College of Grassland Science and Technology
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 grass, 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. 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, in press, doi:10.1093/jxb/eraa325
2. 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. (one of correspondence authors)
3. Yi Xiong, Yanli Xiong, Shangang Jia*, Xiao Ma*. The complete chloroplast genome sequences of two Phalaris species reveal divergence among ploidies/species. Plants, 2020, 9: 748. (one of correspondence authors)
4. 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
5. 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. (co-first author)
6. 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. (one of correspondence authors)
7. 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.
8. 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.
9. Shangang Jia, Aixia Li, Kyla Morton, Penny Avoles-Kianian, Shahryar F. Kianian, Chi Zhang and David Holding. A population of deletion mutants and an integrated mapping and exome-seq pipeline for gene discovery in maize. G3, 2016, 6: 1-11.
10. 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. (Co-first author)
11. 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. (Co-first author)
12. 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.
13. 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.
14. 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.
15. 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.
16. 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.
17. 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:
18. 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.
19. 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.
20. 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.
21. 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.
22. 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.
23. 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.
24. 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.
25. 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.
26. 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.
27. Ibrahim S. Al-Mssallem, Songnian Hu, Xiaowei Zhang, ……, Shangang Jia, ……, & Jun Yu. Genome sequence of the date palm Phoenix dactylifera L. Nature Communications, 2013, 4: 2274.
28. 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.
29. 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.
30. 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.
31. 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.
32. 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.
33. Qingrun Zhang, Guanghua Wu, Elliott Richards, Shangang 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 course of “Seeds science and technology in forage and turf grass” for master students, and the course of “The progress of seed science” for PhD students.