PUBLICATIONS

Google Scholar

ResearchGate

ORCID

Book Chapter

Liu Y, Wang B, Li L, Qiu YL, Xue JY. 2012. Conservative and dynamic evolution of mitochondrial genomes in early land plants. In: Bock R, Knoop V (eds.), Genomics of Chloroplasts and Mitochondria. Springer, Netherlands, pp. 159-174. pdf

Journal Articles (#contributed equally, *corresponding author)

2023

1. Dong S, Zhou X, Peng T, Liu Y*. 2023. Mitochondrial RNA editing sites affect the phylogenetic reconstruction of gymnosperms. Plant Diversity, in press.

2. Xue JY, Li Z, Hu SY, Kao SM, Zhao T, Wang JY, Wang Y, Chen M, Qiu Y, Fan HY, Liu Y*, Shao ZQ*, Van de Peer Y*. 2023. The Saururus chinensis genome provides insights into the evolution of pollination strategies and herbaceousness in magnoliids. The Plant Journal, 113, 1021–1034.

3. Guan Y, Ma L, Wang Q, Zhao J, Wang S, Wu J, Liu Y, Sun H, Huang J. 2023. Horizontally acquired fungal killer protein genes affect cell development in mosses. The Plant Journal, 113, 665–676.

2022

1. 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, 130, 671–685.

2. 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, 130, 951–964.

3. 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.

4. 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]

5. 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.

6. 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.

7. 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.

8. 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.

9. 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. 

10. 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] 

11. 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.

12. 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, 28:2681–2695.

13. 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*. 2022. 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.

14. Wang QH, Dong SS, Zhang JL, Liu Y*, Jia Y*. 2021. Phylogeny of Orthotrichum sl and Ulota sl (Orthotrichaceae, Bryophyta): insights into stomatal evolution. Journal of Systematics and Evolution, 60:876–900.

2021

1. 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.

2. 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.

3. 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.

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

5. 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.

6. 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.

7. 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.

2020

1. 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.

2. 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.

3. 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.

4. 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.

5. 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.

6. 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]

7. 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.

8. 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.

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

10. 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.

2019

1. 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.

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

3. 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.

4. 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.

5. 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.

2018

1. 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.

2. 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.

3. 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.

4. 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 3: 742-743.

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

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

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

2017

1. Antoine S, Liu Y, Sérusiaux E, Goffinet B. 2017. Complete mitogenome sequence of Ricasolia amplissima (Lobariaceae) reveals extensive mitochondrial DNA rearrangement within the Peltigerales (lichenized ascomycetes). The Bryologist 120: 335-339.

2. Carvalho-Silva M, Stech M, Soares-Silva LH, Buck WR, Wickett NJ, Liu Y, Câmara Paulo EAS. 2017. A molecular phylogeny of the Sematophyllaceae s.l. (Hypnales) based on plastid, mitochondrial and nuclear markers, and its taxonomic implications. Taxon 66: 811-831.

3. Xiang KL, Aytaç Z, Liu Y, Espinosa F, Jabbour F, Byng JW, Zhang CF, Erst AS, Wang W. 2017. Recircumscription of Delphinium subg. Delphinium (Ranunculaceae) and implications for its biogeography. Taxon 66: 554-566.

4. Wang W, Ortiz RDC, Jacques FMB, Chung SW, Liu Y, Xiang XG, Chen ZD. 2017. New insights into the phylogeny of Burasaieae (Menispermaceae) with the recognition of a new genus and emphasis on the southern Taiwanese and mainland Chinese disjunction. Molecular Phylogenetics and Evolution 109: 11-20.

2016

1. Johnson MG, Gardner EM, Goffinet B, Liu Y, Medina R, Shaw AJ, Zerega NJC, Wickett NJ. HybPiper: extracting exons and introns for phylogenetics from high-throughput sequencing reads using target enrichment. Applications in Plant Sciences 4, 1600016.

2. Shaw AJ, Devos N, Liu Y, Goffinet B, Cox CJ, Faltberg KI, Shaw B. 2016. Organellar phylogenomics of an emerging model system: Sphagnum (peat moss). Annals of Botany 118, 185-196.

3. Wang W, Lin L, Xiang XG, Ortiz RD, Liu Y, Xiang KL, Yu SX, Xing YW, Chen ZD. 2016. The rise of angiosperm-dominated herbaceous floras: Insights from Ranunculaceae. Scientific Reports 6, 27259.

4. Xiang KL, Wu SD, Yu SX, Liu Y, Jabbour F, Erst AS, Zhao L, Wang W, Chen ZD. 2016. The first comprehensive phylogeny of Coptis (Ranunculaceae) and its implications for character evolution and classification. PLoS ONE 11, e015312.

5. Vigalondo B, Liu Y, Lara F, Draper I, Mazimpaka V, Goffinet B. 2016. Comparing three complete mitochondrial genomes of the moss genus Orthotrichum Hedw. Mitochondrial DNA Part B 1, 176-178.

6. Lewis LR, Liu Y, Rozzi R, Goffinet B. 2016. Infraspecific variation within and across complete organellar genomes and nuclear ribosomal repeats in a moss. Molecular Phylogenetics and Evolution 96, 195-199.

7. Zhao CX, Zhu RL, Liu Y. 2016. Simple sequence repeats in bryophyte mitochondrial genomes. Mitochondrial DNA 27, 191-197.

2015

1. Medina R, Liu Y, Wang LS, Guo S, Hylander K, Goffinet B. 2015. DNA-based geographic circumscription of Physcomitrella s. lat. species (Funariaceae): P. patens new to Asia and P. magdalanae new to Ethiopia. The Bryologist 118, 22-31

2014

1. Liu Y, Cox CJ, Wang W, Goffinet B. 2014. Mitochondrial phylogenomics of early land plants: mitigating the effects of saturation, compositional heterogeneity and codon usage bias. Systematic Biology 63, 862-878. pdf

2. Liu Y, Medina R, Goffinet B. 2014. 350 My of structural stasis in early land plant mitochondrial genomes. Molecular Biology and Evolution 31, 2586-2591. pdf

3. Xiang XG, Wang W, Li RQ, Lin L, Liu Y, Zhou ZK, Li ZY, Chen ZD. 2014. Large-scale phylogenetic analyses reveal fagalean diversification promoted by the interplay of diaspores and environments in the Paleogene. Perspectives in Plant Ecology, Evolution and Systematics 16, 101-110.

4. Liu Y, Forrest LL, Bainard J, Budke JM, Goffinet B. 2013. Organellar genome, nuclear ribosomal DNA repeat unit andmicrosatellites isolated from a small-scale of 454 GS FLX sequencing on two mosses. Molecular Phylogenetics and Evolution 66, 1089-1094. pdf

5. Wang W, Liu Y, Yu SX, Gao TG, Chen ZD. 2013. Gymnaconitum, a new genus of Ranunculaceae endemic to the Qinghai-Tibetan Plateau. Taxon 62, 713-722.

2012

1. Wang W, Ortiz RDC, Jacquesc FMB, Xiang XG, Li HL, Lin L, Li RQ, Liu Y, Soltis PS, Soltis DE, Chen ZD. 2012. Menispermaceae and the diversification of tropical rainforests near the Cretaceous-Paleogene boundary. New Phytologist 195, 470-478.

2. Liu Y, Moskwa NL, Goffinet B. 2012. Development of eight mitochondrial markers for Funariaceae (Musci) and their amplification success in other mosses. American Journal of Botany 99, e62-e65. pdf

3. Liu, Y, Budke JM, Goffinet B. 2012. Phylogenetic inference rejects sporophyte based classification of the Funariaceae (Bryophyta): Rapid radiation suggests rampant homoplasy in sporophyte evolution. Molecular Phylogenetics and Evolution 62, 130-145. pdf

4. Liu Y, Wang B, Cui P, Li L, Xue JY, Yu J, Qiu YL. 2012. The mitochondrial genome of the lycophyte Huperzia squarrosa: The most archaic form in vascular plants. PLoS ONE 7, e35168. pdf

2011

1. Liu Y, Xue JY, Wang B, Li L, Qiu YL. 2011. The mitochondrial genomes of the early land plants Treubia lacunosa and Anomodon rugelii: Dynamic and conservative evolution. PLoS ONE 6, e25836. pdf

2010

1. Qiu YL, Li L, Wang B, Xue JY, Hendry TA, Li RQ, Brown JW, Liu Y, Hudson GT, Chen ZD. 2010. Angiosperm phylogeny inferred from sequences of four mitochondrial genes. Journal of Systematics and Evolution 48, 391-425.

2. Xue JY, Liu Y*, Li L, Wang B, Qiu YL. 2010. The complete mitochondrial genome sequence of the hornwort Phaeoceros laevis: Retention of many ancient pseudogenes and conservative evolution of mitochondrial genomes in hornworts. Current Genetics 56, 53-61. (*contributed equally). pdf

3. Wang B, Yeun LH, Xue JY, Liu Y, Ané JM, Qiu YL. 2010. Presence of three mycorrhizal genes in the common ancestor of land plants suggests a key role of mycorrhizas in the colonization of land by plants. New Phytologist 186, 514-525.

4. Wang QH, Jia Y, Liu Y, Chen ZD. 2010. The systematic position of Meteoriella S. Okamura (Musci) based on molecular and morphological data. Taxon 59, 93-100.

2009

1. Wang B, Xue JY, Li L, Liu Y, Qiu YL. 2009. The complete mitochondrial genome sequence of the liverwort Pleurozia purpurea reveals extremely conservative mitochondrial genome evolution in liverworts. Current Genetics 55, 601-609.

2. Li L, Wang B, Liu Y, Qiu YL. 2009. The complete mitochondrial genome sequence of the hornwort Megaceros aenigmaticus shows a mixed mode of conservative yet dynamic evolution in early land plant mitochondrial genomes. Journal of Molecular Evolution 68, 665-678.

2008 & earlier

1. Liu Y, Jia Y. 2008. Lejeuneaceae (Marchantiophyta) share an indel in chloroplast rps4 gene. Journal of Bryology 30, 174-177.

2. Liu Y, Jia Y, Wang W, Chen ZD, Davis EC, Qiu YL. 2008. Phylogenetic relationships of two endemic genera from East Asia: Trichocoleopsis and Neotrichocolea (Hepaticae). Annals of the Missouri Botanical Garden 95, 463-474. pdf

3. Wang W, Chen ZD, Liu Y, Li RQ, Li JH. 2007. Phylogenetic and biogeographic diversification of Berberidaceae in the northern hemisphere. Systematic Botany 32, 731-742.

4. Jia Y, Liu Y. 2006. Timmia sphaerocarpa (Timmiaceae, Musci), a new species from Tibet, China. Journal of Bryology 28, 350-356.

5. Liu Y, Jia Y, Wang W, Chen ZD, Qiu YL. 2005. A taxonomic reassessment of Microdendron inferred from molecular and morphological evidence. The Bryologist 108, 591-599. pdf

6. Liu Y, Jia Y, Wang MZ. 2005. Glyphomitrium tortifolium, a new species of the Glyphomitriaceae (Musci). Journal of Systematics and Evolution 43, 278-280.

7. Liu Y, Dan HM, Liu CH, Zhang LS. 2004. Effect of temperature and spraying sucrose and auxiliary agent synertrol on pollen germination rate of stone fruit trees. Northern Horticulture 3, 66-67.