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| 1 | Conservation analysis of long non-coding RNAs in plants显示文摘Long non-coding RNAs(lncRNAs) are gene regulators that have vital roles in development and adaptation to the environment in eukaryotes. However, the structural and evolutionary analyses of plant lncRNAs are limited. In this study, we performed an analysis of lncRNAs in five monocot and five dicot species. Our results showed that plant lncRNA genes were generally shorter and had fewer exons than protein-coding genes. The numbers of lncRNAs were positively correlated with the numbers of protein-coding genes in different plant species, despite a high range of variation. Sequence conservation analysis showed that the majority of lncRNAs had high sequence conservation at the intra-species and sub-species levels, reminiscent of protein-coding genes. At the inter-species level, a subset of lncRNAs were highly diverged at the nucleotide level, but conserved by position.Interestingly, we found that plant lncRNAs have identical splicing signals, and those which can form precursors or targets of miRNAs have a conservative identity in different species. We also revealed that most of the lowly expressed lncRNAs were tissue-specific, while those highly conserved were constitutively transcribed. Meanwhile, we characterized a subset of rice lncRNAs that were co-expressed with their adjacent protein-coding genes, suggesting they may play cis-regulatory roles. These results will contribute to understanding the biological significance and evolution of lncRNAs in plants. | Pingchuan Deng Shu Liu Xiaojun Nie Song Weining Liang Wu | 2018 | Science China(Life Sciences)2018，61，2： | 4 |
| 2 | Nuclear translocation of OsMFT1 that is impeded by OsFTIP1 promotes drought toleranee in rice显示文摘Drought is the leading environmental threat affecting crop productivity,and plants have evolved a series of mechanisms to adapt to drought stress.The FT-interacting proteins(FTIPs)and phosphatidylethanola mine.binding proteins(PEBPs)play key roles in developmental processes,whereas their roles in the regulation of stress response are still largely unknown.Here,we report that OsFTIP1 negatively regulates drought response in rice.We showed that OsFTIP1 interacts with rice MOTHER OF FT AND TFL1(OsMFT1),a PEBP that promotes rice tolerance to drought treatment.Further studies discovered that OsMFT1 interacts with two key drought-related transcription factors,OsbZIP66 and OsMYB26,regulating their binding capacity on drought-related genes and thereby enhancing drought toleranee in rice.Interestingly,we found that OsFTIP1 impedes the nucleocytoplasmic translocation of OsMFT1,implying that dynamic modulation of drought-responsive genes by the OsMFT1-OsMYB26 and OsMFT1-OsbZIP66 complexes is integral to OsFTIP1-modulated nuclear accumulation of OsMFT1.Our findings also suggest that OsMFT1 might act as a hitherto unknown nucleocytoplasmic trafficking signal that regulates drought tolerance in rice in response to environmental signals. | Ying Chen Jun Shen Liang Zhangi Haoyue Qi Lijia Yang Huanyu Wang Jiaxuan Wang Yuexing Wang Hao Du Zeng Tao Ting Zhao Pingchuan Deng Qingyao Shu Qian Qian Hao Yu Shiyong Song | 2021 | Molecular Plant2021，14，8： | 2 |
| 3 | A collagen-chitosan hydrogel for endothelial differentiation and angiogenesis显示文摘 | Deng Chao Zhang Pingchuan Vulesevic B | 2010 | Tissue Engingeering2010，16，10： | 1 |
| 4 | Comparative analysis of codon usage patterns in chloroplast genomes of the Asteraceae family显示文摘 | Xiaojun Nie Pingchuan Deng Kewei Feng Peixun Liu Xianghong Du Frank M You Song Weining | 2014 | Plant Molecular Biology Reporter2014，，： | 1 |
| 5 | LncRNAs are cool regulators in cold exposure in plants显示文摘Transcriptomic studies in last two decades showed that more than 70% eukaryotic genomes are transcribed.Those transcripts over 200 nucleotides in length without a coding ability,called long non-coding RNAs (lncRNAs),account for the largest portion of transcribed genomes (Deng et al.,2018). | Pingchuan Deng Liang Wu | 2019 | Science China(Life Sciences)2019，62，7： | 1 |
| 6 | Genome resources for the elite bread wheat cultivar Aikang 58 and mining of elite homeologous haplotypes for accelerating wheat improvement显示文摘Despite recent progress in crop genomics studies,the genomic changes brought about by modern breeding selection are still poorly understood,thus hampering genomics-assisted breeding,especially in polyploid crops with compound genomes such as common wheat(Triticum aestivum).In this work,we constructed genome resources for the modern elite common wheat variety Aikang 58(AK58).Comparative genomics between AK58 and the landrace cultivar Chinese Spring(CS)shed light on genomic changes that occurred through recent varietal improvement.We also explored subgenome diploidization and divergence in common wheat and developed a homoeologous locus-based genome-wide association study(HGWAS)approach,which was more effective than single homoeolog-based GWAS in unraveling agronomic trait-associated loci.A total of 123 major HGWAs loci were detected using a genetic population derived from AK58 and cs.Elite homoeologous haplotypes(HHs),formed by combinations of subgenomic homoeologs of the associated loci,were found in both parents and progeny,and many could substantially improve wheat yield and related traits.We built a website where users can download genome assembly sequence and annotation data for AK58,perform blast analysis,and run JBrowse.Our work enriches genome resources for wheat,provides new insights into genomic changes during modern wheat improve-.ment,and suggests that efficientmining of elite HHs can make a substantial contribuutionto genomics-assisted breeding in common wheat and other polyploid crops. | Jizeng Jia Guangyao Zhao Danping Li Kai Wang Chuizheng Kong Pingchuan Deng Xueqing Yan Xueyong Zhang Zefu Lu Shujuan Xu Yuannian Jiao Kang Chong Xu Liu Dangqun Cui Guangwei Li Yijing Zhang Chunguang Du Liang Wu Tianbao Li Dong Yan Kehui Zhan Feng Chen Zhiyong Wang Lichao Zhang Xiuying Kong Zhengang Ru Daowen Wang Lifeng Gao | 2023 | Molecular Plant2023，16，12： | 0 |
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