The publications of ATCG group

2024

Yingzhen Wang#, Pengwei Li#, Yanyan Zhu, Feng Zhang, Sijia Zhang, Yan He, Ying Wu, Yunzhi Lin, Hongtao Wang, Wangmei Ren, Lihuan Wang, Ying Yang, Runze Wang, Pengpeng Zheng, Yongsheng Liu*, Songhu Wang*, Junyang Yue*. Graph-based pangenome of Actinidia chinensis reveals structural variations mediating fruit degreening. Advanced Science 2024;17:e2400322. (Online: 2024.05.17)    [ PDF ]


Feng Zhang#, Yingzhen Wang#, Yunzhi Lin#, Hongtao Wang, Ying Wu, Wangmei Ren, Lihuan Wang, Ying Yang, Pengpeng Zheng, Songhu Wang, Junyang Yue*, Yongsheng Liu*. Haplotype-resolved genome assembly provides insights into evolutionary history of the Actinidia arguta tetraploid. Molecular Horticulture 2024;4:4. (Online: 2024.02.06)    [ PDF ]


Junyang Yue#, Qinyao Chen#, Sijia Zhang#, Yunzhi Lin, Wangmei Ren, Bingjie Li, Ying Wu, Yingzhen Wang, Yongfeng Zhou*, Yongsheng Liu*. Origin and evolution of the kiwifruit Y chromosome. Plant Biotechnology Journal 2024;22:287–289. (Online: 2023.10.31)    [ PDF ]



2023

Yunzhi Lin#, Chen Ye#, Xingzhu Li, Qinyao Chen, Ying Wu, Feng Zhang, Rui Pan, Sijia Zhang, Shuxia Chen, Xu Wang, Shuo Cao, Yingzhen Wang, Yi Yue*, Yongsheng Liu*, Junyang Yue*. quarTeT: a telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification. Horticulture Research 2023;10:uhad127. (Online: 2023.06.13)    [ PDF ]    [ Website ]


Yingzhen Wang#, Minhui Dong#, Ying Wu, Feng Zhang, Wangmei Ren, Yunzhi Lin, Qinyao Chen, Sijia Zhang, Junyang Yue*, Yongsheng Liu*. Telomere-to-telomere and haplotype-resolved genome of the kiwifruit Actinidia eriantha. Molecular Horticulture 2023;3:4. (Online: 2023.02.17)    [ PDF ]


Junyang Yue#*, Qinyao Chen#, Yingzhen Wang#, Lei Zhang#, Chen Ye, Xu Wang, Shuo Cao, Yunzhi Lin, Wei Huang, He Xian, Hongyan Qin, Yanli Wang, Sijia Zhang, Ying Wu, Songhu Wang, Yi Yue, Yongsheng Liu*. Telomere-to-telomere and gap-free reference genome assembly of the kiwifruit Actinidia chinensis. Horticulture Research 2023;10:uhac264. (Online: 2022.12.02)    [ PDF ]    [ Data ]



2022

Junyang Yue, Yongsheng Liu*. SSR2Marker: an integrated pipeline for identification of SSR markers within any two given genome-scale sequences. Molecular Horticulture 2022;2:11. (Online: 2022.04.22)    [ PDF ]    [ GitHub ]



2021

Longji Wang#, Ting Lei#, Guomin Han#, Junyang Yue#, Xueru Zhang, Qi Yang, Haixiang Ruan, Chunyang Gu, Qiang Zhang, Tao Qian, Niuniu Zhang, Wei Qian, Qi Wang, Xiaojing Pang, Yue Shu, Liping Gao, Yunsheng Wang*. The chromosome-scale reference genome of Rubus chingii Hu provides insight into the biosynthetic pathway of hydrolysable tannins. Plant Journal 2021;107:1466–1477. (Online: 2021.06.26)    [ PDF ]



2020

Junyang Yue#, Jiacheng Liu#, Wei Tang, Ya Qing Wu, Xiaofeng Tang, Wei Li, Ying Yang, Lihuan Wang, Shengxiong Huang, Congbing Fang, Kun Zhao, Zhangjun Fei*, Yongsheng Liu*, Yi Zheng*. Kiwifruit Genome Database (KGD): a comprehensive resource for kiwifruit genomics. Horticulture Research 2020;7:117. (Online: 2020.08.01)    [ PDF ]


Shudong He#, Jinlong Zhao#, Xiaodong Cao, Yongkang Ye, Zeyu Wu, Junyang Yue, Liu Yang, Risheng Jin, Hanju Sun*. Low pH-shifting treatment would improve functional properties of black turtle bean (Phaseolus vulgaris L.) protein isolate with immunoreactivity reduction. Food Chemistry 2020;330:15. (Online: 2020.06.03)


Yufei Yang, Shudong He*, Yongkang Ye, Xiaodong Cao, Haiyan Liu, Zeyu Wu, Junyang Yue, Hanju Sun. Enhanced hydrophobicity of soybean protein isolate by low-pH shifting treatment for the sub-micron gel particles preparation. Industrial Crops and Products 2020;151:1. (Online: 2020.04.27)


Junyang Yue#, Ran Wang#, Xiaojing Ma#, Jiayi Liu, Xiaohui Lu, Sambhaji Balaso Thakar, Ning An, Jia Liu, Enhua Xia*, Yongsheng Liu*. Full-length transcriptome sequencing provides insights into the evolution of apocarotenoid biosynthesis in Crocus sativus. Computational and Structural Biotechnology Journal 2020;18:774–783. (Online: 2020.03.26)    [ PDF ]


王然, 卢晓慧, 刘永胜, 王一君*, 岳俊阳*. 不同产地番红花活性物质的代谢组学研究. 植物生理学报 56:672–680 (2020.03.10). [Ran Wang, Xiaohui Lu, Yongsheng Liu, Yijun Wang*, Junyang Yue*. Metabolomics study of active substances in saffron (Crocus sativus) from different production areas. Plant Physiology Journal 2020;56:672–680. (Online: 2020.03.10)]    [ PDF ]


Xiaojing Ma, Sambhaji Balaso Thakar, Huimin Zhang, Zequan Yu, Li Meng, Junyang Yue*. Bioinformatics analysis of the rhizosphere microbiota of Dangshan Su pear in different soil types. Current Bioinformatics 2020;15:503–514. (Online: 2020.03.09)    [ PDF ]


Yuan Sui, Michael Wisniewski, Samir Droby, Edoardo Piombo, Xuehong Wu*, Junyang Yue*. Genome sequence, assembly, and characterization of the antagonistic yeast Candida oleophila used as a biocontrol agent against post-harvest diseases. Frontiers in Microbiology 2020;11:295. (Online: 2020.02.25)    [ PDF ]


Xiaojing Ma*, Li Meng, Huimin Zhang, Liye Zhou, Junyang Yue, Huixia Zhu, Risheng Yao. Sophorolipid biosynthesis and production from diverse hydrophilic and hydrophobic carbon substrates. Applied Microbiology and Biotechnology 2020;104:77–100. (Online: 2019.11.27)



2019

Xianbao Sun#, Yongkang Ye#, Shudong He*, Zeyu Wu, Junyang Yue, Hanju Sun, Xiaodong Cao*. A novel oriented antibody immobilization based voltammetric immunosensor for allergenic activity detection of lectin in kidney bean by using AuNPs-PEI-MWCNTs modified electrode. Biosensors and Bioelectronics 2019;143:111607. (Online: 2019.10.15)


Wei Tang#, Xuepeng Sun#, Junyang Yue#, Xiaofeng Tang, Chen Jiao, Ying Yang, Xiangli Niu, Min Miao, Danfeng Zhang, Shengxiong Huang, Wei Shi, Mingzhang Li, Congbing Fang, Zhangjun Fei*, Yongsheng Liu*. Chromosome-scale genome assembly of kiwifruit Actinidia eriantha with single-molecule sequencing and chromatin interaction mapping. GigaScience 2019;8:giz027. (Online: 2019.04.01)    [ PDF ]


Lihuan Wang#, Wei Tang#*, Yawen Hu, Yabin Zhang, Jiaqi Sun, Xiuhong Guo, Han Lu, Ying Yang, Congbing Fang, Xiangli Niu, Junyang Yue, Zhangjun Fei, Yongsheng Liu*. A MYB/bHLH complex regulates tissue-specific anthocyanin biosynthesis in the inner pericarp of red-centered kiwifruit Actinidia chinensis cv. Hongyang. Plant Journal 2019;99:359–378. (Online: 2019.03.26)    [ PDF ]



2018

Danfeng Zhang#, Junyang Yue#, Chenyan Hua, Danyang Chen, Yi Han, Yongsheng Liu*. Role of UV-damaged DNA-binding protein-1 (DDB1) in early response to Pseudomonas syringae pv. tomato DC3000 infection in tomato. Canadian Journal of Plant Pathology 2018;40:562–570. (Online: 2018.09.24)    [ PDF ]


Junyang Yue#, Chuanxue Zhu#, Yu Zhou, Xiangli Niu, Min Miao, Xiaofeng Tang, Fadi Chen, Weiping Zhao*, Yongsheng Liu*. Transcriptome analysis of differentially expressed unigenes involved in flavonoid biosynthesis during flower development of Chrysanthemum morifolium 'Chuju'. Scientific Reports 2018;8:13414. (Online: 2018.09.07)    [ PDF ]


Yongbing Ren#, Min Miao#, Yun Meng#, Jiasheng Cao, Tingting Fan, Junyang Yue, Fangming Xiao, Yongsheng Liu*, Shuqing Cao*. DFR1-mediated inhibition of proline degradation pathway regulates drought and freezing tolerance in Arabidopsis. Cell Reports 2018;23:3960–3974. (Online: 2018.06.26)    [ PDF ]


卢晓慧, 朱志明, 岳俊阳*. 藏红花柱头小RNA高通量测序及生物信息学分析. 植物生理学报 54:827–836 (2018.04.26). [Xiaohui Lu, Zhiming Zhu, Junyang Yue*. Bioinformatics analysis for high-throughput sequencing of small RNAs in the stigmas of saffron (Crocus sativus). Plant Physiology Journal 2018;54:827–836. (Online: 2018.04.26)]    [ PDF ]


Xiaoping Gong#, Zhili Zhang#, Junyang Yue#, Wei Tang, Xiaofeng Tang, Zhengming Zeng, Xiangli Niu, Danyang Chen, Xianchun Sang, Fangming Xiao, Guanghua He*, Yongsheng Liu*. Phenotypic characterization, fine mapping, and altered expression profiling of roses1 mutation that affects organ size and water loss through regulating stomatal density in rice. Crop Science 2018;58:486–506. (Online: 2018.01.12)    [ PDF ]



2017

Junyang Yue#, Xiaohui Lu#, Huan Zhang, Jiao Ge, Xueling Gao*, Yongsheng Liu*. Identification of conserved and novel microRNAs in blueberry. Frontiers in Plant Science 2017;8:1155. (Online: 2017.06.30)    [ PDF ]


Junyang Yue#, Danfeng Zhang#, Rongjun Ban#, Xiaojing Ma, Danyang Chen, Guangwei Li, Jia Liu, Michael Wisniewski, Samir Droby, Yongsheng Liu*. PCPPI: a comprehensive database for the prediction of Penicillium-crop protein-protein interactions. Database (Oxford) 2017;2017:baw170. (Online: 2017.02.26)    [ PDF ]



2016

卢晓慧, 聂鹏程, 岳俊阳, 王文才. 农业物联网技术与应用. 中国农业大学出版社 2016. (Online: 2016.12.01)


Junyang Yue#, Wei Xu#, Rongjun Ban#, Shengxiong Huang, Min Miao, Xiaofeng Tang, Guoqing Liu, Yongsheng Liu*. PTIR: Predicted Tomato Interactome Resource. Scientific Reports 2016;6:25047. (Online: 2016.04.28)    [ PDF ]


Wei Tang#, Yi Zheng#, Jing Dong, Jia Yu, Junyang Yue, Fangfang Liu, Xiuhong Guo, Shengxiong Huang, Michael Wisniewski, Jiaqi Sun, Xiangli Niu, Jian Ding, Jia Liu*, Zhangjun Fei, Yongsheng Liu*. Comprehensive transcriptome profiling reveals long noncoding RNA expression and alternative splicing regulation during fruit development and ripening in kiwifruit (Actinidia chinensis). Frontiers in Plant Science 2016;7:335. (Online: 2016.03.29)    [ PDF ]


杨潇怡, 隋媛, 唐晓凤, 曹徐绿, 岳俊阳, 刘永胜*. ZmBK2L3在番茄果实中的特异表达及其功能研究. 合肥工业大学学报(自然科学版) 2016;39:410–414. (Online: 2016.03.00)



2015

Junyang Yue#, Jian Liu#, Rongjun Ban#, Wei Tang, Lin Deng, Zhangjun Fei, Yongsheng Liu*. Kiwifruit Information Resource (KIR): a comparative platform for kiwifruit genomics. Database (Oxford) 2015;2015:bav113. (Online: 2015.12.09)    [ PDF ]


Junyang Yue#, Xiaojing Ma#, Rongjun Ban#, Qianli Huang, Wenjie Wang, Jia Liu, Yongsheng Liu*. FR database 1.0: a resource focused on fruit development and ripening. Database (Oxford) 2015;2015:bav002. (Online: 2015.02.27)    [ PDF ]


Yunye Zhu#, Shengxiong Huang#, Min Miao, Xiaofeng Tang, Junyang Yue, Wenjie Wang, Yongsheng Liu*. Genome-wide identification, sequence characterization, and protein-protein interaction properties of DDB1 (damaged DNA binding protein-1)-binding WD40-repeat family members in Solanum lycopersicum. Planta 2015;241:1337–1350. (Online: 2015.02.14)    [ PDF ]


Junyang Yue#, Wenjie Wang#, Rongjun Ban#, Yunye Zhu, Jia Liu, Yongsheng Liu*. PAAS: Fast retrieval of plant amino acid substitutions and their effects on comparative phenomics. Plant Molecular Biology Reporter 2015;33:748–750. (Online: 2014.08.10)    [ PDF ]



2013

Shengxiong Huang#, Jian Ding#, Dejing Deng#, Wei Tang#, Honghe Sun#, Dongyuan Liu#, Lei Zhang#, Xiangli Niu, Xia Zhang, Meng Meng, Jinde Yu, Jia Liu, Yi Han, Wei Shi, Danfeng Zhang, Shuqing Cao, Zhaojun Wei, Yongliang Cui, Yanhua Xia, Huaping Zeng, Kan Bao, Lin Lin, Ya Min, Hua Zhang, Min Miao, Xiaofeng Tang, Yunye Zhu, Yuan Sui, Guangwei Li, Hanju Sun, Junyang Yue, Jiaqi Sun, Fangfang Liu, Liangqiang Zhou, Lin Lei, Xiaoqin Zheng, Ming Liu, Long Huang, Jun Song, Chunhua Xu, Jiewei Li, Kaiyu Ye, Silin Zhong, Bao-Rong Lu, Guanghua He, Fangming Xiao, Hui-Li Wang, Hongkun Zheng*, Zhangjun Fei*, Yongsheng Liu*. Draft genome of the kiwifruit Actinidia chinensis. Nature Communications 2013;4:2640. (Online: 2013.10.18)    [ PDF ]



2008

Junyang Yue, Jincong Yu, Baishan Fang*. Advances in directed evolution of genetic circuits. Journal of Biotechnology 2008;136:S41–S42. (Online: 2008.10.16)