郭亚龙
博士 研究员 博士生导师
中国科学院植物所 系统与进化植物学国家重点实验室
主要研究方向是植物适应性进化,具体包括三个方面的研究工作:1)进化基因组学;2)自交不亲和系统的进化及物种形成;3)自然变异及适应性进化。
个性化签名
- 姓名:郭亚龙
- 目前身份:在职研究人员
- 担任导师情况:博士生导师
- 学位:博士
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学术头衔:
博士生导师
- 职称:高级-研究员
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学科领域:
植物学
- 研究兴趣:主要研究方向是植物适应性进化,具体包括三个方面的研究工作:1)进化基因组学;2)自交不亲和系统的进化及物种形成;3)自然变异及适应性进化。
郭亚龙,中国科学院植物研究所研究员、博士生导师。1998年在西北师范大学获学士学位,2001年在兰州大学获硕士学位,2005年在中科院植物所获博士学位。2005年至2011年在德国马普发育生物学研究所做博士后研究。2012年获得国家自然科学基金委“优秀青年科学基金”项目资助;2019年获得国家自然科学基金委“杰出青年科学基金”项目资助;2019年获得吴征镒植物学奖“青年创新奖”。目前担任中国科学院大学岗位教授;《Journal of Systematics and Evolution》副主编,《Journal of Integrative Plant Biology》、《BMC Plant Biology》、《植物学报》及《生物多样性》编委;国际拟南芥指导委员会( The Multinational Arabidopsis Steering Committee)自然变异与比较基因组学分会(Natural variation and comparative genomics)共同主席,系统与进化植物学专业委员会委员。主要研究方向是植物适应性进化,具体包括三个方面的研究工作:1)进化基因组学;2)自交不亲和系统的进化及物种形成;3)自然变异及适应性进化。
主要研究工作:
1.进化基因组学
利用全基因组测序的手段,结合进化基因组学、群体遗传学及生物信息学等多学科的方法,重点探讨基因组进化的规律和机制,包括基因组大小的变异(Hu et al., 2011, Nature Genetics)、基因的重复和丢失(Guo et al., 2011, Plant Physiology; Guo, 2013, Plant Journal)、基因的起源(Li et al., 2016, Genome Biology and Evolution)、假基因化(Xu et al., 2019, Plant Cell)、转座子的扩增和丢失(Li et al., 2018, Genome Biology and Evolution)及植物里受平衡选择的基因(Wu et al., 2017, Genome Biology)等。研究的类群以十字花科的拟南芥及其近缘种以及禾本科的水稻及其近缘种为主。
2.自交不亲和系统的进化及物种形成
自交不亲和(self-incompatibility, SI)在很多有花植物中都存在,它的遗传决定位点被称为自交不亲和位点(S locus)。植物可以通过排斥自己的或与自己具有类似自交不亲和位点的花粉从而保持异交。通过群体遗传学、比较基因组学及分子遗传学方法来揭示自交不亲和位点进化的基本规律及其对物种形成的贡献(Guo et al., 2009, PNAS; Guo et al., 2011, Plant Physiology)。对自交不亲和系统的进化及功能方面的深入研究不仅具有重要的理论价值,而且对育种科学有重大的应用价值。下一步的研究主要从物种形成方面展开,重点探讨生殖隔离的形成机制及其与物种形成的关系。
3.自然变异及适应性进化
适应性是生物在变化多样的环境中生存下来的最重要的能力。动物在极端环境下可以逃走而植物却不能。从进化生物学、生态学及分子遗传学各个角度来研究自然变异的规律和机制,进而揭示植物如何适应环境(Guo et al., 2012, Genetics; Han et al., 2015, Molecular Plant; Zou et al., 2017, Genome Biology; Yang et al., 2018, Plant Cell; Niu et al., 2019, PNAS)。
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成果数
31
【期刊论文】Evolution of genes and genomes in the genomics era
Science China Life Sciences,2020,63():602–605
2020年03月13日
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【期刊论文】Transcriptional repression specifies the central cell for double fertilization
PNAS,2020,117(11):6231-6236
2020年03月17日
Double fertilization is a key innovation for the evolutionary success of angiosperms by which the two fertilized female gametes, the egg cell and central cell, generate the embryo and endosperm, respectively. The female gametophyte (embryo sac) enclosed in the sporophyte is derived from a one-celled haploid cell lineage. It undergoes successive events of mitotic divisions, cellularization, and cell specification to give rise to the mature embryo sac, which contains the two female gametes accompanied by two types of accessory cells, namely synergids and antipodals. How the cell fate of the central cell is specified has long been equivocal and is further complicated by the structural diversity of female gametophyte across plant taxa. Here, MADS-box protein AGL80 was verified as a transcriptional repressor that directly suppresses the expression of accessory cell-specific genes to specify the central cell. Further genetic rescue and phylogenetic assay of the AGL80 orthologs revealed a possible conserved mechanism in the Brassicaceae family. Results from this study provide insight into the molecular determination of the second female gamete cell in Brassicaceae.
double fertilization, central cell specification, central cell evolution, transcriptional repression
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【期刊论文】The hornwort genome and early land plant evolution
Nature Plants,2020,6():pages 107–
2020年02月10日
Hornworts, liverworts and mosses are three early diverging clades of land plants, and together comprise the bryophytes. Here, we report the draft genome sequence of the hornwort Anthoceros angustus. Phylogenomic inferences confirm the monophyly of bryophytes, with hornworts sister to liverworts and mosses. The simple morphology of hornworts correlates with low genetic redundancy in plant body plan, while the basic transcriptional regulation toolkit for plant development has already been established in this early land plant lineage. Although the Anthoceros genome is small and characterized by minimal redundancy, expansions are observed in gene families related to RNA editing, UV protection and desiccation tolerance. The genome of A. angustus bears the signatures of horizontally transferred genes from bacteria and fungi, in particular of genes operating in stress-response and metabolic pathways. Our study provides insight into the unique features of hornworts and their molecular adaptations to live on land.
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【期刊论文】Transposable elements drive rapid phenotypic variation in Capsella rubella
PNAS,2019,116(14):6908-6913
2019年04月02日
Rapid phenotypic changes in traits of adaptive significance are crucial for organisms to thrive in changing environments. How such phenotypic variation is achieved rapidly, despite limited genetic variation in species that experience a genetic bottleneck is unknown. Capsella rubella, an annual and inbreeding forb (Brassicaceae), is a great system for studying this basic question. Its distribution is wider than those of its congeneric species, despite an extreme genetic bottleneck event that severely diminished its genetic variation. Here, we demonstrate that transposable elements (TEs) are an important source of genetic variation that could account for its high phenotypic diversity. TEs are (i) highly enriched in C. rubella compared with its outcrossing sister species Capsella grandiflora, and (ii) 4.2% of polymorphic TEs in C. rubella are associated with variation in the expression levels of their adjacent genes. Furthermore, we show that frequent TE insertions at FLOWERING LOCUS C (FLC) in natural populations of C. rubella could explain 12.5% of the natural variation in flowering time, a key life history trait correlated with fitness and adaptation. In particular, we show that a recent TE insertion at the 3′ UTR of FLC affects mRNA stability, which results in reducing its steady-state expression levels, to promote the onset of flowering. Our results highlight that TE insertions can drive rapid phenotypic variation, which could potentially help with adaptation to changing environments in a species with limited standing genetic variation.
Brassicaceae, Capsella rubella, natural variation, rapid phenotypic variation, transposable elements
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【期刊论文】Cysteine-rich peptides promote interspecific genetic isolation in Arabidopsis
Science,2019,364(6443):eaau9564
2019年05月31日
Reproductive isolation is a prerequisite for speciation. Failure of communication between female tissues of the pistil and paternal pollen tubes imposes hybridization barriers in flowering plants. Arabidopsis thaliana LURE1 (AtLURE1) peptides and their male receptor PRK6 aid attraction of the growing pollen tube to the ovule. Here, we report that the knockout of the entire AtLURE1 gene family did not affect fertility, indicating that AtLURE1-PRK6–mediated signaling is not required for successful fertilization within one Arabidopsis species. AtLURE1s instead function as pollen tube emergence accelerators that favor conspecific pollen over pollen from other species and thus promote reproductive isolation. We also identified maternal peptides XIUQIU1 to -4, which attract pollen tubes regardless of species. Cooperation between ovule attraction and pollen tube growth acceleration favors conspecific fertilization and promotes reproductive isolation.
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The Plant Cell,2019,31():1012–1025
2019年05月01日
According to the less-is-more hypothesis, gene loss is an engine for evolutionary change. Loss-of-function (LoF) mutations resulting in the natural knockout of protein-coding genes not only provide information about gene function but also play important roles in adaptation and phenotypic diversification. Although the less-is-more hypothesis was proposed two decades ago, it remains to be explored on a large scale. In this study, we identified 60,819 LoF variants in 1071 Arabidopsis (Arabidopsis thaliana) genomes and found that 34% of Arabidopsis protein-coding genes annotated in the Columbia-0 genome do not have any LoF variants. We found that nucleotide diversity, transposable element density, and gene family size are strongly correlated with the presence of LoF variants. Intriguingly, 0.9% of LoF variants with minor allele frequency larger than 0.5% are associated with climate change. In addition, in the Yangtze River basin population, 1% of genes with LoF mutations were under positive selection, providing important insights into the contribution of LoF mutations to adaptation. In particular, our results demonstrate that LoF mutations shape diverse phenotypic traits. Overall, our results highlight the importance of the LoF variants for the adaptation and phenotypic diversification of plants.
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【期刊论文】Rice FLUORESCENT1 Is Involved in the Regulation of Chlorophyll
Plant and Cell Physiology,2019,60(10):2307–2318
2019年10月01日
Chlorophyll biosynthesis plays essential roles in photosynthesis and plant growth in response to environmental conditions. The accumulation of excess chlorophyll biosynthesis intermediates under light results in the production of reactive oxygen species and oxidative stress. In this study, we identified a rice (Oryza sativa) mutant, oxidation under photoperiod (oxp), that displayed photobleached lesions on its leaves, reduced growth and decreased chlorophyll content during light/dark cycles or following a dark-to-light transition. The oxp mutant accumulated more chlorophyll precursors (5-aminolevulinic acid and protochlorophyllide) than the wild type in the dark, and more singlet oxygen following light exposure. Several singlet-oxygen-responsive genes were greatly upregulated in oxp, whereas the expression patterns of OsPORA and OsPORB, two genes encoding the chlorophyll biosynthesis enzyme NADPH:protochlorop hyllide oxidoreductase, were altered in de-etiolated oxp seedlings. Molecular and complementation studies revealed that oxp is a loss-of-function mutant in LOC_Os01g32730, a homolog of FLUORESCENT (FLU) in Arabidopsis thaliana. Rice PHYTOCHROME-INTERACTING FACTOR-LIKE14 (OsPIL14) transcription factor directly bound to the OsFLU1 promoter and activated its expression. Dark-grown transgenic rice seedlings overexpressing OsPIL14 accumulated more chlorophyll and turned green faster than the wild type upon light illumination. Thus, OsFLU1 is an important regulator of chlorophyll biosynthesis in rice.
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【期刊论文】Parallel Speciation of Wild Rice Associated with Habitat Shifts
Molecular Biology and Evolution,2019,36(5):875–889
2019年05月01日
The occurrence of parallel speciation strongly implies the action of natural selection. However, it is unclear how general a phenomena parallel speciation is since it was only shown in a small number of animal species. In particular, the adaptive process and mechanisms underlying the process of parallel speciation remain elusive. Here, we used an integrative approach incorporating population genomics, common garden, and crossing experiments to investigate parallel speciation of the wild rice species Oryza nivara from O. rufipogon. We demonstrated that O. nivara originated multiple times from different O. rufipogon populations and revealed that different O. nivara populations have evolved similar phenotypes under divergent selection, a reflection of recurrent local adaptation of ancient O. rufipogon populations to dry habitats. Almost completed premating isolation was detected between O. nivara and O. rufipogon in the absence of any postmating barriers between and within these species. These results suggest that flowering time is a “magic” trait that contributes to both local adaptation and reproductive isolation in the origin of wild rice species. Our study thus demonstrates a convincing case of parallel ecological speciation as a consequence of adaptation to new environments.
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Annals of Botany,2019,123(3):441–450
2019年02月15日
Background and Aims Plant elemental composition is of fundamental importance for plant growth and metabolic functions. However, knowledge of how multi-elemental stoichiometry responds to varying nitrogen (N) and phosphorus (P) availabilities remains limited. Methods We conducted experimental manipulations with nine repeat experiments to investigate the effects of N and P supply on the concentrations and variability of six elements, carbon (C), N, P, potassium (K), calcium (Ca) and magnesium (Mg), in leaves of Arabidopsis thaliana. Key Results N supply increased the concentrations of N, K and Mg, decreased the concentration of P, but exerted little influence on the concentrations of C and Ca in green leaves. P supply increased the concentrations of P and Ca, decreased the concentration of C, initially increased and then decreased the concentration of K, but showed little influence on the concentrations of N and Mg in green leaves. Multivariate patterns among the concentrations of these six elements in green leaves was influenced by the type of nutrient supply (i.e. N or P). Elemental variability decreased with increasing elemental concentrations in green leaves at the intraspecific level, supporting the Stability of Limiting Elements Hypothesis that was originally proposed from a meta-analysis of pooled data across species or communities. Compared with green leaves, the senesced leaves showed greater variability in C, N, P, K and Mg concentrations but lower variability in Ca concentration. Conclusions N and P supplies exerted differential influences on the concentrations of C, N, P, K, Ca and Mg in green leaves. The specific C content should be considered when assessing C cycling under global nutrient changes. Stage-dependent patterns of leaf stoichiometric homeostasis differed among elements with various chemical characteristics. These findings can help to improve our understanding of plant eco-physiological responses and acclimation under global nutrient changes from the stoichiometric perspective of multiple elements.
Arabidopsis thaliana,, multiple elements,, N and P supply,, plant stoichiometry,, scaling relationship,, variability
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PNAS,2019,116(9):3494-3501
2019年02月26日
Rice (Oryza sativa L.) is a chilling-sensitive staple crop that originated in subtropical regions of Asia. Introduction of the chilling tolerance trait enables the expansion of rice cultivation to temperate regions. Here we report the cloning and characterization of HAN1, a quantitative trait locus (QTL) that confers chilling tolerance on temperate japonica rice. HAN1 encodes an oxidase that catalyzes the conversion of biologically active jasmonoyl-L-isoleucine (JA-Ile) to the inactive form 12-hydroxy-JA-Ile (12OH-JA-Ile) and fine-tunes the JA-mediated chilling response. Natural variants in HAN1 diverged between indica and japonica rice during domestication. A specific allele from temperate japonica rice, which gained a putative MYB cis-element in the promoter of HAN1 during the divergence of the two japonica ecotypes, enhances the chilling tolerance of temperate japonica rice and allows it to adapt to a temperate climate. The results of this study extend our understanding of the northward expansion of rice cultivation and provide a target gene for the improvement of chilling tolerance in rice.
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