Research Articles
2021
Qianwei Su, Huangyi He, Qi Zhou*. On the origin and evolution of Drosophila new genes during spermatogenesis. bioRxiv. 2021.
He L, Long X, Qi J, Wang Z, Huang Z, Wu S, Zhang X, Luo H, Chen X, Lin J, Yang Q. Shiyu Huang*,Qi Zhou*,Leyun Zheng*.Genome and gene evolution of seahorse species revealed by the chromosome‐level genome of Hippocampus abdominalis. Mol. Ecol. Res.
Peona V, Palacios-Gimenez OM, Blommaert J, Liu J, Haryoko T, Jønsson KA, Irestedt M, Zhou Qi, Jern P, Suh A. The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities.Philos Trans R Soc B. 2021 Sep 13;376(1833):20200186.
Zongji Wang, Jilin Zhang, Xiaoman Xu, Christopher Witt, Yuan Deng, Guangji Chenc, Guanliang Meng, Shaohong Feng,Luohao Xu, Tamas Szekely,Guojie Zhang*,Qi Zhou*.Phylogeny and Sex Chromosome Evolution of Palaeognathae. J Genet Genomics
(2021).
Conte, Matthew A., Frances E. Clark, Reade B. Roberts, Luohao Xu, Wenjing Tao, Qi Zhou, Deshou Wang, Thomas D. Kocher*. Origin of a giant sex chromosome. Mol biol evol.38, no. 4 (2021): 1554-1569.
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.
Wenjing Tao, Luohao Xu*, Lin Zhao, Zexian Zhu, Xin Wu, Qianwen Min, Deshou Wang*, Qi Zhou*. High-quality chromosome-level genomes of two tilapia species reveal their evolution of repeat sequences and sex chromosomes. Mol Ecol Res.21, no. 2 (2021): 543-560.
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.
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.
2020
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.
