Ya-Long Guo
State Key Laboratory of Systematic and Evolutionary Botany
Institute of Botany, Chinese Academy of Sciences
Beijing 100093, China

Research Areas

Our research interests include three areas, evolutionary genomics, speciation, and adaptation. The plant species we study include but not limited to the dicot model species, Arabidopsis thaliana, and related species in the Brassicaceae and the monocot model species, rice (Oryza sativa), and its relatives.


2001 - 2005 Ph.D. in plant systematics and evolution - Molecular systematics of the tribe Oryzeae (Poaceae), Institute of Botany, Chinese Academy of Sciences, China.

1998 - 2001 M.S. in plant physiology - Metabolism of reactive oxygen species under natural drought stress in wheat strains;, Lanzhou University, China.

1994 - 1998 B.A., Undergraduate studies in biology, Northwest Normal University, China.


• 2011 - present Professor, State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.

• 2005 - 2011 Postdoctoral Fellow, Evolutionary genomics and genetics in Arabidopsis relatives, Max-Planck Institute for Developmental Biology, Tübingen, Germany.



1.      Yang FS§, Liu M§, Guo X§, Xu C, Jiang J, Mu W, Fang D, Xu YC, Zhang FM, Wang YH, Yang T, Chen H, Sahu SK, Li R, Wang G, Wang Q, Xu X, Ge S, Liu H*, Guo YL*. 2024. Signatures of adaptation and purifying selection in highland populations of Dasiphora fruticosa. Mol Biol Evol msae099.

2.      Jiang J, Xu YC, Zhang ZQ, Chen JF, Niu XM, Hou XH, Li XT, Wang L, Zhang Y, Ge S, Guo YL*. 2024. Forces driving transposable element load variation during Arabidopsis range expansion. Plant Cell 36: 840-862.

3.      Chen JF§, Xu YC§, Jiang J§, Niu XM, Hou XH, Zhang ZQ, Guo YL*. 2023. Transposable elements and gene expression variation in the intraspecific hybrids of Capsella rubella. Journal of Systematics and Evolution 62: 358-367.

4.      Liu D, Luo S, Li Z, Liang G, Guo YL, Xu Y, Chong K*. 2024. COG3 confers the chilling tolerance to mediate OsFtsH2-D1 module in rice. New Phytol 241: 2143-2157.


5.      Wang MY§, Chen JB§, Wu R§, Guo HL§, Chen Y, Li ZJ, Wei LY, Liu C, He SF, Du MD, Guo YL, Peng YL, Jones JDG, Weigel D, Huang JH*, Zhu WS*. 2023. The plant immune receptor SNC1 monitors helper NLRs targeted by a bacterial effector. Cell Host & Microbe 31: 1792-1803.

6.      Guo X, Wang F, Fang D, Lin Q, Sahu SK, Luo L, Li J, Chen Y, Dong S, Chen S, Liu Y, Luo S, Guo YL, Liu H*. 2023. The genome of Acorus deciphers insights into early monocot evolution. Nature Communications 14: 3662.

7.      Yan ZB*, Tian D*, Han WX, Ji CJ, Hou XH, Guo YL, Fang JY. 2023. Weak transgenerational effects of ancestral nitrogen and phosphorus availabilities on offspring phenotypes in Arabidopsis thaliana. Journal of Plant Research 136: 515–525.

8.      Hu Y§*, Wang X§, Xu Y§, Yang H§, Tong Z§, Tian R§, Xu S§, Yu L*, Guo YL*, Shi P*, Huang S*, Yang G*, Shi S*, Wei F*. 2023. Molecular mechanisms of adaptive evolution in wild animals and plants. Sci China Life Sci 66: 453-495.

9.      Li Y, Liu H, Ma T, Li J, Yuan J, Xu YC, Sun R, Zhang X, Jing Y, Guo YL, Lin R*. 2023. Arabidopsis EXECUTER1 interacts with WRKY transcription factors to mediate plastid-to-nucleus singlet oxygen signaling. Plant Cell 35: 827-851.

10.   Li YH§, Qin C§, Wang L§, Jiao C§, Hong H, Tian Y, Li Y, Xing G, Wang J, Gu Y, Gao X, Li D, Li H, Liu Z, Jing X, Feng B, Zhao T, Guan R, Guo Y, Liu J, Yan Z, Zhang L, Ge T, Li X, Wang X, Qiu H, Zhang W, Luan X, Han Y, Han D, Chang R, Guo YL, Reif JC, Jackson SA*, Liu B*, Tian S*, Qiu LJ*. 2023. Genome-wide signatures of the geographic expansion and breeding of soybean. Sci China Life Sci 66: 350-365.


11.   Huang X§, Wang W§, Gong T§, Wickell D§, Kuo LY, Zhang X, Wen J, Kim H, Lu F, Zhao H, Chen S, Li H, Wu W, Yu C, Chen S, Fan W, Chen S, Bao X, Li L, Zhang D, Jiang L, Yan X, Liao Z, Zhou G, Guo YL, Ralph J, Sederoff RR, Wei H*, Zhu P*, Li FW*, Ming R*, Li Q*. 2022. The flying spider-monkey tree fern genome provides insights into fern evolution and arborescence. Nature Plants 8: 500-512.

12.   Li L§, Chen X§, Fang D§, Dong S§, Guo X§, Li N§, Campos-Dominguez L, Wang W, Liu Y, Lang X, Peng Y, Tian D, Thomas DC, Mu W, Liu M, Wu C, Yang T, Zhang S, Yang L, Yang J, Liu ZJ, Zhang L, Zhang X, Chen F, Jiao Y, Guo YL, Hughes M, Wang W, Liu X, Zhong C, Li A, Sahu SK, Yang H, Wu E, Sharbrough J, Lisby M, Liu X, Xu X, Soltis DE, Van de Peer Y, Kidner C, Zhang S*, Liu H*. 2022. Genomes shed light on the evolution of Begonia, a mega-diverse genus. New Phytologist 234: 295-310.

13.   Liu P, Ye DM, Chen M, Zhang J, Huang XH, Shen LL, Xia KK, Xu XJ, Xu YC, Guo YL, Wang YC*, Huang F*. 2022. Scaling-up and proteomic analysis reveals photosynthetic and metabolic insights toward prolonged H2 photoproduction in Chlamydomonas hpm91 mutant lacking proton gradient regulation 5 (PGR5). Photosynth Res 154: 397-411.

14.   Yan ZB*, Tian D, Huang HY, Sun YF, Hou XH, Han WX, Guo YL, Fang JY. 2022. Interactive effects of plant density and nitrogen availability on the biomass production and leaf stoichiometry of Arabidopsis thaliana. Journal of Plant Ecology DOI: 10.1093/jpe/rtac101.


15.   Geng MF, Wang XH, Wang MX, Cai Z, Meng QL, Wang X, Zhou L, Han JD, Li JL, Zhang FM, Guo YL, Ge S*. 2021. Genome-wide investigation on transcriptional responses to drought stress in wild and cultivated rice. Environmental and Experimental Botany 189, 104555.

16.   Wieters B, Steige KA, He F, Koch EM, Ramos-Onsins SE, Gu H, Guo YL, Sunyaev S, de Meaux J*. 2021. Polygenic adaptation of rosette growth in Arabidopsis thaliana. PLoS Genet 17: e1008748.

17.   Xu YC§, Zhang J§, Zhang DY, Nan YH, Ge S, Guo YL*. 2021. Identification of long noncoding natural antisense transcripts (lncNATs) correlated with drought stress response in wild rice (Oryza nivara). BMC Genomics 22: 424.


18.   Ge S*, Guo YL. 2020. Evolution of genes and genomes in the genomics era. Sci China Life Sci 63: 602-605.

19.   Xu YC, Guo YL*. 2020. Less Is More, Natural Loss-of-Function Mutation Is a Strategy for Adaptation. Plant Communications 1: 100103.

20.   Zhang J, Fu XX, Li RQ, Zhao X, Liu Y, Li MH, Zwaenepoel A, Ma H, Goffinet B, Guan YL, Xue JY, Liao YY, Wang QF, Wang QH, Wang JY, Zhang GQ, Wang ZW, Jia Y, Wang MZ, Dong SS, Yang JF, Jiao YN, Guo YL, Kong HZ, Lu AM, Yang HM, Zhang SZ*, Van de Peer Y*, Liu ZJ*, Chen ZD*. 2020. The hornwort genome and early land plant evolution. Nat Plants 6: 107-118.

21.   Zhang MX, Zhu SS, Xu YC, Guo YL, Yang WC*, Li HJ*. 2020. Transcriptional repression specifies the central cell for double fertilization. Proc Natl Acad Sci U S A 117: 6231-6236.


22.   Cai Z, Zhou L, Ren NN, Xu X, Liu R, Huang L, Zheng XM, Meng QL, Du YS, Wang MX, Geng MF, Chen WL, Jing CY, Zou XH, Guo J, Chen CB, Zeng HZ, Liang YT, Wei XH, Guo YL, Zhou HF, Zhang FM, Ge S*. 2019. Parallel speciation of wild rice associated with habitat shifts. Mol Biol Evol 31: 875-889.

23.   Li Z, Mo W, Jia L, Xu YC, Tang W, Yang W, Guo YL, Lin R*. 2019. Rice FLUORESCENT1 is involved in the regulation of chlorophyll. Plant Cell Physiol 60: 2307-2318.

24.   Mao D, Xin Y, Tan Y, Hu X, Bai J, Liu ZY, Yu Y, Li L, Peng C, Fan T, Zhu Y, Guo YL, Wang S, Lu D, Xing Y, Yuan L*, Chen C*. 2019. Natural variation in the HAN1 gene confers chilling tolerance in rice and allowed adaptation to a temperate climate. Proc Natl Acad Sci U S A 116: 3494-3501.

25.   Niu XM§, Xu YC§, Li ZW, Bian YT, Hou XH, Chen JF, Zou YP, Jiang J, Wu Q, Ge S, Balasubramanian S, Guo YL*. 2019. Transposable elements drive rapid phenotypic variation in Capsella rubella. Proc Natl Acad Sci U S A 116: 6908-6913. (Cover story)

26.   Xu YC, Niu XM, Li XX, He W, Chen JF, Zou YP, Wu Q, Zhang YE, Busch W, Guo YL*. 2019. Adaptation and phenotypic diversification through loss-of-function mutations in Arabidopsis protein-coding genes. Plant Cell 31: 1012-1025.

[For perspectives on this work, see: 1] Caseys C. 2019. Loss-of-function, a strategy for adaptation in Arabidopsis. Plant Cell 31: 935. 2] Faculty of 1000 Biology:]

27.   Yan Z, Hou X, Han W, Ma S, Shen H, Guo YL, Fang J*. 2019. Effects of nitrogen and phosphorus supply on stoichiometry of six elements in leaves of Arabidopsis thaliana. Annals of Botany 123: 441-450.

28.   Yan Z, Eziz A, Tian D, Li X, Hou X, Peng H, Han W, Guo YL, and Fang, J*. 2019. Biomass allocation in response to nitrogen and phosphorus availability: insight from experimental manipulations of Arabidopsis thaliana. Frontiers in Plant Science 10: 598.

29.   Zhong S, Liu M, Wang Z, Huang Q, Hou S, Xu YC, Ge Z, Song Z, Huang J, Qiu X, Shi Y, Xiao J, Liu P, Guo YL, Dong J, Dresselhaus T, Gu H, Qu LJ*. 2019. Cysteine-rich peptides promote interspecific genetic isolation in Arabidopsis. Science 364, 851.

30.   郭亚龙*. 2019. 拟南芥及其近缘种的适应性进化研究. 中国科学:生命科学49: 320-326.


31.   Li ZW§, Hou XH§, Chen JF, Xu YC, Wu Q, González J, Guo YL*. 2018. Transposable elements contribute to the adaptation of Arabidopsis thaliana. Genome Biology and Evolution 10: 2140-2150.

32.   Shen Y, Zhang J, Liu Y, Liu S, Liu Z, Duan Z, Wang Z, Zhu B, Guo YL, and Tian Z*. 2018. DNA methylation footprints during soybean domestication and improvement. Genome Biology 19: 128.

33.   Yan Z, Li X, Tian D, Han W, Hou X, Shen H, Guo YL, Fang J*. 2018. Nutrient addition affects scaling relationship of leaf nitrogen to phosphorus in Arabidopsis thaliana. Functional Ecology 32: 2689-2698.

34.   Yang L§, Wang HN§, Hou XH, Zou YP, Han TS, Niu XM, Zhang J, Zhao Z, Todesco M, Balasubramanian S, Guo YL*. 2018. Parallel evolution of common allelic variants confers flowering diversity in Capsella rubella. Plant Cell 30: 1322-1336.

[For perspectives on this work, see: 1] Moyers BT. 2018. Is Genetic Evolution Predictable? Plant Cell 30: 1171-1172. 2] Faculty of 1000 Biology:]


35.   Li W, Zhang F, Wu R, Jia L, Li G, Guo YL, Liu C, Wang G*. 2017. A novel N-methyltransferase in Arabidopsis appears to feed a conserved pathway for nicotinate detoxification among land plants and is associated with lignin biosynthesis. Plant Physiol 174: 1492-1504.

36.   Wu Q, Han TS, Chen X, Chen JF, Zou YP, Li ZW, Xu YC, Guo YL*. 2017. Long-term balancing selection contributes to adaptation in Arabidopsis and its relatives. Genome Biology 18: 217.

[For perspectives on this work, see: Wang B, Mitchell-Olds T. 2017. Balancing selection and trans-specific polymorphisms. Genome Biology 18(1): 231]

37.   Zou YP§, Hou XH§, Wu Q, Chen JF, Li ZW, Han TS, Niu XM, Yang L, Xu YC, Zhang J, Zhang FM, Tan D, Tian Z, Gu H, Guo YL*. 2017. Adaptation of Arabidopsis thaliana to the Yangtze River basin. Genome Biology 18: 239.


38.   Li ZW, Chen X, Wu Q, Hagmann J, Han TS, Zou YP, Ge S, Guo YL*. 2016. On the origin of de novo genes in Arabidopsis thaliana populations. Genome Biology and Evolution 8: 2190-2202.

39.   Yan Z, Guan H, Han W, Han TS, Guo YL, Fang J*. 2016. Reproductive organ and young tissues show constrained elemental composition in Arabidopsis thaliana. Annals of Botany 117: 431-439.


40.   Han TS, Wu Q, Hou XH, Li ZW, Zou YP, Ge S, Guo YL*. 2015. Frequent introgressions from diploid species contribute to the adaptation of the tetraploid Shepherd’s purse (Capsella bursa-pastoris). Molecular Plant 8: 427-438. (Cover story)

41.   Yan Z, Kim N, Han W, Guo YL, Han TS, Du E, Fang J*. 2015. Effects of nitrogen and phosphorus supply on growth rate, leaf stoichiometry, and nutrient resorption of Arabidopsis thaliana. Plant Soil 388: 147-155.


42.   Guo YL*. 2013. Gene family evolution in green plants with emphasis on the origination and evolution of Arabidopsis thaliana genes. Plant Journal 73: 941-951.

43.   Slotte T, Hazzouri KM, Ågren JA, Koenig D, Maumus F, Guo YL, Steige K, Platts AE, Escobar JS, Newman LK, Wang W, Mandáková T, Vello E, Smith LM, Henz SR, Steffen J, Takuno S, Brandvain Y, Coop G, Andolfatto P, Hu TT, Blanchette M, Clark RM, Quesneville H, Nordborg M, Gaut BS, Lysak MA, Jenkins J, Grimwood J, Chapman J, Prochnik S, Shu S, Rokhsar D, Schmutz J, Weigel D*, Wright SI*. 2013. The Capsella rubella genome and the genomic consequences of rapid mating system evolution. Nature Genetics 45: 831-835.


44.   Guo YL, Todesco M, Hagmann J, Das S, Weigel D*. 2012. Independent FLC mutations as causes of flowering time variation in Arabidopsis thaliana and Capsella rubella. Genetics 192: 729-739.


45.   Guo YL, Fitz J, Schneeberger K, Ossowski S, Cao J, Weigel D*. 2011. Genome-wide comparison of NB-LRR encoding resistance genes in Arabidopsis. Plant Physiology 157: 757-769.

46.   Guo YL§, Zhao X§, Lanz C, Weigel D. 2011. Evolution of S-locus region in Arabidopsis thaliana relatives. Plant Physiology 157: 937-946.

47.   Hollister JD, Smith LM, Guo YL, Ott F, Weigel D*, Gaut BS*. 2011. Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata. Proc. Natl. Acad. Sci. USA 108: 2322-2327.

48.   Hu TT§, Pattyn P§, Bakker EG, Cao J, Cheng JF, Clark RM, Fahlgren N, Fawcett JA, Grimwood J, Gundlach H, Haberer G, Hollister JD, Ossowski S, Ottilar RP, Salamov A, Schneeberger K, Spannagl M, Wang X, Yang L, Nasrallah ME, Bergelson J, Carrington JC, Gaut BS, Schmutz J, Mayer KFX, Van De Peer Y, Grigoriev IV, Nordborg M, Weigel D*, Guo YL*. 2011. The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nature Genetics 43: 476-481.


49.   Wahl V, Brand LH, Guo YL, Schmid M*. 2010. The FANTASTIC FOUR proteins influence shoot meristem size in Arabidopsis thaliana. BMC Plant Biology 10: 285.

50.   Guo YL§, Bechsgaard JS§, Slotte T, Neuffer B, Lascoux M, Weigel D*, Schierup MH*. 2009. Recent speciation of Capsella rubella from C. grandiflora, associated with loss of self-incompatibility and an extreme bottleneck. Proc. Natl. Acad. Sci. USA 106: 5246-5251.

[For perspectives on this work, see: 1) Pannell JR. 2009. Mating-system evolution: genies from a bottleneck. Current Biology 19(9): R369-R370. 2] Faculty of 1000 Biology:]

51.   Tang C, Toomajian C, Sherman-Broyles S, Plagnol V, Guo YL, Hu TT, Clark RM, Nasrallah JB, Weigel D, Nordborg M*. 2007. The evolution of selfing in Arabidopsis thaliana. Science 317: 1070-1072.

[For a perspective on this work, see Faculty of 1000 Biology:]

52.   郭亚龙, 葛颂*. 2006. 稻族的系统发育及其研究进展. 植物分类学报 44: 211-230.

53.   Guo YL, Ge S*. 2005. Molecular phylogeny of Oryzeae (Poaceae) based on DNA sequences from chloroplast, mitochondrial and nuclear genomes. American Journal of Botany 92: 1548-1558.

[For a perspective on this work, see Faculty of 1000 Biology:]

54.   郭亚龙, 葛颂*. 2004. 线粒体nad1基因内含子在稻族系统学研究中的价值兼论Porteresia的系统位置. 植物分类学报 42: 333-344.