PUBLICATIONS

TBtools-II: A "One for All, All for One" Bioinformatics Platform for Biological Big-data Mining

Chengjie Chen ... Zaohai Zeng, Jing Xu, Yuanlong Liu ... Rui Xia*

Taxon-specific, phased siRNAs underlie a speciation locus in monkeyflowers. Science. 2023, 379(6632):576-582.

Mei Liang*, Wenjie Chen , Amy M. LaFountain , Yuanlong Liu , Foen Peng, Rui Xia , H. D. Bradshaw4 , Yaowu Yuan*.

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

陈程杰*,夏瑞*.

Genome-wide identification and expression analysis of carotenoid cleavageoxygenase genes in Litchi (Litchi chinensis Sonn.). BMC Plant Biology. 2022, 22(1):394.

Xiaoqi Yue, Yue Zhang, ... ,Rui Xia,...,Wuqiang Ma* & Kaibing Zhou*.

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

Bo Liu, Guanliang Li, ..., Rui Xia,...

Biogenesis of reproductive PhasiRNAs: exceptions to the rules. Plant Biotechnology Journal. 2022, 21(2):241-243.

Jiakun Zheng, Chengjie Chen, Guanliang Li, Peike Chen, Yuanlong Liu, Rui Xia*.

Flower development and sex determination in horticultural crops. Fruit Research. 2022, 2(1): 1-9.

Jiakun Zheng and Rui Xia*.

A painless way to customize Circos plot: From data preparation to visualization using TBtools. iMeta. 2022, 1(3): e35.

Chengjie Chen, Ya Wu, Rui Xia*.

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.

Shan Yang, Petr Cápal,...,Rui Xia, Muqing Zhang*, Zuhu Deng*.

microRNA-mediated regulation in fruit quality. Current Opinion in Food Science. 2022, 46: 100837.

Xing Huang, Rui Xia*, Yuanlong Liu*.

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.

Guibing Hu#, Junting Feng#, Xu Xiang#,... , Rui Xia* & Jianguo Li*.

MicroRNA482/2118, a miRNA superfamily essential for both disease resistance and plant development. New Phytologist Foundation. 2021, 233(5):2047-2057

Yanqing Zhang#, Muhammad Waseem#, Zaohai Zeng,Jing Xu, Chengjie Chen, Yuanlong Liu,...,Rui Xia*.

The GRAS gene family and its roles in seed development in litchi (Litchi chinensis Sonn). BMS Plant Biology. 2021, 21(1):423.

Jingwen Chen#, Qian Yan#,... Rui Xia*, Zaohai Zeng* and Yuanlong Liu*.

Rambutan genome revealed gene networks for spine formation and aril development. The Plant Journal. 2021, 108(4):1037-1052.

Wenping Zhang#, Jishan Lin#, Jianguo Li#,Shaoquan Zheng#,... Rui Xia, Jisen Zhang, Ray Ming*.

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.

Yanmin Zhu*#,Guanliang Li#,Jugpreet Singh#,..., Rui Xia*.

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.

Daoheng Hu#,Yiming Yu#,Chun Wang#, ...,Rui Xia,...,Kejian Wang*& Jixian Zhai*.

MicroRNAs play important roles in regulating rapid growth of the Phyllostachys edulis culm internode.New phytologist. 2021, 231(6):2215-2230.

Kaili Wang, Yuanyuan Zhang, ..., Rui Xia, Lili Song*, Ai-Min Wu*.

Small RNAs in Plant Immunity and Virulence of Filamentous Pathogens. ANNUAL REVIEWS. 2021, 59:265-288.

Yongli Qiao*, Rui Xia, ..., Wenbo Ma*.

Polyploidy underlies co-option and diversification of biosynthetic triterpene pathways in the apple tribe. PNAS. 2021, 118(20):e2101767118.

Wenbing Su,..., Rui Xia, ... ,Shunquan Lin*,and Zhenhua Liu*.

sRNAanno—a database repository of uniformly annotated small RNAs in plants.Horticulture research. 2021, 8(1):45.

Chengjie Chen#, Jiawei Li#, ..., Rui Xia*.

Long Non-Coding RNAs, the Dark Matter: An Emerging Regulatory Component in Plants. International Journal of Molecular Sciences. 2021, 22(1):86.

Muhammad Waseem, Yuanlong Liu, Rui Xia*.

Chromosome-level reference genome assembly provides insights into aroma biosynthesis in passion fruit (Passiflora edulis). Molecular Ecology Resources. 2020, 21(3):955-968.

Dongna Ma, Shanshan Dong, … Rui Xia*, Xingtan Zhang*.

Evolution and diversification of reproductive phased small interfering RNAs in Oryza species. New Phytologist. 2020, 229(5):2970-2983.

Peng Tian, Xuemei Zhang, Rui Xia,... Blake C. Meyers*, Mingsheng Chen *.

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.

Jinbu Jia#, Ronghuan Ji#, ..., Rui Xia, Bin Liu*, and Jixian Zhai*.

Developmental genetics of corolla tube formation: role of the tasiRNA-ARF pathway and a conceptual model. The Plant Cell. 2020, 32(11):3452-3468.

Baoqing Ding*, Rui Xia, ..., Blake C. Meyers, Yao-Wu Yuan*.

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.

Yuanlong Liu, Chong Teng, Rui Xia*, Blake Meyers*.

TBtools - an integrative toolkit developed for interactive analyses of big biological data. Molecular Plant(2020), 13(8):1194-1202.

Chengjie Chen, ..., Margaret H. Frank, Yehua He, Rui Xia*.

Post-transcriptional splicing of nascent RNA contributes to widespread intron retention in plants.Nature Plants. 2020, 6(7):780-788.

Jinbu Jia#, Yanping Long#, Hong Zhang,..., Rui Xia , Xiaofeng Cao and Jixian Zhai*.

KNOX protein KNAT1 regulates fruitlet abscission in litchi byrepressing ethylene biosynthetic genes. Journal of Experimental Botany. 2020, 71(14):4069-4082.

Minglei Zhao# , Caiqin Li#, Xingshuai Ma, Rui Xia,..., Chun-Lin Shi* and Jianguo Li*.

Evolution of self-compatibility by a mutant Sm-RNase in citrus. Nature Plants. 2020, 6(2):131-142.

Mei Liang, Zonghong Cao, Andan Zhu, Yuanlong Liu,..., Rui Xia..., and Lijun Chai*.

Disruption of miRNAs equences by TALENs and CRISPR/Cas9 induces varied lengths of miRNA production.Plant Biotechnology Journal, 2019. 18(7):1526-1536.

Honghao Bi#, Qili Fei#, Riqing Li, Bo Liu, Rui Xia, Si Nian Char, Blake C. Meyers and Bing Yang*.

Comprehensive Characterization of miRNA and PHAS Loci in the Diploid Strawberry (Fragaria vesca) Genome. Horticultural Plant Journal, 2019, 5(6):255-267

Lei Feng , Rui Xia* , Yuanlong Liu*.

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.

Hong Zhu#, Chengjie Chen#...,Yueming Jiang*, Xuewu Duan*,Rui Xia*.

Jack of many trades:The multifaceted role of miR528 in monocots. Molecular Plant, 2019, 12(8):1044-1046.

Chengjie Chen#, Yuanlong Liu#, Rui Xia*.

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.

Caiqin Li#,Minglei Zhao#,Xingshuai Ma#, ...,Rui Xia,Hong Wu*,Jianguo Li*.

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

Yanqing Zhang,...,Rui Xia*,....

Integrated analysis of high-throughput sequencing data shows abscisic acidresponsive genes and miRNAs in strawberry receptacle fruit ripening. Horticulture Research (2019) 6:26

Dongdong Li#, Wangshu Mou#, Rui Xia, ...,Zhongchi Liu* and Zisheng Luo*.

24-nt reproductive phasiRNAs are broadly present in angiosperms. Nature Communications (2019) 10:627

Rui Xia*, Chengjie Chen, Suresh Pokhre, Wuqiang Ma, … Jianguo Li & Blake C. Meyers*.

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.

Shaopeng Zhao, ..., Chengjie Chen,..., Rui Xia, and Xiurong Wang*.

Small RNAs, emerging regulators critical for thedevelopment of horticultural traits. HorticultureResearch, 2018, 5:63.

Chengjie Chen#, Zaohai Zeng#, Zongrang Liu, Rui Xia*.

Wheat miR9678 Affects Seed Germination byGenerating Phased siRNA and Modulating Abscisic Acid/Gibberellin Signaling. The Plant Cell, 2018, 30(4):796-814.

Guanghui Guo#, Xinye Liu#, ..., Rui Xia,..., Qixin Sun*, Yingyin Yao*.

Coupling of microRNA-directed phasiRNA generation … polyadenylation in small RNA-mediated gene silencing. New Phytologist 2017, 217(4):1535-1550.

Wuqiang Ma, Chengjie Chen, Yuanlong Liu,…, Jianguo Li*, and Rui Xia*.

miR3954 is a trigger of phasiRNAs that affects flowering time in citrus. Plant Journal, 2017, 92(2):263-275.

Yuanlong Liu, Lili Ke, Guizhi Wu, Yuantao Xu, Xiaomeng Wu, Rui Xia, Xiuxing Deng, Qiang Xu*.

The Emergence, Evolution, and Diversification of the miR390-TAS3-ARF Pathway in Land Plants. The Plant Cell, 2017, 29 (6) 1232-1247.

Rui Xia, Jing Xu, Blake C. Meyers*.

Genome-wide identification of histone modifiers and their expression patternsduring fruit abscission in litchi. Frontiersin Plant Science, 2017, 8, 639.

Manjun Peng, Peiyuan Ying, Xuncheng Liu, Caiqin Li, Rui Xia, Jianguo Li*, Minglei Zhao*.

Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce. Nature Communications, 2017, 8:14953.

Sebastian Reyes-Chin-Wo#, Zhiwen Wang#, Xinhua Yang#, …, Rui Xia, …, Richard W Michelmore*.

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.

Peiyuan Ying, …, Rui Xia, Minglei Zhao, Jianguo Li*.

The diversification of plant NBS-LRR defense genes directs the evolution of microRNAs thattarget them. Molecular Biology andEvolution, 2016, 33(10):2692-705.

Yu Zhang, Rui Xia, Hanhui Kuang and Blake C. Meyers*.

SmallRNAs add zing to the zig-zag-zig model of plant defenses. Molecular Plant-Microbe Interactions, 2016, 29(3):165-9.

Qili Fei, YuZhang, Rui Xia, Blake .C. Meyers*.

High-resolution identification and abundance profiling of cassava (Manihot esculenta Crantz) microRNAs. BMC Genomics, 2016, 17:85.

Behnam Khatabi, …, Rui Xia, …, Blake C. Meyers and Vincent N. Fondong*.

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.

Rui Xia, Jing Xu,Siwaret Arikit, Blake Meyers*.

Evolution, functions andmysteries of plant ARGONAUTE proteins. Current Opinion in Plant Biology, 2015, 27:84-90.

Han Zhang*, Rui Xia, Blake C. Meyers, Virginia Walbot.

Novel and recently evolved miRNA clustersregulate expansive F-box genenetworks through phasiRNAs in wild diploid strawberry. Plant Physiology, 2015, 169(1):594-610.

Rui Xia#, Songqing Ye#, Zongrang Liu, Blake C.Meyers, Zhongchi Liu*.

An atlas of soybean small RNAs identifies phased siRNAs from hundreds of coding genes. The Plant Cell, 2014, 26(12):4584-601.

Siwaret Arikit, Rui Xia, …, Blake C. Meyers*.

Phased, secondary siRNAs in post-transcriptional regulatorynetworks. The Plant Cell, 2013, 25: 2400-2415.

Qili Fei, Rui Xia,Blake C. Meyers*.

MicroRNA superfamilies descended from miR390 and their roles in secondary small interfering RNA biogenesis in eudicots. The Plant Cell 2013, 25:1555-1572.

Rui Xia, Blake C. Meyers, Zhongchi Liu, Eric P. Beers, Songqing Ye, Zongrang Liu*.

Apple miRNAs and tasiRNAs with novel regulatory networks. Genome Biology 2012, 13:R47.

Rui Xia, Hong Zhu, Yongqiang An, Eric P Beers and Zongrang Liu*.

Unique expression, processing regulation, and regulatory network of peach (Prunus persica) miRNAs. BMC Plant Biology, 2012, 12:149.

Hong Zhu, Rui Xia,…Zongrang Liu*.

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.

Rui Xia#, … Jianguo Li*.

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.

Hong Zhu, …, Rui Xia and Rongcai Yuan*.

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.

Rui Xia, … Jianguo Li*.

一种改良的扩增cDNA 5' 末端的方法. 园艺学报, 2008, 35: 1533-1538.

夏瑞,陆旺金, 李建国*.

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.

夏瑞,陆旺金, 李建国*, 杜娟.