Dr. Xuewen Wang, PhD - Kunming Institute of Botany, CAS. University of Georgia - Research Scientist

Dr. Xuewen Wang

PhD

Kunming Institute of Botany, CAS. University of Georgia

Research Scientist

Kunming, Yunnan | China P. R.

Main Specialties: Biology

Additional Specialties: genomics, genetics and bioinformatics

Dr. Xuewen Wang, PhD - Kunming Institute of Botany, CAS. University of Georgia - Research Scientist

Dr. Xuewen Wang

PhD

Introduction

He was born and grown up in Hunan province, China. As ranked the top No. 1 high school student at university entry examination, he went to Peking University, the best university in China. He obtained his bachelor degree and Master of Science majored in biology in Peking University. He conducted his postdoc research in University of Georgia during 2008-2012, mainly in the genomes of various energy plants, genetic breeding and bioinformatics research after completing his PhD in 2008 from King’s College London, University of London, majored in molecular genetics. After back to China in 2012 March, he started his career as a leading scientist and director in China Tobacco Gene Research Center, a department of Chinese National Tobacco Monopoly Administration, responsible for Chinese tobacco bioinformatics platform, focusing on tobacco genome sequencing, genetics and bioinformatics research. Since April 2013, he has been working as a leading scientist and group leader for Bennetzen's group in Kunming Institute of Botany (KIB), Chinese Academy of Sciences in China. In 2015 January, he started his senior postdoc in University of Georgia at Bennetzen lab in department of genetics.

Currently, he and his colleagues focus on the studies of the whole genome composition, transcriptome profile and genetic variation of several species of economic importance using advanced Next Generation Sequencing (NGS) technologies and bioinformatics. His research will reveal what the entire genome sequences are, how genes function to determine important crop traits, and how to use the information for molecular breeding.

He has completed or participated in some projects including a Chinese national foreign 1000 plan talent project, 3 US national research projects , 1 US National Science Foundation project, 1 royal society project, 2 Chinese NSFC projects, 1 Education Commission project of Hunan Province, 1 State Tobacco Monopoly Administration project of tobacco genome bioinformatics analysis in 2012, presiding 1 Hunan Poverty alleviation project and 1 XTU research project, 4 national bioinformatics software licensed (the first author signature). He gained multimedia teaching awards from Hunan Province and from XTU respectively, published more than 5 high level of SCI in recent years (with the highest IF 31 as coauthor and the highest IF greater than 5.0 as the first author). He attended dozens of the international academic conference and gave many oral report several. Some of his research papers were published in journals Nature biotechnology, Journal of experimental botany, Development, Bioenergy research, G3 Genes|genomes|genetics and so on. Several articles published were cited by the top academic journals of the world, as Nature genetics, Genome biology, Nature reviews genetics, Current Opinion in Plant biology and so on. He is also a reviewer of international academic journals Journal of experimental botany, plant signaling & behavior, Gene, Molecular Biology Reports, Bioinformatics, BMC Genomics, Plant Diversity, Frontiers in bioinformatics, Frontiers in genetics and Chinese academic journals of Hereditas, biochemistry and Molecular Biology and so on. He is an editor of several international academic journals called Plant Diversity, Frontiers in bioinformatics, Frontiers in genetics.

He is an academic member of Genetic Society of America (GSA), US Bioenergy Science Center (BESC), Society of Experiment Biology (SEB), the International Genetic Association, Chinese Genetic Society, and is a committee member of Chinese Genome Council.
Research interests and undergoing projects:
Research interests are using molecular biology, genomics and bioinformatics to reveal genomic information, transcriptome profile, genetic diversity of germplasm resources of plant species, aiming at deeply disclosing the whole genome sequence information, profiling genes’ expression at the whole genome level and its relationship with the development or important economic traits, providing software and tools such as molecular markers, genetics map for molecular breeding and crop improvement. The research is collaborating closely with the University of Georgia, domestic research institutes and universities. The main researches of interests are listed in the following aspects:
1) Whole genome research
Genome is the entire set of hereditary instructions for building, running, and maintaining an organism, and passing life on to the next generation. Genomics is the study or knowledge of all genomes.

His research interests focus on revealing genome sequence composition, evolution, and diversity of the economically important, scientifically significant species. We have completed the reference genome of foxtail millet published in Nature Biotechnology, 2011. There are several undergoing genomes of crops including Setaria Italica, Eragrestis tef, wheat (Triticum aestivum, Chinese Spring), bamboo (Bambusoideae), and some important plants originated from China, including Camellia Sinensis (drink tea), Camellia Oleifera (oil tea) and Ginkgo biloba.

2) Transcriptome research
Crop traits and responses under different developing stage and various environments are controlled by gene activity namely gene expression.
He is interested in the relationships between gene expression and quality traits at while transcriptomic level. For example, the quality of Camellia Sinensis (drink tea) is associated with the development of the leaves, He is studying on which genes determine the quality of the tea. He will investigate the perspective of genome-wide transcriptome profile plus metabolites to discover the secret of the relationship. Another example is how homoeologous gene functions in a polyploidy (multiple genomes) species. One project of that is which homoeologous genes will be play major role in the process of drought stress in hexaploid wheat with three genomes.

3) Molecular breeding research
Molecular breeding would fundamentally improve the yield and quality of crops. He use the most advanced genotyping technology to score genotypes in crossing populations, natural populations and to conduct genetic variation analysis, to rapidly construct a genetic map and association analysis, to locate the genes’ region responsible for traits and to develop large-scale of molecular markers for breeding. He developed a series of technologies and software for speeding the development of a large number of SSR and SNP molecular markers or variation at very low cost in a short time, to provide direct application tools for germplasm resources and molecular breeding.

4) Bioinformatics research
Bioinformatics technology is a powerful tool in the research of genomics, transcriptomics and molecular breeding. He has a rich experience in professional NGS data analysis and related software development. Some results of NGS analysis are published and referenced in the world top famous academic journals. Four bioinformatics software programmed by him are registered and licensed by Chinese Copyright Administration, such as GMATA, a comprehensive software package for the development of molecular markers at whole genome level.

Primary Affiliation: Kunming Institute of Botany, CAS. University of Georgia - Kunming, Yunnan , China P. R.

Specialties:

Additional Specialties:

Publications

22Publications

269Reads

1Profile Views

395PubMed Central Citations

GMATA: An Integrated Software Package for Genome-Scale SSR Mining, Marker Development and Viewing.

Authors:
Xuewen Wang Le Wang

Front Plant Sci 2016 13;7:1350. Epub 2016 Sep 13.

Key Laboratory of Forensic Genetics and Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Ministry of Public Security Beijing, China.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5020087PMC
http://dx.doi.org/10.3389/fpls.2016.01350DOI Listing
September 2016
21 Reads
9 Citations
3.640 Impact Factor

Using in silico techniques: Isolation and characterization of an insect cuticle-degrading-protease gene from Beauveria bassiana.

Microb Pathog 2016 Aug 8;97:189-97. Epub 2016 Jun 8.

World Agroforestry Centre, East and Central Asia Office, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Rd, Heilongtan, Kunming 650201, Yunnan, China.

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http://dx.doi.org/10.1016/j.micpath.2016.05.024DOI Listing
August 2016
29 Reads
2.000 Impact Factor

GMATA: An Integrated Software Package for Genome-Scale SSR Mining, Marker Development and Viewing

Frontiers in Plant Science. 2016 Augl 7:1350

Frontiers in Plant Science

Simple sequence repeats (SSRs), also referred to as microsatellites, are highly variable tandem DNAs that are widely used as genetic markers. The increasing availability of whole-genome and transcript sequences provides information resources for SSR marker development. However, efficient software is required to efficiently identify and display SSR information along with other gene features at a genome scale. We developed novel software package Genome-wide Microsatellite Analyzing Tool Package (GMATA) integrating SSR mining, statistical analysis and plotting, marker design, polymorphism screening and marker transferability, and enabled simultaneously display SSR markers with other genome features. GMATA applies novel strategies for SSR analysis and primer design in large genomes, which allows GMATA to perform faster calculation and provides more accurate results than existing tools. Our package is also capable of processing DNA sequences of any size on a standard computer. GMATA is user friendly, only requires mouse clicks or types inputs on the command line, and is executable in multiple computing platforms. We demonstrated the application of GMATA in plants genomes and reveal a novel distribution pattern of SSRs in 15 grass genomes. The most abundant motifs are dimer GA/TC, the A/T monomer and the GCG/CGC trimer, rather than the rich G/C content in DNA sequence. We also revealed that SSR count is a linear to the chromosome length in fully assembled grass genomes. GMATA represents a powerful application tool that facilitates genomic sequence analyses. GAMTA is freely available at http://sourceforge.net/projects/gmata/?source=navbar.

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August 2016
5 Reads

DRACULA2 is a dynamic nucleoporin with a role in regulating the shade avoidance syndrome in Arabidopsis.

Development 2016 05 17;143(9):1623-31. Epub 2016 Mar 17.

Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, 08193 Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Ps. Lluís Companys 10, 08010 Barcelona, Spain

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http://dx.doi.org/10.1242/dev.130211DOI Listing
May 2016
21 Reads
1 Citation
6.462 Impact Factor

Characterization of genome-wide variation in Four-row Wax, a waxy maize landrace with a reduced kernel row phenotype

Front. Plant Sci. | doi: 10.3389/fpls.2016.00667

Frontiers in Plant Science

In southwest China, some maize landraces have long been isolated geographically, and have phenotypes that differ from those of widely grown cultivars. These landraces may harbor rich genetic variation responsible for those phenotypes. Four-row Wax is one such landrace, with four rows of kernels on the cob. We resequenced the genome of Four-row Wax, obtaining 50.46 Gb sequence at 21.87× coverage, then identified and characterized 3,252,194 SNPs, 213,181 short InDels (1-5 bp) and 39,631 structural variations (greater than 5 bp). Of those, 312,511 (9.6% of) SNPs were novel compared to the most detailed haplotype map (HapMap) SNP database of maize. Characterization of variations in reported kernel row number (KRN) related genes and KRN QTL regions revealed potential causal mutations in fea2, td1, kn1 and te1. Genome-wide comparisons revealed abundant genetic variations in Four-row Wax, which may be associated with environmental adaptation. The sequence and SNP variations described here enrich genetic resources of maize, and provide guidance into study of seed numbers for crop yield improvement.

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May 2016
5 Reads

Current status and prospects for the study of Nicotiana genomics, genetics, and nicotine biosynthesis genes

Molecular Genetics and Genomics 2015 Jan 13; 290(1) 1-11

Molecular Genetics and Genomics

Nicotiana, a member of the Solanaceae family, is one of the most important research model plants, and of high agricultural and economic value worldwide. To better understand the substantial and rapid research progress with Nicotiana in recent years, its genomics, genetics, and nicotine gene studies are summarized, with useful web links. Several important genetic maps, including a high-density map of N. tabacum consisting of ~2,000 markers published in 2012, provide tools for genetics research. Four whole genome sequences are from allotetraploid species, including N. benthamiana in 2012, and three N. tabacum cultivars (TN90, K326, and BX) in 2014. Three whole genome sequences are from diploids, including progenitors N. sylvestris and N. tomentosiformis in 2013 and N. otophora in 2014. These and additional studies provide numerous insights into genome evolution after polyploidization, including changes in gene composition and transcriptome expression in N. tabacum. The major genes involved in the nicotine biosynthetic pathway have been identified and the genetic basis of the differences in nicotine levels among Nicotiana species has been revealed. In addition, other progress on chloroplast, mitochondrial, and NCBI-registered projects on Nicotiana are discussed. The challenges and prospects for genomic, genetic and application research are addressed. Hence, this review provides important resources and guidance for current and future research and application in Nicotiana.

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January 2015
3 Reads

Linkage maps of lowland and upland tetraploid switchgrass ecotypes

BioEnergy Research Serba 6 (3), 953-965

BioEnergy Research

Switchgrass (Panicum virgatum L.) is a native perennial warm season (C4) grass that has been identified as a promising species for bioenergy research and production. Consequently, biomass yield and feedstock quality improvements are high priorities for switchgrass research. The objective of this study was to develop a switchgrass genetic linkage map using a full-sib pseudo-testcross mapping population derived from a cross between two heterozygous genotypes selected from the lowland cultivar ‘Alamo’ (AP13) and the upland cultivar ‘Summer’ (VS16). The female parent (AP13) map consists of 515 loci in 18 linkage groups (LGs) and spans 1,733 cM. The male parent (VS16) map arranges 363 loci in 17 LGs and spans 1,508 cM. No obvious cause for the lack of one LG in VS16 could be identified. Comparative analyses between the AP13 and VS16 maps showed that the two major ecotypic classes of switchgrass have highly colinear maps with similar recombination rates, suggesting that chromosomal exchange between the two ecotypes should be able to occur freely. The AP13 and VS16 maps are also highly similar with respect to marker orders and recombination levels to previously published switchgrass maps. The genetic maps will be used to identify quantitative trait loci associated with biomass and quality traits. The AP13 genotype was used for the whole genome-sequencing project and the map will thus also provide a tool for the anchoring of the switchgrass genome assembly.

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September 2013
11 Reads

GMATo: A novel tool for the identification and analysis of microsatellites in large genomes.

Bioinformation 2013 8;9(10):541-4. Epub 2013 Jun 8.

China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute, NO.2 Fengyang Street, Hi-tech zone, Zhengzhou 450001, China.

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http://dx.doi.org/10.6026/97320630009541DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3705631PMC
July 2013
11 Reads
22 Citations

Genetic control and comparative genomic analysis of flowering time in Setaria (Poaceae).

G3 (Bethesda) 2013 Feb 1;3(2):283-95. Epub 2013 Feb 1.

Department of Botany, Oklahoma State University, Stillwater, Oklahoma 74078, USA.

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http://dx.doi.org/10.1534/g3.112.005207DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3564988PMC
February 2013
7 Reads
22 Citations
2.511 Impact Factor

A novel high-throughput in vivo molecular screen for shade avoidance mutants identifies a novel phyA mutation.

J Exp Bot 2011 May 11;62(8):2973-87. Epub 2011 Mar 11.

School of Biological Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK.

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http://dx.doi.org/10.1093/jxb/err062DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3202935PMC
May 2011
3 Reads
6 Citations
5.530 Impact Factor

Sex differences in lipid and lipoprotein metabolism: it's not just about sex hormones.

J Clin Endocrinol Metab 2011 Apr;96(4):885-93

Center for Human Nutrition, Washington University School of Medicine, St Louis, Missouri 63110, USA.

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http://dx.doi.org/10.1210/jc.2010-2061DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070248PMC
April 2011
3 Reads
60 Citations
6.210 Impact Factor

Television viewing, computer use, and BMI among U.S. children and adolescents.

J Phys Act Health 2009 ;6 Suppl 1:S28-35

Division of Nutrition, Physical Activity, and Obesity, Centers for Disease Control and Prevention, Atlanta, GA, USA.

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January 2010
5 Reads
26 Citations

Resting energy expenditure changes with weight loss: racial differences.

Obesity (Silver Spring) 2010 Jan 28;18(1):86-91. Epub 2009 May 28.

Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA.

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http://dx.doi.org/10.1038/oby.2009.163DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2798012PMC
January 2010
7 Reads
6 Citations
3.734 Impact Factor

Visible light responsive nitrogen doped anatase TiO2 sheets with dominant {001} facets derived from TiN.

J Am Chem Soc 2009 Sep;131(36):12868-9

Shenyang National Laboratory for Materials Science, Institute of Metal Research, Chinese Academy of Sciences, 72 Wenhua RD, Shenyang 110016, China.

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http://dx.doi.org/10.1021/ja903463qDOI Listing
September 2009
56 Reads
9 Citations
12.113 Impact Factor

Anomalously large anisotropic magnetoresistance in a perovskite manganite.

Proc Natl Acad Sci U S A 2009 Aug 11;106(34):14224-9. Epub 2009 Aug 11.

Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, Zhejiang 315201, People's Republic of China.

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http://dx.doi.org/10.1073/pnas.0907618106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2725015PMC
August 2009
5 Reads
1 Citation
9.810 Impact Factor

Enhanced photocatalytic hydrogen evolution by prolonging the lifetime of carriers in ZnO/CdS heterostructures.

Chem Commun (Camb) 2009 Jun 6(23):3452-4. Epub 2009 May 6.

Shenyang National Laboratory for Materials Science, Institute of Metal Research, Chinese Academy of Sciences, 72 Wenhua Road, Shenyang 110016, P. R. China.

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http://dx.doi.org/10.1039/b904668bDOI Listing
June 2009
15 Reads
6 Citations
6.834 Impact Factor

Drastically enhanced photocatalytic activity in nitrogen doped mesoporous TiO2 with abundant surface states.

J Colloid Interface Sci 2009 Jun 2;334(2):171-5. Epub 2009 Apr 2.

Shenyang National Laboratory for Materials Science, Institute of Metal Research, Chinese Academy of Sciences, 72 Wenhua Road, Shenyang 110016, PR China.

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http://dx.doi.org/10.1016/j.jcis.2009.02.047DOI Listing
June 2009
7 Reads
2 Citations
3.370 Impact Factor

Effect of exercise intensity on abdominal fat loss during calorie restriction in overweight and obese postmenopausal women: a randomized, controlled trial.

Am J Clin Nutr 2009 Apr 11;89(4):1043-52. Epub 2009 Feb 11.

Section on Gerontology and Geriatric Medicine, J Paul Sticht Center on Aging, Department of Internal Medicine, Wake Forest University Health Sciences, Winston-Salem, NC 27157, USA.

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http://dx.doi.org/10.3945/ajcn.2008.26938DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2667455PMC
April 2009
31 Reads
53 Citations
6.770 Impact Factor

Fabrication of a nanocomposite from in situ iron nanoparticle reinforced copper alloy.

Nanotechnology 2009 Feb 26;20(7):075605. Epub 2009 Jan 26.

School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing, People's Republic of China.

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http://dx.doi.org/10.1088/0957-4484/20/7/075605DOI Listing
February 2009
4 Reads
1 Citation
3.821 Impact Factor

The role of crystal phase in determining photocatalytic activity of nitrogen doped TiO2.

J Colloid Interface Sci 2009 Jan 27;329(2):331-8. Epub 2008 Sep 27.

Shenyang National Laboratory for Materials Science, Institute of Metal Research, Chinese Academy of Sciences, 72 Wenhua Road, Shenyang 110016, China.

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http://dx.doi.org/10.1016/j.jcis.2008.09.061DOI Listing
January 2009
12 Reads
3.370 Impact Factor

Energetics of the dipole flip-flop motion in a ferroelectric polymer chain.

J Chem Phys 2007 Mar;126(12):124908

Department of Physics, Florida International University, Miami, Florida 33199, USA.

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http://dx.doi.org/10.1063/1.2646731DOI Listing
March 2007
5 Reads
1 Citation
2.952 Impact Factor

Top co-authors

Gang Liu
Gang Liu

Peking Union Medical College Hospital

4
Paul F Devlin
Paul F Devlin

School of Biological Sciences

2
Tongjian You
Tongjian You

College of Nursing and Health Sciences

2
Feng Li
Feng Li

Tongji Hospital

2
Jiandi Zhang
Jiandi Zhang

Louisiana State University

2
Thomas P Brutnell
Thomas P Brutnell

Donald Danforth Plant Science Center

2
Leon Lenchik
Leon Lenchik

Wake Forest School of Medicine

2