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研究队伍 -- 生物多样性基因组研究研究组
  张国捷    研究员
职  务:
学  历: 理学博士
电  话: +86 871 68125417
传  真:
电子邮件: zhangguojie@mail.kiz.ac.cn
通讯地址: 云南省昆明市五华区教场东路32号 650223    650223
其他主页: http://zhanggjlab.cn/en/pages/our_lab.html
 
  简  历

博士,研究员。现任哥本哈根大学生物系终身教授、中国国家基因库副主任、中国科学院昆明动物研究所生物多样性基因组学研究学科组负责人;生物多样性基因组学和生态演化基因组学领域专家。2005年毕业于厦门大学生物学专业,获理学学士学位;2010年毕业于中科院昆明动物研究所遗传学专业,获理学博士学位;2012年起任丹麦哥本哈根大学助理教授,副教授,2017起任终身教授;同时兼任中国国家基因库副主任。

主要从事生物多样性及生态演化的基因组研究,研究范围包括物种形成的基因组学基础,生态环境与生物协同演化分子机制,以及动物复杂生理性状以及行为学的分子基础。是生物多样性基因组学研究领域的国际领军人物,发起并领导了多个具有重大影响力的国际基因组学研究项目。在基因组演化及其相关的各研究领域开展了大量的开拓性工作,取得了一系列具有重大国际影响力的原创性研究成果,特别是在前沿生命科学领域——生物多样性基因组学和生态演化基因组学方面做出了引领国际的突出学术贡献。在国际高影响力杂志发表论文100余篇,其中包括Science 14篇、Nature 8篇、Nature Genetics 7篇、Cell文章1篇,另有其他Nature子刊十余篇。其中40多篇以第一作者或通讯作者发表。多篇文章被选为封面文章,另有多篇受到F1000 评选为重点推荐文章。文章总引用率超1万次,h-index51i10-index 90。研究成果频繁受到CNN BBC、纽约时报、华盛顿邮报、国家地理等主流媒体热点报道。现担任多个重大国际基因组研究项目负责人,协调人或者委员会成员。长期担任Nature ScienceCell等顶尖国际期刊和各国基金会评审委员。

  研究方向

演化论是生命科学研究中的基础理论,但是我们对于生物体如何响应生理和环境变化并产生适应性表型的分子机制仍然所知甚少。在基因组学技术飞速发展的推动下,本课题组积极开拓生物多样性基因组研究领域,研究物种形成、生物多样性、生物适应性以及物种发育演化等领域的经典问题,揭示这些过程发生的宏观演化趋势和微观演化的分子学动力。我们课题组同时从事动物社会行为和组织的演化方面的研究,并以社会性昆虫作为动物模型,研究社会性昆虫的等级发育和行为可塑性的遗传和表观遗传调控机制。现阶段主要有以下研究方向:

一、生物多样性基因组学研究

地球生命的物种组成、形态、及功能多样性的形成机制是达尔文留给后人的未解之谜,是生命科学研究中最基础的学科之一。生物多样性基因组学是新近发展起来的综合性学科,旨在利用比较基因组学、演化生物学、群体遗传学、发育生物学、生态学等多个学科的理论和技术交叉,系统回答生物形态功能的分子遗传基础、物种协同演化分子机制,以及生物演化与环境互作机制等重要基础问题。课题组先后主导完成了鸟纲演化基因组学研究,中国猕猴和食蟹、蚂蚁、蝙蝠、树鼩、裸鼹鼠、家鸽、海龟、半滑舌鳎、及北极熊等数十个物种的重大基因组演化研究项目,此外还参与了其他众多物种基因组研究,涉及物种范围覆盖了灵长类、哺乳类、两栖爬行类、鸟类、鱼类、及无脊椎动物等演化过程中主要支系代表性物种。这些研究主要回答演化生物学研究中的几个热点问题1) 物种的起源和演化地位;2) 演化历史上关键性状的分子基础;3) 生物极端环境适应机制等。从跨物种宏观水平到同一物种微观水平,从基因组水平到表观遗传水平,从物种的演化历史到物种的形态和功能起源与分子调节机制,进行了广泛而深入的系统性研究。

二、发育基因组学研究

发育生物学是生物科学重要的基础分支学科之一,研究内容包括基因的表达和调控,基因型和表型表达的因果关系等。我们团队利用先进的基因组学手段来回答一些发育生物学的关键问题,主要包括(1)脊椎动物性别决定的遗传学机制;(2)环境性别决定的表观调控机制;(3)鸟类高度保守的基因组元件(avian-specific highly conserved elements, ASHCEs在鸟类特异性状发育过程中的调控作用。

三、社会行为的演化及分子调控机制

人类是一种社会性动物,在演化过程中逐渐形成了高度复杂的社会系统。这种社会系统受到了文化、宗教、政治的深远影响。人类社会系统的产生是否具有生物学基础是自然科学和社会科学研究的重要交叉命题之一。如何从分子层面、表观遗传层面、神经层面、乃至动物行为层面多维度贯穿理解人类社会生物学基础是生物学研究的重要挑战之一。为研究这一命题,该课题组利用与人类类似发展处复杂社会结构的社会性生物作为研究模型,在基因组层面、表观调控层面以及神经生物学层面对社会等级及行为差异展开系统研究。我们以社会性昆虫为模式生物,研究主要包括(1)蚂蚁的社会性基因组演化机制;(2)蚂蚁行为和形态等级分化的遗传和神经生物学基础;(3)超个体的发育和脑基因组学研究;(4)社会性昆虫脑部的3D原位转录组。

  承担科研项目
  专家类别
研究员
  社会任职
  获奖及荣誉

国际奖

2011 Sir Frederick McMaster visiting fellow, CSIRO, Australia

2012 Marie Curie International Incoming Fellowship, European Commission

2015  Lundbeck Fellow, Denmark

2017  The Carlsberg Foundation Distinguished Associate Professor Fellowships

国内奖

2010  深圳市高层次专业人才(国家级)

2011  中国科学院百篇优秀论文

2011  云南省优秀科技论文奖(特等奖)

2013  李汝琪动物遗传学奖(全国每两年两名获奖者)

2014  蝙蝠文章获评2013年中国最具影响力文章之一

2014  指导的学生刘石平获评中国青少年科技创新奖

2014  南粤科技优秀学术论文奖

2014  北极熊基因组文章获评“Cell年度中国论文”

2015  深圳市青年科技奖

2016  深圳市孔雀计划海外高层次人才(B)

  代表论著

通讯作者和第一作者论文(*通讯作者) (1-42)

1.         Avalos A, Pan H, Li C, Acevedo Gonzalez JP, Rendon G, Fields CJ, Brown PJ, Giray T, Robinson GE*, Hudson ME*, Zhang G*. A soft selective sweep during rapid evolution of gentle behaviour in an Africanized honeybee. Nat Commun, 2017, 8:1550.

2.         Hargreaves A, Zhou L, Christensen J, Marlétaz F, Liu S, Li F, Jansen P, Spiga E, Hansen M, Pedersen S, Biswas S, Serikawa K, Fox B, Taylor W, Mulley J, Zhang G*, Heller R*, Holland P*. Genome sequence of a diabetes-prone rodent reveals a mutation hotspot around the ParaHox gene cluster. Proc Natl Acad Sci U S A, 2017, 114(29):7677-7682.

3.         Gao J, Li Q, Wang Z, Zhou Y, Martelli P, Li F, Xiong Z, Wang J, Yang H, Zhang G*. Sequencing, de novo assembling and annotating the genome of the endangered Chinese crocodile lizard Shinisaurus crocodilurus. GigaScience, 2017, 6(7):1-6.

4.         Boomsma J, Brady S, Dunn R, Gadau J, Heinze J, Keller L, Moreau C, Sanders N, Schrader L, Schultz T, Sundstrom L, Ward P, Wcislo W, Zhang G* & The GAGA Consortium. Forum The Global Ant Genomics Alliance (GAGA). Myrmecol News, 2017, 25(2):61-66.

5.         Seki R, Li 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 TM, 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, 2017, 8, 14229.

6.         Xiong Z, Li F, Li Q, Zhou L, Gamble T, Zheng J, Kui L, Li C, Li S, Yang H, Zhang G*. Draft genome of the leopard gecko, Eublepharis macularius. GigaScience, 2016, 5: 49.

7.         Pan H, Yu H, Ravi V, Li C, Lee PA, Lian MM, Tay BH, Brenner S, Wang J, Yang H, Zhang G*, Venkatesh B*. The genome of the largest bony fish, ocean sunfish (Mola mola), provides insights into its fast growth rate. GigaScience, 2016, 5 (1):36.

8.         Wang Z, Lian J, Li Q, Zhang P, Zhou Y, Zhan X, Zhang G*. RES-Scanner: a software package for genome-wide identification of RNA-editing sites. GigaScience, 2016, 5 (1): 37.

9.         Nygaard S, Hu H, Li, C, Schiøtt M, Chen Z, Yang Z, Xie Q, Ma C, Deng Y, Dikow BR, Rabeling C, Nash RD, Wcislo TW, Brady GS, Schultz RT, Zhang G*, Boomsma J*. Reciprocal genomic evolution in the ant-fungus agricultural symbiosis. Nat Commun, 2016, 7.

10.     Zhang G*, Rahbek C, Graves GR, Lei F, Jarvis ED, & Gilbert MT. Genomics: Bird sequencing project takes off. Nature, 2015, 522(7554):34.

11.     Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Alfaro-Nunez A, Narula N, Liu L, Burt D, Ellegren H, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MT, Zhang G, & Avian Phylogenomics C. Phylogenomic analyses data of the avian phylogenomics project. Gigascience, 2015, 4:4.

12.     Zhang J, Li C, Zhou Q, &Zhang G*. Improving the ostrich genome assembly using optical mapping data. Gigascience, 2015, 4:24.

13.     Georges A*, Li Q, Lian J, O'Meally D, Deakin J, Wang Z, Zhang P, Fujita M, Patel HR, Holleley CE, Zhou Y, Zhang X, Matsubara K, Waters P, Graves JA, Sarre SD, & Zhang G*. High-coverage sequencing and annotated assembly of the genome of the Australian dragon lizard Pogona vitticeps. Gigascience, 2015, 4:45.

14.     Kapheim KM, Pan H, Li C, Salzberg SL, Puiu D, Magoc T, Robertson HM, Hudson ME, Venkat A, Fischman BJ, Hernandez A, Yandell M, Ence D, Holt C, Yocum GD, Kemp WP, Bosch J, Waterhouse RM, Zdobnov EM, Stolle E, Kraus FB, Helbing S, Moritz RF, Glastad KM, Hunt BG, Goodisman MA, Hauser F, Grimmelikhuijzen CJ, Pinheiro DG, Nunes FM, Soares MP, Tanaka ED, Simoes ZL, Hartfelder K, Evans JD, Barribeau SM, Johnson RM, Massey JH, Southey BR, Hasselmann M, Hamacher D, Biewer M, Kent CF, Zayed A, Blatti C, 3rd, Sinha S, Johnston JS, Hanrahan SJ, Kocher SD, Wang J*, Robinson GE*, & Zhang G*. Social evolution. Genomic signatures of evolutionary transitions from solitary to group living. Science, 2015, 348(6239):1139-1143.

15.     Zhang G*, Jarvis ED, & Gilbert MT. Avian genomes. A flock of genomes. Introduction. Science, 2014,346(6215):1308-1309.

16.     Zhang G*, Li B, Li C, Gilbert MT, Jarvis ED, Wang J, & Avian Genome C. Comparative genomic data of the Avian Phylogenomics Project. Gigascience, 2014, 3(1):26.

17.     Chen L, Tang L, Xiang H, Jin L, Li Q, Dong Y, Wang W*, & Zhang G*. Advances in genome editing technology and its promising application in evolutionary and ecological studies. Gigascience, 2014, 3:24.

18.     Jarvis ED*, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MS, Zavidovych V, Subramanian S, Gabaldon T, Capella-Gutierrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup M, Lindow B, Warren WC, Ray D, Green RE, Bruford MW, Zhan X, Dixon A, Li S, Li N, Huang Y, Derryberry EP, Bertelsen MF, Sheldon FH, Brumfield RT, Mello CV, Lovell PV, Wirthlin M, Schneider MP, Prosdocimi F, Samaniego JA, Vargas Velazquez AM, Alfaro-Nunez A, Campos PF, Petersen B, Sicheritz-Ponten T, Pas A, Bailey T, Scofield P, Bunce M, Lambert DM, Zhou Q, Perelman P, Driskell AC, Shapiro B, Xiong Z, Zeng Y, Liu S, Li Z, Liu B, Wu K, Xiao J, Yinqi X, Zheng Q, Zhang Y, Yang H, Wang J, Smeds L, Rheindt FE, Braun M, Fjeldsa J, Orlando L, Barker FK, Jonsson KA, Johnson W, Koepfli KP, O'Brien S, Haussler D, Ryder OA, Rahbek C, Willerslev E, Graves GR, Glenn TC, McCormack J, Burt D, Ellegren H, Alstrom P, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W*, Gilbert MT*& Zhang G*. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science, 2014, 346(6215):1320-1331. (Flagship paper in Special Issue of Avian phylogenomics Project)

19.     Zhou Q*, Zhang J, Bachtrog D, An N, Huang Q, Jarvis ED, Gilbert MT, & Zhang G*. Complex evolutionary trajectories of sex chromosomes across bird taxa. Science, 2014, 346(6215):1246338.

20.     Zhang G*, Li C, Li Q, Li B, Larkin DM, Lee C, Storz JF, Antunes A, Greenwold MJ, Meredith RW, Odeen A, Cui J, Zhou Q, Xu L, Pan H, Wang Z, Jin L, Zhang P, Hu H, Yang W, Hu J, Xiao J, Yang Z, Liu Y, Xie Q, Yu H, Lian J, Wen P, Zhang F, Li H, Zeng Y, Xiong Z, Liu S, Zhou L, Huang Z, An N, Wang J, Zheng Q, Xiong Y, Wang G, Wang B, Wang J, Fan Y, da Fonseca RR, Alfaro-Nunez A, Schubert M, Orlando L, Mourier T, Howard JT, Ganapathy G, Pfenning A, Whitney O, Rivas MV, Hara E, Smith J, Farre M, Narayan J, Slavov G, Romanov MN, Borges R, Machado JP, Khan I, Springer MS, Gatesy J, Hoffmann FG, Opazo JC, Hastad O, Sawyer RH, Kim H, Kim KW, Kim HJ, Cho S, Li N, Huang Y, Bruford MW, Zhan X, Dixon A, Bertelsen MF, Derryberry E, Warren W, Wilson RK, Li S, Ray DA, Green RE, O'Brien SJ, Griffin D, Johnson WE, Haussler D, Ryder OA, Willerslev E, Graves GR, Alstrom P, Fjeldsa J, Mindell DP, Edwards SV, Braun EL, Rahbek C, Burt DW, Houde P, Zhang Y, Yang H, Wang J, Avian Genome C, Jarvis ED*, Gilbert MT*& Wang J*. Comparative genomics reveals insights into avian genome evolution and adaptation. Science, 2014,346(6215):1311-1320. (Flagship paper in Special Issue of Avian phylogenomics Project)

21.     Cui J*, Zhao W, Huang Z, Jarvis ED, Gilbert MT, Walker PJ, Holmes EC, & Zhang G*. Low frequency of paleoviral infiltration across the avian phylogeny. Genome Biol, 2014, 15(12):539.

22.     Wang Z, Zhang J, Yang W, An N, Zhang P, Zhang G*, & Zhou Q*. Temporal genomic evolution of bird sex chromosomes. BMC Evol Biol, 2014,14:250.

23.     Poulsen M, Hu H, Li C, Chen Z, Xu L, Otani S, Nygaard S, Nobre T, Klaubauf S, Schindler PM, Hauser F, Pan H, Yang Z, Sonnenberg AS, de Beer ZW, Zhang Y, Wingfield MJ, Grimmelikhuijzen CJ, de Vries RP, Korb J, Aanen DK, Wang J, Boomsma JJ*, & Zhang G*. Complementary symbiont contributions to plant decomposition in a fungus-farming termite. Proc Natl Acad Sci U S A, 2014,111(40):14500-14505.

24.     Li Q, Wang Z, Lian J, Schiott M, Jin L, Zhang P, Zhang Y, Nygaard S, Peng Z, Zhou Y, Deng Y, Zhang W, Boomsma JJ*, & Zhang G*. Caste-specific RNA editomes in the leaf-cutting ant Acromyrmex echinatior. Nat Commun, 2014,5:4943.

25.     Terrapon N, Li C, Robertson HM, Ji L, Meng X, Booth W, Chen Z, Childers CP, Glastad KM, Gokhale K, Gowin J, Gronenberg W, Hermansen RA, Hu H, Hunt BG, Huylmans AK, Khalil SM, Mitchell RD, Munoz-Torres MC, Mustard JA, Pan H, Reese JT, Scharf ME, Sun F, Vogel H, Xiao J, Yang W, Yang Z, Yang Z, Zhou J, Zhu J, Brent CS, Elsik CG, Goodisman MA, Liberles DA, Roe RM, Vargo EL, Vilcinskas A, Wang J, Bornberg-Bauer E, Korb J, Zhang G*, & Liebig J*. Molecular traces of alternative social organization in a termite genome.Nat Commun, 2014, 5:3636.

26.     Shao C, Li Q, Chen S, Zhang P, Lian J, Hu Q, Sun B, Jin L, Liu S, Wang Z, Zhao H, Jin Z, Liang Z, Li Y, Zheng Q, Zhang Y, Wang J, & Zhang G. Epigenetic modification and inheritance in sexual reversal of fish. Genome Res, 2014, 24(4):604-615.

27.     Chen S*, Zhang G, Shao C, Huang Q, Liu G, Zhang P, Song W, An N, Chalopin D, Volff JN, Hong Y, Li Q, Sha Z, Zhou H, Xie M, Yu Q, Liu Y, Xiang H, Wang N, Wu K, Yang C, Zhou Q, Liao X, Yang L, Hu Q, Zhang J, Meng L, Jin L, Tian Y, Lian J, Yang J, Miao G, Liu S, Liang Z, Yan F, Li Y, Sun B, Zhang H, Zhang J, Zhu Y, Du M, Zhao Y, Schartl M*, Tang Q*, & Wang J*. Whole-genome sequence of a flatfish provides insights into ZW sex chromosome evolution and adaptation to a benthic lifestyle. Nat Genet, 2014, 46(3):253-260. (co-first author)

28.     Wang Z, Pascual-Anaya J, Zadissa A, Li W, Niimura Y, Huang Z, Li C, White S, Xiong Z, Fang D, Wang B, Ming Y, Chen Y, Zheng Y, Kuraku S, Pignatelli M, Herrero J, Beal K, Nozawa M, Li Q, Wang J, Zhang H, Yu L, Shigenobu S, Wang J, Liu J, Flicek P, Searle S, Wang J, Kuratani S, Yin Y, Aken B, Zhang G*, & Irie N*. The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan. Nat Genet, 2013,45(6):701-706.

29.     Orlando L, Ginolhac A, Zhang G, Froese D, Albrechtsen A, Stiller M, Schubert M, Cappellini E, Petersen B, Moltke I, Johnson PL, Fumagalli M, Vilstrup JT, Raghavan M, Korneliussen T, Malaspinas AS, Vogt J, Szklarczyk D, Kelstrup CD, Vinther J, Dolocan A, Stenderup J, Velazquez AM, Cahill J, Rasmussen M, Wang X, Min J, Zazula GD, Seguin-Orlando A, Mortensen C, Magnussen K, Thompson JF, Weinstock J, Gregersen K, Roed KH, Eisenmann V, Rubin CJ, Miller DC, Antczak DF, Bertelsen MF, Brunak S, Al-Rasheid KA, Ryder O, Andersson L, Mundy J, Krogh A, Gilbert MT, Kjaer K, Sicheritz-Ponten T, Jensen LJ, Olsen JV, Hofreiter M, Nielsen R, Shapiro B, Wang J, & Willerslev E. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature, 2013,499(7456):74-78. (co-first author)

30.     Fan Y, Huang ZY, Cao CC, Chen CS, Chen YX, Fan DD, He J, Hou HL, Hu L, Hu XT, Jiang XT, Lai R, Lang YS, Liang B, Liao SG, Mu D, Ma YY, Niu YY, Sun XQ, Xia JQ, Xiao J, Xiong ZQ, Xu L, Yang L, Zhang Y, Zhao W, Zhao XD, Zheng YT, Zhou JM, Zhu YB, Zhang GJ*, Wang J*, & Yao YG*. Genome of the Chinese tree shrew. Nat Commun, 2013, 4:1426.

31.     Zhang G*, Cowled C, Shi Z, Huang Z, Bishop-Lilly KA, Fang X, Wynne JW, Xiong Z, Baker ML, Zhao W, Tachedjian M, Zhu Y, Zhou P, Jiang X, Ng J, Yang L, Wu L, Xiao J, Feng Y, Chen Y, Sun X, Zhang Y, Marsh GA, Crameri G, Broder CC, Frey KG, Wang LF*, & Wang J*. Comparative analysis of bat genomes provides insight into the evolution of flight and immunity. Science, 2013,339(6118):456-460.

32.     Bonasio R, Li Q, Lian J, Mutti NS, Jin L, Zhao H, Zhang P, Wen P, Xiang H, Ding Y, Jin Z, Shen SS, Wang Z, Wang W, Wang J, Berger SL*, Liebig J*, Zhang G*, & Reinberg D*. Genome-wide and caste-specific DNA methylomes of the ants Camponotus floridanus and Harpegnathos saltator. Curr Biol, 2012, 22(19):1755-1764.

33.     Qiu Q, Zhang G, Ma T, Qian W, Wang J, Ye Z, Cao C, Hu Q, Kim J, Larkin DM, Auvil L, Capitanu B, Ma J, Lewin HA, Qian X, Lang Y, Zhou R, Wang L, Wang K, Xia J, Liao S, Pan S, Lu X, Hou H, Wang Y, Zang X, Yin Y, Ma H, Zhang J, Wang Z, Zhang Y, Zhang D, Yonezawa T, Hasegawa M, Zhong Y, Liu W, Zhang Y, Huang Z, Zhang S, Long R, Yang H, Wang J, Lenstra JA, Cooper DN, Wu Y, Wang J, Shi P, Wang J, & Liu J. The yak genome and adaptation to life at high altitude. Nat Genet, 2012,44(8):946-949. (co-first author)

34.     Li Y, Robins JH, Ye J, Huang Z, Wen Q, & Zhang G. Adaptive diversity of innate immune receptor family short pentraxins in Murinae. FEBS Lett, 2012, 586(6):798-803.

35.     Kim EB, Fang X, Fushan AA, Huang Z, Lobanov AV, Han L, Marino SM, Sun X, Turanov AA, Yang P, Yim SH, Zhao X, Kasaikina MV, Stoletzki N, Peng C, Polak P, Xiong Z, Kiezun A, Zhu Y, Chen Y, Kryukov GV, Zhang Q, Peshkin L, Yang L, Bronson RT, Buffenstein R, Wang B, Han C, Li Q, Chen L, Zhao W, Sunyaev SR, Park TJ, Zhang G*, Wang J*, & Gladyshev VN*. Genome sequencing reveals insights into physiology and longevity of the naked mole rat. Nature, 2011,479(7372):223-227.

36.     Yan G, Zhang G, Fang X, Zhang Y, Li C, Ling F, Cooper DN, Li Q, Li Y, van Gool AJ, Du H, Chen J, Chen R, Zhang P, Huang Z, Thompson JR, Meng Y, Bai Y, Wang J, Zhuo M, Wang T, Huang Y, Wei L, Li J, Wang Z, Hu H, Yang P, Le L, Stenson PD, Li B, Liu X, Ball EV, An N, Huang Q, Zhang Y, Fan W, Zhang X, Li Y, Wang W, Katze MG, Su B, Nielsen R, Yang H, Wang J, Wang X, & Wang J. Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques. Nat Biotechnol, 2011, 29(11):1019-1023. (co-first author)

37.     Nygaard S, Zhang G, Schiott M, Li C, Wurm Y, Hu H, Zhou J, Ji L, Qiu F, Rasmussen M, Pan H, Hauser F, Krogh A, Grimmelikhuijzen CJ, Wang J, & Boomsma JJ. The genome of the leaf-cutting ant Acromyrmex echinatior suggests key adaptations to advanced social life and fungus farming. Genome Res, 2011, 21(8):1339-1348. (co-first author)

38.     Zhang G*, Pei Z, Ball EV, Mort M, Kehrer-Sawatzki H, & Cooper DN. Cross-comparison of the genome sequences from human, chimpanzee, Neanderthal and a Denisovan hominin identifies novel potentially compensated mutations. Hum Genomics, 2011, 5(5):453-484.

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共同作者的有关重要论文 (43-74)

43.     Shao C, Bao B, Xie Z, Chen X, Li B, Jia X, Yao Q, Ortí G, Li W, Li X, Hamre K, Xu J, Wang L, Chen F, Tian Y, Schreiber AM, Wang N, Wei F, Zhang J, Dong Z, Gao L, Gai J, Sakamoto T, Mo S, Chen W, Shi Q, Li H, Xiu Y, Li Y, Xu W, Shi Z, Zhang G, Power D*, Wang Q*, Schartl M* & Chen S*. The genome and transcriptome of Japanese flounder provide insights into flatfish asymmetry. Nat Genet, 2017, 49(1): 119-124.

44.     Yin W*, Wang Z, Li Q, Lian J, Zhou Y, Lu B, Jin L, Qiu P, Zhang P, Zhu W, Wen B, Huang Y, Lin Z, Qiu B, Su X, Yang H, Zhang G, Yan G, Zhou Q*. Evolutionary trajectories of snake genes and genomes revealed by comparative analyses of five-pacer viper. Nat Commun, 2016, 7: 13107

45.     Sun YB, Xiong ZJ, Xiang XY, Liu SP, Zhou WW, Tu XL, Zhong L, Wang L, Wu DD, Zhang BL, Zhu CL, Yang MM, Chen HM, Li F, Zhou L, Feng SH, Huang C, Zhang GJ, Irwin D, Hillis DM*, Murphy RW, Yang HM, Che J*, Wang J*, & Zhang YP*. Whole-genome sequence of the Tibetan frog Nanorana parkeri and the comparative evolution of tetrapod genomes. Proc Natl Acad Sci U S A, 2015,112(11):E1257-1262.

46.     Dobrynin P, Liu S, Tamazian G, Xiong Z, Yurchenko AA, Krasheninnikova K, Kliver S, Schmidt-Kuntzel A, Koepfli KP, Johnson W, Kuderna LF, Garcia-Perez R, Manuel M, Godinez R, Komissarov A, Makunin A, Brukhin V, Qiu W, Zhou L, Li F, Yi J, Driscoll C, Antunes A, Oleksyk TK, Eizirik E, Perelman P, Roelke M, Wildt D, Diekhans M, Marques-Bonet T, Marker L, Bhak J, Wang J, Zhang G, & O'Brien SJ*. Genomic legacy of the African cheetah, Acinonyx jubatus. Genome Biol, 2015, 16:277.

47.     Nadachowska-Brzyska K, Li C, Smeds L, Zhang G, & Ellegren H*. Temporal Dynamics of Avian Populations during Pleistocene Revealed by Whole-Genome Sequences. Curr Biol, 2015, 25(10):1375-1380.

48.     Eory L, Gilbert MT, Li C, Li B, Archibald A, Aken BL, Zhang G, Jarvis E, Flicek P, & Burt DW. Avianbase: a community resource for bird genomics. Genome Biol, 2015,16:21.

49.     Li X, Fan D, Zhang W, Liu G, Zhang L, Zhao L, Fang X, Chen L, Dong Y, Chen Y, Ding Y, Zhao R, Feng M, Zhu Y, Feng Y, Jiang X, Zhu D, Xiang H, Feng X, Li S, Wang J, Zhang G, Kronforst MR*, & Wang W*. Outbred genome sequencing and CRISPR/Cas9 gene editing in butterflies. Nat Commun, 2015, 6:8212.

50.     Pfenning AR, Hara E, Whitney O, Rivas MV, Wang R, Roulhac PL, Howard JT, Wirthlin M, Lovell PV, Ganapathy G, Mouncastle J, Moseley MA, Thompson JW, Soderblom EJ, Iriki A, Kato M, Gilbert MT, Zhang G, Bakken T, Bongaarts A, Bernard A, Lein E, Mello CV, Hartemink AJ, & Jarvis ED. Convergent transcriptional specializations in the brains of humans and song-learning birds. Science, 2014, 346(6215):1256846.

51.     Meredith RW, Zhang G, Gilbert MT, Jarvis ED, & Springer MS. Evidence for a single loss of mineralized teeth in the common avian ancestor. Science, 2014, 346(6215):1254390.

52.     Green RE, Braun EL, Armstrong J, Earl D, Nguyen N, Hickey G, Vandewege MW, St John JA, Capella-Gutierrez S, Castoe TA, Kern C, Fujita MK, Opazo JC, Jurka J, Kojima KK, Caballero J, Hubley RM, Smit AF, Platt RN, Lavoie CA, Ramakodi MP, Finger JW, Jr., Suh A, Isberg SR, Miles L, Chong AY, Jaratlerdsiri W, Gongora J, Moran C, Iriarte A, McCormack J, Burgess SC, Edwards SV, Lyons E, Williams C, Breen M, Howard JT, Gresham CR, Peterson DG, Schmitz J, Pollock DD, Haussler D, Triplett EW, Zhang G, Irie N, Jarvis ED, Brochu CA, Schmidt CJ, McCarthy FM, Faircloth BC, Hoffmann FG, Glenn TC, Gabaldon T, Paten B, & Ray DA. Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science, 2014, 346(6215):1254449.

53.     You X, Bian C, Zan Q, Xu X, Liu x, Chen J, Wang J, Qiu Y, Li W, Zhang X, Sun Y, Chen S, Hong W, Li Y, Cheng S, Fan G, Shi C, Liang J, Tang TY, Yang C, Ruan Z, Bai J, Peng C, Mu Q, Lu J, Fan M, Yang S, Huang Z, Jiang X, Fang X, Zhang G, Zhang Y, Polgar G, Yu H, Liu Z, Zhang G, Ravi V, Coon SL, Wang J, Yang H, Venkatesh B, Wang J, Shi Q. Mudskipper genomes provide insights into the terrestrial adaptation of amphibious fishes. Nat Commun, 2014, 5: 5594.

54.     Liu S, Lorenzen ED, Fumagalli M, Li B, Harris K, Xiong Z, Zhou L, Korneliussen TS, Somel M, Babbitt C, Wray G, Li J, He W, Wang Z, Fu W, Xiang X, Morgan CC, Doherty A, O'Connell MJ, McInerney JO, Born EW, Dalen L, Dietz R, Orlando L, Sonne C, Zhang G, Nielsen R*, Willerslev E*, & Wang J*. Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears. Cell, 2014,157(4):785-794.

55.     Wang X, Fang X, Yang P, Jiang X, Jiang F, Zhao D, Li B, Cui F, Wei J, Ma C, Wang Y, He J, Luo Y, Wang Z, Guo X, Guo W, Wang X, Zhang Y, Yang M, Hao S, Chen B, Ma Z, Yu D, Xiong Z, Zhu Y, Fan D, Han L, Wang B, Chen Y, Wang J, Yang L, Zhao W, Feng Y, Chen G, Lian J, Li Q, Huang Z, Yao X, Lv N, Zhang G, Li Y, Wang J, Wang J, Zhu B, & Kang L. The locust genome provides insight into swarm formation and long-distance flight. Nat Commun, 2014,5:2957.

56.     Oxley PR*, Ji L, Fetter-Pruneda I, McKenzie SK, Li C, Hu H, Zhang G, & Kronauer DJ*. The genome of the clonal raider ant Cerapachys biroi. Curr Biol, 2014, 24(4):451-458.

57.     Li S, Li B, Cheng C, Xiong Z, Liu Q, Lai J, Carey HV, Zhang Q, Zheng H, Wei S, Zhang H, Chang L, Liu S, Zhang S, Yu B, Zeng X, Hou Y, Nie W, Guo Y, Chen T, Han J, Wang J, Wang J, Chen C, Liu J, Stambrook PJ, Xu M, Zhang G, Gilbert MT, Yang H, Jarvis ED*, Yu J*, & Yan J*. Genomic signatures of near-extinction and rebirth of the crested ibis and other endangered bird species. Genome Biol, 2014, 15(12):557.

58.     Fang X, Seim I, Huang Z, Gerashchenko MV, Xiong Z, Turanov AA, Zhu Y, Lobanov AV, Fan D, Yim SH, Yao X, Ma S, Yang L, Lee SG, Kim EB, Bronson RT, Sumbera R, Buffenstein R, Zhou X, Krogh A, Park TJ, Zhang G, Wang J, & Gladyshev VN. Adaptations to a subterranean environment and longevity revealed by the analysis of mole rat genomes. Cell Rep, 2014,8(5):1354-1364.

59.     Shapiro MD, Kronenberg Z, Li C, Domyan ET, Pan H, Campbell M, Tan H, Huff CD, Hu H, Vickrey AI, Nielsen SC, Stringham SA, Hu H, Willerslev E, Gilbert MT, Yandell M, Zhang G, & Wang J. Genomic diversity and evolution of the head crest in the rock pigeon. Science, 2013, 339(6123):1063-1067.

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62.     Dong Y, Xie M, Jiang Y, Xiao N, Du X, Zhang W, Tosser-Klopp G, Wang J, Yang S, Liang J, Chen W, Chen J, Zeng P, Hou Y, Bian C, Pan S, Li Y, Liu X, Wang W, Servin B, Sayre B, Zhu B, Sweeney D, Moore R, Nie W, Shen Y, Zhao R, Zhang G, Li J, Faraut T, Womack J, Zhang Y, Kijas J, Cockett N, Xu X, Zhao S, Wang J*, & Wang W*. Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). Nat Biotechnol, 2013, 31(2):135-141.

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65.     Young ND, Jex AR, Li B, Liu S, Yang L, Xiong Z, Li Y, Cantacessi C, Hall RS, Xu X, Chen F, Wu X, Zerlotini A, Oliveira G, Hofmann A, Zhang G, Fang X, Kang Y, Campbell BE, Loukas A, Ranganathan S, Rollinson D, Rinaldi G, Brindley PJ, Yang H, Wang J, Wang J, & Gasser RB. Whole-genome sequence of Schistosoma haematobium. Nat Genet, 2012,44(2):221-225.

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近五年发表的10篇代表性论文 (*通讯作者)

1 Avalos A, Pan H, Li C, Acevedo Gonzalez JP, Rendon G, Fields CJ, Brown PJ, Giray T, Robinson GE*, Hudson ME*, Zhang G*. A soft selective sweep during rapid evolution of gentle behaviour in an Africanized honeybee. Nat Commun, 2017, 8:1550.

2 Seki R, Li 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 TM, 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, 2017, 8, 14229.

3 Nygaard S, Hu H, Li, C, Schiøtt M, Chen Z, Yang Z, Xie Q, Ma C, Deng Y, Dikow BR, Rabeling C, Nash RD, Wcislo TW, Brady GS, Schultz RT, Zhang G*, Boomsma J*. Reciprocal genomic evolution in the ant-fungus agricultural symbiosis. Nat Commun, 2016, 7.

4 Kapheim KM, Pan H, Li C, Salzberg SL, Puiu D, Magoc T, Robertson HM, Hudson ME, Venkat A, Fischman BJ, Hernandez A, Yandell M, Ence D, Holt C, Yocum GD, Kemp WP, Bosch J, Waterhouse RM, Zdobnov EM, Stolle E, Kraus FB, Helbing S, Moritz RF, Glastad KM, Hunt BG, Goodisman MA, Hauser F, Grimmelikhuijzen CJ, Pinheiro DG, Nunes FM, Soares MP, Tanaka ED, Simoes ZL, Hartfelder K, Evans JD, Barribeau SM, Johnson RM, Massey JH, Southey BR, Hasselmann M, Hamacher D, Biewer M, Kent CF, Zayed A, Blatti C, 3rd, Sinha S, Johnston JS, Hanrahan SJ, Kocher SD, Wang J*, Robinson GE*, & Zhang G*. Social evolution. Genomic signatures of evolutionary transitions from solitary to group living. Science, 2015, 348(6239):1139-1143.

5 Zhang G*, Rahbek C, Graves GR, Lei F, Jarvis ED, & Gilbert MT. Genomics: Bird sequencing project takes off. Nature, 2015, 522(7554):34.

6 Zhang G*, Jarvis ED, & Gilbert MT. Avian genomes. A flock of genomes. Introduction. Science, 2014, 346(6215):1308-1309.

7 Jarvis ED*, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MS, Zavidovych V, Subramanian S, Gabaldon T, Capella-Gutierrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup M, Lindow B, Warren WC, Ray D, Green RE, Bruford MW, Zhan X, Dixon A, Li S, Li N, Huang Y, Derryberry EP, Bertelsen MF, Sheldon FH, Brumfield RT, Mello CV, Lovell PV, Wirthlin M, Schneider MP, Prosdocimi F, Samaniego JA, Vargas Velazquez AM, Alfaro-Nunez A, Campos PF, Petersen B, Sicheritz-Ponten T, Pas A, Bailey T, Scofield P, Bunce M, Lambert DM, Zhou Q, Perelman P, Driskell AC, Shapiro B, Xiong Z, Zeng Y, Liu S, Li Z, Liu B, Wu K, Xiao J, Yinqi X, Zheng Q, Zhang Y, Yang H, Wang J, Smeds L, Rheindt FE, Braun M, Fjeldsa J, Orlando L, Barker FK, Jonsson KA, Johnson W, Koepfli KP, O'Brien S, Haussler D, Ryder OA, Rahbek C, Willerslev E, Graves GR, Glenn TC, McCormack J, Burt D, Ellegren H, Alstrom P, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W*, Gilbert MT* & Zhang G*. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science, 2014, 346(6215):1320-1331. (Flagship paper in Special Issue of Avian phylogenomics Project)

8 Zhang G*, Li C, Li Q, Li B, Larkin DM, Lee C, Storz JF, Antunes A, Greenwold MJ, Meredith RW, Odeen A, Cui J, Zhou Q, Xu L, Pan H, Wang Z, Jin L, Zhang P, Hu H, Yang W, Hu J, Xiao J, Yang Z, Liu Y, Xie Q, Yu H, Lian J, Wen P, Zhang F, Li H, Zeng Y, Xiong Z, Liu S, Zhou L, Huang Z, An N, Wang J, Zheng Q, Xiong Y, Wang G, Wang B, Wang J, Fan Y, da Fonseca RR, Alfaro-Nunez A, Schubert M, Orlando L, Mourier T, Howard JT, Ganapathy G, Pfenning A, Whitney O, Rivas MV, Hara E, Smith J, Farre M, Narayan J, Slavov G, Romanov MN, Borges R, Machado JP, Khan I, Springer MS, Gatesy J, Hoffmann FG, Opazo JC, Hastad O, Sawyer RH, Kim H, Kim KW, Kim HJ, Cho S, Li N, Huang Y, Bruford MW, Zhan X, Dixon A, Bertelsen MF, Derryberry E, Warren W, Wilson RK, Li S, Ray DA, Green RE, O'Brien SJ, Griffin D, Johnson WE, Haussler D, Ryder OA, Willerslev E, Graves GR, Alstrom P, Fjeldsa J, Mindell DP, Edwards SV, Braun EL, Rahbek C, Burt DW, Houde P, Zhang Y, Yang H, Wang J, Avian Genome C, Jarvis ED*, Gilbert MT* & Wang J*. Comparative genomics reveals insights into avian genome evolution and adaptation. Science, 2014, 346(6215):1311-1320. (Flagship paper in Special Issue of Avian phylogenomics Project)

9 Li Q, Wang Z, Lian J, Schiott M, Jin L, Zhang P, Zhang Y, Nygaard S, Peng Z, Zhou Y, Deng Y, Zhang W, Boomsma JJ*, & Zhang G*. Caste-specific RNA editomes in the leaf-cutting ant Acromyrmex echinatior. Nat Commun, 2014, 5:4943.

10Poulsen M, Hu H, Li C, Chen Z, Xu L, Otani S, Nygaard S, Nobre T, Klaubauf S, Schindler PM, Hauser F, Pan H, Yang Z, Sonnenberg AS, de Beer ZW, Zhang Y, Wingfield MJ, Grimmelikhuijzen CJ, de Vries RP, Korb J, Aanen DK, Wang J*, Boomsma JJ*, & Zhang G*. Complementary symbiont contributions to plant decomposition in a fungus-farming termite. Proc Natl Acad Sci U S A, 2014, 111(40):14500-14505.

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赵若苹  实验师

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高琼华  2016