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Shangang Jia

草业科学与技术学院

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  • Department: 草业科学与技术学院
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Education

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Resume

Curriculum Vitae

Shangang Jia, Associate Professor

College of Grassland Science and Technology, China Agricultural University, Beijing, 100193

Phone: +86-010-62731451

E-mail: shangang.jia@cau.edu.cn

Research Interest

My research interests are to study on “omics”, for example, transcriptomics, genome re-sequencing, metagenomics, epigenomics and etc., in many organisms. Recently, I focused on the genomics and phenomics in grassland plants, especially on forage seed aging.

Education

2007.09-2012.07, Ph.D. in Bioinformatics, Beijing Institute of Genomics, Chinese Academy of Sciences

2004.09-2007.07, M.S. in Genetics, Northwest A & F University

2000.09-2004.07, B.S. in Grass Science, Northwest A & F University

Research Experience

2019.04-Present: Associate Professor, Faculty Member, China Agricultural University, Beijing, China

2014.12-2019.03: Postdoctoral fellow, in Department of Agronomy & Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA.

  • Functional genomics in Quality Protein Maize and mutants caused by gamma-radiation, combining multiple data sets, including whole genome assembly, RNA-seq, exome-seq, LC-MS/MS proteomic profiling, and BSR-seq.

  • Conduct genomic studies on sorghum, soybean, etc.

2013.09-2014.11: Postdoctoral fellow, in Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.

  • Algae taxonomy, in the 1KP project (1000 plants, oneKP, or 1KP).

  • Genome-wide copy number variations in cattle in terms of functional effects and evolution.

  • Marine metagenomics and paleomics in the sediment of deep red sea.

  • Marine protist biodiversity in North Atlantic.

2012.08-2013.08: Postdoctoral fellow, in Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST), Riyadh, Kingdom of Saudi Arabia and Cell department in Beijing Institute of Genomics (BIG).

  • Gut metagenomics in red palm weevil.

Publications

(A)Publications

1.      Rui Song, Ziyao Wang, Hui Wang, Han Zhang, Xuemeng Wang, Hanh Nguyen, David Holding, Bin Yu, Tom Clemente, Shangang Jia*, Chi Zhang*. InMut-Finder: a software tool for insertion identification in mutagenesis using Nanopore long reads. BMC Genomics, accepted. 

2.      Xianjiang Tang, Liangzhi Zhang, Chao Fan, Lei Wang, Haibo Fu, Shi'en Ren, Wenjuan Shen, Shangang Jia*, Guofang Wu*, Yanming Zhang*. Dietary fiber influences bacterial community assembly processes in the gut microbiota of Durco×Bamei crossbred pig. Frontiers in Microbiology, 2021, accepted. 

3.      Lianying Shen, Hang Luo, Xiaoling Wang, Xuemeng Wang, Xiaojing Qiu, Hui Liu, Shanshan Zhou, Kaihua Jia, Shuai Nie, Yutao Bao, Rengang Zhang, Quanzheng Yun, Yinghui Chai, Jinying Lu, Yu Li, Shuwei Zhao, Jian-Feng Mao*, Shangang Jia* and Yongmin Mao*. Chromosome-scale genome assembly for Chinese sour jujube and insights into its genome evolution and domestication signature. Frontiers in Plant Science, 2021, 12: 773090. 

4.      Ruoran Li, Xuli Jia, Jing Zhang, Shangang Jia*, Tao Liu*, Jiangyong Qu*, Xumin Wang*. The complete plastid genomes of seven Sargassaceae species and their phylogenetic analysis. Frontiers in Plant Science, 2021, 12: 747036. 

5.      Xuemeng Wang, Han Zhang, Rui Song, Xin He, Peisheng Mao, Shangang Jia*. Non-destructive Identification of Natural Aging Alfalfa Seeds via Multispectral Imaging Analysis. Sensors, 2021, 21(17): 5804. 

6.      Shien Ren, Chao Fan, Liangzhi Zhang, Xianjiang Tang, Haibo Fu, Chuanfa Liu, Shangang Jia*& Yanming Zhang*. The plant secondary compound swainsonine reshapes gut microbiota in plateau pikas (Ochotona curzoniae). Applied Microbiology and Biotechnology, 2021, 105: 6419-6433. https://doi.org/10.1007/s00253-021-11478-6.

7.      Han Zhang, Xiqiang Liu, Xuemeng Wang, Ming Sun, Rui Song, Peisheng Mao*, Shangang Jia*. Genome-wide identification of GRAS gene family and their responses to abiotic stress in Medicago sativa. International Journal of Molecular Sciences, 2021, 22(14): 7729. 

8.      Ming Sun, Zhixiao Dong, Jian Yang, Wendan Wu, Chenglin Zhang, Jianbo Zhang, Junming Zhao, Yi Xiong, Shangang Jia*, Xiao Ma*. Transcriptomic resources for prairie grass (Bromus catharticus): expressed transcripts, tissue-specific genes, and identification and validation of EST-SSR markers. BMC Plant Biology, 2021, 21: 264. 

9.      Haibo Fu, Liangzhi Zhang, Chao Fan, Chuanfa Liu, Wenjing Li, Jiye Li, Xinquan Zhao*, Shangang Jia*, Yanming Zhang*. Domestication shapes the community structure and functional metagenomic content of the yak fecal microbiota. Frontiers in Microbiology, 2021, 12: 594075. 

10.   Haibo Fu, Liangzhi Zhang, Chao Fan, Chuanfa Liu, Wenjing Li, Qi Cheng, Xinquan Zhao*, Shangang Jia*, Yanming Zhang*. Environment and host species identity shape gut microbiota diversity in sympatric herbivorous mammals. Microbial Biotechnology, 2021, 4(4): 1300-1315. https://doi.org/10.1111/1751-7915.13687 

11.   Chao Fan, Liangzhi Zhang, Haibo Fu, Chuanfa Liu, Wenjing Li, Qi Cheng, He Zhang, Shangang Jia*, Yanming Zhang*. Enterotypes of the gut microbial community and their response to plant secondary compounds in plateau pikas. Microorganisms, 2020, 8: 1131.

12.   Shangang Jia, Abou Yobi, Michael J. Naldrett, Sophie Alvarez, Ruthie Angelovici, Chi Zhang, David R. Holding. Deletion of maize RDM4 suggests a role in endosperm maturation as well as vegetative and stress-responsive growth. Journal of Experimental Botany, 2020, 71(19):5880-5895. doi:10.1093/jxb/eraa325. 

13.   Fengyun Liu, Chao Fan, Liangzhi Zhang, Yuan Li, Haiwen Hou, Yan Ma, Jinhua Fan, Yueqin Tan, Tianyi Wu, Shangang Jia*, Yanming Zhang*. Alterations of Gut Microbiome in Tibetan Patients with Coronary Heart Disease. Frontiers in Cellular and Infection Microbiology, 2020, 10: 373. 

14.   Yi Xiong, Yanli Xiong, Shangang Jia*, Xiao Ma*. The Complete Chloroplast Genome Sequencing and Comparative Analysis of Reed Canary Grass (Phalaris arundinacea) and Hardinggrass (P. aquatica). Plants, 2020, 9: 748. 

15.   Shangang Jia, Guoliang Wang, Guiming Liu, Jiangyong Qu, Beilun Zhao, Xinhao Jin, Lei Zhang, Jinlong Yin, Cui Liu, Guangle Shan, Shuangxiu Wu, Lipu Song, Tao Liu, Xumin Wang, Jun Yu. High-quality de novo genome assembly of Kappaphycus alvarezii based on both PacBio and HiSeq sequencing. BioRxiv, 2019, doi: https://doi.org/10.1101/2020.02.15.950402

16.   Shengjun Li*, Shangang Jia*, Lili Hou*, Hanh Nguyen*, David Holding, Edgar Cahoon, Chi Zhang, Tom Clemente and Bin Yu.Mapping of transgenic alleles in soybean using a Nanopore-based sequencing strategy. Journal of Experimental Botany, 2019, 70: 3825-3833. 

17.   Tao Liu, Xumin Wang, Guoliang Wang, Shangang Jia*, Guiming Liu, Guangle Shan, Shan Chi, Jing Zhang, Yahui Yu, Ting Xue*, Jun Yu*. Evolution of complex thallus alga: genome sequencing of Saccharina japonica. Frontiers in Genetics, 2019, 10: 378. 

18.   Shangang Jia, Kyla Morton, Chi Zhang and David Holding. An exome-seq based tool for mapping and identification of causal genes in maize deletion mutants. Genomics, Proteomics & Bioinformatics, 2018, 16(6): 439-450.

19.   Shangang Jia, Aixia Li, Chi Zhang and David Holding (2017). Deletion mutagenesis and identification of causative mutations in maize. pp. 97-108 in Methods in Molecular Biology. Humana Press, New York.

20.   Shangang Jia, Chi Zhang and David Holding (2017). A mapping-by-sequencing tool for searching causative genes in mutants. 2017 IEEE International Conference on Electro Information Technology (EIT), Lincoln, NE, 2017, pp. 338-340.

21.   Shangang Jia, Aixia Li, Kyla Morton, Penny Avoles-Kianian, Shahryar F. Kianian, Chi Zhang and David Holding (2016). A population of deletion mutants and an integrated mapping and exome-seq pipeline for gene discovery in maize. G3, 2016, 6: 1-11. 

22.   Liangzhi Zhang*, Shangang Jia*, Martin Plath, Yongzhen Huang, Congjun Li, Chuzhao Lei, Xin Zhao, Hong Chen. Impact of parental Bos taurus and Bos indicus origins on copy number variation in traditional Chinese cattle breeds. Genome Biology and Evolution, 2015, 7(8): 2352-2361. 

23.   Liangzhi Zhang*, Shangang Jia*, Mingjuan Yang, Yao Xu, Congjun Li, Jiajie Sun, Yongzhen Huang, Xianyong Lan, Chuzhao Lei, Yang Zhou, Chunlei Zhang, Xin Zhao & Hong Chen. Detection of copy number variations and their effects in Chinese bulls. BMC Genomics, 2014, 15: 480. (IF= 4.041, Co-first author, 生物二区)

24.   Shangang Jia, Xumin Wang, Tianyong Li, Hao Qian, Jing Sun, Liang Wang, Jun Yu, Lufeng Ren, Jinlong Yin, Tao Liu, & Shuangxiu Wu. Phylogenomic analysis of transcriptomic sequences of mitochondria and chloroplasts of essential brown algae (Phaeophyceae) in China. Acta Oceanologica Sinica, 2014, 33: 94-101.

25.   Shangang Jia, Xumin Wang, Hao Qian, Tianyong Li, Jing Sun, Liang Wang, Jun Yu, Xingang Li, Jinlong Yin, Tao Liu, & Shuangxiu Wu. Phylogenomic analysis of transcriptomic sequences of mitochondria and chloroplasts for marine red algae (Rhodophyta) in China. Acta Oceanologica Sinica, 2014, 33: 86-93. 

26.   Shangang Jia*, Xiaowei Zhang*, Guangyu Zhang, An Yin, Sun Zhang, Fusen Li, Lei Wang, Duojun Zhao, Quanzheng Yun, Tala, Jixiang Wang, Gaoyuan Sun, Mohammed Baabdullah, Xiaoguang Yu, Songnian Hu, Ibrahim S. Al-Mssallem, & Jun Yu.Seasonally variable intestinal metagenomes of the red palm weevil (Rhynchophorus ferrugineus). Environmental Microbiology, 2013, 15: 3020-3029. 

27.   Shangang Jia, Xumin Wang, Guiming Liu, Dan Luo, Jing Zhang, Yan Liu, Xiangzhi Lin & Tao Liu.Gene expression analysis of “green tide” alga Ulva prolifera (Chlorophyta) in China. Genes & Genomics, 2011, 33: 173-178. 

28.   Shangang Jia, Yan Zhou, Chuzhao Lei, Ru Yao, Zhiying Zhang, Xingtang Fang, Hong Chen. A new insight into cattle's maternal origin in six Asian countries. Journal of Genetics and Genomics, 2010, 37: 173-180. 

29.   Shangang Jia, Hong Chen, Guixiang Zhang, Zhigang Wang, Chuzhao Lei, Ru Yao, Xu Han. Genetic variation of mitochondrial D-loop region and evolution analysis in some Chinese cattle breeds. Journal of Genetics and Genomics, 2007, 34: 510-518. 

Co-author in the following publications:

1.      Chengming Ou, Mingya Wang, Longyu Hou, Yangyang Zhang, Ming Sun, Shoujiang Sun, Shangang Jia, Peisheng Mao. Responses of Seed Yield Components to the Field Practices for Regulating Seed Yield of Smooth Bromegrass (Bromus inermis Leyss.). Agriculture, 2021, 11(10): 940.

2.      Kun Shi, Xiqiang Liu, Xinyi Pan, Jia Liu, Wenlong Gong, Pan Gong, Mingshu Cao, Shangang Jia, Zan Wang. Unveiling the Complexity of Red Clover (Trifolium pratense L.) Transcriptome and Transcriptional Regulation of Isoflavonoid Biosynthesis Using Integrated Long-and Short-Read RNAseq. International Journal of Molecular Sciences, 22: 12625.

3.      Bei Liu, Di Zhang, Ming Sun, Manli Li, Xiqing Ma, Shangang Jia, Peisheng Mao. PSII activity was inhibited at flowering stage with developing black bracts of oat. International Journal of Molecular Sciences, 2021, 22(10): 5258. 

4.      Zhen Wang, Junmei Kang, Juan Armando Casas-Mollano, Yongchao Dou, Shangang Jia, Qingchuan Yang, Chi Zhang, Heriberto Cerutti. MLK4-mediated phosphorylation of histone H3T3 promotes flowering by transcriptional silencing of FLC/MAF in Arabidopsis thaliana. Plant Journal, 2021, 105(5): 1400-1412. 

5.      Xiaomei Li, Fei Chen, Xuekai Wang, Lin Sun, Linna Guo, Yi Xiong, Yuan Wang, Hongzhang Zhou, Shangang Jia, Fuyu Yang, and Kuikui Ni. Impacts of Low Temperature and Ensiling Period on the Bacterial Community of Oat Silage by SMRT. Microorganisms 2021, 9, 274. 

6.      Tao Liu, Yutong Cui, Xuli Jia, Jing Zhang, Ruoran Li, Yahui Yu, Shangang Jia, Jiangyong Qu, Xumin Wang. OGDA: a comprehensive organelle genome database for algae. Database, 2020, 2020: baaa097. 

7.      Yinyin Weng, Lingqiao Ge, Shangang Jia, Peisheng Mao, Xiqing Ma. Cyclophilin AtROC1S58F confers Arabidopsis cold tolerance by modulating jasmonic acid signaling and antioxidant metabolism. Plant Physiology and Biochemistry, 2020, 152: 81-89. 

8.      Junmei Kang, Huiting Cui, Shangang Jia, Wenwen Liu, Renjie Yu, Zhihai Wu, & Zhen Wang. Arabidopsis thaliana MLK3, a plant-specific casein kinase 1, nNegatively regulates flowering and phosphorylates histone H3 in vitro. Genes, 2020, 11(3): 345. 

9.      Hang Cheng, Xiqing Ma, Shangang Jia, Manli Li, Peisheng Mao. Transcriptomic analysis reveals the changes of energy production and AsA-GSH cycle in oat embryos during seed ageing. Plant Physiology and Biochemistry, 2020, 153: 40-52.

10.   Huifang Yan, Shangang Jia, Peisheng Mao. Melatonin priming alleviates ageing-induced germination inhibition by regulating β-oxidation, protein translation and antioxidant metabolism in oat (Avena sativa L.) seeds. International Journal of Molecular Sciences, 2020, 21(5): 1898. 

11.   Yahui Yu, Jing Zhang, Shangang Jia, Guoliang Wang, Tao Liu, & Xumin Wang. The complete mitogenome of three continuous generations of ‘Rongfu’: a crucial Saccharina cultivation variety. Mitochondrial DNA Part B, 2019, 4(1): 744-745. 

12.   Aixia Li, Shangang Jia, Abou Yobi, Zhengxiang Ge, Shirley Sato, Chi Zhang, Ruthie Angelovici, Tom Clemente, and David Holding. Increased digestibility and protein quality sorghum through editing of an alpha-kafirin gene family. Plant Physiology, 2018, 177: 1425-1438. 

13.   Darshan Bara, Bruce I. Dvorak, David Admiraal, Shangang Jia, Chi Zhang and Xu Li. Tracking the sources of antibiotic resistance genes in an urban stream during wet weather using shotgun metagenomic analyses. Environmental Science & Technology, 2018, 52(16): 9033-9044. 

14.   Paridhi Gulati, Shangang Jia, Aixia Li, David Holding, Dipak Santra, Devin J. Rose. In vitro protein digestibility of cooked proso millet (Pancium miliaceum L.) cultivars and related species from around the world. Journal of Agricultural and Food Chemistry, 2018, 66(27): 7156-7164. 

15.   Kan Liu, Shangang Jia, Qian Du, Chi Zhang. NanoAsPipe: A transcriptome analysis and alternative splicing detection pipeline for MinION long-read RNA-seq. 2017 IEEE International Conference on Bioinformatics and Biomedicine-BIBM, 2017, Kansas City, MI, pp. 1823-1826

16.   Kyla Morton, Shangang Jia, Chi Zhang, David Holding. Proteomic profiling of maize opaque endosperm mutants reveals selective accumulation of lysine-enriched proteins. Journal of Experimental Botany, 2015, 67(5): 1381-1396. 

17.   Ibrahim S. Al-Mssallem, Songnian Hu, Xiaowei Zhang, ……, ShangangJia, ……, & Jun Yu. Genome sequence of the date palm Phoenix dactylifera L. Nature Communications, 2013, 4: 2274. 

18.   An Yin, Linlin Pan, Xiaowei Zhangm Lei Wang, Yuxin Yin, Shangang Jia, Wanfei Liu, Chengqi Xin, Kan Liu, Xiaoguang Yu, Gaoyuan Sun, Khalid Al-hudaib, Songnian Hu, Ibrahim S. Al-Mssallem, Jun Yu. A transcriptomic study of the red palm weevil Rhynchophorus ferrugineus embryogenesis. Insect Science, 2013, 22: 65-82. 

19.   Lei Wang, Xiaowei Zhang, Linlin Pan, Wanfei Liu, Dapeng Wang, Guangyu Zhang, Yuxin Yin, An Yin, Shangang Jia, Xiaoguang Yu, Gaoyuan Sun, Songnian Hu, Ibrahim S. Al-Mssallem, Jun Yu. A large‐scale gene discovery for the red palm weevil Rhynchophorus ferrugineus (Coleoptera: Curculionidae). Insect Science, 2013, 20: 689-702. 

20.   Li Zhang, Xiujuan Xie, Shangang Jia, Mei Xiao, Shudai Lin, Lilong An, Wen Luo, Xinzheng Jia, Qinghua Nie, Xiquan Zhang. Characterization of microRNA * species in Peking duck skin. Journal of Integrative Agriculture, 2013, 12: 1614-1619.

21.   Guixiang Zhang, Youmin Zheng, Zhigang Wang, Xu Han, Shangang Jia, & Hong Chen. Genetic diversity and origin of mitochondria DNA D-loop region of some Chinese indigenous cattle breeds. Hereditas, 2009, 31: 160-168.

22.   Jian Li, Fei Gao, Ning Li, Shengting Li, Guangliang Yin, Geng Tian, Shangang Jia, Kai Wang, Xiuqing Zhang, Huanming Yang, Anders Lade Nielsen & Lars Bolund. An improved method for genome wide DNA methylation profiling correlated to transcription and genomic instability in two breast cancer cell lines. BMC Genomics, 2009, 10: 223. 

23.   Qingrun Zhang, Guanghua Wu, Elliott Richards, Shan'gang Jia & Changqing Zeng. Universal primers for HBV genome DNA amplification across subtypes: a case study for designing more effective viral primers. Virology Journal, 2007, 4: 92. 


(B) Book Chapters

Shangang Jia, Aixia Li, Chi Zhang and David Holding (2017). Deletion mutagenesis and identification of causative mutations in maize. pp. 97-108 in Methods in Molecular Biology. Humana Press, New York.

Teaching Experience

1. “Genomics in grass”, for undergraduate students

2. “Introduction of bioinformatics in grass plant”, for master students

3. Be involved in the courses of “Scientific literature reading & writing in grassland field”, “Forage and turfgrass seeds” and “Modern grass production” for undergraduate students; “Seeds science and technology in forage and turf grass” for master students, and the course of “The progress of seed science” for PhD students.

Teaching research

Social Position

Dynamic activity

Field

Open Course

Project

Thesis

Achievements

The software works Patent

Honor

Enrollment

Enrollment in previous years Application intention

Post：

Duties：

Degree：

Tel： 010-62731451

Email： shangang.jia@cau.edu.cn

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