Faculty and Staff

HU Songnian
E-mail:husn(AT)big.ac.cn

Introduction

Major Research: Genomics, Molecular Biology and Molecular Genetics

1. Genomics

We perform whole genome sequence, including sequencing, assembling, finishing and so on. We also analysis the composing and structure of the whole genome. Now we mainly focused on Microbial Genomes and re-sequencing of important genome such as human, rice and so on.

2. Functional Genomics

We mainly focused on gene expression, regulation in the genome level, gene associated information reorganization and identification and genome diversity and compare.

3. Transcriptomics

We performed comprehensive transcriptomic study both by traditional way, such as EST, SAGE and so on, and new way based on new generation sequencing (Solid), mainly focused on detecting and compare of the transcriptome. For example, we performed a study on the molecular mechanism of heterosis. Based on the compare analysis between F1 and parental line, we detected a lot of heterosis associated genes and analyzed the expression pattern of them which provide us a global view of heterosis associated genes and laid data foundation for further study.

4. Bioinformatics

The development and improvement of bioinformatic tools and construction of associated databases. For example, in the research of genetic molecular mechanism of heterosis, this group mainly adopt bioinformatics methods: improve analysis methods of transcriptome data、mining、 integrating and using network theory study the heherosis molecular mechanism. Now, they have finished improving the SAGE mapping methods and constructed the “HRGD” database.

5. Others

1.MicroRNAs and their functions

The group of microRNA research is focus on miRNAomics in different species, including Trichomonas vaginalis, Apis mellifera, Tribolium castaneum and Bombyx mori. We discovered miRNAs in Protozoa (Trichomonas vaginalis) for the first time using a computational and experimental combined approach. In the miRNA research of Tribolium castaneum and Bombyx mori, we developed an elaborate computational protocol for prediction of insects’miRNA and an effective method for identification of miRNA. Taking a combined approach, we identified 118 conserved miRNAs and 151 novel miRNA candidates from the silkworm genome sequence, the expression pattern shows that molting stages is hotspots of miRNA expression both in sorts and quantities.

2. Data mining of the epigenomics data

Along with the development of the 2rd sequencing technology, we got a great of histone and DNA methylation modification data, e.g. human 20 histone modification profile、the comparative modification profile of human and mouse and so on. How to integrate and mining these raw data? We will construct compute models using data mining tools; propose the hypotheses of the relationship between epigenetic modification and gene expression.

 

Group Leader

Prof. HU Songnian received his Ph.D degree in Plant Molecular Biology from China Agricultural University in 1996. He became the program director and main participator of International Human Genome Projects—Beijing region at BGI in 1999, set up the largest genome sequencing platform in China. In 2001, he lead the team to successfully finish the draft sequence of rice genome (Oryza sativa L. ssp. indica) within 50 days and made major innovations in reducing the sequencing cost and increasing the efficiency. he was awarded “Outstanding Scientific and Technology achievement award for a research group” of Qiu Shi Scientific and Technology Foundation in 2002 and “Outstanding Scientific and Technology achievement award for a research group” of Chinese Academy of Sciences in 2003 due to his standout contribution to “Human Genome Project for China Region”, “China Super Hybrid Rice Genome Project”, and the excellent behavior in setting up large-scale DNA sequencing platform. He has also participated other genome projects carried out at BIG such as “Sino-Danish Porcine Genome Project”, silkworm genome project and chicken genome variation mapping project. He has published more than 60 papers, two monographs and participated in another two monographs.

 

Recent Progress:

  Identification and analysis of mouse non-coding RNA using transcriptome data 

Transcripts are expressed spatially and temporally and they are very complicated, precise and specific; however, most studies are focused on protein-coding related genes. Recently, massively parallel cDNA sequencing (RNA-seq) has emerged to be a new and promising tool for transcriptome research, and numbers of non-coding RNAs (ncRNAs), especially long intergenic non-coding RNAs (lincRNAs), have been widely identified and well characterized as important regulator of diverse biological processes. In this study, we obtained ultra-deep RNA-seq data of 15 mouse tissues and these data gave us the opportunity to study the diversity and dynamic of ncRNA deeply in mouse. Using our developed workflow, we totally identified 16,280 ncRNA genes in mouse. We annotated these ncRNAs by diverse properties and found ncRNAs are generally shorter, have fewer exons, express in lower level and are more strikingly tissue-specific compared with protein-coding genes. Moreover, these ncRNAs show significant enrichments with transcriptional initiation and elongation signals including histone modifications (H3K4me3, H3K27me3 and H3K36me3), RNAPII binding sites and CAGE tags. The Gene Set Enrichment Analysis (GESA) revealed several sets of lincRNAs associated with diverse biological processes such as immune effector process, muscle development and sexual reproduction etc. Taken together, this study provides a new annotation of mouse non-coding genes and gives an opportunity for future functional and evolutionary study of mouse ncRNAs.

The basic genomic features of non-coding genes compared with protein-coding genes. (a) Exon number comparison.(b) Gene length comparison.(c).The expression breadth.(d) The expression dynamics across different tissues.

 

Representative Publications

1. *Al-Mssallem, Ibrahim S.; *Hu, Songnian; Zhang, Xiaowei; Lin, Qiang; Liu, Wanfei; Tan, Jun; Yu,Xiaoguang; Liu, Jiucheng; Pan, Linlin; Zhang, Tongwu; Yin, Yuxin; Xin, Chengqi…… .(2013)Genome sequence of the date palm Phoenix dactylifera L .Nature Communications, pp 1-9.

2. Yu, Lu-jun; Luo, Ying-feng; Liao, Bin; Xie, Li-juan; Chen, Liang; Xiao, Shi; Li, Jin-tian; *Hu,Song-nian; *Shu, Wen-sheng ,(2012)Comparative transcriptome analysis of transporters, phytohormone and lipid metabolism pathways in response to arsenic stress in rice (Oryza sativa) .New Phytologist, pp97-112.

3. Zhang, Huangkai; Gao, Shenghan; Martin, J. Lercher; *Hu, Songnian; Chen, Wei-Hua . (2012)EvolView, an online tool for visualizing, annotating and managing phylogenetic trees ,Nucleic Acids Research. pp 569-572.

4. Zhou, Q.; Yu, X. M.; Lin, H. B.; Wang, L.; Yun, Q. Z.; *Hu, S. N.; Wang, D-M . (2009)Genetic polymorphism, linkage disequilibrium, haplotype structure and novel allele analysis of CYP2C19 and CYP2D6 in Han Chinese .The Pharmacogenomics Journal. pp 380-394

5. Zhao, Wenming; Liu, Wanfei; Tian, Dongmei; Tang, Bixia; Wang, Yanqing; Yu, Caixia; Li, Rujiao; Ling,Yunchao; Wu, Jiayan; *Song, Shuhui; *Hu, Songnian . (2011)wapRNA: a web-based application for the processing of RNA sequences .Bioinformatics. pp 3076-3077.

 

Other Publications

1. Pang, Zhiqian; Zhou, Zhuangzhi; Yin, Dedong; Lv, Qiming; Wang, Lixiang; Xu, Xiao; Wang, Jing; Li,Xiaobing; Zhao, Xianfeng; Jiang, Guanghuai; Lan, Jinping; *Zhu, Lihuang…… . (2013)Transgenic rice plants overexpressing BBTI4 confer partial but broad-spectrum bacterial blight resistance .Journal of Plant Biology. pp 383-390.

2. Hai Wang; Haiyan Hu; Qian Zhang; Yadong Yang; Yanming Li; Yang Hu;Xiuyan Ruan; Yaran Yang; Zhaojun Zhang; Chang Shu; Jiangwei Yan; Edward K.Wakeland; Quanzhen Li; *Songnian Hu; Xiangdong Fang . (2013)Dynamic transcriptomes of human myeloid leukemia cells.Genomics.pp 250-256.

3. Liu, Guozheng; Cao, Dandan; Li, Shuangshuang; Su, Aiguo; Geng, Jianing;Grover, Corrinne E.; *Hu, Songnian; Hua, Jinping . (2013)The Complete Mitochondrial Genome of Gossypium hirsutum and Evolutionary Analysis of Higher Plant Mitochondrial Genomes .PLos One.pp 1-15.

4. Ma, Zhe; Geng, Jianing; Yi, Li; Xu, Bin; Jia, Ruoyu; Li, Yue; Meng, Qingshu; *Fan, Hongjie; *Hu,Songnian . (2013)Insight into the specific virulence related genes and toxin-antitoxin virulent pathogenicity islands in swine streptococcosis pathogen Streptococcus equi ssp zooepidemicus strain ATCC35246.BMC Genomics. pp 1-14.

5. Tsai, Isheng J.; Zarowiecki, Magdalena; Holroyd, Nancy; Garciarrubio, Alejandro; Sanchez-Flores,Alejandro; Brooks, Karen L.; Tracey, Alan; Bobes, Raul J.; Fragoso, Gladis; Sciutto, Edda……. (2013)The genomes of four tapeworm species reveal adaptations to parasitism .Nature . pp 57-63.

6. Zhang, Xiujun; Hao, Lili; Meng, Lijun; Liu, Meiling; Zhao, Lina; Hu, Fen; Ding, Cunbao; Wang, Yang; He,Baoling; Pan, Yuxin; Fang, Wei; Chen, Jing; *Hu, Songnian; Jia, Mengchun. (2013)Digital Gene Expression Tag Profiling Analysis of the Gene Expression Patterns Regulating the Early Stage of Mouse Spermatogenesis.PLos One.pp 1-11.

7. He, Lin; Jiang, Hui; Cao, Dandan; Liu, Lihua; Hu, Songnian; *Wang, Qun. (2013)Comparative Transcriptome Analysis of the Accessory Sex Gland and Testis from the Chinese Mitten Crab (Eriocheir sinensis).PLos One.pp 1-13

8. Lina Ma; Linghu Nie; Jing Liu; Bing Zhang; Shuhui Song; Min Sun; Jin Yang; Yadong Yang; Xiangdong Fang;Songnian Hu; Yongliang Zhao; Jun Yu. (2012)An RNA-seq-based Gene Expression Profiling of Radiation-induced Tumorigenic Mammary Epithelial Cells.Genomics Proteomics Bioinformatics.pp 326-335.

9. Chen, Xuan; Hu, Yang; Zheng, Huoqing; Cao, Lianfei; Niu, Defang; Yu,Dongliang; Sun, Yongqiao; *Hu,Songnian; *Hu, Fuliang. (2012)Transcriptome comparison between honey bee queen- and worker-destined larvae.Insect Biochemistry and Molecular Biology. pp 665-673.

10. *Guo, Ai-Jiang; Liu, Kan; Gong, Wei; Luo, Xue-Nong; Yan, Hong-Bin; Zhao, Song-Buo; *Hu, Song-Nian; Jia, Wan-Zhong .Molecular identification of Diphyllobothrium latum and a brief review of diphyllobothriosis in China. Acta Parasitologica.pp 293-296.

11. Han, Jing; Zhang, Fan; Hou, Jing; Liu, Xiaoqing; Li, Ming; Liu, Hailong; Cai, Lei; Zhang, Bing; Chen, Yaping; Zhou, Jian; *Hu, Songnian; *Xiang, Hua . (2012)Complete Genome Sequence of the Metabolically Versatile Halophilic Archaeon Haloferax mediterranei, a Poly(3-Hydroxybutyrate-co-3-Hydroxyvalerate) Producer. Journal of Bacteriology.pp 4463-4464.

12. *Zhang, Tongwu; Hu, Songnian; Zhang, Guangyu; Pan, Linlin; Zhang, Xiaowei; Al-Mssallem, Ibrahim S.; Yu,Jun. (2012)The Organelle Genomes of Hassawi Rice (Oryza sativa L.) and Its Hybrid in Saudi Arabia: Genome Variation, Rearrangement, and Origins. PLos One.2012/7/31.

13. Zhang, Guangyu; Pan, Linlin; Yin, Yuxin; Liu, Wanfei; Huang, Dawei; Zhang, Tongwu; Wang, Lei; Xin, Chengqi; Lin, Qiang; Sun, Gaoyuan; Ba Abdullah, M. M; Zhang, Xiaowei; *Hu, Songnian…. (2012)Large-Scale Collection and Annotation of Gene Models for Date Palm (Phoenix Dactylifera, L). Plant Molecular Biology.pp 521-536.

14. Fang, Yongjun; Wu, Hao; Zhang, Tongwu; Yang, Meng; Yin, Yuxin; Pan, Linlin; Yu, Xiaoguang; *Zhang,Xiaowei; *Hu, Songnian; *Ibrahim S. (2012)Al-Mssallem; *Yu, Jun ,A Complete Sequence and Transcriptomic Analyses of Date Palm (Phoenix dactylifera L.) Mitochondrial Genome. PLos One.

15. Yu, Dongliang; Wang, Yue; Fang, Xu; *Hu, Songnian; *Tang, Petrus; Fu, Yan . (2012)Acquisition of hydrogenosomal presequences: examples from Trichomonas vaginalis .FEMS Microbiology Letters.pp127-131.

16. Peng Cui; Qiang Lin; Feng Ding; *Songnian Hu; Jun Yu. (2012)The Transcript-centric Mutations in Human Genomes.Genomics, Proteomics & Bioinformatics. pp 11-22.

17. Zhang, Tongwu; Fang, Yongjun; Wang, Xumin; Deng, Xin; Zhang, Xiaowei; *Hu, Songnian; Yu, Jun. (2012)The Complete Chloroplast and Mitochondrial Genome Sequences of Boea hygrometrica: Insights into the Evolution of Plant Organellar Genomes.PLos One.

18. Zhang, Tongwu; Zhang, Xiaowei; Hu, Songnian; *Yu, Jun. (2011)An efficient procedure for plant organellar genome assembly, based on whole genome data from the 454 GS FLX sequencing platform.Plant Methods.

  

Group Members

Staff:

Dr.ZHANG Xiaowei, Associate Professor

Dr.LUO Yingfeng, Associate Professor

Dr.GENG Jianing

Dr.GE Xiaomeng

Dr.GAO Shenghan

Ms.TAN Xinyu, Senior Engineer

Graduate Students:

ZHAO Yuhui, 2008

WANG Sen, 2010

WANG Xiliang, 2010

MEI Hailiang, 2010

WEI Ting, 2010

ZENG Jingyao, 2010

HE Zilong, 2011

LIANG Yuan, 2012

CAO Dandan, 2012

ZENG Liping, 2013

LIANG Hao, 2013

WU Shuangyang, 2013