36 results on '"Bobin Liu"'
Search Results
2. Genome-wide identification, evolution and expression analysis of the aspartic protease gene family during rapid growth of moso bamboo (Phyllostachys edulis) shoots
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Xiaqin Wang, Xinyang Yan, Shubin Li, Yun Jing, Lianfeng Gu, Shuangquan Zou, Jin Zhang, and Bobin Liu
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Aspartic protease ,Moso bamboo ,Programmed cell death ,Rapid growth ,Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Aspartic proteases (APs) are a class of aspartic peptidases belonging to nine proteolytic enzyme families whose members are widely distributed in biological organisms. APs play essential functions during plant development and environmental adaptation. However, there are few reports about APs in fast-growing moso bamboo. Result In this study, we identified a total of 129 AP proteins (PhAPs) encoded by the moso bamboo genome. Phylogenetic and gene structure analyses showed that these 129 PhAPs could be divided into three categories (categories A, B and C). The PhAP gene family in moso bamboo may have undergone gene expansion, especially the members of categories A and B, although homologs of some members in category C have been lost. The chromosomal location of PhAPs suggested that segmental and tandem duplication events were critical for PhAP gene expansion. Promoter analysis revealed that PhAPs in moso bamboo may be involved in plant development and responses to environmental stress. Furthermore, PhAPs showed tissue-specific expression patterns and may play important roles in rapid growth, including programmed cell death, cell division and elongation, by integrating environmental signals such as light and gibberellin signals. Conclusion Comprehensive analysis of the AP gene family in moso bamboo suggests that PhAPs have experienced gene expansion that is distinct from that in rice and may play an important role in moso bamboo organ development and rapid growth. Our results provide a direction and lay a foundation for further analysis of plant AP genes to clarify their function during rapid growth.
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- 2021
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3. Genome-Wide Identification and Co-Expression Analysis of ARF and IAA Family Genes in Euscaphis konishii: Potential Regulators of Triterpenoids and Anthocyanin Biosynthesis
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Bobin Liu, Juanli Zhu, Lina Lin, Qixin Yang, Bangping Hu, Qingying Wang, Xiao-Xing Zou, and Shuang-Quan Zou
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Euscaphis konishii ,Aux/IAA ,ARF ,triterpenoids ,anthocyanin ,fruit development ,Genetics ,QH426-470 - Abstract
Euscaphis konishii is an evergreen plant that is widely planted as an industrial crop in Southern China. It produces red fruits with abundant secondary metabolites, giving E. konishii high medicinal and ornamental value. Auxin signaling mediated by members of the AUXIN RESPONSE FACTOR (ARF) and auxin/indole-3-acetic acid (Aux/IAA) protein families plays important roles during plant growth and development. Aux/IAA and ARF genes have been described in many plants but have not yet been described in E. konishii. In this study, we identified 34 EkIAA and 29 EkARF proteins encoded by the E. konishii genome through database searching using HMMER. We also performed a bioinformatic characterization of EkIAA and EkARF genes, including their phylogenetic relationships, gene structures, chromosomal distribution, and cis-element analysis, as well as conserved motifs in the proteins. Our results suggest that EkIAA and EkARF genes have been relatively conserved over evolutionary history. Furthermore, we conducted expression and co-expression analyses of EkIAA and EkARF genes in leaves, branches, and fruits, which identified a subset of seven EkARF genes as potential regulators of triterpenoids and anthocyanin biosynthesis. RT-qPCR, yeast one-hybrid, and transient expression analyses showed that EkARF5.1 can directly interact with auxin response elements and regulate downstream gene expression. Our results may pave the way to elucidating the function of EkIAA and EkARF gene families in E. konishii, laying a foundation for further research on high-yielding industrial products and E. konishii breeding.
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- 2022
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4. Functional and morphological evolution in gymnosperms: A portrait of implicated gene families
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Amanda R. De La Torre, Anthony Piot, Bobin Liu, Benjamin Wilhite, Matthew Weiss, and Ilga Porth
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biotechnology ,functional evolution ,gene families ,gymnosperms ,PDR gene family ,reproductive biology ,Evolution ,QH359-425 - Abstract
Abstract Gymnosperms diverged from their sister plant clade of flowering plants 300 Mya. Morphological and functional divergence between the two major seed plant clades involved significant changes in their reproductive biology, water‐conducting systems, secondary metabolism, stress defense mechanisms, and small RNA‐mediated epigenetic silencing. The relatively recent sequencing of several gymnosperm genomes and the development of new genomic resources have enabled whole‐genome comparisons within gymnosperms, and between angiosperms and gymnosperms. In this paper, we aim to understand how genes and gene families have contributed to the major functional and morphological differences in gymnosperms, and how this information can be used for applied breeding and biotechnology. In addition, we have analyzed the angiosperm versus gymnosperm evolution of the pleiotropic drug resistance (PDR) gene family with a wide range of functionalities in plants' interaction with their environment including defense mechanisms. Some of the genes reviewed here are newly studied members of gene families that hold potential for biotechnological applications related to commercial and pharmacological value. Some members of conifer gene families can also be exploited for their potential in phytoremediation applications.
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- 2020
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5. Insights of Molecular Mechanism of Xylem Development in Five Black Poplar Cultivars
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Lei Zhang, Bobin Liu, Jin Zhang, and Jianjun Hu
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Populus ,developing xylem ,transcriptome ,cell wall ,transcriptional regulation ,Plant culture ,SB1-1110 - Abstract
Black poplar (Populus deltoides, P. nigra, and their hybrids) is the main poplar cultivars in China. It offers interesting options of large-scale biomass production for bioenergy due to its rapid growth and high yield. Poplar wood properties were associated with chemical components and physical structures during wood formation. In this study, five poplar cultivars, P. euramericana ‘Zhonglin46’ (Pe1), P. euramericana ‘Guariento’ (Pe2), P. nigra ‘N179’ (Pn1), P. deltoides ‘Danhong’ (Pd1), and P. deltoides ‘Nanyang’ (Pd2), were used to explore the molecular mechanism of xylem development. We analyzed the structural differences of developing xylem in the five cultivars and profiled the transcriptome-wide gene expression patterns through RNA sequencing. The cross sections of the developing xylem showed that the cell wall thickness of developed fiber in Pd1 was thickest and the number of xylem vessels of Pn1 was the least. A total of 10,331 differentially expressed genes were identified among 10 pairwise comparisons of the five cultivars, most of them were related to programmed cell death and secondary cell wall thickening. K-means cluster analysis and Gene Ontology enrichment analysis showed that the genes highly expressed in Pd1 were related to nucleotide decomposition, metabolic process, transferase, and microtubule cytoskeleton; whereas the genes highly expressed in Pn1 were involved in cell wall macromolecule decomposition and polysaccharide binding processes. Based on a weighted gene co-expression network analysis, a large number of candidate regulators for xylem development were identified. And their potential regulatory roles to cell wall biosynthesis genes were validated by a transient overexpression system. This study provides a set of promising candidate regulators for genetic engineering to improve feedstock and enhance biofuel conversion in the bioenergy crop Populus.
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- 2020
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6. Characterization of the Populus Rab family genes and the function of PtRabE1b in salt tolerance
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Jin Zhang, Yu Li, Bobin Liu, Lijuan Wang, Li Zhang, Jianjun Hu, Jun Chen, Huanquan Zheng, and Mengzhu Lu
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Populus ,Rab GTPase ,Phylogenetic analysis ,Co-expression network ,Subcellular localization ,Salt tolerance ,Botany ,QK1-989 - Abstract
Abstract Background Rab proteins form the largest family of the Ras superfamily of small GTP-binding proteins and regulate intracellular trafficking pathways. However, the function of the Rab proteins in woody species is still an open question. Results Here, a total of 67 PtRabs were identified in Populus trichocarpa and categorized into eight subfamilies (RabA-RabH). Based on their chromosomal distribution and duplication blocks in the Populus genome, a total of 27 PtRab paralogous pairs were identified and all of them were generated by whole-genome duplication events. Combined the expression correlation and duplication date, the PtRab paralogous pairs that still keeping highly similar expression patterns were generated around the latest large-scale duplication (~ 13 MYA). The cis-elements and co-expression network of unique expanded PtRabs suggest their potential roles in poplar development and environmental responses. Subcellular localization of PtRabs from each subfamily indicates each subfamily shows a localization pattern similar to what is revealed in Arabidopsis but RabC shows a localization different from their counterparts. Furthermore, we characterized PtRabE1b by overexpressing its constitutively active mutant PtRabE1b(Q74L) in poplar and found that PtRabE1b(Q74L) enhanced the salt tolerance. Conclusions These findings provide new insights into the functional divergence of PtRabs and resources for genetic engineering resistant breeding in tree species.
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- 2018
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7. Overexpression of PtrMYB121 Positively Regulates the Formation of Secondary Cell Wall in Arabidopsis thaliana
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Ying Liu, Jiayin Man, Yinghao Wang, Chao Yuan, Yuyu Shi, Bobin Liu, Xia Hu, Songqing Wu, Taoxiang Zhang, and Chunlan Lian
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PtrMYB121 ,secondary cell wall ,transcription factor ,lignin ,cellulose ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
MYB transcription factors have a wide range of functions in plant growth, hormone signaling, salt, and drought tolerances. In this study, two homologous transcription factors, PtrMYB55 and PtrMYB121, were isolated and their functions were elucidated. Tissue expression analysis revealed that PtrMYB55 and PtrMYB121 had a similar expression pattern, which had the highest expression in stems. Their expression continuously increased with the growth of poplar, and the expression of PtrMYB121 was significantly upregulated in the process. The full length of PtrMYB121 was 1395 bp, and encoded protein contained 464 amino acids including conserved R2 and R3 MYB domains. We overexpressed PtrMYB121 in Arabidopsis thaliana, and the transgenic lines had the wider xylem as compared with wild-type Arabidopsis. The contents of cellulose and lignin were obviously higher than those in wild-type materials, but there was no significant change in hemicellulose. Quantitative real-time PCR demonstrated that the key enzyme genes regulating the synthesis of lignin and cellulose were significantly upregulated in the transgenic lines. Furthermore, the effector-reporter experiment confirmed that PtrMYB121 bound directly to the promoters of genes relating to the synthesis of lignin and cellulose. These results suggest that PtrMYB121 may positively regulate the formation of secondary cell wall by promoting the synthesis of lignin and cellulose.
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- 2020
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8. Evolutionary Divergence of Duplicated Hsf Genes in Populus
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Bobin Liu, Jianjun Hu, and Jin Zhang
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Populus ,heat shock transcription factors ,gene duplication ,gene expression ,alternative splicing ,single nucleotide polymorphism ,protein structure ,co-expression network ,Cytology ,QH573-671 - Abstract
Heat shock transcription factors (Hsfs), which function as the activator of heat shock proteins (Hsps), play multiple roles in response to environmental stress and the development of plants. The Hsf family had experienced gene expansion via whole-genome duplication from a single cell algae to higher plants. However, how the Hsf gene family went through evolutionary divergence after genome duplication is unknown. As a model wood species, Populus trichocarpa is widely distributed in North America with various ecological and climatic environments. In this study, we used P. trichocarpa as materials and identified the expression divergence of the PtHsf gene family in developmental processes, such as dormant bud formation and opening, catkins development, and in response to environments. Through the co-expression network, we further discovered the divergent co-expressed genes that related to the functional divergence of PtHsfs. Then, we studied the alternative splicing events, single nucleotide polymorphism distribution and tertiary structures of members of the PtHsf gene family. In addition to expression divergence, we uncovered the evolutionary divergence in the protein level which may be important to new function formations and for survival in changing environments. This study comprehensively analyzed the evolutionary divergence of a member of the PtHsf gene family after genome duplication, paving the way for further gene function analysis and genetic engineering.
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- 2019
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9. Sequencing of Euscaphis konishii Endocarp Transcriptome Points to Molecular Mechanisms of Endocarp Coloration
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Xueyan Yuan, Weihong Sun, Xiaoxing Zou, Bobin Liu, Wei Huang, Zeming Chen, Yanlei Li, Meng-Yuan Qiu, Zhong-Jian Liu, Yanling Mao, and Shuang-Quan Zou
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endocarp coloration ,Euscaphis konishii ,transcriptome ,anthocyanin biosynthesis ,chlorophyll degradation ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
Flower and fruit colors are of vital importance to the ecology and economic market value of plants. The mechanisms of flower and fruit coloration have been well studied, especially among ornamental flower plants and cultivated fruits. As people pay more attention to exocarp coloration, the endocarp coloration in some species has often been ignored. Here, we report on the molecular mechanism of endocarp coloration in three development stages of Euscaphis konishii. The results show that endocarp reddening is closely related to anthocyanin accumulation, and a total of 86,120 unigenes were assembled, with a mean length of 893 bp (N50 length of 1642 bp). We identified a large number of differentially expressed genes associated with endocarp coloration, including anthocyanin biosynthesis, carotenoid biosynthesis, and chlorophyll breakdown. The genes participating in each step of the anthocyanin biosynthesis were found in the transcriptome dataset, but a few genes were found in the carotenoid biosynthesis and chlorophyll breakdown. In addition, the candidate R2R3-MYB transcription factors and candidate glutathione S-transferase transport genes, which likely regulate the anthocyanin biosynthesis, were identified. This study offers a platform for E. konishii functional genomic research and provides a reference for revealing the regulatory mechanisms of endocarp reddening.
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- 2018
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10. Insights into cryptochrome modulation of <scp>ABA</scp> signaling to mediate dormancy regulation in Marchantia polymorpha
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Jiakai Liao, Ban Deng, Qixin Yang, Yu Li, Yuxiang Zhang, Jiajing Cong, Xiaqin Wang, Markus V. Kohnen, Zhong‐Jian Liu, Meng‐Zhu Lu, Deshu Lin, Lianfeng Gu, and Bobin Liu
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Physiology ,Plant Science - Published
- 2023
11. Genome-wide Identification and Expression Profile Analysis of Laccase Family Genes in theHypsizygus marmoreus
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Gang Wang, Cheng Wang, HongBo Wang, Ying Zhu, Yuanyuan Wang, Yu chen, Lin Ma, Zijun Sun, Bobin Liu, and Fang Liu
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Laccase exists widely in plants and fungi. It is a copper-containing polyphenol oxidase that can degrade lignin, oxidate, and phenolic substances, inhibit heterophytes, promote fruiting body formation, and improve the quality of mushrooms. In this study, 18 laccase genes were identified from the whole genome of a white strain (HM62) ofHypsizygus marmoreus, and the mapping, structure, and evolution of laccase genes were analyzed at the whole genome level, while the spatiotemporal expression was evaluated at different developmental stages. The laccase genes mainly distributed on chromosomes 1, 2, 3, 4, 6, 9, and 10, and 9 genes were clustered linearly on chromosome 6, indicating gene doubling. Phylogenetic tree analysis showed that the laccase gene family was divided into three subfamilies. The spatiotemporal expression analysis of the laccase gene family showed thatHmLac09andHmLac10were highly expressed in different periods and might be involved in lignin degradation and fruit body formation, respectively. The expression levels ofHmLac02, HmLac05, HmLac08, andHmLac17genes in gray or gray and white heterozygous strains were higher than those in white strains, which might be related to the difference in lignin decomposition in gray strains, and one of the factors leading to different growth rates. The present study investigated the characterization of theH. marmoreuslaccase gene family, extending our understanding of laccase mediated fruiting body development and growth rate mechanisms in this fungi.
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- 2022
12. A time-resolved transcriptome analysis reveals regulation of Arabidopsis seed dormancy by the transcription factors WOX11/12
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Jiakai Liao, Ban Deng, Xinyu Cai, Qixin Yang, Bangping Hu, Jiajing Cong, Yuxiang Zhang, Gang Wang, Guiliang Xin, Yuting Li, Li Yang, Daizhen Zhang, Jin Zhang, and Bobin Liu
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Physiology ,Plant Science - Abstract
The induction of seed dormancy and its release involve a finely regulated genetic program controlled by various environmental and developmental cues that are critical for plant survival and population expansion. Light plays a key role in seed dormancy and germination, but the molecular mechanisms underlying the control of dormancy are unclear. In the present study, high-resolution temporal RNA-seq in Arabidopsis identified WOX11 as encoding a hub transcription factor during the seed dormancy induction and release stages. This gene might have evolved from gymnosperms and expanded in angiosperms with highly conserved expression patterns in seeds. WOX11 and its homolog WOX12 were highly expressed from 2 d after pollination, and mRNA abundance was greatly increased during the seed dormancy induction and release stages. Further, we found that WOX11 plays a role in the regulation of seed dormancy downstream of phytochrome B (PHYB)-mediated red-light signaling during the induction stage, indicating that WOX11/12 are newly identified components of red-light signaling transduction. Taken together, our results suggest that WOX11/12-mediated PHYB signaling regulates seed dormancy in Arabidopsis, and provide insights into the developmental regulation and evolutionary adaptation of plants to changes in the light environment.
- Published
- 2022
13. Time-course transcriptome analysis reveals regulation of Arabidopsis seed dormancy by the transcription factors WOX11/12.
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Jiakai Liao, Ban Deng, Xinyu Cai, Qixin Yang, Bangping Hu, Jiajing Cong, Yuxiang Zhang, Gang Wang, Guiliang Xin, Yuting Li, Li Yang, Daizhen Zhang, Jin Zhang, and Bobin Liu
- Abstract
The induction of seed dormancy and its release involve a finely regulated genetic program controlled by various environmental and developmental cues that are critical for plant survival and population expansion. Light plays a key role in seed dormancy and germination, but the molecular mechanisms underlying the control of dormancy are unclear. In the present study, high-resolution temporal RNA-seq in Arabidopsis identified WOX11 as encoding a hub transcription factor during the seed dormancy induction and release stages. This gene might have evolved from gymnosperms and expanded in angiosperms with highly conserved expression patterns in seeds. WOX11 and its homolog WOX12 were highly expressed from 2 d after pollination, and mRNA abundance was greatly increased during the seed dormancy induction and release stages. Further, we found that WOX11 plays a role in the regulation of seed dormancy downstream of phytochrome B (PHYB)-mediated red-light signaling during the induction stage, indicating that WOX11/12 are newly identified components of red-light signaling transduction. Taken together, our results suggest that WOX11/12-mediated PHYB signaling regulates seed dormancy in Arabidopsis, and provide insights into the developmental regulation and evolutionary adaptation of plants to changes in the light environment. [ABSTRACT FROM AUTHOR]
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- 2023
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14. An essential role for Arabidopsis Trs33 in cell growth and organization in plant apical meristems
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Jun Chen, Jianbo Li, Shutang Zhao, Lijuan Wang, Jin Zhang, Weina Wang, Bobin Liu, Xingyun Qi, Huanquan Zheng, and Mengzhu Lu
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0106 biological sciences ,0301 basic medicine ,Transcription, Genetic ,Meristem ,Arabidopsis ,Vesicular Transport Proteins ,Golgi Apparatus ,Plant Science ,GTPase ,Biology ,01 natural sciences ,03 medical and health sciences ,Gene Expression Regulation, Plant ,Auxin ,Plant Cells ,Cell Proliferation ,chemistry.chemical_classification ,Indoleacetic Acids ,Arabidopsis Proteins ,Membrane Transport Proteins ,General Medicine ,Plants, Genetically Modified ,Subcellular localization ,biology.organism_classification ,Cell biology ,Protein Transport ,Fertility ,030104 developmental biology ,chemistry ,PIN1 ,RNA Interference ,Rab ,Agronomy and Crop Science ,Functional divergence ,010606 plant biology & botany - Abstract
Trafficking protein particle (TRAPP) complexes subunit gene AtTrs33 plays an important role in keeping apical meristematic activity and dominance in Arabidopsis. TRAPP complexes, composed of multimeric subunits, are guanine-nucleotide exchange factors for certain Rab GTPases and are believed to be involved in the regulation of membrane trafficking, but the cases in Arabidopsis are largely unknown. Trs33, recently proposed to be a component of TRAPP IV, is non-essential in yeast cells. A single copy of Trs33 gene, AtTrs33, was identified in Arabidopsis. GUS activity assay indicated that AtTrs33 was ubiquitously expressed. Based on a T-DNA insertion line, we found that loss-of-function of AtTrs33 is lethal for apical growth. Knock-down or knock-in of AtTrs33 affects apical meristematic growth and fertility, which indicates that AtTrs33 plays an important role in keeping apical meristematic activity and dominance in Arabidopsis. Analysis of auxin responses and PIN1/2 localization indicate that impaired apical meristematic activity and dominance were caused by altered auxin responses through non-polarized PIN1 localization. The present study reported that AtTrs33 plays an essential role in Arabidopsis cell growth and organization, which is different with its homologue in yeast. These findings provide new insights into the functional divergence of TRAPP subunits.
- Published
- 2019
15. Genome-Wide Identification and Co-Expression Analysis of
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Bobin, Liu, Juanli, Zhu, Lina, Lin, Qixin, Yang, Bangping, Hu, Qingying, Wang, Xiao-Xing, Zou, and Shuang-Quan, Zou
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fungi ,Genetics ,food and beverages ,ARF ,fruit development ,Aux/IAA ,triterpenoids ,Euscaphis konishii ,anthocyanin ,Original Research - Abstract
Euscaphis konishii is an evergreen plant that is widely planted as an industrial crop in Southern China. It produces red fruits with abundant secondary metabolites, giving E. konishii high medicinal and ornamental value. Auxin signaling mediated by members of the AUXIN RESPONSE FACTOR (ARF) and auxin/indole-3-acetic acid (Aux/IAA) protein families plays important roles during plant growth and development. Aux/IAA and ARF genes have been described in many plants but have not yet been described in E. konishii. In this study, we identified 34 EkIAA and 29 EkARF proteins encoded by the E. konishii genome through database searching using HMMER. We also performed a bioinformatic characterization of EkIAA and EkARF genes, including their phylogenetic relationships, gene structures, chromosomal distribution, and cis-element analysis, as well as conserved motifs in the proteins. Our results suggest that EkIAA and EkARF genes have been relatively conserved over evolutionary history. Furthermore, we conducted expression and co-expression analyses of EkIAA and EkARF genes in leaves, branches, and fruits, which identified a subset of seven EkARF genes as potential regulators of triterpenoids and anthocyanin biosynthesis. RT-qPCR, yeast one-hybrid, and transient expression analyses showed that EkARF5.1 can directly interact with auxin response elements and regulate downstream gene expression. Our results may pave the way to elucidating the function of EkIAA and EkARF gene families in E. konishii, laying a foundation for further research on high-yielding industrial products and E. konishii breeding.
- Published
- 2021
16. The Euscaphis japonica genome and the evolution of malvids
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Zhi-Wen Wang, Shuangquan Zou, Meng-Yuan Qiu, Yu-Ting Jiang, Yifan Wang, Yi-Xun Yue, Yves Van de Peer, Zou Xiaoxing, Lin Ni, Shuang Xiang, Xi Wu, Lin Xiao, Xing-Yu Liao, Xue-Die Liu, Hui Ni, Le Din, Qi-Gong Zhang, Wei-Hong Sun, Yifan Li, Huang Wei, Zhong-Jian Liu, Xiaokai Ma, Zhen Li, Pei-Lan Zhang, De-Qiang Chen, Xiang-Qing Din, Bobin Liu, and Diyang Zhang
- Subjects
EXPRESSION ,SYNTHASE GENE ,Population ,PROTEIN ,Plant Science ,Genome ,Japonica ,Coalescent theory ,Evolution, Molecular ,MULTIPLE SEQUENCE ALIGNMENT ,Magnoliopsida ,Abscission ,Genetics ,TOOL ,PHYLOGENETIC ANALYSIS ,PROANTHOCYANIDIN BIOSYNTHESIS ,Fruit dehiscence ,education ,genome ,Gene ,education.field_of_study ,biology ,Phylogenetic tree ,fungi ,Biology and Life Sciences ,food and beverages ,Cell Biology ,OLEANOLIC ACID ,ARABIDOPSIS ,biology.organism_classification ,Euscaphis japonica ,humanities ,Evolutionary biology ,Fruit ,malvids ,MADS-BOX GENES ,Genome, Plant ,population history - Abstract
Malvids is one of the largest clades of rosids, includes 58 families and exhibits remarkable morphological and ecological diversity. Here, we report a high-quality chromosome-level genome assembly for Euscaphis japonica, an early-diverging species within malvids. Genome-based phylogenetic analysis suggests that the unstable phylogenetic position of E. japonica may result from incomplete lineage sorting and hybridization event during the diversification of the ancestral population of malvids. Euscaphis japonica experienced two polyploidization events: the ancient whole genome triplication event shared with most eudicots (commonly known as the γ event) and a more recent whole genome duplication event, unique to E. japonica. By resequencing 101 samples from 11 populations, we speculate that the temperature has led to the differentiation of the evergreen and deciduous of E. japonica and the completely different population histories of these two groups. In total, 1012 candidate positively selected genes in the evergreen were detected, some of which are involved in flower and fruit development. We found that reddening and dehiscence of the E. japonica pericarp and long fruit-hanging time promoted the reproduction of E. japonica populations, and revealed the expression patterns of genes related to fruit reddening, dehiscence and abscission. The key genes involved in pentacyclic triterpene synthesis in E. japonica were identified, and different expression patterns of these genes may contribute to pentacyclic triterpene diversification. Our work sheds light on the evolution of E. japonica and malvids, particularly on the diversification of E. japonica and the genetic basis for their fruit dehiscence and abscission.
- Published
- 2021
17. Functional and morphological evolution in gymnosperms: A portrait of implicated gene families
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Benjamin Wilhite, Ilga Porth, Bobin Liu, Anthony Piot, Amanda R. De La Torre, and Matthew Weiss
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0106 biological sciences ,0301 basic medicine ,gene families ,gymnosperms ,Range (biology) ,lcsh:Evolution ,functional evolution ,Biology ,010603 evolutionary biology ,01 natural sciences ,Genome ,03 medical and health sciences ,stress ,Gymnosperm ,lcsh:QH359-425 ,Genetics ,PDR gene family ,Gene family ,Clade ,Secondary metabolism ,Gene ,Ecology, Evolution, Behavior and Systematics ,fungi ,reproductive biology ,food and beverages ,15. Life on land ,biology.organism_classification ,030104 developmental biology ,Evolutionary biology ,General Agricultural and Biological Sciences ,Special Issue Reviews and Syntheses ,Functional divergence ,biotechnology - Abstract
Gymnosperms diverged from their sister plant clade of flowering plants 300 Mya. Morphological and functional divergence between the two major seed plant clades involved significant changes in their reproductive biology, water‐conducting systems, secondary metabolism, stress defense mechanisms, and small RNA‐mediated epigenetic silencing. The relatively recent sequencing of several gymnosperm genomes and the development of new genomic resources have enabled whole‐genome comparisons within gymnosperms, and between angiosperms and gymnosperms. In this paper, we aim to understand how genes and gene families have contributed to the major functional and morphological differences in gymnosperms, and how this information can be used for applied breeding and biotechnology. In addition, we have analyzed the angiosperm versus gymnosperm evolution of the pleiotropic drug resistance (PDR) gene family with a wide range of functionalities in plants' interaction with their environment including defense mechanisms. Some of the genes reviewed here are newly studied members of gene families that hold potential for biotechnological applications related to commercial and pharmacological value. Some members of conifer gene families can also be exploited for their potential in phytoremediation applications.
- Published
- 2019
18. PtWOX11 acts as master regulator conducting the expression of key transcription factors to induce de novo shoot organogenesis in poplar
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Mengzhu Lu, Gerald A. Tuskan, Zhaohe Yang, Bobin Liu, Markus V. Kohnen, Akihiro Matsui, Motoaki Seki, Shubin Li, Lianfeng Gu, Jin Zhang, Xinyang Yan, Kalika Prasad, and Yoshito Oka
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0301 basic medicine ,Callus formation ,Organogenesis ,Plant Science ,Real-Time Polymerase Chain Reaction ,Plant Roots ,03 medical and health sciences ,Plant Growth Regulators ,Gene Expression Regulation, Plant ,Arabidopsis ,Genetics ,Transcription factor ,Plant Proteins ,biology ,fungi ,food and beverages ,Sequence Analysis, DNA ,General Medicine ,Meristem ,biology.organism_classification ,Cell biology ,Populus ,030104 developmental biology ,Callus ,Shoot ,Homeobox ,Agronomy and Crop Science ,Plant Shoots ,Transcription Factors - Abstract
WUSCHEL-RELATED HOMEOBOX 11 establishes the acquisition of pluripotency during callus formation and accomplishes de novo shoot formation by regulating key transcription factors in poplar. De novo shoot regeneration is a prerequisite for propagation and genetic engineering of elite cultivars in forestry. However, the regulatory mechanism of de novo organogenesis is poorly understood in tree species. We previously showed that WUSCHEL (WUS)-RELATED HOMEOBOX 11 (PtWOX11) of the hybrid poplar clone 84K (Populus alba × P. glandulosa) promotes de novo root formation. In this study, we found that PtWOX11 also regulates de novo shoot regeneration in poplar. The overexpression of PtWOX11 enhanced de novo shoot formation, whereas overexpression of PtWOX11 fused with the transcriptional repressor domain (PtWOX11-SRDX) or reduced expression of PtWOX11 inhibited this process, indicating that PtWOX11 promotes de novo shoot organogenesis. Although PtWOX11 promotes callus formation, overexpression of PtWOX11 and PtWOX11-SRDX also produced increased and decreased numbers of de novo shoots per unit weight, respectively, implying that PtWOX11 promotes de novo shoot organogenesis partially by regulating the intrinsic mechanism of shoot development. RNA-seq and qPCR analysis further revealed that PtWOX11 activates the expression of PLETHORA1 (PtPLT1) and PtPLT2, whose Arabidopsis paralogs establish the acquisition of pluripotency, during incubation on callus-inducing medium. Moreover, PtWOX11 activates the expression of shoot-promoting factors and meristem regulators such as CUP-SHAPED COTYLEDON2 (PtCUC2), PtCUC3, WUS and SHOOT MERISTEMLESS to fulfill shoot regeneration during incubation on shoot-inducing medium. These results suggest that PtWOX11 acts as a central regulator of the expression of key genes to cause de novo shoot formation. Our studies further provide a possible means to genetically engineer economically important tree species for their micropropagation.
- Published
- 2018
19. Genome-wide identification, evolution and expression analysis of the aspartic protease gene family during rapid growth of moso bamboo (Phyllostachys edulis) shoots
- Author
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Yun Jing, Xiaqin Wang, Jin Zhang, Xinyang Yan, Shuangquan Zou, Shubin Li, Lianfeng Gu, and Bobin Liu
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Bamboo ,lcsh:QH426-470 ,lcsh:Biotechnology ,Moso bamboo ,Poaceae ,Genome ,Gene Expression Regulation, Plant ,lcsh:TP248.13-248.65 ,Phaps ,Genetics ,Gene family ,Rapid growth ,Gene ,Phylogeny ,Programmed cell death ,Plant Proteins ,biology ,Proteolytic enzymes ,biology.organism_classification ,lcsh:Genetics ,Phyllostachys edulis ,Aspartic protease ,Tandem exon duplication ,Biotechnology ,Research Article ,Peptide Hydrolases - Abstract
Background Aspartic proteases (APs) are a class of aspartic peptidases belonging to nine proteolytic enzyme families whose members are widely distributed in biological organisms. APs play essential functions during plant development and environmental adaptation. However, there are few reports about APs in fast-growing moso bamboo. Result In this study, we identified a total of 129 AP proteins (PhAPs) encoded by the moso bamboo genome. Phylogenetic and gene structure analyses showed that these 129 PhAPs could be divided into three categories (categories A, B and C). The PhAP gene family in moso bamboo may have undergone gene expansion, especially the members of categories A and B, although homologs of some members in category C have been lost. The chromosomal location of PhAPs suggested that segmental and tandem duplication events were critical for PhAP gene expansion. Promoter analysis revealed that PhAPs in moso bamboo may be involved in plant development and responses to environmental stress. Furthermore, PhAPs showed tissue-specific expression patterns and may play important roles in rapid growth, including programmed cell death, cell division and elongation, by integrating environmental signals such as light and gibberellin signals. Conclusion Comprehensive analysis of the AP gene family in moso bamboo suggests that PhAPs have experienced gene expansion that is distinct from that in rice and may play an important role in moso bamboo organ development and rapid growth. Our results provide a direction and lay a foundation for further analysis of plant AP genes to clarify their function during rapid growth.
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- 2021
20. Insights of Molecular Mechanism of Xylem Development in Five Black Poplar Cultivars
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Bobin Liu, Jianjun Hu, Lei Zhang, and Jin Zhang
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0106 biological sciences ,0301 basic medicine ,Plant Science ,lcsh:Plant culture ,01 natural sciences ,Black poplar ,Cell wall ,03 medical and health sciences ,Botany ,Gene expression ,lcsh:SB1-1110 ,transcriptional regulation ,Gene ,Hybrid ,Original Research ,biology ,fungi ,Xylem ,food and beverages ,biology.organism_classification ,Polysaccharide binding ,developing xylem ,030104 developmental biology ,Populus ,cell wall ,Secondary cell wall ,transcriptome ,010606 plant biology & botany - Abstract
Black poplar (Populus deltoides, P. nigra, and their hybrids) is the main poplar cultivars in China. It offers interesting options of large-scale biomass production for bioenergy due to its rapid growth and high yield. Poplar wood properties were associated with chemical components and physical structures during wood formation. In this study, five poplar cultivars, P. euramericana 'Zhonglin46' (Pe1), P. euramericana 'Guariento' (Pe2), P. nigra 'N179' (Pn1), P. deltoides 'Danhong' (Pd1), and P. deltoides 'Nanyang' (Pd2), were used to explore the molecular mechanism of xylem development. We analyzed the structural differences of developing xylem in the five cultivars and profiled the transcriptome-wide gene expression patterns through RNA sequencing. The cross sections of the developing xylem showed that the cell wall thickness of developed fiber in Pd1 was thickest and the number of xylem vessels of Pn1 was the least. A total of 10,331 differentially expressed genes were identified among 10 pairwise comparisons of the five cultivars, most of them were related to programmed cell death and secondary cell wall thickening. K-means cluster analysis and Gene Ontology enrichment analysis showed that the genes highly expressed in Pd1 were related to nucleotide decomposition, metabolic process, transferase, and microtubule cytoskeleton; whereas the genes highly expressed in Pn1 were involved in cell wall macromolecule decomposition and polysaccharide binding processes. Based on a weighted gene co-expression network analysis, a large number of candidate regulators for xylem development were identified. And their potential regulatory roles to cell wall biosynthesis genes were validated by a transient overexpression system. This study provides a set of promising candidate regulators for genetic engineering to improve feedstock and enhance biofuel conversion in the bioenergy crop Populus.
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- 2020
21. Identification and Characterization of the PEBP Family Genes in Moso Bamboo (Phyllostachys heterocycla)
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Bei Xiong, Jiakai Liao, Bobin Liu, Markus V. Kohnen, Zhaohe Yang, Qiang Zhu, Chentao Lin, Lianfeng Gu, Yoshito Oka, Lei Chen, and Xi Zhen
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0106 biological sciences ,0301 basic medicine ,China ,Bamboo ,Plant molecular biology ,Perennial plant ,Meristem ,Arabidopsis ,lcsh:Medicine ,Germination ,Phosphatidylethanolamine Binding Protein ,Flowers ,Biology ,Genes, Plant ,Poaceae ,01 natural sciences ,Article ,Plant breeding ,03 medical and health sciences ,Gene Expression Regulation, Plant ,Botany ,Amino Acid Sequence ,lcsh:Science ,Gene ,Phylogeny ,Plant Proteins ,Multidisciplinary ,lcsh:R ,food and beverages ,Monocarpic ,Plant ,biology.organism_classification ,Plant Leaves ,Plant Breeding ,Phyllostachys ,030104 developmental biology ,Gene Expression Regulation ,Genes ,Seeds ,lcsh:Q ,010606 plant biology & botany - Abstract
Moso bamboo is one of the economically most important plants in China. Moso bamboo is a monocarpic perennial that exhibits poor and slow germination. Thus, the flowering often causes destruction of moso bamboo forestry. However, how control of flowering and seed germination are regulated in moso bamboo is largely unclear. In this study, we identified 5 members (PhFT1-5) of the phosphatidyl ethanolamine-binding proteins (PEBP) family from moso bamboo genome that regulate flowering, flower architecture and germination, and characterized the function of these PEBP family genes further in Arabidopsis. Phylogenetic analysis revealed that 3 (PhFT1, PhFT2 and PhFT3), 1 (PhFT4) and 1 (PhFT5) members belong to the TFL1-like clade, FT-like clade, and MFT-like clade, respectively. These PEBP family genes possess all structure necessary for PEBP gene function. The ectopic overexpression of PhFT4 and PhFT5 promotes flowering time in Arabidopsis, and that of PhFT1, PhFT2 and PhFT3 suppresses it. In addition, the overexpression of PhFT5 promotes seed germination rate. Interestingly, the overexpression of PhFT1 suppressed seed germination rate in Arabidopsis. The expression of PhFT1 and PhFT5 is significantly higher in seed than in tissues including leaf and shoot apical meristem, implying their function in seed germination. Taken together, our results suggested that the PEBP family genes play important roles as regulators of flowering and seed germination in moso bamboo and thereby are necessary for the sustainability of moso bamboo forest.
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- 2019
22. A CRY-BIC negative-feedback circuitry regulating blue light sensitivity of Arabidopsis
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Qing Liu, Liu Bin, Yun-Jeong Han, Jing Wang, Minami Matsui, Wenjin He, Qin Wang, Zhaohe Yang, Bobin Liu, Xu Wang, Liangfeng Gu, Zecheng Zuo, Chentao Lin, Jun Su, Jeong-Il Kim, and Yoshito Oka
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Photoreceptors, Plant ,0301 basic medicine ,Light ,Ubiquitin-Protein Ligases ,Arabidopsis ,Plant Science ,Biology ,Models, Biological ,Article ,03 medical and health sciences ,Cryptochrome ,Gene Expression Regulation, Plant ,Genes, Reporter ,Transcription (biology) ,Botany ,Genetics ,Gene ,Feedback, Physiological ,Phytochrome ,Arabidopsis Proteins ,fungi ,Nuclear Proteins ,Promoter ,Cell Biology ,biology.organism_classification ,Cell biology ,Chromatin ,Cryptochromes ,Basic-Leucine Zipper Transcription Factors ,030104 developmental biology ,Seedlings ,Cryptochrome-1 - Abstract
Cryptochromes are blue light receptors that regulate various light responses in plants. Arabidopsis cryptochrome 1 (CRY1) and cryptochrome 2 (CRY2) mediate blue light inhibition of hypocotyl elongation and long-day (LD) promotion of floral initiation. It has been reported recently that two negative regulators of Arabidopsis cryptochromes, Blue light Inhibitors of Cryptochromes 1 and 2 (BIC1 and BIC2), inhibit cryptochrome function by blocking blue light-dependent cryptochrome dimerization. However, it remained unclear how cryptochromes regulate the BIC gene activity. Here we show that cryptochromes mediate light activation of transcription of the BIC genes, by suppressing the activity of CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), resulting in activation of the transcription activator ELONGATED HYPOCOTYL 5 (HY5) that is associated with chromatins of the BIC promoters. These results demonstrate a CRY-BIC negative-feedback circuitry that regulates the activity of each other. Surprisingly, phytochromes also mediate light activation of BIC transcription, suggesting a novel photoreceptor co-action mechanism to sustain blue light sensitivity of plants under the broad spectra of solar radiation in nature.
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- 2017
23. The WUSCHEL-related homeobox 5a (PtoWOX5a) is involved in adventitious root development in poplar
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Lijuan Wang, Jianjun Hu, Mengzhu Lu, Jin Zhang, Pei Sun, Huixia Jia, Jianbo Li, and Bobin Liu
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0106 biological sciences ,0301 basic medicine ,Physiology ,Vegetative reproduction ,Plant Science ,Biology ,Plant Roots ,01 natural sciences ,03 medical and health sciences ,Gene Expression Regulation, Plant ,Botany ,Transcription factor ,Psychological repression ,Plant Proteins ,Cyclin ,fungi ,Lateral root ,Plants, Genetically Modified ,Phenotype ,Cell biology ,Complementation ,Populus ,030104 developmental biology ,Homeobox ,Transcription Factors ,010606 plant biology & botany - Abstract
Adventitious rooting is an essential step in vegetative propagation. Currently, the mechanism that regulates adventitious root (AR) development in woody plants is poorly understood. This work demonstrates that Populus tomentosa WUSCHEL-related homeobox 5a (PtoWOX5a) transcription factor is involved in AR development in poplar. PtoWOX5a was specifically expressed in the AR tip and lateral root tip during AR and lateral root regeneration from the stem segment. Phenotypic complementation experiments indicated that the PtoWOX5a can functionally complement AtWOX5 in quiescent center (QC) cells. Overexpression of PtoWOX5a introduces significant developmental phenotypes in roots and leaves, such as increased AR number, decreased AR length, swollen AR tip and lateral root tip, and decreased leaf number and area. The conserved mechanism of D-type cyclins (CYCD) repression mediated by WOX5 was confirmed in poplar. The co-expression network of PtWOX5a was constructed, which provided clues to reveal the molecular mechanism of PtoWOX5a in AR development in poplar. Taken together, our results suggest that the PtoWOX5a is involved in AR development though cooperating with a series of functional genes.
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- 2017
24. Overexpression of PtrMYB121 Positively Regulates the Formation of Secondary Cell Wall in Arabidopsis thaliana
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Shi Yuyu, Chunlan Lian, Bobin Liu, Man Jiayin, Zhang Taoxiang, Yinghao Wang, Songqing Wu, Ying Liu, Xia Hu, and Chao Yuan
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0106 biological sciences ,0301 basic medicine ,Arabidopsis ,01 natural sciences ,lcsh:Chemistry ,chemistry.chemical_compound ,Cell Wall ,Gene Expression Regulation, Plant ,Arabidopsis thaliana ,Lignin ,MYB ,lcsh:QH301-705.5 ,transcription factor ,Phylogeny ,Spectroscopy ,Plant Proteins ,biology ,food and beverages ,General Medicine ,Plants, Genetically Modified ,PtrMYB121 ,cellulose ,Computer Science Applications ,Cell biology ,Populus ,secondary cell wall ,Secondary cell wall ,lignin ,Article ,Catalysis ,Inorganic Chemistry ,03 medical and health sciences ,Xylem ,Amino Acid Sequence ,Physical and Theoretical Chemistry ,Cellulose ,Molecular Biology ,Transcription factor ,fungi ,Organic Chemistry ,Promoter ,biology.organism_classification ,Biosynthetic Pathways ,030104 developmental biology ,lcsh:Biology (General) ,lcsh:QD1-999 ,chemistry ,010606 plant biology & botany - Abstract
MYB transcription factors have a wide range of functions in plant growth, hormone signaling, salt, and drought tolerances. In this study, two homologous transcription factors, PtrMYB55 and PtrMYB121, were isolated and their functions were elucidated. Tissue expression analysis revealed that PtrMYB55 and PtrMYB121 had a similar expression pattern, which had the highest expression in stems. Their expression continuously increased with the growth of poplar, and the expression of PtrMYB121 was significantly upregulated in the process. The full length of PtrMYB121 was 1395 bp, and encoded protein contained 464 amino acids including conserved R2 and R3 MYB domains. We overexpressed PtrMYB121 in Arabidopsis thaliana, and the transgenic lines had the wider xylem as compared with wild-type Arabidopsis. The contents of cellulose and lignin were obviously higher than those in wild-type materials, but there was no significant change in hemicellulose. Quantitative real-time PCR demonstrated that the key enzyme genes regulating the synthesis of lignin and cellulose were significantly upregulated in the transgenic lines. Furthermore, the effector-reporter experiment confirmed that PtrMYB121 bound directly to the promoters of genes relating to the synthesis of lignin and cellulose. These results suggest that PtrMYB121 may positively regulate the formation of secondary cell wall by promoting the synthesis of lignin and cellulose.
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- 2020
25. Signaling mechanisms of plant cryptochromes in Arabidopsis thaliana
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Yoshito Oka, Chentao Lin, Zhaohe Yang, Bobin Liu, Adam Gomez, and Liu Bin
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0106 biological sciences ,0301 basic medicine ,endocrine system ,Light Signal Transduction ,animal structures ,Light ,Arabidopsis ,Plant Science ,01 natural sciences ,Article ,03 medical and health sciences ,Protein Domains ,Cryptochrome ,Gene Expression Regulation, Plant ,Transcription (biology) ,Phosphorylation ,Transcription factor ,Genetics ,biology ,Arabidopsis Proteins ,fungi ,food and beverages ,Plant physiology ,biology.organism_classification ,Hypocotyl ,Ubiquitin ligase ,Cell biology ,Cryptochromes ,030104 developmental biology ,Etiolation ,biology.protein ,Photomorphogenesis ,sense organs ,Transcription Factors ,010606 plant biology & botany - Abstract
Cryptochromes (CRY) are flavoproteins that direct a diverse array of developmental processes in response to blue light in plants. Conformational changes in CRY are induced by the absorption of photons and result in the propagation of light signals to downstream components. In Arabidopsis, CRY1 and CRY2 serve both distinct and partially overlapping functions in regulating photomorphogenic responses and photoperiodic flowering. For example, both CRY1 and CRY2 regulate the abundance of transcription factors by directly reversing the activity of E3 ubiquitin ligase on CONSTITUTIVE PHOTOMORPHOGENIC 1 and SUPPRESSOR OF PHYA-105 1 complexes in a blue light-dependent manner. CRY2 also specifically governs a photoperiodic flowering mechanism by directly interacting with a transcription factor called CRYPTOCHROME-INTERACTING BASIC-HELIX-LOOP-HELIX. Recently, structure/function analysis of CRY1 revealed that the CONSTITUTIVE PHOTOMORPHOGENIC 1 independent pathway is also involved in CRY1-mediated inhibition of hypocotyl elongation. CRY1 and CRY2 thus not only share a common pathway but also relay light signals through distinct pathways, which may lead to altered developmental programs in plants.
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- 2016
26. Sequencing of
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Xueyan, Yuan, Weihong, Sun, Xiaoxing, Zou, Bobin, Liu, Wei, Huang, Zeming, Chen, Yanlei, Li, Meng-Yuan, Qiu, Zhong-Jian, Liu, Yanling, Mao, and Shuang-Quan, Zou
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Chlorophyll ,anthocyanin biosynthesis ,Pigmentation ,Sequence Analysis, RNA ,Gene Expression Profiling ,chlorophyll degradation ,fungi ,food and beverages ,Reproducibility of Results ,Molecular Sequence Annotation ,Genes, Plant ,Carotenoids ,Article ,Euscaphis konishii ,Anthocyanins ,Gene Ontology ,Gene Expression Regulation, Plant ,Fruit ,Multigene Family ,Protein Interaction Maps ,Transcriptome ,Malvaceae ,endocarp coloration ,Transcription Factors - Abstract
Flower and fruit colors are of vital importance to the ecology and economic market value of plants. The mechanisms of flower and fruit coloration have been well studied, especially among ornamental flower plants and cultivated fruits. As people pay more attention to exocarp coloration, the endocarp coloration in some species has often been ignored. Here, we report on the molecular mechanism of endocarp coloration in three development stages of Euscaphis konishii. The results show that endocarp reddening is closely related to anthocyanin accumulation, and a total of 86,120 unigenes were assembled, with a mean length of 893 bp (N50 length of 1642 bp). We identified a large number of differentially expressed genes associated with endocarp coloration, including anthocyanin biosynthesis, carotenoid biosynthesis, and chlorophyll breakdown. The genes participating in each step of the anthocyanin biosynthesis were found in the transcriptome dataset, but a few genes were found in the carotenoid biosynthesis and chlorophyll breakdown. In addition, the candidate R2R3-MYB transcription factors and candidate glutathione S-transferase transport genes, which likely regulate the anthocyanin biosynthesis, were identified. This study offers a platform for E. konishii functional genomic research and provides a reference for revealing the regulatory mechanisms of endocarp reddening.
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- 2018
27. Characterization of the Populus Rab family genes and the function of PtRabE1b in salt tolerance
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Jun Chen, Jin Zhang, Yu Li, Li Zhang, Bobin Liu, Lijuan Wang, Huanquan Zheng, Jianjun Hu, and Mengzhu Lu
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0301 basic medicine ,Populus trichocarpa ,Subfamily ,Plant Science ,Genes, Plant ,Chromosomes, Plant ,03 medical and health sciences ,lcsh:Botany ,Arabidopsis ,Gene duplication ,Promoter Regions, Genetic ,Gene ,Conserved Sequence ,Phylogeny ,Plant Proteins ,Genetics ,Co-expression network ,Phylogenetic analysis ,biology ,Subcellular localization ,fungi ,Salt-Tolerant Plants ,Salt Tolerance ,biology.organism_classification ,lcsh:QK1-989 ,Populus ,030104 developmental biology ,rab GTP-Binding Proteins ,Rab ,Ras superfamily ,Transcriptome ,Rab GTPase ,Functional divergence ,Research Article - Abstract
Background Rab proteins form the largest family of the Ras superfamily of small GTP-binding proteins and regulate intracellular trafficking pathways. However, the function of the Rab proteins in woody species is still an open question. Results Here, a total of 67 PtRabs were identified in Populus trichocarpa and categorized into eight subfamilies (RabA-RabH). Based on their chromosomal distribution and duplication blocks in the Populus genome, a total of 27 PtRab paralogous pairs were identified and all of them were generated by whole-genome duplication events. Combined the expression correlation and duplication date, the PtRab paralogous pairs that still keeping highly similar expression patterns were generated around the latest large-scale duplication (~ 13 MYA). The cis-elements and co-expression network of unique expanded PtRabs suggest their potential roles in poplar development and environmental responses. Subcellular localization of PtRabs from each subfamily indicates each subfamily shows a localization pattern similar to what is revealed in Arabidopsis but RabC shows a localization different from their counterparts. Furthermore, we characterized PtRabE1b by overexpressing its constitutively active mutant PtRabE1b(Q74L) in poplar and found that PtRabE1b(Q74L) enhanced the salt tolerance. Conclusions These findings provide new insights into the functional divergence of PtRabs and resources for genetic engineering resistant breeding in tree species. Electronic supplementary material The online version of this article (10.1186/s12870-018-1342-1) contains supplementary material, which is available to authorized users.
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- 2018
28. AtBET5 is essential for exine pattern formation and apical meristem organization in Arabidopsis
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Jianbo Li, Shutang Zhao, Jun Chen, Lijuan Wang, Xingyun Qi, Huanquan Zheng, Mengzhu Lu, Jin Zhang, Bobin Liu, and Hongying Li
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0106 biological sciences ,0301 basic medicine ,Endosome ,Recombinant Fusion Proteins ,Meristem ,Arabidopsis ,Vesicular Transport Proteins ,Plant Science ,01 natural sciences ,03 medical and health sciences ,symbols.namesake ,Biopolymers ,Sporopollenin ,Plant Growth Regulators ,Auxin ,RNA interference ,Genes, Reporter ,Genetics ,Guanine Nucleotide Exchange Factors ,Gene ,chemistry.chemical_classification ,biology ,Indoleacetic Acids ,Arabidopsis Proteins ,Membrane Transport Proteins ,General Medicine ,Golgi apparatus ,biology.organism_classification ,Carotenoids ,Cell biology ,Mutagenesis, Insertional ,030104 developmental biology ,chemistry ,symbols ,Pollen ,RNA Interference ,Agronomy and Crop Science ,010606 plant biology & botany - Abstract
BET5 is a component of trafficking protein particle (TRAPP) which has been studied extensively in non-plant organisms where they are involved in membrane trafficking within Golgi and between Golgi and early endosomes. Recent analysis of TRAPP in different classes of organisms indicates that TRAPP function might exhibit differences among organisms. A single copy of the BET5 gene named AtBET5 was found in the Arabidopsis genome based on sequence similarity. Developmental phenotype and the underlying mechanisms have been characterized upon transcriptional knock-down lines generated by both T-DNA insertion and RNAi. Pollen grains of the T-DNA insertional line present reduced fertility and pilate exine instead of tectate exine. Perturbation of the AtBET5 expression by RNAi leads to apical meristematic organization defects and reduced fertility as well. The reduced fertility was due to the pollination barrier caused by an altered composition and structure of pollen walls. Auxin response in root tip cells is altered and there is a severe disruption in polar localization of PIN1-GFP, but to a less extent of PIN2-GFP in the root tips, which causes the apical meristematic organization defects and might also be responsible for the secretion of sporopollenin precursor or polar targeting of sporopollenin precursor transporters.
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- 2018
29. Additional file 15: of Characterization of the Populus Rab family genes and the function of PtRabE1b in salt tolerance
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Zhang, Jin, Li, Yu, Bobin Liu, Lijuan Wang, Zhang, Li, Jianjun Hu, Chen, Jun, Huanquan Zheng, and Mengzhu Lu
- Abstract
Table S6 qRT-PCR Primers used in this study. (DOCX 18 kb)
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- 2018
- Full Text
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30. Additional file 7: of Characterization of the Populus Rab family genes and the function of PtRabE1b in salt tolerance
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Zhang, Jin, Li, Yu, Bobin Liu, Lijuan Wang, Zhang, Li, Jianjun Hu, Chen, Jun, Huanquan Zheng, and Mengzhu Lu
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Table S2. Probe sets corresponding to PtRab genes. (DOCX 22 kb)
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- 2018
- Full Text
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31. Coordination of Cryptochrome and Phytochrome Signals in the Regulation of Plant Light Responses
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Bobin Liu, Chentao Lin, Jiakai Liao, Zhaohe Yang, Jun Su, and Yoshito Oka
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0301 basic medicine ,Crop and Pasture Production ,de-etiolation ,phytochrome ,cryptochrome ,gene expression ,photoperiodic flowering ,Environmental Science and Management ,1.1 Normal biological development and functioning ,law.invention ,03 medical and health sciences ,Cryptochrome ,law ,Underpinning research ,Arabidopsis ,Genetics ,Transcription factor ,biology ,Phytochrome ,biology.organism_classification ,Cell biology ,Ubiquitin ligase ,030104 developmental biology ,Etiolation ,biology.protein ,Suppressor ,Photomorphogenesis ,Generic health relevance ,Agronomy and Crop Science - Abstract
In nature, plants integrate a wide range of light signals from solar radiation to adapt to the surrounding light environment, and these light signals also regulate a variety of important agronomic traits. Blue light-sensing cryptochrome (cry) and red/far-red light-sensing phytochrome (phy) play critical roles in regulating light-mediated physiological responses via the regulated transcriptional network. Accumulating evidence in the model plant Arabidopsis has revealed that crys and phys share two mechanistically distinct pathways to coordinately regulate transcriptional changes in response to light. First, crys and phys promote the accumulation of transcription factors that regulate photomorphogenesis, such as HY5 and HFR1, via the inactivation of the CONSTITUTIVE PHOTOMORPHOGENIC1/SUPPRESSOR OF PHYA-105 E3 ligase complex by light-dependent binding. Second, photoactive crys and phys directly interact with PHYTOCHROME INTERACTING FACTOR transcription factor family proteins to regulate transcriptional activity. The coordinated regulation of these two pathways (and others) by crys and phys allow plants to respond with plasticity to fluctuating light environments in nature.
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- 2017
32. A survey of Populus PIN-FORMED family genes reveals their diversified expression patterns
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Bobin Liu, Jin Zhang, Mengzhu Lu, Huanquan Zheng, Lin Wang, Jun Chen, and Jianbo Li
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Physiology ,Secondary growth ,Plant Science ,Gene Expression Regulation, Plant ,Auxin ,Arabidopsis ,Botany ,Cambium ,PIN proteins ,Gene ,Phylogeny ,Plant Proteins ,chemistry.chemical_classification ,biology ,fungi ,Gene Expression Regulation, Developmental ,Membrane Transport Proteins ,food and beverages ,biology.organism_classification ,Cell biology ,Protein Transport ,Transmembrane domain ,Populus ,chemistry ,Multigene Family ,Plant hormone - Abstract
The plant hormone auxin is a key regulator of plant development, and its uneven distribution maintained by polar intercellular auxin transport in plant tissues can trigger a wide range of developmental processes. Although the roles of PIN-FORMED (PIN) proteins in intercellular auxin flow have been extensively characterized in Arabidopsis, their roles in woody plants remain unclear. Here, a comprehensive analysis of PIN proteins in Populus is presented. Fifteen PINs are encoded in the genome of Populus, including four PIN1s, one PIN2, two PIN3s, three PIN5s, three PIN6s, and two PIN8s. Similar to Arabidopsis AtPIN proteins, PtPINs share conserved topology and transmembrane domains, and are either plasma membrane- or endoplasmic reticulum-localized. The more diversified expansion of the PIN family in Populus, comparing to that in Arabidopsis, indicates that some auxin-regulated developmental processes, such as secondary growth, may exhibit unique features in trees. More importantly, different sets of PtoPINs have been found to be strongly expressed in the roots, leaves, and cambium in Populus; the dynamic expression patterns of selected PtoPINs were further examined during the regeneration of shoots and roots. This genome-wide analysis of the Populus PIN family provides important cues for their potential roles in tree growth and development.
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- 2014
33. Hsf and Hsp gene families in Populus: genome-wide identification, organization and correlated expression during development and in stress responses
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Yan Wang, Huanquan Zheng, Mengzhu Lu, Jin Zhang, Bobin Liu, Li Zhang, Jun Chen, and Jianbo Li
- Subjects
endocrine system ,Transcription, Genetic ,Amino Acid Motifs ,Heat shock protein (Hsp) ,Biology ,Genes, Plant ,Bioinformatics ,Expression analysis ,Conserved sequence ,Gene Expression Regulation, Plant ,Stress, Physiological ,Gene Duplication ,Heat shock protein ,Arabidopsis ,Genetics ,Coexpression ,Gene family ,Gene Regulatory Networks ,Gene ,Conserved Sequence ,Phylogeny ,Regulation of gene expression ,Gene Expression Profiling ,fungi ,Chromosome Mapping ,biology.organism_classification ,Gene expression profiling ,Populus ,Organ Specificity ,Multigene Family ,Heat shock factor (Hsf) ,DNA microarray ,Genome, Plant ,Research Article ,Biotechnology - Abstract
Background Heat shock proteins (Hsps) are molecular chaperones that are involved in many normal cellular processes and stress responses, and heat shock factors (Hsfs) are the transcriptional activators of Hsps. Hsfs and Hsps are widely coordinated in various biological processes. Although the roles of Hsfs and Hsps in stress responses have been well characterized in Arabidopsis, their roles in perennial woody species undergoing various environmental stresses remain unclear. Results Here, a comprehensive identification and analysis of Hsf and Hsp families in poplars is presented. In Populus trichocarpa, we identified 42 paralogous pairs, 66.7% resulting from a whole genome duplication. The gene structure and motif composition are relatively conserved in each subfamily. Microarray and quantitative real-time RT-PCR analyses showed that most of the Populus Hsf and Hsp genes are differentially expressed upon exposure to various stresses. A coexpression network between Populus Hsf and Hsp genes was generated based on their expression. Coordinated relationships were validated by transient overexpression and subsequent qPCR analyses. Conclusions The comprehensive analysis indicates that different sets of PtHsps are downstream of particular PtHsfs and provides a basis for functional studies aimed at revealing the roles of these families in poplar development and stress responses. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1398-3) contains supplementary material, which is available to authorized users.
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- 2015
34. WUSCHEL-related Homeobox genes in Populus tomentosa: diversified expression patterns and a functional similarity in adventitious root formation
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Bobin Liu, Mengzhu Lu, Huanquan Zheng, Jun Chen, Lin Wang, Jianbo Li, and Jin Zhang
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Populus trichocarpa ,Protein family ,Active Transport, Cell Nucleus ,Expression ,Genes, Plant ,Plant Roots ,Chromosomes, Plant ,Gene Expression Regulation, Plant ,Arabidopsis ,Gene Duplication ,Genetics ,Homeobox ,Regeneration ,Promoter Regions, Genetic ,Gene ,Phylogeny ,Regulation of gene expression ,Homeodomain Proteins ,biology ,Adventitious root ,Gene Expression Profiling ,fungi ,Meristem ,biology.organism_classification ,Gene expression profiling ,Protein Transport ,Populus ,Phenotype ,WOX ,Wuschel-related ,Multigene Family ,Plant Shoots ,Biotechnology ,Research Article - Abstract
Background WUSCHEL (WUS)-related homeobox (WOX) protein family members play important roles in the maintenance and proliferation of the stem cell niche in the shoot apical meristem (SAM), root apical meristem (RAM), and cambium (CAM). Although the roles of some WOXs in meristematic cell regulation have been well studied in annual plants such as Arabidopsis and rice, the expression and function of WOX members in woody plant poplars has not been systematically investigated. Here, we present the identification and comprehensive analysis of the expression and function of WOXs in Populus tomentosa. Results A genome-wide survey identified 18 WOX encoding sequences in the sequenced genome of Populus trichocarpa (PtrWOXs). Phylogenetic and gene structure analysis revealed that these 18 PtrWOXs fall into modern/WUS, intermediate, and ancient clades, but that the WOX genes in P. trichocarpa may have expanded differently from the WOX genes in Arabidopsis. In the P. trichocarpa genome, no WOX members could be closely classified as AtWOX3, AtWOX6, AtWOX7, AtWOX10, and AtWOX14, but there were two copies of WOX genes that could be classified as PtrWUS, PtrWOX2, PtrWOX4, PtrWOX5, PtrWOX8/9, and PtrWOX11/12, and three copies of WOX genes that could be classified as PtrWOX1 and PtrWOX13. The use of primers specific for each PtrWOX gene allowed the identification and cloning of 18 WOX genes from P. tomentosa (PtoWOXs), a poplar species physiologically close to P. trichocarpa. It was found that PtoWOXs and PtrWOXs shared very high amino acid sequence identity, and that PtoWOXs could be classified identically to PtrWOXs. We revealed that the expression patterns of some PtoWOXs were different to their Arabidopsis counterparts. When PtoWOX5a and PtoWOX11/12a, as well as PtoWUSa and PtoWOX4a were ectopically expressed in transgenic hybrid poplars, the regeneration of adventitious root (AR) was promoted, indicating a functional similarity of these four WOXs in AR regeneration. Conclusions This is the first attempt towards a systematical analysis of the function of WOXs in P. tomentosa. A diversified expression, yet functional similarity of PtoWOXs in AR regeneration is revealed. Our findings provide useful information for further elucidation of the functions and mechanisms of WOXs in the development of poplars.
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- 2014
35. Genome-wide analysis of the Populus Hsp90 gene family reveals differential expression patterns, localization, and heat stress responses
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Jin Zhang, Mengzhu Lu, Li Zhang, Jun Chen, Bobin Liu, and Jianbo Li
- Subjects
Intracellular Space ,Hsp90 ,Biology ,Genome ,Expression analysis ,Chromosomes, Plant ,Evolution, Molecular ,Species Specificity ,Heat shock protein ,Gene Duplication ,Gene duplication ,Genetics ,Gene family ,HSP90 Heat-Shock Proteins ,Gene ,Phylogeny ,Genomic organization ,Phylogenetic analysis ,Gene Expression Profiling ,Genomics ,Subcellular localization ,Gene structure ,Protein Transport ,Populus ,DNA microarray ,Heat-Shock Response ,Biotechnology ,Research Article - Abstract
Background Members of the heat shock protein 90 (Hsp90) class of proteins are evolutionarily conserved molecular chaperones. They are involved in protein folding, assembly, stabilization, activation, and degradation in many normal cellular processes and under stress conditions. Unlike many other well-characterized molecular chaperones, Hsp90s play key roles in signal transduction, cell-cycle control, genomic silencing, and protein trafficking. However, no systematic analysis of genome organization, gene structure, and expression compendium has been performed in the Populus model tree genus to date. Results We performed a comprehensive analysis of the Populus Hsp90 gene family and identified 10 Populus Hsp90 genes, which were phylogenetically clustered into two major groups. Gene structure and motif composition are relatively conserved in each group. In Populus trichocarpa, we identified three paralogous pairs, among which the PtHsp90-5a/PtHsp90-5b paralogous pair might be created by duplication of a genome segment. Subcellular localization analysis shows that PtHsp90 members are localized in different subcellular compartments. PtHsp90-3 is localized both in the nucleus and in the cytoplasm, PtHsp90-5a and PtHsp90-5b are in chloroplasts, and PtHsp90-7 is in the endoplasmic reticulum (ER). Furthermore, microarray and semi-quantitative real-time RT-PCR analyses show that a number of Populus Hsp90 genes are differentially expressed upon exposure to various stresses. Conclusions The gene structure and motif composition of PtHsp90s are highly conserved among group members, suggesting that members of the same group may also have conserved functions. Microarray and RT-PCR analyses show that most PtHsp90s were induced by various stresses, including heat stress. Collectively, these observations lay the foundation for future efforts to unravel the biological roles of PtHsp90 genes.
- Published
- 2013
36. Hsf and Hsp gene families in Populus: genomewide identification, organization and correlated expression during development and in stress responses.
- Author
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Jin Zhang, Bobin Liu, Jianbo Li, Li Zhang, Yan Wang, Huanquan Zheng, Mengzhu Lu, and Jun Chen
- Subjects
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POPLAR genetics , *GENE expression in plants , *HEAT shock proteins , *HEAT shock factors , *PERENNIALS , *GENETIC overexpression - Abstract
Background: Heat shock proteins (Hsps) are molecular chaperones that are involved in many normal cellular processes and stress responses, and heat shock factors (Hsfs) are the transcriptional activators of Hsps. Hsfs and Hsps are widely coordinated in various biological processes. Although the roles of Hsfs and Hsps in stress responses have been well characterized in Arabidopsis, their roles in perennial woody species undergoing various environmental stresses remain unclear. Results: Here, a comprehensive identification and analysis of Hsf and Hsp families in poplars is presented. In Populus trichocarpa, we identified 42 paralogous pairs, 66.7% resulting from a whole genome duplication. The gene structure and motif composition are relatively conserved in each subfamily. Microarray and quantitative real-time RT-PCR analyses showed that most of the Populus Hsf and Hsp genes are differentially expressed upon exposure to various stresses. A coexpression network between Populus Hsf and Hsp genes was generated based on their expression. Coordinated relationships were validated by transient overexpression and subsequent qPCR analyses. Conclusions: The comprehensive analysis indicates that different sets of PtHsps are downstream of particular PtHsfs and provides a basis for functional studies aimed at revealing the roles of these families in poplar development and stress responses. [ABSTRACT FROM AUTHOR]
- Published
- 2015
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