Publications

2019

  • Guanghui Zheng, Wei Wei, Yongping Li, Lijun Kan, Fuxi Wang, Xi Zhang, Feng Li, Zhongchi Liu, and Chunying Kang (2019) Conserved and novel roles of miR164-CUC2 regulatory module in specifying leaf and floral organs morphology in strawberry New Phytologist Jun 10. doi: 10.1111/nph.15982. [Epub ahead of print].
  • Rui Xia, Chengjie Chen, Suresh Pokhrel, Wuqiang Ma, Kun Huang, Parth Patel, Fuxi Wang, Zhongchi Liu, Jianguo Li, and Blake C. Meyers (2019) 24-nt reproductive phasiRNAs are broadly present in angiosperms. Nature Communications 2019 Feb 7;10(1):627. doi: 10.1038/s41467-019-08543-0.
  • Abigail Simmons, Kellie A. Davies, Wanpeng Wang, Zhongchi Liu,  Dominique C. Bergmann (2019) SOL1 and SOL2 Regulate Fate Transition and Cell Divisions in the Arabidopsis Stomatal Lineage. Development. 2019 Feb 4;146(3). pii: dev171066. doi: 10.1242/dev.171066.
  • Haley Wight, Junhui Zhou, Muzi Li, Sridhar Hanennhalli, Stephen M. Mount and Zhongchi Liu (2019) Draft Genome Assembly and Annotation of Red Raspberry Rubus idaeus. BioRxiv doi: https://doi.org/10.1101/546135
  • Galimba, K., Bullock, D., Dardick, C., Liu, Z., Callahan, A. (2019) Gibberellic Acid induced parthenocarpic 'Honeycrisp' apple (Malus domestica) exhibit reduced ovary width and lower acidity. Horticulture Research 6:41.
  • Shahan, R., Li, D. and Liu, Z. (2019) Identification of genes preferentially expressed in wild strawberry receptacle fruit and demonstration of their promoter activities. Horticulture Research 6:50.
  • Zhou, J., Li, D., Wang., G., Wang, F., Kunjal, M., Joldersma, D., and Liu, Z. (2019) Application and future perspective of CRISPR/Cas9 genome editing in fruit crops Jorunal of Integrative Plant Biology Feb. 21; https://doi.org/10.1111/jipb.12793.
  • Yongping Li, Mengting Pi, Qi Gao, Zhongchi Liu and Chunying Kang (2019) Updated annotation of the wild strawberry Fragaria vesca V4 genome. Horticulture Research 6:61

2018

  • Dongdong Li, Wangshu Mou, Rui Xia, Li Li, Chris Zawora, Tiejin Ying1, Linchun Mao, Zhongchi Liu, Zisheng Luo, (2019) Integrated analysis of high-throughput sequencing data shows abscisic acid-responsive genes and miRNAs in strawberry receptacle fruit ripening. Horticulture Research Feb 1;6:26. doi: 10.1038/s41438-018-0100-8
  • Jia Feng, Cheng Dai, Huifeng Luo, Yafan Han, Zhongchi Liu#, Chunying Kang# (2018) Dynamic spatial-temporal expression of TARs and YUCs in auxin biosynthesis underpins fruit development in strawberry. Journal of Experimental Botany Oct 27. doi: 10.1093/jxb/ery384. [Epub ahead of print]
  • Matthew D. Fischer, Emmanuel Mgboji, and Zhongchi Liu# (2018) Pyrite cloning: a single tube and programmed reaction cloning with restriction enzymes. Plant Methods Oct 17;14:91. doi: 10.1186/s13007-018-0359-7. eCollection 2018.
  • Rachel Shahan*, Chris Zawora*, John Sittmann, Haley Wight, Wanpeng Wang, Steve Mount, and Zhongchi Liu# (2018) Consensus network analysis identifies key regulators of flower and fruit development in wild strawberry Plant Physiology DOI: https://doi.org/10.1104/pp.18.00086 (*: co first author)
  • Maria Fernanda Laranjeira-Silva, Wanpeng Wang, Tamika K. Samuel, Fernando Y. Maeda1, Vladimir Michailowsky, Iqbal Hamza, Zhongchi Liu and Norma W. Andrews (2018) A MFS-like plasma membrane transporter promotes Leishmania virulence by protecting the parasites from iron toxicity. PLoS Pathog. 2018 Jun 15;14(6):e1007140. doi: 10.1371/journal.ppat.1007140.
  • Wanpeng Wang, Paja Sijacic, Pengbo Xu, Hongli Lian, Zhongchi Liu# (2018) Arabidopsis TSO1 and MYB3R1 form a regulatory module to coordinate cell proliferation with differentiation in shoot and root.  Proc Natl Acad Sci U S A. 2018 Mar 13. pii: 201715903. doi: 10.1073/pnas.1715903115. [Epub ahead of print].
  • Junhui Zhou, Guoming Wang, and Zhongchi Liu# (2018) Efficient genome-editing of wild strawberry genes, vector development, and validation. Plant Biotechnology Journal Mar 25. doi: 10.1111/pbi.12922. [Epub ahead of print]
  • Courtney A. Hollender, Thierry Pascal, Amy Tabb, Toto Hadiarto,  Chinnathambi Srinivasan,  Wanpeng Wang, Zhongchi Liu, Ralph Scorza, and Chris Dardick (2018). Loss of a highly conserved Sterile Alpha Motif domain gene (WEEP) results in pendulous branch growth in peach and plum trees. Proc Natl Acad Sci U S A May 15;115(20):E4690-E4699. doi: 10.1073/pnas.1704515115.
  • Huifeng Luo, Cheng Dai, Yongping Li, Jia Feng, Zhongchi Liu, and Chunying Kang (2018). RAP codes for a GST anthocyanin transporter that is essential for the foliage and fruit coloration in strawberry. J Exp Bot. 2018 Mar 10. doi: 10.1093/jxb/ery096. [Epub ahead of print]
  • ­Chunying Kang# and Zhongchi Liu# (2018) An easy-to-follow pipeline for long non-coding RNA identification: a case study in diploid strawberry Fragaria vesca during development. Methods in Mol. Biol. (In press).
  • Joldersma D, Liu Z.# (2018) Plant genetics enters the nano age? J Integr Plant Biol. 2018 Feb 27. doi: 10.1111/jipb.12646. [Epub ahead of print]
  • Dirk Joldersma and Zhongchi Liu# (2018). The making of virgin fruit: the molecular and genetic basis of parthenocarpy. J Exp Bot. 2018 Jan 10. doi: 10.1093/jxb/erx446.

2017

  • Caruana JC, Sittmann JW, Wang W, Liu Z.# (2017) Suppressor of Runnerless Encodes a DELLA Protein that Controls Runner Formation for Asexual Reproduction in Strawberry. Mol Plant, 2017 Nov 20. pii: S1674-2052(17)30334-9. doi: 10.1016 (two highlight articles: Flowering Newsletter and Mol Plant Spotlight)
  • Yongping Li, Wei Wei, Jia Feng, Huifeng Luo, Mengting Pi, Zhongchi Liu, Chunying Kang (2017) Genome re-annotation of the wild strawberry Fragaria vesca using extensive Illumina- and SMRT-based RNA-seq datasets. DNA Research, dsx038, https://doi.org/10.1093/dnares/dsx038
  • Charles Hawkins, Julie Caruana, Jiaming Li, Omar Darwish, Chris Zawora, Jun Wu, Nadim Alkharouf, and Zhongchi Liu# (2017) An eFP Browser for Visualizing Strawberry Fruit and Flower Transcriptomes. Horticulture Research Horticulture Research 4, Article number: 17029 doi:10.1038/hortres.2017.29.
  • Xinlei Li, Jiyuan Li, Zhengqi Fan, Zhongchi Liu, Takayuki Tanaka, Hengfu Yin. (2017) Global analysis of gene expression defines faded whorl specification into the domestication of different types of double flowers in Camellia. Scientific report 7, Article number: 3197 doi:10.1038/s41598-017-03575-2

2016

  • Yongping Li, Cheng Dai, Chungen Hu, Zhongchi Liu, and Chunying Kang (2016) Global identification of alternative splicing via comparative analysis of SMRT- and Illumina-based RNA-seq in strawberry. Plant Journal Dec 20. doi: 10.1111/tpj.13462.
  • Xue Gong, Jing Han Hong, Miguel Flores-Vergara, Huangwei Chu, Jun Lim, Robert Franks, Zhongchi Liu, and Jian Xu (2016) SEUSS integrates gibberellin signaling with transcriptional inputs from the SHR-SCR-SCL3 module to regulate middle cortex formation in the Arabidopsis root. Plant Physiology 2016 Jan 27.
  • Charles Hawkins, Julie Caruana, Erin Schiksnis, and Zhongchi Liu (2016) Genome-scale DNA variant analysis identifies a SNP that underlies the yellow fruit color in wild strawberry. Scientific Report Jul 5;6:29017. doi: 10.1038/srep29017
  • Hengfu Yin, Zhengqi Fan, Xinlei Li, Jiangying Wang, Weixin Liu, Bin Wu, Zhen Yin, Liping Liu, Zhongchi Liu, and Jiyuan Li. (2016) Phylogenetic tree-informed microRNAome analysis uncovers conserved and lineage-specific miRNAs in Camellia during floral organ development. Journal of Experimental Botany. doi: 10.1093/jxb/erw095 First published online: March 7, 2016

2015

  • Omar Darwish, Rachel Shahan, Zhongchi Liu, Janet P. Slovin, Nadim W. Alkharouf (2015). Reannotation of the Strawberry (Fragaria vesca) Genome. BMC Genomics 16(1):29.
  • Rui Xia, Songqing Ye, Zongrang Liu, Blake Meyers, and Zhongchi Liu (2015) Novel and recently evolved miRNA clusters regulate expansive F-box gene networks through phasiRNAs in wild diploid strawberry. Plant Physiology 169(1):594-610.
  • Fan Z, Li J, Li X, Wu B, Liu Z, Yin H (2015) Genome-wide transcriptome profiling provides insights into floral bud development of summer-flowering Camellia azalea. Sci Rep. 2015 May 15;5:9729
  • Kang, C. and Liu, Z. (2015) Global identification and analysis of long non-coding RNAs in diploid strawberry Fragaria vesca during flower and fruit development. BMC Genomics 16(1):815.
  • Zhongchi Liu and Rober Franks (2015) “Molecular Basis of Fruit Development”. Frontiers in Plant Science 05 February 2015 | doi: 10.3389/fpls.2015.00028

2014

  • Wen, Zhifeng; Yang, Yazhou; Zhang, Jinjin; Wang, Xiping; Singer, Stacy; Liu, Zhongchi; Yang, Yingjun; Liu, Zongrang (2014) Highly interactive nature of flower-specific enhancers and promoters, and its potential impact on tissue-specific expression and engineering of multiple genes or agronomic traits. Plant Biotechnology Journal 12(7):951-962.
  • Sun Y, Fan Z, Li X, Liu Z, Li J, Yin H (2014) Distinct double flower varieties in Camellia japonica exhibit both expansion and contraction of C-class gene expression. BMC plant biology 14(1):288.
  • Hawkins C and Liu Z (2014) A Model for an Early Role of Auxin in Arabidopsis Gynoecium Morphogenesis. Frontiers in Plant Science 5:328
  • Hollender CA, Kang C, Darwish O, Geretz A., Matthews BF, Slovin, J, Alkharouf N, and Liu Z. (2014). Floral transcriptomes in woodland strawberry uncover developing receptacle and anther gene networks. Plant Physiology, 165(3):1062-1075..
  • 2013
  • O. Darwish, J. P. Slovin, C. Kang, C. A. Hollender, A. Geretz, S. Houston, Z. Liu, N. W. Alkharouf (2013). SGR: an online genomic resource for the woodland strawberry. BMC Plant Biology Dec 23;13;223
  • Kang C, Darwish O, Geretz A., Shahan R, Alkharouf N, and Liu Z. (2013) Genome-Scale Transcriptomic Insights into Early-Stage Fruit Development in Woodland Strawberry Fragaria vesca. Plant Cell 25(6):1960-78.
  • Xia R, Meyers BC, Liu Z, Beers EP, Ye S, Liu Z. (2013) MicroRNA Superfamilies Descended from miR390 and Their Roles in Secondary Small Interfering RNA Biogenesis in Eudicots. Plant Cell 25(5):1555-72
  • Yin H, Gao P, Liu C, Yang J, Liu Z, Luo D. (2013) SUI-family genes encode phosphatidylserine synthases and regulate stem development in rice. Planta Jan;237(1):15-27.
  • 2012
  • C. A. Hollender, A. Geretz, J.P. Slovin., Z. Liu (2012) Flower and early fruit development in diploid strawberry, Fragaria vesca. Planta Jun;235(6):1123-39.
  • 2011
  • Sijacic, P., Wang, W., and Liu, Z. (2011). Recessive antimorphic alleles overcome functionally redundant loci to reveal TSO1 function in Arabidopsis flowers and meristems. PLoS Genetics Nov;7(11):e1002352. doi: 10.1371/journal.pgen.1002352.
  • Grigorova, B, Mara, C., Hollender, C., Sijacic, P., X. Chen, and Liu, Z. (2011). LEUNIG and SEUSS regulate miR172 in Arabidopsis Flowers. Development Jun;138(12):2451-6.
  • Bui, M., Lim, N., Sijacic, P. and Liu, Z. (2011). LEUNIG-HOMOLOG and LEUNIG promote seed mucilage extrusion in Arabidopsis. JIPB 2011 Mar 1. doi: 10.1111/j.1744-7909.2011.01036.x. [Epub ahead of print]
  • 2010
  • Courtney Hollender and Zhongchi Liu (2010) Bimolecular Fluorescence Complementation (BiFC) Assay for Protein-Protein Interaction in Onion Cells Using the Helios Gene Gun. J. Vis. Exp. 2010 Jun 12;(40)
  • Paja Sijacjc and Z. Liu (2010) Novel insights from live imaging in shoot meristem development. Journal of Integrative Plant Biology 52 (4) 393-9.
  • Chloe Mara, Boyana Grigorova, and Zhongchi Liu (2010) Floral-dip transformation of Arabidopsis thaliana to examine pTSO2:: b-glucuronidase reporter expression. J Vis Exp. 2010 Jun 11;(40).
  • Z. Liu and C. Mara (2010) Regulation of floral homeotic genes. Invited review for a special issue on flower development. Seminars in Cell and Developmental Biology, Feb;21(1):80-86.
  • 2009
  • Minh Bui and Zhongchi Liu. (2009) Simple Allele-discriminating PCR For Cost-effective and Rapid Genotyping and Mapping. Plant Methods 5:1.
  • 2008 and before
  • Jayashree Sitaraman*, Minh Bui*, and Zhongchi Liu. (2008) LEUNIG_HOMOLOG and LEUNIG are partially redundant during Arabidopsis embryo and floral development. Plant Physiology 147(2):672-681 (pdf). *: equal contribution.
  • Courtney Hollender and Zhongchi Liu (2008). Histone Deacetylase Genes in Arabidopsis Development. Journal of Integrative Plant Biology 50(7):875-85.
  • Z. Liu and V. Karmarkar. (2008) Gro-Tup1 family co-repressors in plant development. Trends in Plant Science 13(3):137-144 (pdf).
  • Zongreng Liu and Zhongchi Liu. (2008) Precise and efficient ablation of male and female organs in engineering plant sterility for complete containment of transgene flow. Plant Cell Reports 27(5):855-863 (pdf).
  • Vaniyambadi .V. Sridhar, Anandkumar Surendrarao, and Z. Liu (2006). APETALA1 and SEPALLATA3 interact with SEUSS to mediate transcription repression during flower development. Development 133, 3159-3166 (pdf).
  • R. Franks, Z. Liu and R. Fischer. (2006) Petal polarity and shape regulation in Arabidopsis requires SEUSS and LEUNIG. Planta 224(4):801-11(pdf)
  • C. Wang and Z. Liu (2006). Arabidopsis Ribonucleotide Reductase are Critical for Cell Cycle Progression, DNA Damage Repair, and Plant Development. Plant Cell 18:350-365. (pdf)
  • Z. Liu (2005) Regulatory Mechanisms for Floral Organ Identity Specification in Higher Plants. In Gene Expression and Regulation, a Current Scientific Frontiers Book (Ed. J. Ma). Higher Education Press, Beijing and Blackwell Publishing.
  • Sridhar, V.V., Surendrarao, A., Gonzalez, D., Conlan, R.S., and Liu, Z. (2004) Transcriptional repression of target genes by LEUNIG and SEUSS, two interacting regulatory proteins for Arabidopsis flower development. Proc Natl Acad Sci U S A. 101: 11494-11499. (pdf)
  • Bao, X., Franks, R.G., Levin, J.Z., and Liu, Z. (2004) Repression of AGAMOUS by BELLRINGR, in Floral and Inflorescence Meristems. Plant Cell 16: 1478-14. (pdf)
  • Franks, R. Wang, C., Levin, J. Z., and Liu, Z. (2002) SEUSS, a member of a novel family of plant regulatory proteins, represses floral homeotic gene expression with LEUNIG. Development 129: 253-263. (pdf) (with Cover)
  • Franks, R.G. and Liu, Z. 2001) Floral homeotic gene regulation. Horticultural Reviews vol. 27: 41-77.
  • Song, J., Leung, T., Ehler, L. K., Wang, C., Liu, Z. (2000) Regulation of meristem organization and cell division by TSO1, an Arabidopsis gene with cysteine-rich repeats. Development 127:2207-2217. (pdf)
  • Liu, Z., Franks, R.G. and Klink, V. P. (2000) Regulation of marginal tissue formation by LEUNIG and AINTEGUMENTA. Plant Cell 12: 1893-1902. (pdf) (with Cover)
  • Conner, J. and Liu Z. (2000) LEUNIG, a putative transcriptional co-repressor that regulates AGAMOUS expression during flower development. Proc Natl Acad Sci U S A 97: 12902-12907. (pdf)
  • Scovel, G., Altshuler, T., Liu, Z., and Vainstein, A. (2000) The EVERGREEN gene is essential for flower initiation in carnation. J. of Heredity 91: 487-491.
  • Liu, Z., Running, M. R., and Meyerowitz, E. M. (1997) TSO1 function in cell division during Arabidopsis flower development. Development 124: 665-672. (pdf)
  • Liu, Z., and Meyerowitz, E. M. (1995) LEUNIG regulates AGAMOUS expression in Arabidopsis flowers. Development 121: 975-991.