Early land plant evolution, bryophyte phylogeny, phylogenomics, comparative genomics

Jul 2007   Ph.D. in Botany

Institute of Botany, Chinese Academy of Sciences, Beijing, China.

Jul 2001   B.S. in Horticulture

Department of Horticulture, China Agricultural University, Beijing, China.

   

Jan 2015-May 2016   Assistant Research Professor

Department of EEB, University of Connecticut, Storrs, CT

 

Sep 2009-Dec 2014   Postdoctoral Research Fellow

Department of EEB, University of Connecticut, Storrs, CT

Mar 2008-Aug 2009  Postdoctoral Research Fellow

Department of EEB, University of Michigan, Ann Arbor, MI

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1.     Kirbis A, Rahmatpour N, Dong S, Yu J, van Gessel N, Waller M, Reski R, Lang D, Rensing SA, Temsch EM, Wegrzyn J, Goffinet B, Liu Y, Szövényi P. 2022. Genome dynamics in mosses: Extensive synteny coexists with a highly dynamic gene space. bioRxiv, 10.1101/2022.05.17.492078.

2.     Habib S, Gong Y, Dong S, Lindstrom A, Stevenson DW, Liu Y, Wu H, Zhang S. 2022. Phylotranscriptomics reveal the spatio-temporal distribution and morphological evolution of Macrozamia, an Australian endemic genus of Cycadales. Annals of Botany, in press.

3.     Dong S, Yu J, Zhang L, Goffinet B, Liu Y^*. 2022. Phylotranscriptomics of liverworts: revisiting the backbone phylogeny and ancestral gene duplications. Annals of Botany, in press.

4.     Wang QH, Zhang J, Liu Y, Jia Y, Jiao YN, Xu B, Chen ZD. 2022. Diversity, phylogeny and adaptation of bryophytes: insights from genomic and transcriptomic data. Journal of Experimental Botany, 73: 4306–4322.

5.     Liu Y^*, Wang S, Li L, Yang T, Dong S, Wei T, Wu S, Liu Y, Gong Y, et al., Zhang S. 2022. The Cycas genome and the early evolution of seed plants. Nature Plants, 8:389–401. 【Featured on cover】

6.     Yang T, Sahu SK, Yang L, Liu Y, Mu W, Liu X, Strube ML, Liu H, Zhong B. 2022. Comparative Analyses of 3,654 Plastid genomes unravel insights into evolutionary dynamics and phylogenetic discordance of green plants. Frontiers in Plant Science, 13: 808156–808156.

7.     Yu J, Cai Y, Zhu Y, Zeng Y, Dong S, Zhang K, Wang S, Li L, Goffinet B, Liu H, Liu Y^*. 2022. Chromosome-level genome assemblies of two Hypnales (mosses) reveal high intergeneric synteny. Genome Biology and Evolution, 14: evac020, https://doi.org/10.1093/gbe/evac020.

8.     Li L, Chen X, Fang D, Dong S, Guo X, Li N, Campos-Dominguez L, Wang W, Liu Y, et al., Liu H. 2022. Genomes shed light on the evolution of Begonia, a mega-diverse genus. New Phytologist, 234: 295–310.

9.     Sheng W, Dong SS, Liu Y, Ma WZ, Wu YH. 2022. Sciaromiopsis sinensis (Amblystegiaceae), revised to a member of Brachythecium (Brachytheciaceae). The Bryologist, 125:148–156.

10.  Dong S, Li H, Goffinet B, Liu Y^*. 2022. Exploring the impact of RNA editing on mitochondrial phylogenetic analyses in liverworts, an early land plant lineage. Journal of Systematics and Evolution, 60:16–22.

11.  Dong S, Wang Y, Xia N, Liu Y, Liu M, Lian L, Li N, Li L, Lang X, Gong Y, et al., Zhang SZ. 2022. Plastid and nuclear phylogenomic incongruences and biogeographic implications of Magnolia sl (Magnoliaceae). Journal of Systematics and Evolution, 60:1–15.【Featured on cover】

12.  Wang S, Liang H, Wang H, Li L, Xu Y, Liu Y, Liu M, Wei J, Ma T, Le C. Yang J, He C, Liu J, Zhao JM, Zhao Y, Lisby M, Sahu SK, Liu H. 2022. The chromosome‐scale genomes of Dipterocarpus turbinatus and Hopea hainanensis (Dipterocarpaceae) provide insights into fragrant oleoresin biosynthesis and hardwood formation. Plant Biotechnology Journal, 20:538–553.

13.  Wu ETY, Liu Y, Jennings L, Dong S, Davies TJ. 2021. Detecting the phylogenetic signal of glacial refugia in a bryodiversity hotspot outside the tropics. Diversity and Distributions, 00:1–15.

14.  Li HL, Wu L, Dong Z, Jiang Y, Jiang S, Xing H, Li Q, Liu G, Tian S, Wu Z, Wu B, Li Z, Zhao P, Zhang Y, Tang J, Xu J, Huang K, Liu X, Zhang W, Liao Q, Ren Y, Huang X, Li Q, Li C, Wang Y, Xavier-Ravi B, Li H, Liu Y, Wan T, Liu Q, Zou Y, Jian J, Xia Q, Liu Y. 2021. Haplotype-resolved genome of diploid ginger (Zingiber officinale) and its unique gingerol biosynthetic pathway. Horticulture Research, 8:1–13.

15.  Habib S, Dong S, Liu Y, Liao W, Zhang S. 2021. The complete mitochondrial genome of Cycas debaoensis revealed unexpected static evolution in gymnosperm species. PloS ONE, 16, e0255091.

16.  Frangedakis E, Guzman-Chavez F, Rebmann M, Markel K, Yu Y, Perraki A, Tse SW, Liu Y, Rever J, Sauret-Gueto S, Goffinet B, Schneider H, Haseloff J. 2021. Construction of DNA Tools for Hyperexpression in Marchantia Chloroplasts. ACS Synthetic Biology 10:1651−1666.

17.  Dong S, Zhang S, Zhang L, Wu H, Goffinet B, Liu Y^*. 2021. Plastid genomes and phylogenomics of liverworts (Marchantiophyta): Conserved genome structure but highest relative plastid substitution rate in land plants. Molecular Phylogenetics and Evolution, 161, 107171.

18.  Dong S, Liu Y^*. 2021. The mitochondrial genomes of bryophytes. Bryophyte Diversity and Evolution, 43, 112–126.

19.  Dong S, Liu M, Liu Y, Chen F, Yang T, Chen L, Zhang X, Guo X, Fang D, Li L, et al., Zhang SZ. 2021. The genome assembly and annotation of Magnolia biondii Pamp., a phylogenetically, economically, and medicinally important ornamental tree species. Horticulture Research 8:38.

20.  Wei T, Van Treuren R, Liu X, Zhang Z, Chen J, Liu Y, et al., Liu H. 2021. Whole-genome resequencing of 445 Lactuca accessions reveals the domestication history of cultivated lettuce. Nature Genetics 53:752–760.

21.  Xue JY, Dong S, Wang MQ, Song TQ, Zhou GC, Li Z, Van de Peer Y, Shao ZQ, Wang W, Chen M, et al., Liu Y^*, Wang Q^*, Hang YY^*. 2021. Mitochondrial genes from eighteen angiosperms fill sampling gaps for phylogenomic inferences of the early diversification of flowering plants. Journal of Systematics and Evolution, 60:773–788.

22.  Yu J, Li LZ, Wang SB, Dong SS, Chen ZQ, Patel N, Goffinet B, Liu H, Liu Y^*. 2020. Draft genome of the aquatic moss Fontinalis antipyretica (Fontinalaceae, Bryophyta). Gigabyte, doi: 10.46471/gigabyte.8.

23.  Wang QH, Dong SS, Zhang JL, Liu Y^*, Jia Y^*. 2020. Phylogeny of Orthotrichum sl and Ulota sl (Orthotrichaceae, Bryophyta): insights into stomatal evolution. Journal of Systematics and Evolution, doi.org/10.1111/jse.12713.

24.  Sheng W, Yue X R, Li N, Liu Y, Wu YH. Comparison of eight complete plastid genomes from three moss families Amblystegiaceae, Calliergonaceae and Pylaisiaceae. Mitochondrial DNA Part B, 2020, 5: 3109–3111.

25.  Sun G, Bai S, Guan Y, Wang Q, Liu Y, Liu H, Goffinet B, Zhou Y, Paoletti M, Hu X, Hass FB, Fernandez-Pozo N, Czyrt A, Sun H, Rensing SA, Huang J. 2020. Are fungi-derived genomic regions related to antagonism towards fungi in mosses? New Phytologist, 228:1169–1175.

26.  Xue JY, Wang Y, Chen M, Dong SS, Shao ZQ*, Liu Y*. 2020. Maternal Inheritance of U’s Triangle and Evolutionary Process of Brassica Mitochondrial Genomes. Frontiers in Plant Science, 11:805.

27.  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. Nature Plants 6:107–118.【Featured on cover】

28.  Chen X, Fang D, Wu C, Liu B, Liu Y, Sahu SK, Song B, Yang S, Yang T, Wei J, Wang X, et al. 2020. Comparative plastome analysis of root-and stem-feeding parasites of Santalales untangle the footprints of feeding mode and lifestyle transitions. Genome Biology and Evolution 12:3663–3676.

29.  Dong SS, Chen L, Liu Y, Wang YL, Zhang SZ, Yang LL, Lang XA, Zhang SZ. 2020. The draft mitochondrial genome of Magnolia biondii and mitochondrial phylogenomics of angiosperms. PLoS ONE 15: e0231020.

30.  Wang W, Liu Y. 2020. The current status, problems, and policy suggestions for reconstructing the plant tree of life. Biodiversity Science 28: 176–188.

31.  Xue JY, Zhao T, Liu Y, Zhang YX, Zhang GQ, Chen HF, Zhou GC, Zhang SZ, Shao ZQ. 2020. Genome-Wide Analysis of NBS-LRR Genes of Four Orchids Revealed Extremely Low Numbers of Disease Resistance Genes. Frontiers in Genetics 10:1286.

32.  Zhang L, Chen F, Zhang X, Li Z, Zhao Y, Lohaus R, Chang X, Dong W, Ho SYW, Liu X, Song A, Chen J, Guo W, Wang Z, Zhuang Y, Wang H, Chen X, Hu J, Liu Y, Qin Y, Wang K, Dong S, Liu Y, Zhang S, Yu X, Wu Q, Wang L, Yan X, Jiao Y, Kong H, Zhou X, Yu C, Chen Y, Li F, Wang J, Chen W, Chen X, Jia Q, Zhang C, Jiang Y, Zhang W, Liu G, Fu J, Chen F, Ma H, Van de Peer Y, Tang H. 2020. The water lily genome and the early evolution of flowering plants. Nature 577: 79–84.

33.  Liu Y, Johnson MG, Cox CJ, Medina R, Devos N, Vanderpoorten A, Hedenäs L, Bell NE, Shevock JR, Aguero B, Quandt D, Wickett NJ, Shaw AJ, Goffinet B*. 2019. Resolution of the ordinal phylogeny of mosses using targeted exons from organellar and nuclear genomes. Nature Communications 10:1485.

34.  Dong SS, Zhao CX, Zhang SZ, Zhang L, Wu H, Liu H, Zhu RL, Jia Y, Goffinet B, Liu Y*. 2019. Mitochondrial genomes of the early land plant lineage liverworts (Marchantiophyta): conserved genome structure, and ongoing low frequency recombination. BMC Genomics 20: 953.

35.  Dong SS, Zhao CX, Zhang SZ, Wu H, Mu WX, Wei T, Li N, Wan T, Liu H, Cui J, Zhu RL, Goffinet B, Liu Y*. 2019. The amount of RNA editing sites in liverwort organellar genes is correlated with GC content and nuclear PPR protein diversity. Genome Biology and Evolution 11: 3233–3239.

36.  Medina R, Johnson MG, Liu Y, Wickett NJ, Shaw AJ, Goffinet B. 2019. Phylogenomic delineation of Physcomitrium (Bryophyta: Funariaceae) based on targeted sequencing of nuclear exons and their flanking regions rejects the retention of Physcomitrella, Physcomitridium and Aphanorrhegma. Journal of Systematics and Evolution 57: 404–417.

37.  Dong SS, He Q, Zhang SZ, Wu H, Goffinet B, Liu Y*. 2019. The mitochondrial genomes of Bazzania tridens and Riccardia planiflora further confirm conservative evolution of mitogenomes in liverworts. The Bryologist 122: 130-139.

38.  Liao X, Liu Y, Liu H. 2018. The complete plastid genomes of two Fabaceae orphan crops from Africa. Mitochondrial DNA Part B 4:93-94.

39.  Shi YC, Liu Y, Zhang SZ, Zou R, Tang JM, Mu WX, Yang P, Dong SS. 2018. Assembly and comparative analysis of the complete mitochondrial genome sequence of Sophora japonica ‘JinhuaiJ2’. PLoS ONE 13: e0202485.

40.  Dong SS, Zhao CX, Chen F, Liu YH, Zhang SZ, Wu H, Zhang LS, Liu Y^*. 2018. The complete mitochondrial genome of the early flowering plant Nymphaea colorata is highly repetitive with low recombination. BMC Genomics 19: 614.

41.  Yao ZX, Yang JF, Liu Y, Dong SS, Wu H, Zhang SZ. 2018. The complete chloroplast genome of Magnolia sinostellata (Magnoliaceae), a rare and endangered species of China. Mitochondrial DNA Part B: Resources 3: 742-743.

42.  Wan T, Liu ZM, Li LF, Leitch AR, Leitch IJ, Liu ZJ, Xin HP, Gong YB, Liu Y, Wang WC, et al. 2018. A genome for gnetophytes and early evolution of seed plants. Nature Plants 4: 82-89.

43.  Dong S, Xue JY, Zhang SZ, Zhang L, Wu H, Chen ZD, Goffinet B, Liu Y^*. 2018. Complete mitochondrial genome sequence of Anthoceros angustus: conservative evolution of the mitogenome in hornworts. The Bryologist 121: 14-22.

44.  Medina R, Johnson MG, Liu Y, Wilding N, Hedderson TA, Wickett N, Goffinet B. 2018. Evolutionary dynamism in bryophytes: Phylogenomic inferences confirm rapid radiation in the moss family Funariaceae. Molecular Phylogenetics and Evolution 120: 240-247.

现指导学生

蔡语清  硕士研究生  086000-生物与医药  

2019    Sullivant Award (American Bryological and Lichenological Society)

2018    Contribution Award from the XIX International Botanical Congress

2018    "Phoenix Tree" Talent of Yantian award, Shenzhen

2017    Overseas High-Caliber Personnel award, Shenzhen