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Using Genome-Referenced Expressed Sequence Tag Assembly to Analyze the Origin and Expression Patterns of Gossypium hirsutum Transcripts

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Journal of Integrative plant Biology 2013年第7期55卷 576-585页

作者： Xiang Jin Qin Li Guanghui Xiao Yu-Xian Zhu State Key Laboratory of Protein and plant gene research College of Life SciencesPeking University national center for plant gene research(Beijing)

We assembled a total of 297,239 Gossypium hirsutum （Gh, a tetraploid cotton, AADD） expressed sequence tag （EST） sequences that were available in the national center for Biotechnology Information database, with reference to the recently published G. raimondii （Gr, a diploid cotton, DD） genome, and obtained 49,125 Unigenes. The average lengths of the U nigenes were increased from 804 and 791 bp in two previous EST assemblies to 1,019 bp in the current analysis. The number of putative cotton Unigenes with lengths of 3 kb or more increased from 25 or 34 to 1,223. As a result, thousands of originally independent G. hirsutum ESTs were aligned to produce large contigs encoding transcripts with very long open reading frames, indicating that the G. raimondii genome sequence provided remarkable advantages to assemble the tetraploid cotton transcriptome. Significant different distribution patterns within several GO terms, including transcription factor activity, were observed between D- and A-derived assemblies. Tran- scriptome analysis showed that, in a tetraploid cotton cell, 29,547 Unigenes were possibly derived from the D subgenome while another 19,578 may come from the A subgenome. Finally, some of the in silico data were confirmed by reverse transcription polymerase chain reaction experiments to show the changes in transcript levels for several gene families known to play key role in cotton fiber development. We believe that our work provides a useful platform for functional and evolutionary genomic studies in cotton.

关键词： Cotton fiber deep sequencing expressed sequence tag assembly functional genomics Gossypium.

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Structural Insights into N^6-methyladenosine (m^6A) Modification in the Transcriptome

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Genomics, Proteomics & Bioinformatics 2018年第2期16卷 85-98页

作者： Jinbo Huang Ping Yin national Key Laboratory of Crop genetic Improvement and national center of plant gene research Huazhong Agricultural University

More than 100 types of chemical modifications in RNA have been well documented. Recently, several modifications, such as N6-methyladenosine （m^6A）, have been detected in mRNA, opening the window into the realm of epitranscriptomies. The m^6A modification is the most abundant modification in mRNA and non-coding RNA （ncRNA）. At the molecular level, m^6A affects almost all aspects of mRNA metabolism, including splicing, translation, and stability, as well as microRNA （miRNA） maturation, playing essential roles in a range of cellular processes. The m^6A modification is regulated by three classes of proteins generally referred to as the ＂writer＂（adenosine methyltransferase）, ＂eraser＂（m^6A demethylating enzyme）, and ＂reader＂（m^6A-binding protein）. The m^6A modification is reversibly installed and removed by writers and erasers, respectively. Readers, which are members of the YT521-B homology （YTH） family proteins, selectively bind to RNA and affect its fate in an m^6A-dependent manner. In this review, we summarize the structures of the functional proteins that modulate the m^6A modification, and provide our insights into the m^6A-mediated gene regulation.

关键词： Epitranscriptomics M^6A modification Writer Reader Eraser

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The Arabidopsis Anaphase-Promoting Complex/Cyclosome Subunit 1 is Critical for Both Female Gametogenesis and Embryogenesis

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Journal of Integrative plant Biology 2013年第1期55卷 64-74页

作者： Yanbing Wang Yingnan Hou Hongya Gu Dingming Kang Zhang-Liang Chen Jingjing Liu Li-Jia Qu State Key Laboratory of Protein and plant gene research College of Life Sciences Peking University College of Agronomy and Biotechnology China Agricultural University The national plant gene research center

Anaphase-promoting complex/cyclosome （APC/C）, a multisubunit E3 ligase, plays a critical role in cell cycle control, but the functional characterization of each subunit has not yet been completed. To investigate the function of APC1 in Arabidopsis, we analyzed four mutant alleles of APC1, and found that mutation in APC1 resulted in significantly reduced plant fertility, accumulation of cyclin B, and disrupted auxin distribution in embryos. The three mutant alleles apcl-1, apcl-2 and apcl-3 shared variable defects in female gametogenesis including degradation, abnormal nuclear number, and disrupted polarity of nuclei in the embryo sac as well as in embryogenesis, in which embryos were arrested at multiple stages. All of these defects are similar to those previously identified in apc4. The mutant apcl-4, in which the T-DNA was inserted after the transmembrane domain at the C-terminus, showed much more severe phenotypes; that is, most of the ovules were arrested at the one-nucleate female gametophyte stage （stage FG1）. In the apcl apc4 double mutants, the fertility was further reduced by one-third in apcl-ll＋ apc4-1/＋, and in some cases no ovules even survived in siliques of apcl-4/＋ apc4-1/＋. Our data thus suggest that APC1, an essential component of APC/C, plays a synergistic role with APC4 both in female gametogenesis and in embryogenesis.

关键词： Arabidopsis anaphase-promoting complex/cyclosome (APC/C) APC1 APC4 female gametogenesis embryogenesis synergistic role

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Rice MtN3/saliva/SWEET gene family: Evolution,expression profiling, and sugar transport

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Journal of Integrative plant Biology 2014年第6期56卷 559-570页

作者： Meng Yuan Junwei Zhao Renyan Huang Xianghua Li Jinghua Xiao Shiping Wang national Key Laboratory of Crop genetic Improvement National Center of Plant Gene Research (Wuhan) Huazhong Agricultural University

The rice MtN3/saliva/SWEET gene family consists of 21 paralogs. However, their functions in physiological processes are largely unknown, although at least three of the 21 paralogs are used by pathogenic bacteria to infect rice. Here, we report the evolutionary features, transcriptional characteristics, and putative functions in sugar transport of this gene family. The wild rice accessions in this study included those with AA, BB, CC, BBCC, CCDD, EE, and GG genomes, which appeared approximately 0.58-14.6 million years ago. The structures, chromosomal locations, phylogenetic relationships, and homologous distribution among the accessions suggest that the number of rice MtN3/saliva/SWEET paralogs gradual y increased as the Oryza genus evolved, and one third of the paralogs may have originated recently. These paralogs are differentially expressed in vegetative and reproductive tissues, in the leaf senescence process, and in signaling dependent on gibberel ic acid, cytokinin, or 1-naphthalene acetic acid （an analog of auxin）, suggesting that they may be associated with multiple physiological processes. Four paralogs could transport galactose in yeast, which suggests that they may have a similar function in rice. These results will help to elucidate their roles and biochemical functions in rice development, adaptation to environment, host-pathogen interaction, and so forth.

关键词： Evolution MtN3/saliva domain Oryza sotivo transporter

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The key residues of OsTFIIAγ5/Xa5 protein captured by the argininerich TFB domain of TALEs compromising rice susceptibility and bacterial pathogenicity

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Journal of Integrative Agriculture 2019年第6期18卷 1178-1188页

作者： TIAN Jing-jing HUI Shu-gang SHI Ya-rui YUAN Meng national Key Laboratory of Crop genetic Improvement National Center of Plant Gene Research (Wuhan)Huazhong Agricultural University

Xanthomonas bacteria secrete transcription activator-like effector(TALE)proteins into host cells to activate plant disease susceptibility genes to cause disease,and the process is dependent on interaction between bacteria TFB domain of TALEs and host plant basal transcription factor IIA gamma subunit(TFIIAγ).The key domain or residues of plant TFIIAγand core residues of bacteria TFB domain that are indispensable for TFIIAγ-TALEs interaction in the process of TALE-carrying Xanthomonas invasion plants are ***,we showed that the thirdα-helix domain of OsTFIIAγ5/Xa5,especially the 38th,39th,40th and 42th residues were key sites for capturing by TALEs of Xanthomonas oryzae ***(Xoo),the causal agent of rice bacterial blight *** latter segment of Xoo TFB domain harboring seventy-two amino acid residues was vital for TALE specific binding with host plant OsTFIIAγ5/*** of some residues in this core region of TFB domain completely compromised capacity of TALEs capturing rice OsTFIIAγ5/*** rich and conserved arginine residues in this core region of TFB domain were responsible for TALE-dependent plant susceptibility gene activation and virulence of *** results provide a potential strategy for improving resistance to TALE-carrying pathogens in plants by site-specific modification of key residues of host plant TFIIAγ.

关键词： Xanthomonas transcription activator-like effector PthXo1 TFB rice

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GID1 modulates stomatal response and submergence tolerance involving abscisic acid and gibberellic acid signaling in rice

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Journal of Integrative plant Biology 2015年第11期57卷 954-968页

作者： Hao Du Yu Chang Fei Huang Lizhong Xiong national Key Laboratory of Crop genetic Improvement and national center of plant gene research(Wuhan) Huazhong Agricultural University

plant responses to abiotic stresses are coordinated by arrays of growth and developmental programs. Gibberellic acid （GA） and abscisic acid （ABA） play critical roles in the developmental programs and environmental responses, respectively, through complex signaling and metabolism networks. However, crosstalk between the two phytohormones in stress responses remains largely unknown. In this study, we report that GIBBERELLIN-INSENSITIVE DWARF 1 （GID1）, a soluble receptor for GA, regulates stomata[ develop- ment and patterning in rice （Oryza sativa L.）. The gidl mutant showed impaired biosynthesis of endogenous ABA under drought stress conditions, but it exhibited enhanced sensi- tivity to exogenous ABA. Scanning electron microscope and infrared thermal image analysis indicated an increase in the stomatal conductance in the gidl mutant under drought conditions. Interestingly, the gidl mutant had increased levels of chlorophyll and carbohydrates under submergence conditions, and showed enhanced reactive oxygen species （ROS）-scavenging ability and submergence tolerance compared with the wild-type. Further analyses suggested that the function of GID1 in submergence responses is partially dependent on ABA, and GA signaling by GID1 is involved in submergence tolerance by modulating carbohydrate consumption. Taken together, these findings suggest GID1 plays distinct roles in stomatal response and submergence tolerance through both the ABA and GA signaling pathways in rice.

关键词： Abscisic acid carbohydrateconsumption gibberellic acid stomata Oryza sativa

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The regulatory network mediated by circadian clock genes is related to heterosis in rice

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Journal of Integrative plant Biology 2015年第3期57卷 300-312页

作者： Guojing Shen Wei Hu Bo Zhang Yongzhong Xing national Key Laboratory of Crop genetic Improvement and national center of plant gene research (Wuhan) Huazhong Agricultural University

Exploitation of heterosis in rice（Oryza sativa L.） has contributed greatly to global food *** this study,we generated three sets of reciprocal F1 hybrids of indica and japonica subspecies to evaluate the relationship between yield heterosis and the circadian *** were no differences in trait performance or heterosis between the reciprocal hybrids,indicating no maternal effects on *** indica-indica and indica-japonica reciprocal F1 hybrids exhibited pronounced heterosis for chlorophyll and starch content in leaves and for grain yield/*** contrast,the japonica-japonica F1 hybrids showed low *** three circadian clock genes investigated expressed in an above-high-parent pattern（AHP）at seedling stage in all the *** five genes downstream of the circadian clock,and involved in chlorophyll and starch metabolic pathways,were expressed in AHP in hybrids with strong better-parent heterosis（BPH）.Similarly,three of these research Arfive genes in the japonica-japonica F1 hybrids showing low BPH were expressed in positive overdominance,but the other two genes were expressed in additive or negative *** results indicated that the expression patterns of circadian clock genes and their downstream genes are associated with heterosis,which suggests that the circadian rhythm pathway may be related to heterosis in rice.

关键词： Circadian clock better-parent heterosis biomass overdominance yield

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The tRNA 3'-end Processing Enzyme tRNase Z2Contributes to Chloroplast Biogenesis in Rice

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Journal of Integrative plant Biology 2013年第11期55卷 1104-1118页

作者： Tuan Long Dong Guo Dong He Wenjie Shen Xianghua Li national Key Laboratory of Crop genetic Improvement and national center of plant gene research (Wuhan) Huazhong Agricultural University

tRNase Z （TRZ） is a ubiquitous endonuclease that removes the 3＇-trailer from precursor tRNAs during maturation. In yeast and animals, TRZ regulates the cell cycle via its （t）RNA processing activity; however, its physiological function in higher plants has not been well characterized. This study describes the identification of a rice （Oryza sativa） TRZ2 mutant; plants homozygous for the osatrz2 mutation were albinos with deficient chlorophyll content. A microscopic analysis of the mutant plants revealed that the transition of proplastids to chloroplasts was arrested at an early stage, and the number and size of the plastids in callus cells was substantially decreased. A genetic complementation test and an RNA interference analysis confirmed that disruption of OsaTRZ2 was responsible for the mutant phenotype. OsaTRZ2 is expressed in all rice tissues, but is preferentially expressed in leaves, sheathes, and calli. OsaTRZ2 was subcellularly localized in chloroplasts, and displayed tRNA 3＇-end processing activity in both in vitro and in vivo assays. In the osatrz2 mutants, transcription of plastid-encoded and nucleus- encoded RNA polymerases was severely reduced and moderately increased, respectively. These results suggest that the tRNA 3＇ processing activity of OsaTRZ2 contributes to chloroplast biogenesis.

关键词： Chloroplast biogenesis rice tRNA processing tRNase Z.

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Characterization of a Purine Permease Family gene OsPUP7 Involved in Growth and Development Control in Rice

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Journal of Integrative plant Biology 2013年第11期55卷 1119-1135页

作者： Zhuyun Qi Lizhong Xiong national Key Laboratory of Crop genetic Improvement and national center of plant gene research (Wuhan) Huazhong Agricultural University

In this study, PUP-type cytokinin transporter genes were identified in rice （Oryza sativa L.）. The Oryza sativa purine permease （OsPUP） family has 12 members that show similar predicted protein sequences with AtPUPs. To reveal the functions of OsPUP genes, we searched the T-DNA mutant library of rice and found one mutant for the member OsPUP7. The T-DNA insertion caused a new transcript that encodes a protein with 26 amino acids different from the native OsPUP7 at the C-terminus. The mutant showed multiple phenotypic changes including increased plant height, big seeds, and delayed flowering. The mutant also showed increased sensitivity to drought and salt stresses and treatments with kinetin and abscisic acid. OsPUP7is expressed mainly in the vascular bundle, pistil, and stamens. The measurement of cytokinins （CKs） showed that CK content in the mutant spikelets accumulated higher than that in the wild type. Moreover, uptake experiment in the yeast fcy2 mutant suggested that OsPUP7 has the ability to transport caffeine, a CK derivative. Our results indicate that the PUP transport system also exists in rice, and OsPUP7has an important role in the transport of CK, thus affecting developmental process and stress responses.

关键词： Abiotic stress cytokinin purine permease transporter rice.

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Validation and Characterization of Ghd7.1, a Major Quantitative Trait Locus with Pleiotropic Effects on Spikelets per Panicle, plant Height, and Heading Date in Rice (Oryza sativa L.)

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Journal of Integrative plant Biology 2013年第10期55卷 917-927页

作者： Touming Liu Haiyang Liu Huang Zhang Yongzhong Xing national Key Laboratory of Crop genetic Improvement and national center of plant gene research (Wuhan) Huazhong Agricultural University

A quantitative trait locus （QTL） that affects heading date （HD） and the number of spikelets per panicle （SPP） was previously identified in a small region on chromosome 7 in rice （Oryza sativa L.）. In order to further characterize the QTL region, near isogenic lines （NILs） were quickly obtained by self-crossing recombinant inbred line 189, which is heterozygous in the vicinity of the target region. The pleiotropic effects of QTL Ghd7.1 on plant height （PH）, SPP, and HD, were validated using an NIL-F2 population. Ghd7.1 explained 50.2%, 45.3%, and 76.9% of phenotypic variation in PH, SPP, and HD, respectively. Ghd7.1 was precisely mapped to a 357-kb region on the basis of analysis of the progeny of the NIL-F2 population. Day-length treatment confirmed that Ghd7.1 is sensitive to photoperiod, with long days delaying heading up to 12.5 d. Identification of panicle initiation and development for the pair of NILs showed that Ghd7.1 elongated the photoperiod-sensitive phase more than 10 d, but did not change the basic vegetative phase and the reproductive growth phase. These findings indicated that Ghd7.1 regulates SPP by controlling the rate of panicle differentiation rather than the duration of panicle development.

关键词： Day-length treatment pleiotropic effects photoperiod sensitive phase rice.

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