Research Articles

 

2021

 

Zhou Y, Shearwin-Whyatt L, Li J, Zhou Q.et al. Platypus and echidna genomes reveal mammalian biology and evolution. Nature (2021). https://doi.org/10.1038/s41586-020-03039-0

 

Li J, Zhang J , Liu J, Zhou Y, Cai C, Xu LH, Zhou Q, A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals, GigaScience, Volume 10, Issue 1, January 2021, giaa142, https://doi.org/10.1093/gigascience/giaa142

 

Liu J, Wang Z,Li J, Xu LH,Zhou Q,A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes,Genome Res,31 (1),January 2021,http://doi:10.1101/gr.271569.120

 

2020

 

Tao W, Xu LH, Zhao L, Zhou Q.et al. High-quality chromosome-level genomes of two tilapia species reveal their evolution of repeat sequences and sex chromosomes. Mol Ecol Resour. 2020; 00: 1– 18. https://doi.org/10.1111/1755-0998.13273

 

Matthew A Conte, Frances E Clark, Reade B Roberts,Xu L, Tao W, Zhou Q, Deshou Wang, Thomas D Kocher, Origin of a Giant Sex Chromosome, Molecular Biology and Evolution,  msaa319, https://doi.org/10.1093/molbev/msaa319

 

Feng S, Stiller J, Deng Y ,Zhou Q. et al. Dense sampling of bird diversity increases power of comparative genomics. Nature 587, 252–257 (2020). https://doi.org/10.1038/s41586-020-2873-9

 

Xu LH,Irestedt M, Zhou Q. 2020.Sequence Transpositions Restore Genes on the Highly Degenerated W Chromosomes of Songbirds . Genes 11, no. 11: 1267.

 

Wang ZJ, Chen GJ, Zhang GJ, Zhou Q. Dynamic evolution of transposable elements, demographic history, and gene content of paleognathous birds. Zoological Research. 2020 Oct:1-11. DOI: 10.24272/j.issn.2095-8137.2020.175.

 

Xu LH, Zhou Q.The Female-Specific W Chromosomes of Birds Have Conserved Gene Contents but Are Not Feminized. Genes, 2020. 11(10): p. 1126.

 

Liu J, Ali M, Zhou Q. Establishment and evolution of heterochromatin.Annals of the New York Academy of Sciences.2020. 1476(1): p.59-77.

 

2019

 

Xu L, Auer G, Peona V, Suh A, Deng Y, Feng S, Zhang G, Blom MPK, Christidis L, Prost S, Irestedt M, Zhou Q. Dynamic evolutionary history and gene content of sex chromosomes across diverse songbirds. Nat Ecol Evol 3, 834-844. 

 

2018

 

Zhang JY, Zhou Q.  On the regulatory evolution of new genes throughout their life history. Mol Biol Evol. doi: 10.1093/molbev/msy206.

 

Lin JQ, Zhou Q, Yang HQ, Fang LM, Tang KY, Sun L, Wan QH, Fang SG.  Molecular mechanism of temperature-dependent sex determination and differentiation in Chinese alligator revealed by developmental transcriptome profiling. Sci Bull. 4: 209-212.

 

2017

 

Seki R, L. C., Fang Q, Hayashi S, Egawa S, Hu J, Xu L, Pan H, Kondo M, Sato T, Matsubara H, Kamiyama N, Kitajima K, Saito D, Liu Y, Gilbert MTP, Zhou Q, Xu X, Shiroishi T, Irie N, Tamura K, Zhang G. Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features. Nat Commun. 

 

2016

 

Gibilisco L, Zhou Q, Mahajan S, Bachtrog D. Alternative Splicing within and between Drosophila Species, Sexes, Tissues, and Developmental Stages. PLoS Genet.​​​​​ 2016 Dec 9;12(12):e1006464.

doi: 10.1371/journal.pgen.1006464.eCollection 2016 Dec.

 

Yin W, Wang ZJ, Li QY, Lian JM, Zhou Y, Lu BZ, Jin LJ, Qiu PX, Zhang P, Zhu WB, Wen B, Huang YJ, Lin ZL, Qiu BT, Su XW, Yang HM, Zhang GJ, Yan GM, Zhou Q*. Evolutionary trajectories of snake genes and genomes revealed by comparative analyses of five-pacer viper. Nat Commun. 7:13107.  *correspondence author

  

2015

 

Zhou Q, Bachtrog D. Ancestral chromatin configuration constrains chromatin evolution on differentiating sex chromosomes in Drosophila. PLoS Genet. 11(6): e1005331.

 

Zhang J, Li C, Zhou Q, Zhang G. Improving the ostrich genome assembly using optical mapping data.

Gigascience. 2015; 4: 24. Published online 2015 May 12. doi: 10.1186/s13742-015-0062-9

 

2014

 

Zhou Q*, Zhang J, Bachtrog D, An N, Huang Q, Jarvis ED, Gilbert MTP, Zhang G.  Sex chromosomes demonstrate complex evolutionary trajectories across bird taxa. Science. 346: 1332  *correspondence author

 Highlighted by The Scientist, Faculty of 1000

 

Avian Genomics Consortium* Whole genome analyses resolve the early branches in the tree of life of modern birds. Science. 346: 1320-1331 *together with other 103 co-authors

 

2013

 

Zhou Q, Ellison EC, Kaiser BV, Alekseyenko AA, Gorchakov AA, Bachtrog D  The epigenome of evolving sex chromosomes: dosage compensation and heterochromatin formation. PloS Biol. 11(11): e1001711

 Highlighted by Nature Review Genetics

 

Alekseyenko AA, Ellison CE, Gorchakov AA, Zhou Q, Kaiser VB, Toda N, Walton Z, Peng S, Park PJ, Bachtrog D, Kuroda MI . Conservation and de novo acquisition of dosage compensation on newly evolved sex chromosomes in Drosophila. Genes. Dev 27: 853-858.

 

2012​

 

Zhou Q, Bachtrog D. Sex-specific adaptation drives early sex chromosome evolution in Drosophila. Science. 337: 341-345.Highlighted by The Scientists and Science online podcast

 

Zhou Q, Bachtrog D.  Chromosome-wide gene silencing initiates Y degeneration in Drosophila.Curr Biol. 22: 522-525.

 

Zhan Z, Ding Y, Zhao R, Zhang Y, Yu H, Zhou Q, Yang S, Xiang H, Wang W . Rapid functional divergence of a newly evolved polyubiquitin gene in Drosophila and its role in the trade-off between male fecundity and lifespan. Mol Biol Evol. 29: 1407-1416.

 

2011

 

Kaiser VB, Zhou Q, Bachtrog D.  Nonrandom gene loss from the Drosophila miranda neo-Y chromosome. Genome Biol Evol. 3: 1329-1337.

 

2010

 

Ding Y, Zhao L, Yang S, Jiang Y, Chen Y, Zhao R, Zhang Y, Zhang G, Dong Y, Yu H, Zhou Q, Wang W.  A young Drosophila duplicate gene plays essential roles in spermatogenesis by regulating several Y-linked male fertility genes. PLoS Genet. 6: e1001255.

 

2008

 

Zhou Q, Zhang G, Zhang Y, Xu S, Zhao R, Zhan Z, Li X, Ding Y, Yang S, Wang W.  On the origin of new genes in Drosophila. Genome Res. 18: 1446-1455.

Highlighted by Nature Review Genetics

 

Zhou Q, Wang J, Huang L, Nie W, Wang J, Liu Y, Zhao X, Yang F, Wang W. Neo-sex chromosomes in the black muntjac recapitulate incipient evolution of mammalian sex chromosomes.Genome. Biol 9: R98.

 

Invited Review Articles

 

Ding Y, Zhou Q*, Wang W (2012) Origins of new genes and evolution of their novel functions. Annu Rev Ecol Evol Syst. 43: 345-363. *co-first author

 

Zhou Q, Wang W (2008) On the origin and evolution of new genes--a genomic and experimental perspective. J Genet Genomics. 35: 639-648.

 

Book Chapters

 

Zhang J., Li J., Zhou Q. (2017) Genomic and Transcriptomic Analyses of Avian Sex Chromosomes and Sex-Linked Genes. In: Sheng G. (eds) Avian and Reptilian Developmental Biology. Methods in Molecular Biology, vol 1650. Humana Press, New York, NY

​

Wang W, Zhou Q, Li X Origin of New Genes. In: Zhang G, editor. Molecular Genetics: Beijing Normal University Publishing Group. pp. in press

 

 

Articles in Press or Preparation

 

Zhou Q, Walton Z, Dunn J, Bachtrog D (2015) Proteom evolution of young sex chromosomes of Drosophila uncoverred by ribosomal footprinting. in preparation

​

Zhou Q*, Wang Z, Jin L, Li Q, Bachtrog D, Zhang G (2015) Genome, venome and sex chromosome evolution of a viper snake. in preparation * correspondence author