Research Interest/Area of Expertise
Our primary research interest is to develop a better understanding of the highly dynamic genomic changes and their corresponding functional consequences. To accomplish this research, we conduct comparative genomic studies using next-generation sequencing, experimental and bioinformatics approaches. Much of our published work has been carried out on bacterial pathogens and eukaryotic mitochondria, and has focused on the exchange of genetic material between more or less distantly related genomes.
We plan to continue the investigation of genome evolution and associated functional consequences in both prokaryotes and eukaryotes.
1) Determine how horizontal gene transfer and homologous recombination change the genome architecture in bacteria and eukaryotic mitochondria.
2) Investigate horizontal transfer and dynamics of antibiotic resistance genes in nature using metagenomics approaches.
3) Investigate the evolution and epidemiology of bacterial pathogens via comparative genomics.
4) Investigate the functional genomics of mitochondrial mutations in yeast
Education – Degrees, Licenses, Certifications
Ph.D. McMaster University
M.Sc. NanKai University
B. Sc. NanKai University
Awards and Grants
Su HJ, Barkman TJ, Hao W, Jones SS, Naumann J, Skippington E, Wafula EK, Hu JM, Palmer JD, dePamphilis CW (2018)
A novel genetic code and record-setting AT-richness in the highly reduced plastid genome of the holoparasitic plant Balanophora.
Proc Natl Acad Sci U S A
Mafiz A, Perera LN, He Y, Zhang W, Xiao S, Hao W, Sun S, Zhou K, Zhang Y
(2018) A case study on soil antibiotic resistome in an urban community garden.
Int J Antimicrob Agents
(34) Xiao S#, Nguyen DT#, Wu B, Hao W* (2017) Genetic drift and indel mutation in the evolution of yeast mitochondrial genome size. Genome Biology and Evolution 9:3088-3099. [Pubmed] [Reprint] [Supplementary Data]
(33) Wu B, Macielog AI, Hao W* (2017) Origin and spread of spliceosomal introns: insights from the fungal clade Zymoseptoria. Genome Biology and Evolution 9:2658-2667. [Pubmed] [Reprint]
(32) Ha SW, Ju D, Hao W, Xie Y*. (2016) Rapidly translated polypeptides are preferred substrates for cotranslational protein degradation. J Biol Chem 291:9827-9834. [Pubmed] [Reprint]
(31) Bhagwat AS*, Hao W, Townes JP, Lee H, Tang H, Foster PL (2016) Strand-biased cytosine deamination at the replication fork causes cytosine to thymine mutations in Escherichia coli. Proc Natl Acad Sci U S A 113:2176-2181. [Pubmed] [Reprint]
(30) Wu B, Buljic A, Hao W* (2015) Extensive horizontal transfer and homologous recombination generate highly chimeric mitochondrial genomes in yeast. Molecular Biology and Evolution 32:2559-2570. [Pubmed] [Reprint]
(29) Wu B, Hao W* (2015) A dynamic mobile DNA family in the yeast mitochondrial genome. G3: Genes | Genomes | Genetics 5:1273-1282. [Pubmed] [Reprint]
(28) Kim T, Hao W* (2014) DiscML: an R package for estimating evolutionary rates of discrete characters using maximum likelihood. BMC Bioinformatics 15: 320. [Pubmed] [Reprint] [Program Link]
(27) Wu B, Hao W* (2014) Horizontal transfer and gene conversion as an important driving force in shaping the landscape of mitochondrial intron. G3: Genes | Genomes | Genetics 4:605-612. [Pubmed] [Reprint]
(26) Kong Y, Ma JH, Warren K, Tsang RS, Low DE, Jamieson FB, Alexander DC, Hao W* (2013) Homologous recombination drives both sequence diversity and gene content variation in Neisseria meningitidis. Genome Biology and Evolution 5:1611-1627. [Pubmed] [Reprint] [Supplementary Data]
(25) Hao W* (2013) Unrecognized fine-scale recombination can mimic the effects of adaptive radiation. Gene 518:483-488. [Pubmed] [Reprint]
(24) Hao W* (2013) Extensive genomic variation within clonal bacterial groups resulted from homologous recombination. Mobile Genetic Elements 3:e23463. [Pubmed] [Reprint]
(23) Hao W* Allen VG, Jamieson FB, Low DE and Alexander DC (2012) Phylogenetic incongruence in E. coli O104: Understanding the evolutionary relationships of emerging pathogens in the face of homologous recombination. PLoS One 7: e33971. [Pubmed] [Reprint] [Supplementary Data]
(22) Hao W* (2012) Fast rates of evolution in bacteria due to horizontal gene transfer, in Rapidly Evolving Genes and Genetic Systems, Oxford University Press, (Book Chapter) [Publisher's website]
(21) Alexander DC, Hao W, Gilmour M, Zittermann S, Sarabia A, Melano R, Peralta A, Lombos M, Warren K, Amatnieks Y, Virey E, Ma JH, Jamieson FB, Low DE and Allen VG (2012) Escherichia coli O104:H4 infections associated with international travel. Emerging Infectious Diseases 18:473-476. [Pubmed] [Reprint]
(20) Hao W* and Palmer JD (2011) HGT turbulence: Confounding phylogenetic influence of duplicative horizontal transfer and differential gene conversion. Mobile Genetic Elements 1:256-261. [Pubmed] [Reprint]
(19) Hao W, Ma JH, Warren K, Tsang RS, Low DE, Jamieson FB and Alexander DC (2011) Extensive genomic variation within clonal complexes of Neisseria meningitidis. Genome Biology and Evolution 3:1406-1418. [Pubmed] [Reprint] [Supplementary Data]
(17) Mower JP*, Stefanovic S, Hao W, Gummow JS, Jain K, Ahmed D and Palmer JD (2010) Horizontal acquisition of multiple mitochondrial genes from a parasitic plant followed by gene conversion with host mitochondrial genes. BMC Biology 8: 150. [Pubmed] [Reprint] [Commentary by Archibald and Richards]
(16) Hao W#, Richardson AO#, Zheng Y and Palmer JD* (2010) Gorgeous mosaic of mitochondrial genes created by horizontal transfer and gene conversion. Proc Natl Acad Sci U S A 107: 21576-21581. [Pubmed] [Reprint] [Commentary by Archibald and Richards]
(15) Hao W* and Golding GB (2010) Inferring bacterial genome flux while considering truncated genes. Genetics 186: 411-426. [Pubmed] [Reprint]
(14) Hao W* (2010) OrgConv: detection of gene conversion using consensus sequences and its application in plant mitochondrial and chloroplast homologs. BMC Bioinformatics 11: 114. [Pubmed] [Reprint] [Program Link]
(13) Hao W* and Golding GB* (2010) Pattern of horizontal gene transfer in bacteria, in Microbial Population Genetics, Horizon Scientific Press. (book chapter) [Publisher's website]
(12) Hao W and Palmer JD* (2009) Fine-scale mergers of chloroplast and mitochondrial genes create functional, transcompartmentally chimeric mitochondrial genes. Proc Natl Acad Sci U S A 106: 16728-16733. [Pubmed] [Reprint]
(11) Hao W and Golding GB* (2009) Does gene translocation accelerate the evolution of laterally transferred genes? Genetics 182:1365-1375. [Pubmed] [Reprint]
(10) Hao W and Golding GB* (2008) High rates of lateral gene transfer are not due to false diagnosis of gene absence. Gene 421:27-31. [Pubmed]
(9) Hao W and Golding GB* (2008) Uncovering rate variation of lateral gene transfer during bacterial genome evolution. BMC Genomics 9: 235. [Pubmed] [Reprint]
(8) Higgs PG*, Hao W and Golding GB (2007) Identification of conflicting selective effects on highly expressed genes. Evolutionary Bioinformatics 2: 1-13. [Pubmed] [Reprint]
(7) Marri PR#, Hao W# and Golding GB* (2007) The role of laterally transferred genes in adaptive evolution. BMC Evolutionary Biology 7(Suppl 1):S8 (14 pages). [Pubmed] [Reprint]
(6) Hao W and Golding GB* (2006) The fate of laterally transferred genes: Life in the fast lane to adaptation or death. Genome Research 16:636-643. [Pubmed] [Reprint] [Highlighted by I. King Jordan]
(5) Marri PR#, Hao W# and Golding GB* (2006) Gene gain and gene loss in Streptococcus: Is it driven by habitat? Molecular Biology and Evolution 23: 2379-2391. [Pubmed] [Reprint]
(4) Hao W and Golding GB* (2006) Asymmetrical evolution of Cytochrome bd subunits. Journal of Molecular Evolution 62: 132-142. [Pubmed]
(3) Lee YK, Hao W, Ho PS, Nordling MM, Low CS, Kok TM and Rafter J* (2005) Human fecal water modifies adhesion of intestinal bacteria to caco-2 cells. Nutrition and Cancer 52: 35-42. [Pubmed]
(2) Hao W and Golding GB* (2004) Patterns of bacterial gene movement. Molecular Biology and Evolution 21: 1294-1307. [Pubmed] [Reprint]
(1) Hao W and Lee YK* (2004) Microflora of the gastrointestinal tract: A Review, in Public Health Microbiology: Methods and Protocols (Methods in Molecular Biology), pps. 491-502 Humana Press, Totowa, NJ. (book chapter) [Pubmed]