主要发表文章:
Zhongjie Liu, Nan Wang, Ying Su, Qiming Long, Yanling Peng, Lingfei Shangguan, Fan Zhang, Shuo Cao, Xu Wang, Mengqing Ge, Hui Xue, Zhiyao Ma, Wenwen Liu, Xiaodong Xu, Chaochao Li, Xuejing Cao, Bilal Ahmad, Xiangnian Su, Yuting Liu, Guizhou Huang, Mengrui Du, Zhenya Liu, Yu Gan, Lei Sun, Xiucai Fan, Chuan Zhang, Haixia Zhong, Xiangpeng Leng, Yanhua Ren, Tianyu Dong, Dan Pei, Xinyu Wu, Zhongxin Jin, Yiwen Wang, Chonghuai Liu, Jinfeng Chen, Brandon Gaut, Sanwen Huang, Jinggui Fang*, Hua Xiao* & Yongfeng Zhou*. Grapevine pangenome facilitates trait genetics and genomic breeding. Nature Genetics (2024). https://doi.org/10.1038/s41588-024-01967-5 [葡萄泛基因组促进性状遗传和基因组育种]
Xu Wang, Zhongjie Liu, Fan Zhang, Hua Xiao, Shuo Cao, Hui Xue, Wenwen Liu, Ying Su, Zhenya Liu, Haixia Zhong, Fuchun Zhang, Bilal Ahmad, Qiming Long, Yingchun Zhang, Yuting Liu, Yu Gan, Ting Hou, Zhongxin Jin, Xinyu Wu, Guotian Liu, Yiwen Wang, Yanling Peng, and Yongfeng Zhou*. Integrative genomics reveals the polygenic basis of seedlessness in grapevine[J]. Current Biology, 2023: 2023.12. 22.573032. [整合基因组学揭示了葡萄无核基础的多基因性]
Xiaoxia Li, Xiaofan Dai, Huiying He, Yang Lv, Longbo Yang, Wenchuang He, Congcong Liu, Hua Wei, Xiangpei Liu, Qiaoling Yuan, Xianmeng Wang, Tianyi Wang, Bintao Zhang, Hong Zhang, Wu Chen, Yue Leng, Xiaoman Yu, Hongge Qian, Bin Zhang, Mingliang Guo, Zhipeng Zhang, Chuanlin Shi, Qianqian Zhang, Yan Cui, Qiang Xu, Xinglan Cao, Dandan Chen, Yongfeng Zhou*, Qian Qian*, Lianguang Shang*, A pan-TE map highlights transposable elements underlying domestication and agronomic traits in Asian rice, National Science Review, 2024;, nwae188, https://doi.org/10.1093/nsr/nwae188 [泛TE图谱突出了亚洲水稻驯化和农艺性状背后的转座因子]
Peng Y, Wang Y, Liu Y, et al. The genomic and epigenomic dynamics of hemizygous genes across crops with contrasting mating systems[J]. bioRxiv, 2024: 2024.05. 24.595664. [不同配种制度下半合子基因在作物间的基因组和表观基因组动力学]
Ying Su, Xuanwen Yang, Yuwei Wang, Jialei Li, Qiming Long, Shuo Cao, Xu Wang, Zhenya Liu, Siyang Huang, Zhuyifu Chen, Yanling Peng, Fan Zhang, Hui Xue, Xuejing Cao, Mengyan Zhang, Gulbar Yisilam, Zhenzhou Chu, Yuan Gao, Yongfeng Zhou*, Zhongjie Liu*, Hua Xiao*, Xinmin Tian*, Phased Telomere-to-Telomere Reference Genome and Pangenome Reveal an Expansion of Resistance Genes during Apple Domestication, Plant Physiology, 2024;, kiae258, https://doi.org/10.1093/plphys/kiae258 [端粒-端粒参考基因组和泛基因组揭示了苹果驯化过程中抗性基因的扩增]
Fan Zhang, Ruicai Long, Zhiyao Ma, Hua Xiao, Xiaodong Xu, Zhongjie Liu, Chunxue Wei, Yiwen Wang, Yanling Peng, Xuanwen Yang, Xiaoya Shi, Shuo Cao, Mingna Li, Ming Xu, Fei He, Xueqian Jiang, Tiejun Zhang, Zhen Wang, Xianran Li, Long-Xi Yu, Junmei Kang, Zhiwu Zhang, Yongfeng Zhou*, Qingchuan Yang*, Evolutionary genomics of climatic adaptation and resilience to climate change in alfalfa, Molecular Plant, Volume 17, Issue 6, 2024, Pages 867-883, ISSN 1674-2052, https://doi.org/10.1016/j.molp.2024.04.013. [苜蓿气候适应和气候变化复原力的进化基因组学研究]
Xuanwen Yang, Ying Su, Siyang Huang, Qiandong Hou, Pengcheng Wei, Yani Hao, Jiaqi Huang, Hua Xiao, Zhiyao Ma, Xiaodong Xu, Xu Wang, Shuo Cao, Xuejing Cao, Mengyan Zhang, Xiaopeng Wen, Yuhua Ma, Yanling Peng, Yongfeng Zhou*, Ke Cao*, Guang Qiao*, Comparative population genomics reveals convergent and divergent selection in the Apricot-Peach-Plum-Mei Complex, Horticulture Research, 2024;, uhae109, https://doi.org/10.1093/hr/uhae109 [比较群体基因组学揭示了杏-桃-李-梅复合体的趋同选择和发散选择]
Tianhao Zhang, Wenjing Peng, Hua Xiao, Shuo Cao, Zhuyifu Chen, Xiangnian Su, Yuanyuan Luo, Zhongjie Liu, Yanling Peng, Xiping Yang, Guo-Feng Jiang*, Xiaodong Xu*, Zhiyao Ma*, Yongfeng Zhou*. (2024). Population genomics highlights structural variations in local adaptation to saline coastal environments in woolly grape. Journal of Integrative Plant Biology. [结构变异促进野生葡萄适应高盐海滨环境]
Qiming Long, Shuo Cao, Guizhou Huang, Xu Wang, Zhongjie Liu, Wenwen Liu, Yiwen Wang, Hua Xiao, Yanling Peng, Yongfeng Zhou, Population comparative genomic analyses unveil gene gain and loss during grapevine domestication, Plant Physiology, 2024;, kiae039, https://doi.org/10.1093/plphys/kiae039 [群体比较基因组学发现葡萄驯化过程中基因的得失]
Gan Y, Liu Z, Zhang F, et al. Deep learning based genomic breeding of pest-resistant grapevine[J]. bioRxiv, 2024: 2024.03. 16.585323. [基于深度学习的抗虫葡萄基因组育种]
Yanhong Song, Yanling Peng, Lifeng Liu, Gang Li, Xia Zhao, Xu Wang, Shuo Cao, Aline Muyle, Yongfeng Zhou*, Houcheng Zhou*. Phased gap-free genome assembly of octoploid cultivated strawberry illustrates the genetic and epigenetic divergence among subgenomes[J]. Horticulture Research, 2023: uhad203. [八倍体栽培草莓的分阶段无间隙基因组组装说明了亚基因组之间的遗传和表观遗传差异]
Hua Xiao, Zhongjie Liu, Nan Wang, Brandon S. Gaut, and Yongfeng Zhou*. Reply to Blanco-Pastor: Introgression and heterozygosity complicated grapevine domestication[J]. PNAS, 2023, 120(49): e2314162120. [渗入和杂合性复杂的葡萄驯化]
Yue JY, Chen QY, Zhang SJ, Lin YZ, Ren WM, Li BJ, Wu Y, Wang YZ, Zhou YF*, Liu YS* (2023) Origin and evolution of the kiwifruit Y chromosome. Plant Biotechnology Journal https://doi.org/10.1111/pbi.14213 [猕猴桃Y染色体的起源和进化]
Huang HR, Liu X, Arshad R, Wang X, Li WM, Zhou YF*, Ge XJ* (2023) Telomere-to-telomere haplotype-resolved reference genome reveals subgenome divergence and disease resistance in triploid Cavendish banana. Horticulture Research uhad153. [T2T单倍型解析参考基因组揭示了三倍体卡文迪什香蕉的亚基因组分化和抗病性]
Wang N, Cao ST, Liu ZJ, Xiao H, Hu JB, Xu XD, Chen P, Ma ZY, Ye JL, Chai LJ, Guo WW, Larkin RM, Xu Q, Morrell PL, Zhou YF*, Deng XX* (2023) Genomic conservation of crop wild relatives: A case study of citrus. PLoS genetics 19(6): e1010811. [作物野生亲缘种的基因组保护:柑橘的案例研究]
Xiao H, Liu ZJ, Wang N, Long QM, Cao S, Huang GZ, Liu WW, Peng YL, Riaz S, Walker AW, Gaut BS*, Zhou YF* (2023) Adaptive and maladaptive introgression in grapevine domestication. PNAS 120(24): e2222041120. [葡萄栽培中的适应性和不适应性渐渗]
Shi XY, Cao S, Wang X, Huang SY, Wang Y, Liu ZJ, Liu WW, Leng XP, Peng YL, Wang N, Wang YW, Ma ZY, Xu XD, Zhang F, Xue H, Zhong HX, Wang Y, Zhang KK, Velt A, Avia K, Holtgräwe D, Grimplet J, Matus JT, Ware D, Wu XY, Wang HB, Liu CH, Fang YL, Rustenholz C*, Cheng ZM*, Xiao H*, Zhou YF* (2023) The complete reference genome for grapevine (Vitis vinifera L.) genetics and breeding. Horticulture Research 10(05): uhad061. [葡萄遗传和育种的完整参考基因组]
Morales-Cruz A, Aguirre-Liguori J, Massonnet M, Minio A, Zaccheo M, Cochetel N, Walker A, Riaz S, Zhou YF*, Cantu D*, Gaut BS* (2023) Multigenic resistance to Xylella fastidiosa in wild grapes (Vitis sps.) and its implications within a changing climate. Communications Biology 6(1): 580. [野生葡萄对苛养木杆菌的多基因抵抗及其在气候变化中的影响]
Zhong HX, Liu ZJ, Zhang FC, Zhou XM, Sun XX, Li YY, Liu WW, Xiao H, Wang N, Lu H, Pan MQ*, Wu XY*, Zhou YF* (2022) Metabolomic and transcriptomic analyses reveal the effects of self-and hetero-grafting on anthocyanin biosynthesis in grapevine. Horticulture Research 9: uhac103. [代谢组学和转录组学分析揭示了自体嫁接和异体嫁接对葡萄栽培中花青素生物合成的影响]
Kou Y, Liao Y, Toivainen T, Lv Y, Tian X, Emerson JJ, Gaut BS*, Zhou YF* (2020) Evolutionary genomics of structural variation in Asian rice (Oryza sativa) domestication. Molecular Biology and Evolution 37:3507–3524. [亚洲水稻驯化中结构变异的进化基因组学]
Zhou YF*, Gaut BS* (2020) Large chromosomal variants drive adaptation in sunflowers. Nature plants 6:734–735. [大型染色体变异推动向日葵的适应性演化]
Zhou YF, Muyle A, Gaut BS* (2019) Evolutionary genomics and the domestication of grapes. The grape genome, Dario Cantu and M. Andrew Walker (Eds). [进化基因组学与葡萄的驯化]
Zhou YF, Minio A, Solares E, Lyu Y, Cantu D*, Gaut BS* (2019) Population genetics of structural variation in grapevine domestication. Nature plants, 5, 965–979. [葡萄栽培中结构变异的种群遗传学]
Gaut BS, Seymour D, Liu QP, Zhou YF* (2018) Demography and its effects on genomic variation in crop domestication. Nature plants 4: 512–520. [群体统计学及其对作物驯化中基因组变异的影响]
Tian XM, Wang QY, Zhou YF* (2018) Euphorbia section Hainanensis (Euphorbiaceae), a new section endemic to the Hainan Island of China from biogeographical, karyological, and phenotypical evidence. Frontiers in Plant Science 9: 660. [海南大戟组:来自生物地理学、核型学和表型学证据的中国海南岛特有新组]
Zhou YF, Massonnet M, Sanjak J, Cantu D, Gaut BS* (2017) Evolutionary genomics of grape (Vitis vinifera ssp. vinifera) domestication. PNAS 114: 11715-11720. [葡萄驯化的进化基因组学]
Zhou YF, Duvaux L, Ren G, Zhang LR, Savolainen O, Liu J* (2017) Importance of incomplete lineage sorting and introgression in the origin of shared genetic variation between two closely related pines with overlapping distributions. Heredity 118: 211-220. [不完全谱系分选和内引入在两种重叠分布的密切相关松树共享遗传变异的起源中的重要性]
Zhou YF (2014) Demographic history and climatic adaptation in ecological divergence between two closely related parapatric pine species. Acta Universitatis Ouluensis. A, Scientiae rerum naturalium, ISSN: 0355-3191. [两种密切相关的副生态学松树物种的人口历史和气候适应在生态分化中的作用]
周永锋. Local adaptation to climate in Pinus densata complex[D]. 兰州大学, 2014. [高山松复合体的气候适应]
Zhou YF, Zhang LR, Liu JQ, Wu GL, Savolainen O* (2014) Climatic adaptation and ecological divergence between two closely related pines species in Southeast China. Molecular Ecology 23: 3504–3522. [东南中国两种密切相关的松树物种的气候适应和生态分化]
Zhou YF, Abbott RJ, Jiang ZY, Du, FK, Milne RI, Liu JQ (2010) Gene flow and species delimitation: a case study of two pine species with overlapping distributions in southeast China. Evolution 64: 2342- 2352. [基因流动与物种界定:东南中国重叠分布的两种松树物种的案例研究]
合作发表文章:
He H, Leng Y, Cao X, et al. The pan-tandem repeat map highlights multiallelic variants underlying gene expression and agronomic traits in rice[J]. Nature Communications, 2024, 15(1): 7291. [泛串联重复序列图谱揭示了水稻基因表达和农艺性状背后的多等位变异]
Chao-Chao Li, Yi Bao, Ting Hou, Jia-Cui Li, Zhi-Yao Ma, Nan Wang, Xiao-Meng Wu, Kai-Dong Xie, Yong-Feng Zhou & Wen-Wu Guo. Insights into chloroplast genome evolution in Rutaceae through population genomics[J]. Horticulture Advances, 2024, 2(1): 1-14. [芜科植物叶绿体基因组进化的群体基因组学研究]
He W, He H, Yuan Q, et al. Widespread inversions shape the genetic and phenotypic diversity in rice[J]. Science bulletin, 2024, 69(5): 593-596. [广泛的倒位形成了水稻的遗传和表型多样性]
Yu Q, Hu J, Hu X, et al. Demographic patterns of two related desert shrubs with overlapping distributions in response to past climate changes[J]. Frontiers in Plant Science, 15: 1345624. [两种相关荒漠灌木重叠分布的人口分布模式对过去气候变化的响应]
Lv Y, Liu C, Li X, et al. A centromere map based on super pan‐genome highlights the structure and function of rice centromeres[J]. Journal of Integrative Plant Biology. [基于超级全基因组的着丝点图突显了水稻着丝点的结构和功能]
Wang N, Chen P, Xu Y, et al. Phased genomics reveals hidden somatic mutations and provides insight into fruit development in sweet orange[J]. Horticulture Research, 2024, 11(2): uhad268. [分阶段基因组学揭示了隐藏的体细胞突变,并提供了甜橙果实发育的见解]
Chen J, Liu Y, Liu M, et al. Pangenome analysis reveals genomic variations associated with domestication traits in broomcorn millet[J]. Nature Genetics, 2023: 1-12. [全基因组分析揭示了与黍稷驯化特征相关的基因组变异]
Wang TY, He WC, Li XX, et al. A rice variation map derived from 10 548 rice accessions reveals the importance of rare variants[J]. NAR, 2023 [从10548个水稻材料制作的水稻变异图谱揭示了罕见变种的重要性]
Kekun Zhang, Mengrui Du, Hongyan Zhang, Xiaoqian Zhang, Shuo Cao, Xu Wang, Wenrui Wang, Xueqiang Guan, Penghui Zhou, Jin Li, Wenguang Jiang, Meiling Tang, Qiuling Zheng, Muming Cao, Yongfeng Zhou, Keqin Chen, Zhongjie Liu, Yulin Fang, The haplotype-resolved T2T genome of teinturier cultivar Yan73 reveals the genetic basis of anthocyanin biosynthesis in grapes, Horticulture Research, Volume 10, Issue 11, November 2023, uhad205, https://doi.org/10.1093/hr/uhad205 [Yan73的单倍型解析T2T基因组揭示了葡萄花青素生物合成的遗传基础]
Zhang X, Chen Y, Wang L, et al. Pangenome of water caltrop reveals structural variations and asymmetric subgenome divergence after allopolyploidization[J]. Horticulture Research, 2023: uhad203. [菱角异源多倍体后的泛基因组结构变异和亚基因组不对称分化]
Liu X, Arshad R, Wang X, et al. The phased telomere-to-telomere reference genome of Musa acuminata, a main contributor to banana cultivars[J]. Scientific Data, 2023, 10(1): 631. [小果野蕉( Musa acuminata)T2T基因组]
Liu W, Mu H, Yuan L, et al. VvBBX44 and VvMYBA1 form a regulatory feedback loop to balance anthocyanin biosynthesis in grape[J]. Horticulture Research, 2023, 10(10): uhad176. [VvBBX44和VvMYBA1形成调控反馈回路平衡葡萄花青素的生物合成]
Shang L, He W, Wang T, et al. A complete assembly of the rice Nipponbare reference genome[J]. Molecular Plant, 2023, 16(8): 1232-1236. [水稻“日本晴”参考基因组的完整组装]
Jin M, North H L, Peng Y, et al. Adaptive evolution to the natural and anthropogenic environment in a global invasive crop pest, the cotton bollworm[J]. The Innovation, 2023, 4(4). [全球入侵作物害虫棉铃虫对自然和人为环境的自适应进化]
Wu Y, Li D, Hu Y, et al. Phylogenomic discovery of deleterious mutations facilitates hybrid potato breeding[J]. Cell, 2023, 186(11): 2313-2328. e15. [系统基因组学发现有害突变有助于杂交马铃薯育种]
Li N, He Q, Wang J, et al. Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species[J]. Nature Genetics, 2023, 55(5): 852-860. [超级泛基因组分析突显了野生和栽培番茄物种之间的基因组多样性和结构变异]
Wang N, Li C, Kuang L, et al. Pan-mitogenomics reveals the genetic basis of cytonuclear conflicts in citrus hybridization, domestication, and diversification[J]. Proceedings of the National Academy of Sciences, 2022, 119(43): e2206076119. [全线粒体基因组学揭示了柑橘杂交、驯化和多样化中细胞核冲突的遗传基础]
Ma Z Y, Nie Z L, Liu X Q, et al. Phylogenetic relationships, hybridization events, and drivers of diversification of East Asian wild grapes as revealed by phylogenomic analyses[J]. Journal of Systematics and Evolution, 2023, 61(2): 273-283. [系统发育分析揭示了东亚野生葡萄的系统发育关系、杂交事件和多样化驱动因素]
Shang L, Li X, He H, et al. A super pan-genomic landscape of rice[J]. Cell Research, 2022, 32(10): 878-896. [水稻的超级泛基因组景观]
Tang D, Jia Y, Zhang J, et al. Genome evolution and diversity of wild and cultivated potatoes[J]. Nature, 2022, 606(7914): 535-541. [野生和栽培马铃薯的基因组演化和多样性]
Wang N, Song X, Ye J, et al. Structural variation and parallel evolution of apomixis in citrus during domestication and diversification[J]. National Science Review, 2022, 9(10): nwac114. [柑橘在驯化和多样化过程中无性繁殖的结构变异和平行进化]
Liao Y, Wang J, Zhu Z, et al. The 3D architecture of the pepper genome and its relationship to function and evolution[J]. Nature Communications, 2022, 13(1): 3479. [辣椒基因组的三维结构及其与功能和进化的关系]
Morales-Cruz A, Aguirre-Liguori J A, Zhou Y, et al. Introgression among North American wild grapes (Vitis) fuels biotic and abiotic adaptation[J]. Genome biology, 2021, 22(1): 1-27. [北美野生葡萄之间的渐渗推动了生物和非生物适应]
Massonnet M, Cochetel N, Minio A, et al. The genetic basis of sex determination in grapes[J]. Nature communications, 2020, 11(1): 2902. [葡萄性别决定的遗传基础]
Vondras A M, Minio A, Blanco-Ulate B, et al. The genomic diversification of grapevine clones[J]. BMC genomics, 2019, 20: 1-19. [葡萄克隆的基因组多样化]
Lv Y, Hu F, Zhou Y, et al. Maize transposable elements contribute to long non-coding RNAs that are regulatory hubs for abiotic stress response[J]. BMC genomics, 2019, 20: 1-17. [玉米可转移元件对长非编码RNA的贡献,它们是非生物胁迫响应的调控中心]
Fan B, Zhou Y, Ma Q, et al. The bet-hedging strategies for seedling emergence of Calligonum mongolicum to adapt to the extreme desert environments in northwestern China[J]. Frontiers in Plant Science, 2018, 9: 1167. [毛茛属幼苗出苗的分散投注策略,以适应中国西北极端沙漠环境]
Liu QP, Zhou YF, Morrell P, Gaut BS* (2017) Deleterious variants in Asian rice and the potential cost of domestication. Molecular Biology and Evolution 34: 908-924. [亚洲水稻中的有害变异和驯化潜在成本]
Ren G P, Abbott R J, Zhou Y F, et al. Genetic divergence, range expansion and possible homoploid hybrid speciation among pine species in Northeast China[J]. Heredity, 2012, 108(5): 552-562. [中国东北松树物种的遗传分化、分布范围扩展和可能的同源二倍体杂交物种分化]
Jiang Z Y, Peng Y L, Hu X X, et al. Cytoplasmic DNA variation in and genetic delimitation of Abies nephrolepis and Abies holophylla in northeastern China[J]. Canadian Journal of Forest Research, 2011, 41(7): 1555-1561. [中国东北地区云杉和全叶云杉的细胞质DNA变异和遗传界定]
张利锐, 彭艳玲, 任广朋, 等. Population genetic diversity and species divergence of Pinus massoniana and P. hwangshanensis at two nucleotide loci[J]. 植物生态学报, 2011, 35(5): 531. [马尾松和黄山松两个核基因位点的群体遗传多样性和种间分化]
Li Y, Stocks M, Hemmilä S, et al. Demographic histories of four spruce (Picea) species of the Qinghai-Tibetan Plateau and neighboring areas inferred from multiple nuclear loci[J]. Molecular biology and evolution, 2010, 27(5): 1001-1014. [从多个核位点推断的青藏高原及邻近地区四种云杉(Picea)物种的人口历史]
Wang P, Meng F, Yang Y, et al. Amur grape genome sequence[J]. bioRxiv, 2023: 2023.10. 09.561595. [一个高质量的山葡萄(Vitis amurensis Rupr.)基因组组装有助于深入了解山葡萄的分化和性别决定]
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