EasyMetagenome: A user‐friendly and flexible pipeline for shotgun metagenomic analysis in microbiome research

Authors: Defeng Bai, Tong Chen, Jiani Xun, Chuang Ma, Hao Luo, Haifei Yang, Chen Cao, Xiaofeng Cao, Jianzhou Cui, Yuan‐Ping Deng, Zhaochao Deng, Wenxin Dong, Wenxue Dong, Juan Du, Qunkai Fang, Wei Fang, Yue Fang, Fangtian Fu, Min Fu, Yi‐Tian Fu, He Gao, Jingping Ge, Qinglong Gong, Lunda Gu, Peng Guo, Yuhao Guo, Tang Hai, Hao Liu, Jieqiang He, Zi‐Yang He, Huiyu Hou, Can Huang, Shuai Ji, ChangHai Jiang, Gui‐Lai Jiang, Lingjuan Jiang, Ling N. Jin, Yuhe Kan, Da Kang, Jin Kou, Ka‐Lung Lam, Changchao Li, Chong Li, Fuyi Li, Liwei Li, Miao Li, Xin Li, Ye Li, Zheng‐Tao Li, Jing Liang, Yongxin Lin, Changzhen Liu, Danni Liu, Fengqin Liu, Jia Liu, Tianrui Liu, Tingting Liu, Xinyuan Liu, Yaqun Liu, Bangyan Liu, Minghao Liu, Wenbo Lou, Yaning Luan, Yuanyuan Luo, Hujie Lv, Tengfei Ma, Zongjiong Mai, Jiayuan Mo, Dongze Niu, Zhuo Pan, Heyuan Qi, Zhanyao Shi, Chunjiao Song, Fuxiang Sun, Yan Sun, Sihui Tian, Xiulin Wan, Guoliang Wang, Hongyang Wang, Hongyu Wang, Huanhuan Wang, Jing Wang, Jun Wang, Kang Wang, Leli Wang, Shao‐kun Wang, Xinlong Wang, Yao Wang, Zufei Xiao, Huichun Xing, Yifan Xu, Shu‐yan Yan, Li Yang, Song Yang, Yuanming Yang, Xiaofang Yao, Salsabeel Yousuf, Hao Yu, Yu Lei, Zhengrong Yuan, Meiyin Zeng, Chunfang Zhang, Chunge Zhang, Huimin Zhang, Jing Zhang, Na Zhang, Tianyuan Zhang, Yi‐Bo Zhang, Yupeng Zhang, Zheng Zhang, Mingda Zhou, Yuanping Zhou, Chengshuai Zhu, Lin Zhu, Yue Zhu, Zhihao Zhu, Hongqin Zou, Anna Zuo, Wenxuan Dong, Tao Wen, Shifu Chen, Guoliang Li, Yunyun Gao, Yong‐Xin Liu

Source: iMeta, Vol 4, Iss 1, Pp n/a-n/a (2025)

Subject Terms: metagenome, microbiome, microbiota, pipeline, visualization, Computer applications to medicine. Medical informatics, R858-859.7

File Description: electronic resource

Relation: https://doaj.org/toc/2770-596X

Access URL: https://doaj.org/article/9e02ebd1b25b4e5fb372b6e50eee325f

Heterologous Overexpression of Apple MdKING1 Promotes Fruit Ripening in Tomato

Authors: Qianyu Yue, Xinyue Yang, Pengda Cheng, Jieqiang He, Wenyun Shen, Yixuan Li, Fengwang Ma, Chundong Niu, Qingmei Guan

Source: Plants, Vol 12, Iss 15, p 2848 (2023)

Subject Terms: MdKING1, tomato, fruit ripening, ethylene, carotenoid, Botany, QK1-989

File Description: electronic resource

Relation: https://www.mdpi.com/2223-7747/12/15/2848; https://doaj.org/toc/2223-7747

Access URL: https://doaj.org/article/68c16d5bbffe44aeb3b32b50b756f500

Transcriptomic Analysis Revealed the Discrepancy between Early-Ripening ‘Geneva Early’ and Late-Ripening ‘Hanfu’ Apple Cultivars during Fruit Development and Ripening

Authors: Qianyu Yue, Jieqiang He, Xinyue Yang, Pengda Cheng, Abid Khan, Wenyun Shen, Yi Song, Shicong Wang, Fengwang Ma, Qingmei Guan

Source: Horticulturae, Vol 9, Iss 5, p 570 (2023)

Subject Terms: apple (Malus × domestica Borkh.), transcriptome, fruit development, early-ripening, late-ripening, Plant culture, SB1-1110

File Description: electronic resource

Relation: https://www.mdpi.com/2311-7524/9/5/570; https://doaj.org/toc/2311-7524

Access URL: https://doaj.org/article/2d8b08220894496ab7e7f3ffc11cf494

Transcriptional Effects of Rootstock on Scion after Drought: A Case Study of Using MdGH3 RNAi as the Rootstock

Authors: Jieqiang He, Junxing Guo, Lijuan Jiang, Wenjing An, Fengwang Ma, Qingmei Guan, Chundong Niu

Source: Horticulturae, Vol 8, Iss 12, p 1212 (2022)

Subject Terms: transcriptome, apple, drought stress, GH3, grafting, Plant culture, SB1-1110

File Description: electronic resource

Relation: https://www.mdpi.com/2311-7524/8/12/1212; https://doaj.org/toc/2311-7524

Access URL: https://doaj.org/article/7bb24c0b47454f859bafce3302fb709a

Profiling of N6-Methyladenosine (m6A) Modification Landscape in Response to Drought Stress in Apple (Malus prunifolia (Willd.) Borkh)

Authors: Xiushan Mao, Nan Hou, Zhenzhong Liu, Jieqiang He

Source: Plants, Vol 11, Iss 1, p 103 (2021)

Subject Terms: epitranscriptome, gene expression, m6A methylation, drought stress, apple, Botany, QK1-989

File Description: electronic resource

Relation: https://www.mdpi.com/2223-7747/11/1/103; https://doaj.org/toc/2223-7747

Access URL: https://doaj.org/article/09607421b6514613af0924ed3d850c4c

Global hypermethylation of the N⁶-methyladenosine RNA modification associated with apple heterografting.

Authors: Jidi Xu¹ jieqiang.he.dawn@gmail.com, Jieqiang He¹, Bichun Hu¹, Nan Hou¹, Junxing Guo¹, Caixia Wang¹, Xuewei Li¹, Zhongxing Li¹, Jingjing Zha², Ting Zhang², Chuang Ma², Fengwang Ma¹, Qingmei Guan¹ qguan@nwafu.edu.cn

Source: Plant Physiology. Dec2023, Vol. 193 Issue 4, p2513-2537. 25p.

Methylation of a MITE insertion in the MdRFNR1-1 promoter is positively associated with its allelic expression in apple in response to drought stress.

Authors: Chundong Niu, Lijuan Jiang, Fuguo Cao, Chen Liu, Junxing Guo, Zitong Zhang, Qianyu Yue, Nan Hou, Zeyuan Liu, Xuewei Li, Tahir, Muhammad Mobeen, Jieqiang He, Zhongxing Li, Chao Li, Fengwang Ma, Qingmei Guan

Source: Plant Cell; Oct2022, Vol. 34 Issue 10, p3983-4006, 24p

The positive feedback regulatory loop of miR160-Auxin Response Factor 17-HYPONASTIC LEAVES 1 mediates drought tolerance in apple trees.

Authors: Xiaoxia Shen^1,2, Jieqiang He¹, Yikun Ping¹, Junxing Guo¹, Nan Hou¹, Fuguo Cao¹, Xuewei Li¹, Dali Geng¹, Shicong Wang¹, Pengxiang Chen¹, Gege Qin¹, Fengwang Ma¹, Qingmei Guan¹ qguan@nwafu.edu.cn

Source: Plant Physiology. Mar2022, Vol. 188 Issue 3, p1686-1708. 23p.

Zinc-finger protein MdBBX7/MdCOL9, a target of MdMIEL1 E3 ligase, confers drought tolerance in apple.

Authors: Pengxiang Chen, Fang Zhi, Xuewei Li, Wenyun Shen, Mingjia Yan, Jieqiang He, Chana Bao, Tianle Fan, Shuangxi Zhou, Fengwang Ma, Qingmei Guan

Source: Plant Physiology; Feb2022, Vol. 188 Issue 2, p540-559, 20p