Background: The pig is an economically important food source, amounting to approximately 40% of all meat consumed worldwide. Pigs also serve as an important model organism because of their similarity to humans at the anatomical, physiological and genetic level, making them very useful for studying a variety of human diseases. A pig strain of particular interest is the miniature pig, specifically the Wuzhishan pig (WZSP), as it has been extensively inbred. Its high level of homozygosity offers increased ease for selective breeding for specific traits and a more straightforward understanding of the genetic changes that underlie its biological characteristics. WZSP also serves as a promising means for applications in surgery, tissue engineering, and xenotransplantation. Here, we report the sequencing and analysis of an inbreeding WZSP genome.Results: Our results reveal some unique genomic features, including a relatively high level of homozygosity in the diploid genome, an unusual distribution of heterozygosity, an over-representation of tRNA-derived transposable elements, a small amount of porcine endogenous retrovirus, and a lack of type C retroviruses. In addition, we carried out systematic research on gene evolution, together with a detailed investigation of the counterparts of human drug target genes.Conclusion: Our results provide the opportunity to more clearly define the genomic character of pig, which could enhance our ability to create more useful pig models. © 2012 Fang et al.; licensee BioMed Central Ltd.

Xiaodong Fang    Mou Yulian    Zhiyong Huang    Li Yong    Lijuan Han    Zhang Yanfeng    Yue Feng    Yuanxin Chen    Xuanting Jiang    Wei Zhao    Xiaoqing Sun    Zhiqiang Xiong    Lan Yang    Liu Huan    Dingding Fan    Mao Likai    Ren Lijie    Liu Chuxin    Wang Juan    Kui Li    Wang Guangbiao    Yang Shulin    Liangxue Lai    Guo jie Zhang    Yingrui Li    王俊    Lars Bolund    杨焕明     Jian Wang    Feng Shutang    Songgang Li    Yutao Du   

GigaScience

2012

Background: There is a rapidly increasing amount of de novo genome assembly using next-generation sequencing (NGS) short reads; however, several big challenges remain to be overcome in order for this to be efficient and accurate. SOAPdenovo has been successfully applied to assemble many published genomes, but it still needs improvement in continuity, accuracy and coverage, especially in repeat regions.Findings: To overcome these challenges, we have developed its successor, SOAPdenovo2, which has the advantage of a new algorithm design that reduces memory consumption in graph construction, resolves more repeat regions in contig assembly, increases coverage and length in scaffold construction, improves gap closing, and optimizes for large genome. Conclusions: Benchmark using the Assemblathon1 and GAGE datasets showed that SOAPdenovo2 greatly surpasses its predecessor SOAPdenovo and is competitive to other assemblers on both assembly length and accuracy. We also provide an updated assembly version of the 2008 Asian (YH) genome using SOAPdenovo2. Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp, respectively, which is 3-fold and 50-fold longer than the first published version. The genome coverage increased from 81.16% to 93.91%, and memory consumption was ~2/3 lower during the point of largest memory consumption. © 2012 Luo et al.; licensee BioMed Central Ltd.

Ruibang Luo    Binghang Liu    Yinlong Xie    Zhenyu Li    Huang Weihua    Jianying Yuan    He Guangzhu    Chen Yanxiang    Pan Qi    Liu Yunjie    Tang Jingbo    Wu Gengxiong    Hao Zhang    Yujian Shi    Liu Yong    Chang Yu    Bo Wang    Yao Lu    Han Changlei    David Cheung    Siu ming Yiu    Peng Shaoliang    Xiaoqian Zhu    Liu Guangming    廖湘科    Yingrui Li    杨焕明     Jian Wang    Takwah Lam    王俊   

GigaScience

2012

Yeyang Su    Guo Zhaozheng    杨焕明    

Asian Biotechnology and Development Review

2012

杨焕明    

Prometheus (United Kingdom)

2012

OBJECTIVE: Emerging evidence has shown the association of aberrant microRNA-375 (miR-375) expression with tumourigenesis in many types of human malignancy. This prospective study characterized the contribution of miR-375 to the initiation and progression of nonsmall cell lung cancer (NSCLC). METHODS: The real-time reverse transcription–polymerase chain reaction was used to examine miR-375 levels prospectively in 96 pairs of samples of NSCLC tissue and adjacent noncancerous tissue (> 2 cm from cancer tissue). The relationship between miR-375 levels and clinico pathological features was also explored. RESULTS: MiR-375 was downregulated in 89% (85/96) of NSCLC samples compared with matched noncancerous tissue samples. Decreased miR-375 correlated significantly with advanced disease stage and lymphatic metastasis. Univariate and multivariate Cox proportional hazard regression analyses revealed that underexpression of miR-375 was an unfavourable prognostic factor for overall survival in NSCLC. CONCLUSIONS: This study suggested that miR-375 is a novel prognostic indicator in NSCLC and might be a potential target for diagnosis and gene therapy.

Li    Qingping Jiang    Xia    杨焕明     Chengping Hu   

Journal of International Medical Research

2012

Transitional cell carcinoma (TCC) is the most common type of bladder cancer. Here we sequenced the exomes of nine individuals with TCC and screened all the somatically mutated genes in a prevalence set of 88 additional individuals with TCC with different tumor stages and grades. In our study, we discovered a variety of genes previously unknown to be mutated in TCC. Notably, we identified genetic aberrations of the chromatin remodeling genes (UTX, MLL-MLL3, CREBBP-EP300, NCOR1, ARID1A and CHD6) in 59% of our 97 subjects with TCC. Of these genes, we showed UTX to be altered substantially more frequently in tumors of low stages and grades, highlighting its potential role in the classification and diagnosis of bladder cancer. Our results provide an overview of the genetic basis of TCC and suggest that aberration of chromatin regulation might be a hallmark of bladder cancer. © 2011 Nature America, Inc. All rights reserved.

桂耀庭    Guangwu Guo    Huang Y.    Xueda Hu    Aifa Tang    Gao Shengjie    Renhua Wu    陈超    Xianxin Li    Zhou Liang    Minghui He    Zesong Li    Xiaojuan Sun    Jia Wenlong    Chen Jinnong    Yang Shangming    Zhou Fang-Jian    Xiaokun Zhao    Wan Shengqing    Rui Ye    Chaozhao Liang    Liu Zhisheng    Huang Peide    Liu Chunxiao    Hui Jiang    Wang Yong    Hancheng Zheng    Sun Liang    Liu Xingwang    Zhimao Jiang    Feng Dafei    Jing Chen    Wu Song    Zou Jing    Zhang Zhongfu    Yang Ruilin    Zhao Jun    Xu Congjie    Yin Weihua    Guan Zhichen    Jiongxian Ye    Hongjiang Zhang    Jingxiang Li    Karsten Kristiansen    Nickerson Michael L.    Dan Theodorescu    李英睿    Xiuqing Zhang    Songgang Li    汪建    杨焕明     王军    Zhiming Cai   

Nature Genetics

2011

Germline inactivating mutations of the breast cancer associated gene 1 (BRCA1) predispose to breast cancer and account for most cases of familiar breast and/or ovarian cancer. The pig is an excellent model for medical research as well as testing of new methods and drugs for disease prevention and treatment. We have generated cloned BRCA1 knockout (KO) Yucatan miniature piglets by targeting exon 11 using recombinant adeno-associated virus (rAAV)-mediated gene targeting and somatic cell nuclear transfer by Handmade Cloning (HMC). We found a very high targeting rate of rAAV-mediated BRCA1 KO. Approximately 35% of the selected cells were BRCA1 targeted. One BRCA1 KO cell clone (5D1), identified by PCR and Southern blot, was used as nuclear donor for HMC. Reconstructed embryos were transferred to three recipient sows which gave birth to 8 piglets in total. Genotyping identified seven piglets as BRCA1 heterozygotes (BRCA1 ), and one as wild type. The BRCA1 expression was decreased at the mRNA level in BRCA1 fibroblasts. However, all BRCA1 piglets died within 18 days after birth. The causes of perinatal mortality remain unclear. Possible explanations may include a combination of the BRCA1 haploinsufficiency, problems of epigenetic reprogramming, presence of the marker gene, single cell clone effects, and/or the special genetic background of the minipigs. © 2010 Springer Science+Business Media B.V.

Luo Yonglun    Li Juan    Liu Ying    Lin Lin    Yutao Du    Shengting Li    杨焕明     Gábor Vajta    Henrik Callesen    Lars Bolund    Sørensen Charlotte B.   

Transgenic Research

2011

Animal breeding via Somatic Cell Nuclear Transfer (SCNT) has enormous potential in agriculture and biomedicine. However, concerns about whether SCNT animals are as healthy or epigenetically normal as conventionally bred ones are raised as the efficiency of cloning by SCNT is much lower than natural breeding or In-vitro fertilization (IVF). Thus, we have conducted a genome-wide gene expression and DNA methylation profiling between phenotypically normal cloned pigs and control pigs in two tissues (muscle and liver), using Affymetrix Porcine expression array as well as modified methylation-specific digital karyotyping (MMSDK) and Solexa sequencing technology. Typical tissue-specific differences with respect to both gene expression and DNA methylation were observed in muscle and liver from cloned as well as control pigs. Gene expression profiles were highly similar between cloned pigs and controls, though a small set of genes showed altered expression. Cloned pigs presented a more different pattern of DNA methylation in unique sequences in both tissues. Especially a small set of genomic sites had different DNA methylation status with a trend towards slightly increased methylation levels in cloned pigs. Molecular network analysis of the genes that contained such differential methylation loci revealed a significant network related to tissue development. In conclusion, our study showed that phenotypically normal cloned pigs were highly similar with normal breeding pigs in their gene expression, but moderate alteration in DNA methylation aspects still exists, especially in certain unique genomic regions. © 2011 Gao et al.

Gao Fei    Luo Yonglun    Shengting Li    Jian Li    Lin Lin    Nielsen Anders Lade    Sørensen Charlotte B.    Gábor Vajta    王军    Xiuqing Zhang    Yutao Du    杨焕明     Lars Bolund   

PLoS ONE

2011

Professor Huanming Yang is co-founder and president of BGI Shenzhen (formally the Beijing Institute of Genomics). BGI made China's contribution to the human genome project. From 1% of the human genome project, it is now a key player in many of the world's megasequencing projects. Professor Yang also has a strong interest in bioethics and society. He is a former member of UNESCO's international bioethics committee and has recently been appointed to President Obama's international research panel of the presidential commission for the study of bioethical issues. © 2011 Copyright Taylor and Francis Group, LLC.

杨焕明    

Prometheus (United Kingdom)

2011

Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2.25 gigabases (Gb)) cover approximately 94% of the whole genome, and the remaining gaps (0.05 Gb) seem to contain carnivore-specific repeats and tandem repeats. Comparisons with the dog and human showed that the panda genome has a lower divergence rate. The assessment of panda genes potentially underlying some of its unique traits indicated that its bamboo diet might be more dependent on its gut microbiome than its own genetic composition. We also identified more than 2.7 million heterozygous single nucleotide polymorphisms in the diploid genome. Our data and analyses provide a foundation for promoting mammalian genetic research, and demonstrate the feasibility for using next-generation sequencing technologies for accurate, cost-effective and rapid de novo assembly of large eukaryotic genomes. © 2010 Macmillan Publishers Limited. All rights reserved.

李瑞强    Wei Fan    Geng Tian    Hongmei Zhu    贺林    Cai Jing    Huang Quanfei    Qingle Cai    Bo li    Bai Yinqi    Zhihe Zhang    张亚平    Wen Wang    Jun Li    魏辅文    Heng Li    Min Jian    Li Jianwen    张兆雷    Rasmus wedel Nielsen    李大伟    Wanjun Gu    Yang Zhentao    Xuan Zhaoling    Oliver Ryder    Leung Frederick Chi-Ching    Yan Zhou    Cao Jianjun    Sun Xiao    Fu Yonggui    Xiaodong Fang    Xiaosen Guo    bo Wang    Rong Hou    Fujun Shen    Mu Bo    Peixiang Ni    Lin Runmao    Qian Wubin    WANG Guo-dong    Chang Yu    Nie Wenhui    Wang Jinhuan    Wu Zhigang    Huiqing Liang    Jiumeng Min    Wu Qi    Shifeng Cheng    Jue Ruan    Wang Mingwei    Shi Zhongbin    Wen Ming    Binghang Liu    Xiaoli Ren    Huisong Zheng    董东    Cook Kathleen    Shan Gao    Hao Zhang    Carolin Kosiol    Xie Xueying    Lu Zuhong    Hancheng Zheng    李英睿    Cynthia Steiner    Tommy tsan yuk Lam    Lin Siyuan    Qinghui Zhang    Guoqing Li    Tian Jing    Gong Timing    Hongde Liu    Zhang Dejin    方林    Chen Ye    Zhang Juanbin    Hu Wenbo    徐安龙    Ren Yuanyuan    Guo jie Zhang    Michael william Bruford    Qibin Li    Lijia Ma    Guo Y.    An Na    Hu Yujie    Zheng Yang    师咏勇    Li Zhiqiang    Liu Qing    Chen Yanling    Zhao Jing    Qu Ning    Shancen Zhao    Tian Feng    Wang Xiaoling    Wang Haiyin    Xu Lizhi    Xiao Liu    Tomáš Vinař    Wang Yajun    Takwah Lam    Siu ming Yiu    Shiping Liu    Hemin Zhang    Li Desheng    Huang Yan    Wang Xia    Yang Guohua    Jiang Zhi    Junyi Wang    Nan Qin    Li Li    Jingxiang Li    Lars Bolund    Karsten Kristiansen    Gane ka shu Wong    Maynard Olson    Xiuqing Zhang    Songgang Li    杨焕明     Wang    Jun Wang   

Nature

2010