNAs in plants.Horticulture research. 2021, 8(1):45.
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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.
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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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.
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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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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.
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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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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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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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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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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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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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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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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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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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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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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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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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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.
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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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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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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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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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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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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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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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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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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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