6 results on '"Liu, Zhongchi"'
Search Results
2. Allelic Variation of MYB10 Is the Major Force Controlling Natural Variation in Skin and Flesh Color in Strawberry (Fragaria spp.) Fruit.
- Author
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Castillejo, Cristina, Waurich, Veronika, Wagner, Henning, Ramos, Rubén, Oiza, Nicolás, Muñoz, Pilar, Triviño, Juan C., Caruana, Julie, Liu, Zhongchi, Cobo, Nicolás, Hardigan, Michael A., Knapp, Steven J., Vallarino, José G., Osorio, Sonia, Martín-Pizarro, Carmen, Posé, David, Toivainen, Tuomas, Hytönen, Timo, Oh, Youngjae, and Barbey, Christopher R.
- Published
- 2020
- Full Text
- View/download PDF
3. Genome-Scale Transcriptomic Insights into Early-Stage Fruit Development in Woodland Strawberry Fragaria vesca.
- Author
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Kang, Chunying, Darwish, Omar, Geretz, Aviva, Shahan, Rachel, Alkharouf, Nadim, and Liu, Zhongchi
- Subjects
FRUIT development ,SEED coats (Botany) ,WOODLOTS ,TRANSCRIPTOMES ,FORESTS & forestry ,STRAWBERRIES ,NUCLEOTIDE sequencing ,PLANT hormones - Abstract
Fragaria vesca , a diploid woodland strawberry with a small and sequenced genome, is an excellent model for studying fruit development. The strawberry fruit is unique in that the edible flesh is actually enlarged receptacle tissue. The true fruit are the numerous dry achenes dotting the receptacle's surface. Auxin produced from the achene is essential for the receptacle fruit set, a paradigm for studying crosstalk between hormone signaling and development. To investigate the molecular mechanism underlying strawberry fruit set, next-generation sequencing was employed to profile early-stage fruit development with five fruit tissue types and five developmental stages from floral anthesis to enlarged fruits. This two-dimensional data set provides a systems-level view of molecular events with precise spatial and temporal resolution. The data suggest that the endosperm and seed coat may play a more prominent role than the embryo in auxin and gibberellin biosynthesis for fruit set. A model is proposed to illustrate how hormonal signals produced in the endosperm and seed coat coordinate seed, ovary wall, and receptacle fruit development. The comprehensive fruit transcriptome data set provides a wealth of genomic resources for the strawberry and Rosaceae communities as well as unprecedented molecular insight into fruit set and early stage fruit development. [ABSTRACT FROM AUTHOR]
- Published
- 2013
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4. MicroRNA Superfamilies Descended from miR390 and Their Roles in Secondary Small Interfering RNA Biogenesis in Eudicots.
- Author
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Xia, Rui, Meyers, Blake C., Liu, Zhongchi, Beers, Eric P., Ye, Songqing, and Liu, Zongrang
- Subjects
SMALL interfering RNA ,PENTATRICOPEPTIDE repeat genes ,NON-coding RNA ,EUDICOTS ,MICRORNA ,RNA splicing - Abstract
Trans -acting small interfering RNAs (tasiRNAs) are a major class of small RNAs performing essential biological functions in plants. The first reported tasiRNA pathway, that of miR173- TAS1/2 , produces tasiRNAs regulating a set of pentatricopeptide repeat (PPR) genes and has been characterized only in Arabidopsis thaliana to date. Here, we demonstrate that the microRNA (miRNA)- trans -acting small interfering RNA gene (TAS)-pentatricopeptide repeat-containing gene (PPR)-small interfering RNA pathway is a highly dynamic and widespread feature of eudicots. Nine eudicot plants, representing six different plant families, have evolved similar tasiRNA pathways to initiate phased small interfering RNA (phasiRNA) production from PPR genes. The PPR phasiRNA production is triggered by different 22-nucleotide miRNAs , including miR7122, miR1509, and fve-PPRtri1/2, and through distinct mechanistic strategies exploiting miRNA direct targeting or indirect targeting through TAS -like genes (TASL), one-hit or two-hit, or even two layers of tasiRNA – TASL interactions. Intriguingly, although those miRNA triggers display high sequence divergence caused by the occurrence of frequent point mutations and splicing shifts, their corresponding MIRNA genes show pronounced identity to the Arabidopsis MIR173 , implying a common origin of this group of miRNAs (super-miR7122). Further analyses reveal that super-miR7122 may have evolved from a newly defined miR4376 superfamily, which probably originated from the widely conserved miR390. The elucidation of this evolutionary path expands our understanding of the course of miRNA evolution, especially for relatively conserved miRNA families. [ABSTRACT FROM AUTHOR]
- Published
- 2013
- Full Text
- View/download PDF
5. Arabidopsis ribonucleotide reductases are critical for cell cycle progression, DNA damage repair, and plant development.
- Author
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Wang C and Liu Z
- Subjects
- Amino Acid Sequence, Apoptosis, Arabidopsis enzymology, Arabidopsis growth & development, Arabidopsis Proteins chemistry, Gene Expression Profiling, Gene Expression Regulation, Developmental, Gene Expression Regulation, Plant, Gene Silencing, Genes, Plant genetics, Molecular Sequence Data, Mutation genetics, Plant Leaves anatomy & histology, Plant Leaves cytology, Plant Leaves ultrastructure, Protein Subunits, RNA, Messenger genetics, RNA, Messenger metabolism, Radiation Tolerance, Ribonucleotide Reductases chemistry, Seedlings anatomy & histology, Seedlings radiation effects, Seedlings ultrastructure, Ultraviolet Rays, Arabidopsis cytology, Arabidopsis genetics, Arabidopsis Proteins metabolism, Cell Cycle, DNA Damage, DNA Repair, Ribonucleotide Reductases metabolism
- Abstract
Ribonucleotide reductase (RNR), comprising two large (R1) and two small (R2) subunits, catalyzes a rate-limiting step in the production of deoxyribonucleotides needed for DNA replication and repair. Previous studies in yeast and mammals indicated that defective RNR often led to cell cycle arrest, growth retardation, and p53-dependent apoptosis, whereas abnormally increased RNR activities led to higher mutation rates. Because plants are constantly exposed to environmental mutagens and plant cells are totipotent, an understanding of RNR function in plants is important. We isolated and characterized mutations in all three R2 genes (TSO2, RNR2A, and RNR2B) in Arabidopsis thaliana. tso2 mutants had reduced deoxyribonucleoside triphosphate (dNTP) levels and exhibited developmental defects, including callus-like floral organs and fasciated shoot apical meristems. tso2 single and tso2 rnr2a double mutants were more sensitive to UV-C light, and tso2 rnr2a seedlings exhibited increased DNA damage, massive programmed cell death, and release of transcriptional gene silencing. Analyses of single and double r2 mutants demonstrated that a normal dNTP pool and RNR function are critical for the plant response to mutagens and proper plant development. The correlation between DNA damage accumulation and the subsequent occurrence of apoptotic nuclei in tso2 rnr2a double mutants suggests that perhaps plants, like animals, can initiate programmed cell death upon sensing DNA damage.
- Published
- 2006
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6. Repression of AGAMOUS by BELLRINGER in floral and inflorescence meristems.
- Author
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Bao X, Franks RG, Levin JZ, and Liu Z
- Subjects
- Alleles, Amino Acid Sequence, Arabidopsis metabolism, Arabidopsis Proteins chemistry, Arabidopsis Proteins genetics, Base Sequence, Flowers metabolism, Genes, Plant genetics, Meristem metabolism, Molecular Sequence Data, Mutation genetics, Phenotype, Protein Binding, Protein Structure, Tertiary, Repressor Proteins chemistry, Repressor Proteins genetics, AGAMOUS Protein, Arabidopsis genetics, Arabidopsis genetics, Arabidopsis Proteins metabolism, Flowers genetics, Gene Expression Regulation, Plant, Meristem genetics, Repressor Proteins metabolism
- Abstract
A common aspect of gene regulation in all developmental systems is the sustained repression of key regulatory genes in inappropriate spatial or temporal domains. To understand the mechanism of transcriptional repression of the floral homeotic gene AGAMOUS (AG), we identified two mutations in the BELLRINGER (BLR) gene based on a striking floral phenotype, in which homeotic transformations from sepals to carpels are found in flowers derived from old terminating shoots. Furthermore, this phenotype is drastically enhanced by growth at a high temperature and by combining blr with mutants of LEUNIG and SEUSS, two putative transcriptional corepressors of AG. We showed that the floral phenotype of blr mutants is caused by derepression of AG, suggesting that BLR functions as a transcription repressor. Because BLR encodes a BELL1-like (BELL) homeobox protein, direct binding of BLR to AG cis-regulatory elements was tested by gel-shift assays, and putative BLR binding motifs were identified. In addition, these putative BLR binding motifs were shown to be conserved in 17 of the 29 Brassicaceae species by phylogenetic footprinting. Because BELL homeobox proteins are a family of plant-specific transcription factors with 12 members in Arabidopsis thaliana, our findings will facilitate the identification of regulatory targets of other BELL proteins and help determine their biological functions. The age-dependent and high temperature-enhanced derepression of AG in blr mutants led us to propose that AG expression might be regulated by a thermal time-dependent molecular mechanism., (Copyright 2004 American Society of Plant Biologists)
- Published
- 2004
- Full Text
- View/download PDF
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