Research Articles
2021
Stöck M, Kratochvíl L, Kuhl H, Rovatsos M, Evans BJ, Suh A, Valenzuela N, Veyrunes F, Zhou Qi, Gamble T, Capel B, Schartl M, Guiguen Y. A brief review of vertebrate sex evolution with a pledge for integrative research: towards 'sexomics'. Philos Trans R Soc Lond B Biol Sci. 2021 Aug 30;376(1832):20200426.
Zhou Qi*. Y chromosome evolution spurs behavioural diversity in male fish. Nat. Ecol. Evol.,2021,News & Views
Valentina Peona*; Mozes P K Blom; Luohao Xu; Reto Burri; Shawn Sullivan; Ignas Bunikis; Ivan Liachko; Tri Haryoko; Knud A Jønsson; Zhou Qi; Martin Irestedt; Alexander Suh*, Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird-of-paradise, Mol.Ecol .Resour., 2021, 21(1): 263-286.
Li Jing; Zhang Jilin; Liu Jing; Zhou Yang; Cai Cheng; Xu Luohao; Dai Xuelei; Feng Shaohong; Guo Chunxue; Rao Jinpeng; Wei Kai; Erich D Jarvis; Jiang Yu; Zhou Zhengkui; Zhang Guojie; Zhou Qi*, A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals, Gigascience, 2021, 10(1): 142.
Liu Jing #; Wang Zongji #; Xu Luohao; Liu Jiaqi; Shaohong Feng; Chunxue Guo; Shengchan Chen; Zhanjun Ren; Jinpeng Rao; Kai Wei; Yuezhou Chen; Erich Jarvis; Zhang Guojie ; Zhou Qi*, A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes, Genome Res., 2021, 31(1): gr. 271569.120.
Zhou, Yang #; Shearwin-Whyatt, Linda #; Li, Jing #; Song, Zhenzhen; Hayakawa, Takashi; Stevens, David; Fenelon, Jane C.; Peel, Emma; Cheng, Yuanyuan; Pajpach, Filip; Bradley, Natasha; Suzuki, Hikoyu; Nikaido, Masato; Damas, Joana; Daish, Tasman; Perry, Tahlia; Zhu, Zexian; Geng, Yuncong; Rhie, Arang; Sims, Ying; Wood, Jonathan; Haase, Bettina; Mountcastle, Jacquelyn; Fedrigo, Olivier; Li, Qiye; Yang, Huanming; Wang, Jian; Johnston, Stephen D.; Phillippy, Adam M.; Howe, Kerstin; Jarvis, Erich D.;Ryder, Oliver A.;Kaessmann, Henrik;Donnelly, Peter;Korlach, Jonas;Lewin, Harris A.;Graves, Jennifer;Belov, Katherine;Renfree, Marilyn B.;Grutzner, Frank*;Zhou Qi*;Zhang, Guojie*, Platypus and echidna genomes reveal mammalian biology and evolution, Nature, 2021, 1-7.
2020
Wang Zong-Ji; Chen Guang-Ji; Zhou Qi*; Zhang Guo-Jie*, Dynamic evolution of transposable elements, demographic history, and gene content of paleognathous birds, Zool. Res., 2020, 42(1): 51-61.
Matthew A Conte; Frances E Clark; Reade B Roberts; Luohao Xu; Wenjing Tao; Zhou Qi; Deshou Wang; Thomas D Kocher*, Origin of a giant sex chromosome, Mol. Biol. Evol., 2020,38(4), 1554-1569.
Feng, Shaohong; Stiller, Josefin; Deng, Yuan; Armstrong, Joel; Fang, Qi; Reeve, Andrew Hart; Xie, Duo; Chen, Guangji; Guo, Chunxue; Faircloth, Brant C.; Petersen, Bent; Wang, Zongji; Zhou,Qi; Diekhans, Mark; Chen, Wanjun; Andreu-Sanchez, Sergio; Margaryan, Ashot; Howard, Jason Travis; Parent, Carole; Pacheco, George; Sinding, Mikkel-Holger S.; Puetz, Lara; Cavill, Emily; Ribeiro, Angela M.; Eckhart, Leopold; Fjeldsa, Jon; Hosner, Peter A.; Brumfield, Robb T.; Christidis, Les; Bertelsen, Mads F...., Paten, Benedict*,Zhang, Guojie*,Dense sampling of bird diversity increases power of comparative genomics, Nature, 2020, 587(7833): 252-+.
Xu, Luohao*; Irestedt, Martin; Zhou Qi, Sequence Transpositions Restore Genes on the Highly Degenerated W Chromosomes of Songbirds, Genes, 2020, 11(11): 1267.
Tao, Wenjing; Xu, Luohao*; Zhao, Lin; Zhu, Zexian; Wu, Xin; Min, Qianwen; Wang, Deshou*; Zhou Qi*, High-quality chromosome-level genomes of two tilapia species reveal their evolution of repeat sequences and sex chromosomes, Mol. Ecol. Resour., 2020, 21(2): 543-560.
Xu Luohao; Zhou Qi*, The Female-Specific W Chromosomes of Birds Have Conserved Gene Contents but Are Not Feminized, Genes, 2020, 11(10).
Liu Jing; Mujahid Ali;Zhou Qi*, Establishment and evolution of heterochromatin, ANN NY ACAD SCI , 2020.
2019
Xu, Luohao; Auer, Gabriel; Peona, Valentina; Suh, Alexander; Deng, Yuan; Feng, Shaohong; Zhang, Guojie; Blom, Mozes P K; Christidis, Les; Prost, Stefan; Irestedt, Martin*; Zhou,Qi*, Dynamic evolutionary history and gene content of sex chromosomes across diverse songbirds, Nat. Ecol. Evol., 2019, 3(5): 834-844.
Zhang Jiayu; Zhou Qi*, On the Regulatory Evolution of New Genes Throughout Their Life History, Mol. Biol. Evol., 2019, 36(1): 15-27.
吴芮封; 徐小曼; 周琦*, 性别决定机制和性染色体的演化, 中国科学:生命科学 , 2019, (04): 403-420.
2018
Lin Jian Qing#; Zhou Qi#; Yang Hai Qiong; Fang Li Ming; Tang Ke Yi; Sun Li; Wan Qiu Hong; Fang Sheng Guo*, Molecular mechanism of temperature-dependent sex determination and differentiation in Chinese alligator revealed by developmental transcriptome profiling, Sci. Bull., 2018, 63(4): 209-212.
Lyu Jialan#; Wang Zehua#; Wang Fang; Miao Chen; Nan Zi; Zhang Jiayu; Xi Yongmei; Zhou Qi; Yang Xiaohang; Ge Wanzhong*, The histone deacetylase HDAC1 positively regulates Notch signaling during Drosophila wing development, Biology open. 2018, 7(2): UNSP bio029637.
2017
Seki Ryohei#; Li Cai#; Fang Qi; Hayashi Shinichi; Egawa Shiro; Hu Jiang; Xu Luohao; Pan Hailin; Kondo Mao; Sato Tomohiko; Matsubara Haruka; Kamiyama Namiko; Kitajima Keiichi; Saito Daisuke; Liu Yang; Gilbert M Thomas P; Zhou Qi; Xu Xing; Shiroishi Toshihiko; Irie Naoki*; Tamura Koji*; Zhang Guojie*, Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features, Nat. Commun., 2017, 8: 14229-14229.
Zhang Jilin; Li Jing; Zhou Qi*, Genomic and Transcriptomic Analyses of Avian Sex Chromosomes and Sex-Linked Genes, Humana Press, New York, NY,69-85, 2017.
2016
Gibilisco Lauren; Zhou Qi; Mahajan Shivani; Bachtrog Doris*, Alternative Splicing within and between Drosophila Species, Sexes, Tissues, and Developmental Stages, PLoS Genet., 2016, 12(12).
Yin Wei#; Wang Zong-Ji#; Li Qi-Ye; Lian Jin-Ming; Zhou Yang; Lu Bing-Zheng; Jin Li-Jun; Qiu Peng-Xin; Zhang Pei; Zhu Wen-Bo; Wen Bo; Huang Yi-Jun; Lin Zhi-Long; Qiu Bi-Tao; Su Xing-Wen; Yang Huan-Ming; Zhang Guo-Jie; Yan Guang-Mei*; Zhou Qi*, Evolutionary trajectories of snake genes and genomes revealed by comparative analyses of five-pacer viper, Nat. Commun., 2016, 7: 13107-13107.
2015
Zhou, Qi; Bachtrog, Doris*, Ancestral Chromatin Configuration Constrains Chromatin Evolution on Differentiating Sex Chromosomes in Drosophila, PLoS Genet., 2015, 11(6): e1005331.
Zhang Jilin; Li Cai; Zhou Qi; Zhang Guojie*, Improving the ostrich genome assembly using optical mapping data, GigaScience, 2015, 4: 24.
2014
Wang Zongji; Zhang Jilin; Yang Wei; An Na; Zhang Pei; Zhang Guojie*; Zhou Qi*, Temporal genomic evolution of bird sex chromosomes, Bmc. Evol. Biol., 2014, 14: 250.
Zhou Qi#*; Zhang Jilin#; Bachtrog Doris#; An Na; Huang Quanfei; Jarvis Erich D.; Gilbert M. Thomas P.; Zhang Guojie*, Complex evolutionary trajectories of sex chromosomes across bird taxa, Science, 2014, 346(6215): 1332.
Jarvis, Erich D.#*; Mirarab, Siavash#; Aberer, Andre J.; Li, Bo; Houde, Peter; Li, Cai; Ho, Simon Y. W.; Faircloth, Brant C.; Nabholz, Benoit; Burt, Dave; Ellegren, Hans; Alstrom, Per; Edwards, Scott V.; Stamatakis, Alexandros; Mindell, David P.; Cracraft, Joel; Braun, Edward L.; Howard, Jason T.; Suh, Alexander; Weber, Claudia C.; da Fonseca, Rute R.;Howard, Jason T.;Suh, Alexander;...Zhou Qi;... Warnow Tandy*; Jun Wang*; Gilbert, M. Thomas P.*; Zhang Guojie*,Whole-genome analyses resolve early branches in the tree of life of modern birds, Science, 2014, 346(6215): 1320-1331.
Zhang Guojie#*; Li Cai#; Li Qiye; Li Bo; Larkin Denis M.; Lee Chul; Storz Jay F.; Antunes Agostinho; Greenwold Matthew J.; Mindell David P.; Edwards Scott V.; Braun Edward L.; Rahbek Carsten; Burt David W.; Houde Peter; Zhang Yong; Yang Huanming; Wang Jian; Meredith Robert W.; Odeen Anders; Cui Jie; Zhou Qi; Xu Luohao; Pan Hailin;Wang Zongji;Jin Lijun;Zhang Pei;Hu Haofu;Yang Wei;Hu Jiang;...Jarvis Erich D.*; Gilbert M. Thomas P.*; Wang Jun*, Comparative genomics reveals insights into avian genome evolution and adaptation, Science, 2014, 346(6215): 1311-1320.
Lott, Susan E*; Villalta, Jacqueline E; Zhou, Qi; Bachtrog, Doris; Eisen, Michael B, Sex-specific embryonic gene expression in species with newly evolved sex chromosomes, PLoS Genet., 2014, 10(2).
2013
Zhou Qi; Ellison Christopher E; Kaiser Vera B; Alekseyenko Artyom A; Gorchakov Andrey A; Bachtrog Doris*, The epigenome of evolving Drosophila neo-sex chromosomes: dosage compensation and heterochromatin formation, PLoS Biol., 2013, 11(11).
Alekseyenko, Artyom A.#; Ellison, Christopher E.#; Gorchakov, Andrey A.#; Zhou Qi; Kaiser, Vera B.; Toda, Nick; Walton, Zaak; Peng, Shouyong; Park, Peter J.; Bachtrog, Doris*; Kuroda, Mitzi I.*, Conservation and de novo acquisition of dosage compensation on newly evolved sex chromosomes in Drosophila, Gen. Dev., 2013, 27(8): 853-858.
2012
Zhou Qi; Bachtrog Doris*, Sex-Specific Adaptation Drives Early Sex Chromosome Evolution in Drosophila, Science, 2012, 337(6092): 341-345.
Zhan Zubing; Ding Yun; Zhao Ruopin; Zhang Yue; Yu Haijing; Zhou Qi; Yang Shuang; Xiang Hui*; Wang Wen*, 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., 2012, 29(5): 1407-1416.
Zhou Qi#; Huang, Quan-fei#; Zhu, Hong-mei*; Zhao, Li; Zhang, Guo-jie; Roy, Scott W.; Vicoso, Beatriz; Xuan, Zhao-lin; Ruan, Jue; Zhang, Yue; Zhao, Ruo-ping; Ye, Chen; Zhang, Xiu-qing; Wang, Jun*; Wang, Wen*; Bachtrog, Doris*, Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans, BMC. Genomics，2012, 13: 109.
Zhou Qi; Bachtrog, Doris*, Chromosome-Wide Gene Silencing Initiates Y Degeneration in Drosophila, Curr.Bio., 2012, 22(6): 522-525.
Assis, Raquel*; Zhou, Qi; Bachtrog, Doris, Sex-Biased Transcriptome Evolution in Drosophila, Genome. Biol. Evol. , 2012, 4(11): 1189-1200.
Ding, Yun#; Zhou Qi#; Wang, Wen*, Origins of New Genes and Evolution of Their Novel Functions, ANNU REV ECOL EVOL S , 2012, 43: 345-363.
2011
Kaiser, Vera B.*; Zhou Qi; Bachtrog, Doris, Nonrandom Gene Loss from the Drosophila miranda Neo-Y Chromosome, Genome. Biol. Evol.,2011, 3: 1329-1337.
2010
Ding, Yun#; Zhao, Li#; Yang, Shuang; Jiang, Yu; Chen, Yuan; Zhao, Ruoping; Zhang, Yue; Zhang, Guojie; Dong, Yang; Yu, Haijing; Zhou Qi; Wang Wen*, A Young Drosophila Duplicate Gene Plays Essential Roles in Spermatogenesis by Regulating Several Y- Linked Male Fertility Genes, PLoS Genet., 2010, 6(12): e1001255.
2008
Zhou Qi; Wang, Wen*, On the origin and evolution of new genes-a genomic and experimental perspective, J GENET GENOMICS, 2008, 35(11): 639-648.
Yang, Shuang#; Arguello, J. Roman#; Li, Xin; Ding, Yun; Zhou Qi; Chen, Ying; Zhang, Yue; Zhao, Ruoping; Brunet, Frederic; Peng, Lixin; Long, Manyuan*; Wang, Wen*, Repetitive element-mediated recombination as a mechanism for new gene origination in Drosophila, PLoS Genet., 2008, 4(1): e3.
Zhou Qi#; Wang, Jun#; Huang, Ling#; Nie, Wenhui; Wang, Jinhuan; Liu, Yan; Zhao, Xiangyi; Yang, Fengtang*; Wang Wen*, Neo-Sex chromosomes in the black muntjac recapitulate incipient evolution of mammalian sex chromosomes, Genome.Biol., 2008, 9(6): R98.
2006
Zhou Qi#; Huang, Ling#; Zhang, Jianguo#; Zhao, Xiangyi; Zhang, Qingpeng; Song, Fei; Chi, Jianxiang; Yang, Fengtang*; Wan Wen*, Comparative genomic analysis links karyotypic evolution with genomic evolution in the Indian Muntjac (Muntiacus muntjak vaginalis), Chromosoma, 2006, 115(6): 427-436.
Yu, Haijing*; Jiang, Huifeng; Zhou Qi; Yang, Jufen; Cun, Yina; Su, Bing; Xiao, Chunjie; Wang, Wen, Origination and evolution of a human-specific transmembrane protein gene, c1orf37-dup, Hum. Mol. Genet., 2006, 15(11): 1870-1875.
2004
周琦; 王文*, DNA水平自然选择作用的检测, 动物学研究, 2004, (01): 73-80.
