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Ochiai KK, Hanawa D, Ogawa HA, Tanaka H, Uesaka K, Edzuka T, Shirae-Kurabayashi M, Toyoda A, Itoh T, Goshima G. Genome sequence and cell biological toolbox of the highly regenerative, coenocytic green feather alga Bryopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38642374 DOI: 10.1111/tpj.16764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 02/10/2024] [Accepted: 03/27/2024] [Indexed: 04/22/2024]
Abstract
Green feather algae (Bryopsidales) undergo a unique life cycle in which a single cell repeatedly executes nuclear division without cytokinesis, resulting in the development of a thallus (>100 mm) with characteristic morphology called coenocyte. Bryopsis is a representative coenocytic alga that has exceptionally high regeneration ability: extruded cytoplasm aggregates rapidly in seawater, leading to the formation of protoplasts. However, the genetic basis of the unique cell biology of Bryopsis remains poorly understood. Here, we present a high-quality assembly and annotation of the nuclear genome of Bryopsis sp. (90.7 Mbp, 27 contigs, N50 = 6.7 Mbp, 14 034 protein-coding genes). Comparative genomic analyses indicate that the genes encoding BPL-1/Bryohealin, the aggregation-promoting lectin, are heavily duplicated in Bryopsis, whereas homologous genes are absent in other ulvophyceans, suggesting the basis of regeneration capability of Bryopsis. Bryopsis sp. possesses >30 kinesins but only a single myosin, which differs from other green algae that have multiple types of myosin genes. Consistent with this biased motor toolkit, we observed that the bidirectional motility of chloroplasts in the cytoplasm was dependent on microtubules but not actin in Bryopsis sp. Most genes required for cytokinesis in plants are present in Bryopsis, including those in the SNARE or kinesin superfamily. Nevertheless, a kinesin crucial for cytokinesis initiation in plants (NACK/Kinesin-7II) is hardly expressed in the coenocytic part of the thallus, possibly underlying the lack of cytokinesis in this portion. The present genome sequence lays the foundation for experimental biology in coenocytic macroalgae.
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Affiliation(s)
- Kanta K Ochiai
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Toba, 517-0004, Japan
| | - Daiki Hanawa
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Harumi A Ogawa
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Toba, 517-0004, Japan
| | - Hiroyuki Tanaka
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Kazuma Uesaka
- Centre for Gene Research, Nagoya University, Nagoya, 464-8602, Japan
| | - Tomoya Edzuka
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Toba, 517-0004, Japan
| | - Maki Shirae-Kurabayashi
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Toba, 517-0004, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Gohta Goshima
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Toba, 517-0004, Japan
- Department of Biological Science, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan
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Li H, Gong P, Xu X, Zhou X, Li F. Knockout of the virus replication-related genes UbEF1B and CCR4/NOT3 by CRISPR/Cas9 confers high-efficiency and broad-spectrum resistance to geminiviruses in Nicotiana benthamiana. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:793-795. [PMID: 38147372 PMCID: PMC10955485 DOI: 10.1111/pbi.14265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 11/14/2023] [Accepted: 11/27/2023] [Indexed: 12/27/2023]
Affiliation(s)
- Hao Li
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
| | - Pan Gong
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
- State Key Laboratory of Rice BiologyInstitute of Biotechnology, Zhejiang UniversityHangzhouZhejiangChina
| | - Xiongbiao Xu
- Guangxi Key Laboratory of Sugarcane Biology, College of AgricultureGuangxi UniversityNanningChina
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
- State Key Laboratory of Rice BiologyInstitute of Biotechnology, Zhejiang UniversityHangzhouZhejiangChina
| | - Fangfang Li
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
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He J, Zeng C, Li M. Plant Functional Genomics Based on High-Throughput CRISPR Library Knockout Screening: A Perspective. ADVANCED GENETICS (HOBOKEN, N.J.) 2024; 5:2300203. [PMID: 38465224 PMCID: PMC10919289 DOI: 10.1002/ggn2.202300203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/19/2023] [Indexed: 03/12/2024]
Abstract
Plant biology studies in the post-genome era have been focused on annotating genome sequences' functions. The established plant mutant collections have greatly accelerated functional genomics research in the past few decades. However, most plant genome sequences' roles and the underlying regulatory networks remain substantially unknown. Clustered, regularly interspaced short palindromic repeat (CRISPR)-associated systems are robust, versatile tools for manipulating plant genomes with various targeted DNA perturbations, providing an excellent opportunity for high-throughput interrogation of DNA elements' roles. This study compares methods frequently used for plant functional genomics and then discusses different DNA multi-targeted strategies to overcome gene redundancy using the CRISPR-Cas9 system. Next, this work summarizes recent reports using CRISPR libraries for high-throughput gene knockout and function discoveries in plants. Finally, this work envisions the future perspective of optimizing and leveraging CRISPR library screening in plant genomes' other uncharacterized DNA sequences.
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Affiliation(s)
- Jianjie He
- Department of BiotechnologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhan430074China
- Key Laboratory of Molecular Biophysics of the Ministry of EducationWuhan430074China
| | - Can Zeng
- Department of BiotechnologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhan430074China
- Key Laboratory of Molecular Biophysics of the Ministry of EducationWuhan430074China
| | - Maoteng Li
- Department of BiotechnologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhan430074China
- Key Laboratory of Molecular Biophysics of the Ministry of EducationWuhan430074China
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Ke S, Jiang Y, Zhou M, Li Y. Genome-Wide Identification, Evolution, and Expression Analysis of the WD40 Subfamily in Oryza Genus. Int J Mol Sci 2023; 24:15776. [PMID: 37958759 PMCID: PMC10648978 DOI: 10.3390/ijms242115776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/23/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
The WD40 superfamily is widely found in eukaryotes and has essential subunits that serve as scaffolds for protein complexes. WD40 proteins play important regulatory roles in plant development and physiological processes, such as transcription regulation and signal transduction; it is also involved in anthocyanin biosynthesis. In rice, only OsTTG1 was found to be associated with anthocyanin biosynthesis, and evolutionary analysis of the WD40 gene family in multiple species is less studied. Here, a genome-wide analysis of the subfamily belonging to WD40-TTG1 was performed in nine AA genome species: Oryza sativa ssp. japonica, Oryza sativa ssp. indica, Oryza rufipogon, Oryza glaberrima, Oryza meridionalis, Oryza barthii, Oryza glumaepatula, Oryza nivara, and Oryza longistaminata. In this study, 383 WD40 genes in the Oryza genus were identified, and they were classified into four groups by phylogenetic analysis, with most members in group C and group D. They were found to be unevenly distributed across 12 chromosomes. A total of 39 collinear gene pairs were identified in the Oryza genus, and all were segmental duplications. WD40s had similar expansion patterns in the Oryza genus. Ka/Ks analyses indicated that they had undergone mainly purifying selection during evolution. Furthermore, WD40s in the Oryza genus have similar evolutionary patterns, so Oryza sativa ssp. indica was used as a model species for further analysis. The cis-acting elements analysis showed that many genes were related to jasmonic acid and light response. Among them, OsiWD40-26/37/42 contained elements of flavonoid synthesis, and OsiWD40-15 had MYB binding sites, indicating that they might be related to anthocyanin synthesis. The expression profile analysis at different stages revealed that most OsiWD40s were expressed in leaves, roots, and panicles. The expression of OsiWD40s was further analyzed by qRT-PCR in 9311 (indica) under various hormone treatments and abiotic stresses. OsiWD40-24 was found to be responsive to both phytohormones and abiotic stresses, suggesting that it might play an important role in plant stress resistance. And many OsiWD40s might be more involved in cold stress tolerance. These findings contribute to a better understanding of the evolution of the WD40 subfamily. The analyzed candidate genes can be used for the exploration of practical applications in rice, such as cultivar culture for colored rice, stress tolerance varieties, and morphological marker development.
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Affiliation(s)
| | | | | | - Yangsheng Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (S.K.); (Y.J.); (M.Z.)
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Cantila AY, Thomas WJW, Bayer PE, Edwards D, Batley J. Predicting Cloned Disease Resistance Gene Homologs (CDRHs) in Radish, Underutilised Oilseeds, and Wild Brassicaceae Species. PLANTS (BASEL, SWITZERLAND) 2022; 11:3010. [PMID: 36432742 PMCID: PMC9693284 DOI: 10.3390/plants11223010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/01/2022] [Accepted: 11/02/2022] [Indexed: 06/16/2023]
Abstract
Brassicaceae crops, including Brassica, Camelina and Raphanus species, are among the most economically important crops globally; however, their production is affected by several diseases. To predict cloned disease resistance (R) gene homologs (CDRHs), we used the protein sequences of 49 cloned R genes against fungal and bacterial diseases in Brassicaceae species. In this study, using 20 Brassicaceae genomes (17 wild and 3 domesticated species), 3172 resistance gene analogs (RGAs) (2062 nucleotide binding-site leucine-rich repeats (NLRs), 497 receptor-like protein kinases (RLKs) and 613 receptor-like proteins (RLPs)) were identified. CDRH clusters were also observed in Arabis alpina, Camelina sativa and Cardamine hirsuta with assigned chromosomes, consisting of 62 homogeneous (38 NLR, 17 RLK and 7 RLP clusters) and 10 heterogeneous RGA clusters. This study highlights the prevalence of CDRHs in the wild relatives of the Brassicaceae family, which may lay the foundation for rapid identification of functional genes and genomics-assisted breeding to develop improved disease-resistant Brassicaceae crop cultivars.
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Cognitive control of song production by humpback whales. Anim Cogn 2022; 25:1133-1149. [PMID: 36058997 DOI: 10.1007/s10071-022-01675-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 08/04/2022] [Accepted: 08/12/2022] [Indexed: 11/01/2022]
Abstract
Singing humpback whales are highly versatile vocalizers, producing complex sequences of sounds that they vary throughout adulthood. Past analyses of humpback whale song have emphasized yearly variations in structural features of songs made collectively by singers within a population with comparatively little attention given to the ways that individual singers vary consecutive songs. As a result, many researchers describe singing by humpback whales as a process in which singers produce sequences of repeating sound patterns. Here, we show that such characterizations misrepresent the degree to which humpback whales flexibly and dynamically control the production of sounds and sound patterns within song sessions. Singers recorded off the coast of Hawaii continuously morphed units along multiple acoustic dimensions, with the degree and direction of morphing varying across parallel streams of successive units. Individual singers also produced multiple phrase variants (structurally similar, but acoustically distinctive sequences) within song sessions. The precision with which individual singers maintained some acoustic properties of phrases and morphing trajectories while flexibly changing others suggests that singing humpback whales actively select and adjust acoustic elements of their songs in real time rather than simply repeating stereotyped sound patterns within song sessions.
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Mining of Cloned Disease Resistance Gene Homologs (CDRHs) in Brassica Species and Arabidopsis thaliana. BIOLOGY 2022; 11:biology11060821. [PMID: 35741342 PMCID: PMC9220128 DOI: 10.3390/biology11060821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 05/15/2022] [Accepted: 05/24/2022] [Indexed: 01/23/2023]
Abstract
Simple Summary Developing cultivars with resistance genes (R genes) is an effective strategy to support high yield and quality in Brassica crops. The availability of clone R gene and genomic sequences in Brassica species and Arabidopsis thaliana provide the opportunity to compare genomic regions and survey R genes across genomic databases. In this paper, we aim to identify genes related to cloned genes through sequence identity, providing a repertoire of species-wide related R genes in Brassica crops. The comprehensive list of candidate R genes can be used as a reference for functional analysis. Abstract Various diseases severely affect Brassica crops, leading to significant global yield losses and a reduction in crop quality. In this study, we used the complete protein sequences of 49 cloned resistance genes (R genes) that confer resistance to fungal and bacterial diseases known to impact species in the Brassicaceae family. Homology searches were carried out across Brassica napus, B. rapa, B. oleracea, B. nigra, B. juncea, B. carinata and Arabidopsis thaliana genomes. In total, 660 cloned disease R gene homologs (CDRHs) were identified across the seven species, including 431 resistance gene analogs (RGAs) (248 nucleotide binding site-leucine rich repeats (NLRs), 150 receptor-like protein kinases (RLKs) and 33 receptor-like proteins (RLPs)) and 229 non-RGAs. Based on the position and distribution of specific homologs in each of the species, we observed a total of 87 CDRH clusters composed of 36 NLR, 16 RLK and 3 RLP homogeneous clusters and 32 heterogeneous clusters. The CDRHs detected consistently across the seven species are candidates that can be investigated for broad-spectrum resistance, potentially providing resistance to multiple pathogens. The R genes identified in this study provide a novel resource for the future functional analysis and gene cloning of Brassicaceae R genes towards crop improvement.
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Jiang N, Li SZ, Zhang YWQ, Habib MR, Xiong T, Xu S, Dong H, Zhao QP. The identification of alternative oxidase in intermediate host snails of Schistosoma and its potential role in protecting Oncomelania hupensis against niclosamide-induced stress. Parasit Vectors 2022; 15:97. [PMID: 35313980 PMCID: PMC8935807 DOI: 10.1186/s13071-022-05227-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 03/03/2022] [Indexed: 11/21/2022] Open
Abstract
Background Snail intermediate hosts are mandatory for the transmission of schistosomiasis, which has to date infected more than 200 million people worldwide. Our previous studies showed that niclosamide treatment caused the inhibition of aerobic respiration and oxidative phosphorylation, and the disruption of energy supply, in one of the intermediate hosts of schistosomiasis, Oncomelania hupensis, which eventually led to the death of the snails. Meanwhile, the terminal oxidase in the mitochondrial respiratory chain, alternative oxidase (AOX), was significantly up-regulated, which was thought to counterbalance the oxidative stress and maintain metabolic homeostasis in the snails. The aims of the present study are to identify the AOXs in several species of snails and investigate the potential activation of O. hupensis AOX (OhAOX) under niclosamide-induced stress, leading to enhanced survival of the snail when exposed to this molluscicide. Methods The complete complementary DNA was amplified from the AOXs of O. hupensis and three species of Biomphalaria; the sequence characteristics were analysed and the phylogenetics investigated. The dynamic expression and localisation of the AOX gene and protein in O. hupensis under niclosamide-induced stress were examined. In addition, the expression pattern of genes in the mitochondrial respiratory complex was determined and the production of reactive oxygen species (ROS) calculated. Finally, the molluscicidal effect of niclosamide was compared between snails with and without inhibition of AOX activity. Results AOXs containing the invertebrate AOX-specific motif NP-[YF]-XPG-[KQE] were identified from four species of snail, which phylogenetically clustered together into Gastropoda AOXs and further into Mollusca AOXs. After niclosamide treatment, the levels of OhAOX messenger RNA (mRNA) and OhAOX protein in the whole snail were 14.8 and 2.6 times those in untreated snails, respectively, but varied widely among tissues. Meanwhile, the level of cytochrome C reductase mRNA showed a significant decrease in the whole snail, and ROS production showed a significant decrease in the liver plus gonad (liver-gonad) of the snails. At 24 h post-treatment, the mortality of snails treated with 0.06–0.1 mg/L niclosamide and AOX inhibitor was 56.31–76.12% higher than that of snails treated with 0.1 mg/L niclosamide alone. Conclusions AOX was found in all the snail intermediate hosts of Schistosoma examined here. AOX was significantly activated in O. hupensis under niclosamide-induced stress, which led to a reduction in oxidative stress in the snail. The inhibition of AOX activity in snails can dramatically enhance the molluscicidal effect of niclosamide. A potential target for the development of an environmentally safe snail control method, which acts by inhibiting the activity of AOX, was identified in this study. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-022-05227-5.
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Affiliation(s)
- Ni Jiang
- Department of Parasitology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China.,Joint Inspection Center of Precision Medicine, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, China
| | - Shi-Zhu Li
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, National Center for Tropical Diseases Research, WHO Collaborating Center for Tropical Diseases, Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, China.
| | - Yang-Wen-Qing Zhang
- Department of Parasitology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Mohamed R Habib
- Medical Malacology Department, Theodor Bilharz Research Institute, Giza, Egypt
| | - Tao Xiong
- Department of Microbiology, School of Medical Sciences, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Sha Xu
- Department of Parasitology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Huifen Dong
- Department of Parasitology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Qin-Ping Zhao
- Department of Parasitology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China.
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Hassani SB, Trontin JF, Raschke J, Zoglauer K, Rupps A. Constitutive Overexpression of a Conifer WOX2 Homolog Affects Somatic Embryo Development in Pinus pinaster and Promotes Somatic Embryogenesis and Organogenesis in Arabidopsis Seedlings. FRONTIERS IN PLANT SCIENCE 2022; 13:838421. [PMID: 35360299 PMCID: PMC8960953 DOI: 10.3389/fpls.2022.838421] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Although full sequence data of several embryogenesis-related genes are available in conifers, their functions are still poorly understood. In this study, we focused on the transcription factor WUSCHEL-related HOMEOBOX 2 (WOX2), which is involved in determination of the apical domain during early embryogenesis, and is required for initiation of the stem cell program in the embryogenic shoot meristem of Arabidopsis. We studied the effects of constitutive overexpression of Pinus pinaster WOX2 (PpWOX2) by Agrobacterium-mediated transformation of P. pinaster somatic embryos and Arabidopsis seedlings. Overexpression of PpWOX2 during proliferation and maturation of somatic embryos of P. pinaster led to alterations in the quantity and quality of cotyledonary embryos. In addition, transgenic somatic seedlings of P. pinaster showed non-embryogenic callus formation in the region of roots and subsequently inhibited root growth. Overexpression of PpWOX2 in Arabidopsis promoted somatic embryogenesis and organogenesis in a part of the transgenic seedlings of the first and second generations. A concomitant increased expression of endogenous embryogenesis-related genes such as AtLEC1 was detected in transgenic plants of the first generation. Various plant phenotypes observed from single overexpressing transgenic lines of the second generation suggest some significant interactions between PpWOX2 and AtWOX2. As an explanation, functional redundancy in the WOX family is suggested for seed plants. Our results demonstrate that the constitutive high expression of PpWOX2 in Arabidopsis and P. pinaster affected embryogenesis-related traits. These findings further support some evolutionary conserved roles of this gene in embryo development of seed plants and have practical implications toward somatic embryogenesis induction in conifers.
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Affiliation(s)
- Seyedeh Batool Hassani
- Department of Plant Systematics and Evolution, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Juliane Raschke
- Department of Plant Systematics and Evolution, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Kurt Zoglauer
- Department of Plant Systematics and Evolution, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Andrea Rupps
- Department of Plant Systematics and Evolution, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
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Thilini Chethana KW, Peng J, Li X, Xing Q, Liu M, Zhang W, Hyde KD, Zhao W, Yan J. LtEPG1, a Secretory Endopolygalacturonase Protein, Regulates the Virulence of Lasiodiplodia theobromae in Vitis vinifera and Is Recognized as a Microbe-Associated Molecular Patterns. PHYTOPATHOLOGY 2020; 110:1727-1736. [PMID: 32460690 DOI: 10.1094/phyto-04-20-0118-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The Lasiodiplodia theobromae genome encodes numerous glycoside hydrolases involved in organic matter degradation and conducive to pathogen infection, whereas their molecular mechanisms are still largely unknown. Here, we identified the glycoside hydrolase family 28 endopolygalacturonase LtEPG1 in L. theobromae and characterized its function in detail. LtEPG1 acts as a virulence factor during L. theobromae infection. Overexpression and silencing of LtEPG1 in L. theobromae led to significantly increased and decreased lesion areas, respectively. Further, the high transcript level of LtEPG1 during the infection process supported its virulence function. Polygalacturonase activity of LtEPG1 was substantiated by detecting its ability to degrade pectin. Furthermore, LtEPG1 functioned as microbe-associated molecular patterns during the infection process. Both transient expression of LtEPG1 in planta and infiltration of purified LtEPG1 triggered cell death in Nicotiana benthamiana. Site-directed mutation of LtEPG1 indicated that the enzymatic activity of LtEPG1 is independent from its elicitor activity. A protein kinase, KINβ1, was shown to interact in the yeast two-hybrid system with LtEPG1. This interaction was further confirmed in vitro using a pull-down assay. Our data indicate that LtEPG1 functions as a polygalacturonase and also serves as an elicitor with two independent mechanisms. Moreover, LtEPG1 may be able to manipulate host immune responses by regulating the KINβ1-mediated signal pathway and consequently promote its own successful infection and symptom development.
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Affiliation(s)
- K W Thilini Chethana
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
- College of Plant Protection, China Agricultural University, Beijing 100097, China
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Junbo Peng
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Xinghong Li
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Qikai Xing
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Mei Liu
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Wei Zhang
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Kevin D Hyde
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Wensheng Zhao
- College of Plant Protection, China Agricultural University, Beijing 100097, China
| | - Jiye Yan
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
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The gain-of-function allele bamA E470K bypasses the essential requirement for BamD in β-barrel outer membrane protein assembly. Proc Natl Acad Sci U S A 2020; 117:18737-18743. [PMID: 32675245 DOI: 10.1073/pnas.2007696117] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The outer membrane (OM) of gram-negative bacteria confers innate resistance to toxins and antibiotics. Integral β-barrel outer membrane proteins (OMPs) function to establish and maintain the selective permeability of the OM. OMPs are assembled into the OM by the β-barrel assembly machine (BAM), which is composed of one OMP-BamA-and four lipoproteins-BamB, C, D, and E. BamB, C, and E can be removed individually with only minor effects on barrier function; however, depletion of either BamA or BamD causes a global defect in OMP assembly and results in cell death. We have identified a gain-of-function mutation, bamA E470K , that bypasses the requirement for BamD. Although bamD::kan bamA E470K cells exhibit growth and OM barrier defects, they assemble OMPs with surprising robustness. Our results demonstrate that BamD does not play a catalytic role in OMP assembly, but rather functions to regulate the activity of BamA.
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Rahman M, Baten A, Mauleon R, King GJ, Liu L, Barkla BJ. Identification, characterization and epitope mapping of proteins encoded by putative allergenic napin genes from Brassica rapa. Clin Exp Allergy 2020; 50:848-868. [PMID: 32306538 DOI: 10.1111/cea.13612] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 03/25/2020] [Accepted: 04/13/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Brassica rapeseed crops contain high concentrations of oil in the seed. The remaining meal, following oil extraction, has a high protein content, but is of low value due to the presence of high amounts of napin seed storage proteins. These 2S albumin-like proteins are difficult to digest and have been identified as major allergens in humans. OBJECTIVE To comprehensively characterize the napin gene (NG) family in Brassica rapa and to gain an understanding of the structural basis of allergenicity of the expressed proteins. METHODS To identify candidate napin genes in B rapa, 2S albumin-like napin genes of Arabidopsis thaliana were used as query sequences to search for similarity against the B rapa var. pekinensis Chiifu-401 v2 and the var. trilocularis R-o-18 v1.5 genomes. Multiple sequence alignment (MSA) and epitope modelling was carried out to determine structural and evolutionary relationships of NGs and their potential allergenicity. RESULTS Four candidate napin genes in R-o-18 and ten in Chiifu-401 were identified with high sequence similarity to A thaliana napin genes. Multiple sequence alignment revealed strong conservation among the candidate genes. An epitope survey indicated high conservation of allergenic epitope motifs with known 2S albumin-like allergens. CONCLUSION Napin is thought to be responsible for a high prevalence of food allergies. Characterization of the napin gene family in B rapa will give important insight into the protein structure, and epitope modelling will help to advance studies into allergenicity including the development of precise diagnostic screenings and therapies for this potential food allergy as well as the possible manipulation of napin levels in the seed by gene editing technology.
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Affiliation(s)
- Mahmudur Rahman
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia
| | - Abdul Baten
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia.,Grasslands Research Centre, AgResearch Ltd, Palmerston North, New Zealand
| | - Ramil Mauleon
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia
| | - Lei Liu
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia
| | - Bronwyn J Barkla
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia
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Kim S, Nie H, Jun B, Kim J, Lee J, Kim S, Kim E, Kim S. Functional genomics by integrated analysis of transcriptome of sweet potato (Ipomoea batatas (L.) Lam.) during root formation. Genes Genomics 2020; 42:581-596. [PMID: 32240514 DOI: 10.1007/s13258-020-00927-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 03/26/2020] [Indexed: 12/30/2022]
Abstract
BACKGROUND Sweet potato is easily propagated by cuttings. But the molecular biological mechanism of adventitious root formation are not yet clear. OBJECTIVE To understand the molecular mechanisms of adventitious root formation from stem cuttings in sweet potato. METHODS RNA-seq analysis was performed using un-rooted stem (0 day) and rooted stem (3 days). Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, comparison with Arabidopsis transcription factors (TFs) of DEGs were conducted to investigate the characteristics of genes and TFs involved in root formation. In addition, qRT-PCR analysis using roots at 0, 3, 6, 9, and 12 days after planting was performed to confirm RNA-seq reliability and related genes expression. RESULTS 42,459 representative transcripts and 2092 DEGs were obtained through the RNA-seq analysis. The DEGs indicated the GO terms related to the single-organism metabolic process and cell periphery, and involved in the biosynthesis of secondary metabolites, and phenylpropanoid biosynthesis in KEGG pathways. The comparison with Arabidopsis thaliana TF database showed that 3 TFs (WRKY, NAC, bHLH) involved in root formation of sweet potato. qRT-PCR analysis, which was conducted to confirm the reliability of RNA-seq analysis, indicated that some metabolisms including oxidative stress and wounding, transport, hormone may be involved in adventitious root formation. CONCLUSIONS The detected genes related to secondary metabolism, some hormone (auxin, gibberellin), transports, etc. and 3 TFs (WRKY, NAC, bHLH) may have functions in adventitious roots formation. This results provide valuable resources for future research on the adventitious root formation of sweet potato.
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Affiliation(s)
- Sujung Kim
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Korea
| | - Hualin Nie
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Korea
| | - Byungki Jun
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Korea.,NH Seed Research Development Center, Nonghyup Agribusiness Group Incorporation, Anseong, 17558, Korea
| | - Jiseong Kim
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Korea
| | - Jeongeun Lee
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Korea
| | - Seungill Kim
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Korea
| | - Ekyune Kim
- College of Pharmacy, Catholic University of Daegu, Gyeongsan, Gyeongbuk, 38430, Korea
| | - Sunhyung Kim
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Korea.
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Natural variation in DNA methylation homeostasis and the emergence of epialleles. Proc Natl Acad Sci U S A 2020; 117:4874-4884. [PMID: 32071208 DOI: 10.1073/pnas.1918172117] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In plants and mammals, DNA methylation plays a critical role in transcriptional silencing by delineating heterochromatin from transcriptionally active euchromatin. A homeostatic balance between heterochromatin and euchromatin is essential to genomic stability. This is evident in many diseases and mutants for heterochromatin maintenance, which are characterized by global losses of DNA methylation coupled with localized ectopic gains of DNA methylation that alter transcription. Furthermore, we have shown that genome-wide methylation patterns in Arabidopsis thaliana are highly stable over generations, with the exception of rare epialleles. However, the extent to which natural variation in the robustness of targeting DNA methylation to heterochromatin exists, and the phenotypic consequences of such variation, remain to be fully explored. Here we describe the finding that heterochromatin and genic DNA methylation are highly variable among 725 A. thaliana accessions. We found that genic DNA methylation is inversely correlated with that in heterochromatin, suggesting that certain methylation pathway(s) may be redirected to genes upon the loss of heterochromatin. This redistribution likely involves a feedback loop involving the DNA methyltransferase, CHROMOMETHYLASE 3 (CMT3), H3K9me2, and histone turnover, as highly expressed, long genes with a high density of CMT3-preferred CWG sites are more likely to be methylated. Importantly, although the presence of CG methylation in genes alone may not affect transcription, genes containing CG methylation are more likely to become methylated at non-CG sites and silenced. These findings are consistent with the hypothesis that natural variation in DNA methylation homeostasis may underlie the evolution of epialleles that alter phenotypes.
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Lin Y, Yi X, Tang S, Chen W, Wu F, Yang X, Jiang X, Shi H, Ma J, Chen G, Chen G, Zheng Y, Wei Y, Liu Y. Dissection of Phenotypic and Genetic Variation of Drought-Related Traits in Diverse Chinese Wheat Landraces. THE PLANT GENOME 2019; 12:1-14. [PMID: 33016597 DOI: 10.3835/plantgenome2019.03.0025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 08/30/2019] [Indexed: 05/10/2023]
Abstract
Variations in 16 seedling traits under normal and drought conditions were investigated. Extremely resistant and sensitive accessions were identified for future analyses. Under normal and drought conditions, 57 and 29 QTL were identified, respectively. A total of 77 candidate genes were identified, and four were validated by qRT-PCR. Drought is one of the most important abiotic stressors affecting wheat (Triticum aestivum L.) production. To improve wheat yield, a better understanding of the genetic control of traits governing drought resistance is paramount. Here, using 645 wheat landraces, we evaluated 16 seedling traits related to root and shoot growth and water content under normal and drought (induced by polyethylene glycol) conditions. Extremely resistant and sensitive accessions were identified for future drought-resistance breeding and further genetic analyses. A genome-wide association study was performed for the 16 traits using 52,118 diversity arrays technology sequencing (DArT-seq) markers. A total of 57 quantitative trait loci (QTL) were detected for seven traits under normal conditions, whereas 29 QTL were detected for eight traits under drought conditions. On the basis of these markers, we identified 56 candidate genes for six seedling traits under normal conditions, and 21 candidate genes for seven seedling traits under drought conditions. Four candidate genes were validated under normal and drought conditions using quantitative reverse transcription polymerase chain reaction (qRT-PCR) data. The co-localization of the flowering date and drought-related traits indicates that the regulatory networks of flowering may also respond to drought stress or are associated with the correlated responses of these traits. The phenotypic and genetic elucidation of drought-related traits will assist future gene discovery efforts and provide a basis for breeding drought-resistant wheat cultivars.
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Affiliation(s)
- Yu Lin
- Triticeae Research Institute, Sichuan Agricultural Univ., Wenjiang, Chengdu, 611130, China
| | - Xin Yi
- College of Environmental Sciences, Sichuan Agricultural Univ., Wenjiang, Chengdu, 611130, China
| | - Si Tang
- Triticeae Research Institute, Sichuan Agricultural Univ., Wenjiang, Chengdu, 611130, China
| | - Wei Chen
- Triticeae Research Institute, Sichuan Agricultural Univ., Wenjiang, Chengdu, 611130, China
| | - Fangkun Wu
- Triticeae Research Institute, Sichuan Agricultural Univ., Wenjiang, Chengdu, 611130, China
| | - Xilan Yang
- Triticeae Research Institute, Sichuan Agricultural Univ., Wenjiang, Chengdu, 611130, China
| | - Xiaojun Jiang
- Triticeae Research Institute, Sichuan Agricultural Univ., Wenjiang, Chengdu, 611130, China
| | - Haoran Shi
- Triticeae Research Institute, Sichuan Agricultural Univ., Wenjiang, Chengdu, 611130, China
| | - Jian Ma
- Triticeae Research Institute, Sichuan Agricultural Univ., Wenjiang, Chengdu, 611130, China
| | - Guangdeng Chen
- Triticeae Research Institute, Sichuan Agricultural Univ., Wenjiang, Chengdu, 611130, China
| | - Guoyue Chen
- College of resources, Sichuan Agricultural Univ., Wenjiang, Chengdu, 611130, China
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural Univ., Wenjiang, Chengdu, 611130, China
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural Univ., Wenjiang, Chengdu, 611130, China
| | - Yaxi Liu
- Triticeae Research Institute, Sichuan Agricultural Univ., Wenjiang, Chengdu, 611130, China
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Cloning and expression analysis of three critical triterpenoid pathway genes in Osmanthus fragrans. ELECTRON J BIOTECHN 2018. [DOI: 10.1016/j.ejbt.2018.08.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Phylogenetic analyses and in-seedling expression of ammonium and nitrate transporters in wheat. Sci Rep 2018; 8:7082. [PMID: 29728590 PMCID: PMC5935732 DOI: 10.1038/s41598-018-25430-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 04/18/2018] [Indexed: 02/03/2023] Open
Abstract
Plants deploy several ammonium transporter (AMT) and nitrate transporter (NRT) genes to acquire NH4+ and NO3− from the soil into the roots and then transport them to other plant organs. Coding sequences of wheat genes obtained from ENSEMBL were aligned to known AMT and NRT sequences of Arabidopsis, barley, maize, rice, and wheat to retrieve homologous genes. Bayesian phylogenetic relationships among these genes showed distinct classification of sequences with significant homology to NRT1, NRT2, and NRT3 (NAR2). Inter-species gene duplication analysis showed that eight AMT and 77 NRT genes were orthologous to the AMT and NRT genes of aforementioned plant species. Expression patterns of these genes were studied via whole transcriptome sequencing of 21-day old seedlings of five spring wheat lines. Eight AMT and 52 NRT genes were differentially expressed between root and shoot; and 131 genes did not express neither in root nor in shoot of 21-day old seedlings. Homeologous genes in the A, B, and D genomes, characterized by high sequence homology, revealed that their counterparts exhibited different expression patterns. This complement and evolutionary relationship of wheat AMT and NRT genes is expected to help in development of wheat germplasm with increased efficiency in nitrogen uptake and usage.
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Suzuki T, Kawai T, Takemura S, Nishiwaki M, Suzuki T, Nakamura K, Ishiguro S, Higashiyama T. Development of the Mitsucal computer system to identify causal mutation with a high-throughput sequencer. PLANT REPRODUCTION 2018; 31:117-128. [PMID: 29497825 DOI: 10.1007/s00497-018-0331-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 02/16/2018] [Indexed: 06/08/2023]
Abstract
Development of Mitsucal. Recent advances in DNA sequencing technology have facilitated whole-genome sequencing of mutants and variants. However, the analyses of large sequence datasets using a computer remain more difficult than operating a sequencer. Forward genetic approach is powerful even in sexual reproduction to identify key genes. Therefore, we developed the Mitsucal computer system for identifying causal genes of mutants, using whole-genome sequence data. Mitsucal includes a user-friendly web interface to configure analysis variables, such as background and crossed strains. Other than configuration, users are only required to upload short reads. All results are presented through a web interface where users can easily obtain a short list of candidate mutations. In the present study, we present three examples of Arabidopsis mutants defective in sexual reproduction in which Mitsucal is used to identify causal mutation. One mutant was screened from seeds of a transgenic line with a reporter gene to elucidate the mechanisms involved in the regulation of seed oil storage. The identified gene codes for a protein may be involved in mRNA splicing. Other two mutants had defects in the surface walls on pollen termed exine. Both causal genes were identified, and mutants were found to be allele of known mutants. These results show that Mitsucal could facilitate identification of causal genes.
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Affiliation(s)
- Takamasa Suzuki
- Division of Biological Sciences, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan.
- Exploratory Research for Advanced Technology (ERATO), Higashiyama Live-Holonics Project, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan.
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501, Japan.
| | - Tsutae Kawai
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501, Japan
| | - Shunsuke Takemura
- Laboratory of Biochemistry, Graduate School of Bio-agricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Marie Nishiwaki
- Laboratory of Biochemistry, Graduate School of Bio-agricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Toshiya Suzuki
- Laboratory of Biochemistry, Graduate School of Bio-agricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Kenzo Nakamura
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501, Japan
| | - Sumie Ishiguro
- Laboratory of Biochemistry, Graduate School of Bio-agricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Tetsuya Higashiyama
- Division of Biological Sciences, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
- Exploratory Research for Advanced Technology (ERATO), Higashiyama Live-Holonics Project, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
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Hou DY, Shi LC, Yang MM, Li J, Zhou S, Zhang HX, Xu HW. De novo transcriptomic analysis of leaf and fruit tissue of Cornus officinalis using Illumina platform. PLoS One 2018; 13:e0192610. [PMID: 29451882 PMCID: PMC5815590 DOI: 10.1371/journal.pone.0192610] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 01/27/2018] [Indexed: 01/06/2023] Open
Abstract
Cornus officinalis is one of the most widely used medicinal plants in China and other East Asian countries to cure diseases such as liver, kidney, cardiovascular diseases and frequent urination for thousands of years. It is a Level 3 protected species, and is one of the 42 national key protected wild species of animals and plants in China. However, the genetics and molecular biology of C. officinalis are poorly understood, which has hindered research on the molecular mechanism of its metabolism and utilization. Hence, enriching its genomic data and information is very important. In recent years, the fast-growing technology of next generation sequencing has provided an effective path to gain genomic information from nonmodel species. This study is the first to explore the leaf and fruit tissue transcriptome of C. officinalis using the Illumina HiSeq 4000 platform. A total of 57,954,134 and 60,971,652 clean reads from leaf and fruit were acquired, respectively (GenBank number SRP115440). The pooled reads from all two libraries were assembled into 56,392 unigenes with an average length 856 bp. Among these, 41,146 unigenes matched with sequences in the NCBI nonredundant protein database. The Gene Ontology database assigned 24,336 unigenes with biological process (83.26%), cellular components (53.58%), and molecular function (83.93%). In addition, 10,808 unigenes were assigned a KOG functional classification by the KOG database. Searching against the KEGG pathway database indicated that 18,435 unigenes were mapped to 371 KEGG pathways. Moreover, the edgeR database identified 4,585 significant differentially expressed genes (DEGs), of which 1,392 were up-regulated and 3,193 were down-regulated in fruit tissue compared with leaf tissue. Finally, we explored 581 transcription factors with 50 transcription factor gene families. Most DEGs and transcription factors were related to terpene biosynthesis and secondary metabolic regulation. This study not only represented the first de novo transcriptomic analysis of C. officinalis but also provided fundamental information on its genes and biosynthetic pathway. These findings will help us explore the molecular metabolism mechanism of terpene biosynthesis in C. officinalis.
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Affiliation(s)
- Dian-Yun Hou
- Agricultural College, Henan University of Science and Technology, Luoyang, Henan Province, China
- The Luoyang Engineering Research Center of Breeding and Utilization of Dao-di Herbs, Luoyang, Henan Province, China
- * E-mail:
| | - Lin-Chun Shi
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Meng-Meng Yang
- Agricultural College, Henan University of Science and Technology, Luoyang, Henan Province, China
- The Luoyang Engineering Research Center of Breeding and Utilization of Dao-di Herbs, Luoyang, Henan Province, China
| | - Jiong Li
- Chinese Medicinal Materials Production Technology Service Center, Department of Agriculture of Henan Province, Zhengzhou, Henan Province, China
| | - Shuang Zhou
- Agricultural College, Henan University of Science and Technology, Luoyang, Henan Province, China
- The Luoyang Engineering Research Center of Breeding and Utilization of Dao-di Herbs, Luoyang, Henan Province, China
| | - Hong-Xiao Zhang
- Agricultural College, Henan University of Science and Technology, Luoyang, Henan Province, China
- The Luoyang Engineering Research Center of Breeding and Utilization of Dao-di Herbs, Luoyang, Henan Province, China
| | - Hua-Wei Xu
- Agricultural College, Henan University of Science and Technology, Luoyang, Henan Province, China
- The Luoyang Engineering Research Center of Breeding and Utilization of Dao-di Herbs, Luoyang, Henan Province, China
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Wu J, Zhu J, Wang L, Wang S. Genome-Wide Association Study Identifies NBS-LRR-Encoding Genes Related with Anthracnose and Common Bacterial Blight in the Common Bean. FRONTIERS IN PLANT SCIENCE 2017; 8:1398. [PMID: 28848595 PMCID: PMC5552710 DOI: 10.3389/fpls.2017.01398] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 07/26/2017] [Indexed: 05/03/2023]
Abstract
Nucleotide-binding site and leucine-rich repeat (NBS-LRR) genes represent the largest and most important disease resistance genes in plants. The genome sequence of the common bean (Phaseolus vulgaris L.) provides valuable data for determining the genomic organization of NBS-LRR genes. However, data on the NBS-LRR genes in the common bean are limited. In total, 178 NBS-LRR-type genes and 145 partial genes (with or without a NBS) located on 11 common bean chromosomes were identified from genome sequences database. Furthermore, 30 NBS-LRR genes were classified into Toll/interleukin-1 receptor (TIR)-NBS-LRR (TNL) types, and 148 NBS-LRR genes were classified into coiled-coil (CC)-NBS-LRR (CNL) types. Moreover, the phylogenetic tree supported the division of these PvNBS genes into two obvious groups, TNL types and CNL types. We also built expression profiles of NBS genes in response to anthracnose and common bacterial blight using qRT-PCR. Finally, we detected nine disease resistance loci for anthracnose (ANT) and seven for common bacterial blight (CBB) using the developed NBS-SSR markers. Among these loci, NSSR24, NSSR73, and NSSR265 may be located at new regions for ANT resistance, while NSSR65 and NSSR260 may be located at new regions for CBB resistance. Furthermore, we validated NSSR24, NSSR65, NSSR73, NSSR260, and NSSR265 using a new natural population. Our results provide useful information regarding the function of the NBS-LRR proteins and will accelerate the functional genomics and evolutionary studies of NBS-LRR genes in food legumes. NBS-SSR markers represent a wide-reaching resource for molecular breeding in the common bean and other food legumes. Collectively, our results should be of broad interest to bean scientists and breeders.
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Affiliation(s)
| | | | | | - Shumin Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural SciencesBeijing, China
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The molecular mechanisms of Monascus purpureus M9 responses to blue light based on the transcriptome analysis. Sci Rep 2017; 7:5537. [PMID: 28717254 PMCID: PMC5514072 DOI: 10.1038/s41598-017-05990-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 06/16/2017] [Indexed: 01/14/2023] Open
Abstract
Light is an important environmental factor that regulates various physiological processes of fungi. To thoroughly study the responses of Monascus to blue light, transcriptome sequencing was performed on mRNAs isolated from samples of Monascus purpureus M9 cultured under three conditions: darkness (D); exposure to blue light for 15 min/d (B15); and exposure to blue light for 60 min/d over 8 days (B60). The number of differentially expressed genes between the three pairs of samples-B15 vs D, B60 vs B15, and B60 vs D-was 1167, 1172, and 220, respectively. KEGG analysis showed the genes involved in primary metabolism including carbon and nitrogen metabolism were downregulated by B15 light treatment, whereas B15 upregulated expression of genes involved with aromatic amino acid metabolism, which associated with development, and branched chain amino acid metabolism, and fatty acid degradation, which can produce the biosynthetic precursors of pigments. When exposed to B60 conditions, genes with roles in carbohydrate metabolism and protein synthesis were upregulated as part of a stress response to blue light. Based on this study, we propose a predicted light-stimulated signal transduction pathway in Monascus. Our work is the first comprehensive investigation concerning the mechanism of Monascus responses to blue light.
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Ben Romdhane W, Ben-Saad R, Meynard D, Verdeil JL, Azaza J, Zouari N, Fki L, Guiderdoni E, Al-Doss A, Hassairi A. Ectopic Expression of Aeluropus littoralis Plasma Membrane Protein Gene AlTMP1 Confers Abiotic Stress Tolerance in Transgenic Tobacco by Improving Water Status and Cation Homeostasis. Int J Mol Sci 2017; 18:E692. [PMID: 28338609 PMCID: PMC5412278 DOI: 10.3390/ijms18040692] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 03/12/2017] [Accepted: 03/20/2017] [Indexed: 01/15/2023] Open
Abstract
We report here the isolation and functional analysis of AlTMP1 gene encoding a member of the PMP3 protein family. In Aeluropus littoralis, AlTMP1 is highly induced by abscisic acid (ABA), cold, salt, and osmotic stresses. Transgenic tobacco expressing AlTMP1 exhibited enhanced tolerance to salt, osmotic, H₂O₂, heat and freezing stresses at the seedling stage. Under greenhouse conditions, the transgenic plants showed a higher level of tolerance to drought than to salinity. Noteworthy, AlTMP1 plants yielded two- and five-fold more seeds than non-transgenic plants (NT) under salt and drought stresses, respectively. The leaves of AlTMP1 plants accumulated lower Na⁺ but higher K⁺ and Ca2+ than those of NT plants. Tolerance to osmotic and salt stresses was associated with higher membrane stability, low electrolyte leakage, and improved water status. Finally, accumulation of AlTMP1 in tobacco altered the regulation of some stress-related genes in either a positive (NHX1, CAT1, APX1, and DREB1A) or negative (HKT1 and KT1) manner that could be related to the observed tolerance. These results suggest that AlTMP1 confers stress tolerance in tobacco through maintenance of ion homeostasis, increased membrane integrity, and water status. The observed tolerance may be due to a direct or indirect effect of AlTMP1 on the expression of stress-related genes which could stimulate an adaptive potential not present in NT plants.
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Affiliation(s)
- Walid Ben Romdhane
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, 11451 Riyadh, Saudi Arabia.
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax, University of Sfax, B.P 1177, 3018 Sfax, Tunisia.
- Current Address: Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, 11451 Riyadh, Saudi Arabia..
| | - Rania Ben-Saad
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax, University of Sfax, B.P 1177, 3018 Sfax, Tunisia.
| | - Donaldo Meynard
- CIRAD-UMR AGAP (Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement), Avenue Agropolis, 34398 Montpellier CEDEX 5, France.
| | - Jean-Luc Verdeil
- CIRAD-UMR AGAP (Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement), Avenue Agropolis, 34398 Montpellier CEDEX 5, France.
| | - Jalel Azaza
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax, University of Sfax, B.P 1177, 3018 Sfax, Tunisia.
| | - Nabil Zouari
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax, University of Sfax, B.P 1177, 3018 Sfax, Tunisia.
| | - Lotfi Fki
- Laboratory of Plant Biotechnology Applied to Crop Improvement, Faculty of Sciences of Sfax, University of Sfax, B.P 802, 3038 Sfax, Tunisia.
| | - Emmanuel Guiderdoni
- CIRAD-UMR AGAP (Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement), Avenue Agropolis, 34398 Montpellier CEDEX 5, France.
| | - Abdullah Al-Doss
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, 11451 Riyadh, Saudi Arabia.
| | - Afif Hassairi
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, 11451 Riyadh, Saudi Arabia.
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax, University of Sfax, B.P 1177, 3018 Sfax, Tunisia.
- Current Address: Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, 11451 Riyadh, Saudi Arabia..
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Niu YF, Ye C, He J, Han F, Guo LB, Zheng HF, Chen GB. Reproduction and In-Depth Evaluation of Genome-Wide Association Studies and Genome-Wide Meta-analyses Using Summary Statistics. G3 (BETHESDA, MD.) 2017; 7:943-952. [PMID: 28122950 PMCID: PMC5345724 DOI: 10.1534/g3.116.038877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 01/16/2017] [Indexed: 11/21/2022]
Abstract
In line with open-source genetics, we report a novel linear regression technique for genome-wide association studies (GWAS), called Open GWAS algoriTHm (OATH). When individual-level data are not available, OATH can not only completely reproduce reported results from an experimental model, but also recover underreported results from other alternative models with a different combination of nuisance parameters using naïve summary statistics (NSS). OATH can also reliably evaluate all reported results in-depth (e.g., p-value variance analysis), as demonstrated for 42 Arabidopsis phenotypes under three magnesium (Mg) conditions. In addition, OATH can be used for consortium-driven genome-wide association meta-analyses (GWAMA), and can greatly improve the flexibility of GWAMA. A prototype of OATH is available in the Genetic Analysis Repository (https://github.com/gc5k/GEAR).
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Affiliation(s)
- Yao-Fang Niu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 Zhejiang, China
| | - Chengyin Ye
- Department of Health Management, College of Medicine, Hangzhou Normal University, Hangzhou, 310021 Zhejiang, China
| | - Ji He
- Department of Neurology, Peking University Third Hospital, Beijing 100191, China
| | - Fang Han
- Department of Pulmonary and Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China
| | - Long-Biao Guo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 Zhejiang, China
| | - Hou-Feng Zheng
- Institute of Aging Research, College of Medicine, Hangzhou Normal University, Hangzhou, 310021 Zhejiang, China
- The Affiliated Hospital of Hangzhou Normal University, Hangzhou, 310015 Zhejiang, China
| | - Guo-Bo Chen
- Evergreen Landscape and Architecture Studio, Hangzhou, 310026 Zhejiang, China
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24
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Kawaharada Y, James EK, Kelly S, Sandal N, Stougaard J. The Ethylene Responsive Factor Required for Nodulation 1 (ERN1) Transcription Factor Is Required for Infection-Thread Formation in Lotus japonicus. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:194-204. [PMID: 28068194 DOI: 10.1094/mpmi-11-16-0237-r] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Several hundred genes are transcriptionally regulated during infection-thread formation and development of nitrogen-fixing root nodules. We have characterized a set of Lotus japonicus mutants impaired in root-nodule formation and found that the causative gene, Ern1, encodes a protein with a characteristic APETALA2/Ethylene Responsive Factor (AP2/ERF) transcription-factor domain. Phenotypic characterization of four ern1 alleles shows that infection pockets are formed but root-hair infection threads are absent. Formation of root-nodule primordia is delayed and no normal transcellular infection threads are found in the infected nodules. Corroborating the role of ERN1 (ERF Required for Nodulation1) in nodule organogenesis, spontaneous nodulation induced by an autoactive CCaMK and cytokinin-induced nodule primordia were not observed in ern1 mutants. Expression of Ern1 is induced in the susceptible zone by Nod factor treatment or rhizobial inoculation. At the cellular level, the pErn1:GUS reporter is highly expressed in root epidermal cells of the susceptible zone and in the cortical cells that form nodule primordia. The genetic regulation of this cellular expression pattern was further investigated in symbiotic mutants. Nod factor induction of Ern1 in epidermal cells was found to depend on Nfr1, Cyclops, and Nsp2 but was independent of Nin and Nf-ya1. These results suggest that ERN1 functions as a transcriptional regulator involved in the formation of infection threads and development of nodule primordia and may coordinate these two processes.
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Affiliation(s)
- Yasuyuki Kawaharada
- 1 Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C, Denmark; and
| | - Euan K James
- 2 The James Hutton Institute, Invergowrie, Dundee DD2 5DA, U.K
| | - Simon Kelly
- 1 Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C, Denmark; and
| | - Niels Sandal
- 1 Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C, Denmark; and
| | - Jens Stougaard
- 1 Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C, Denmark; and
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25
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Chen M, Wu J, Wang L, Mantri N, Zhang X, Zhu Z, Wang S. Mapping and Genetic Structure Analysis of the Anthracnose Resistance Locus Co-1HY in the Common Bean (Phaseolus vulgaris L.). PLoS One 2017; 12:e0169954. [PMID: 28076395 PMCID: PMC5226810 DOI: 10.1371/journal.pone.0169954] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 12/27/2016] [Indexed: 11/20/2022] Open
Abstract
Anthracnose is a destructive disease of the common bean (Phaseolus vulgaris L.). The Andean cultivar Hongyundou has been demonstrated to possess strong resistance to anthracnose race 81. To study the genetics of this resistance, the Hongyundou cultivar was crossed with a susceptible genotype Jingdou. Segregation of resistance for race 81 was assessed in the F2 population and F2:3 lines under controlled conditions. Results indicate that Hongyundou carries a single dominant gene for anthracnose resistance. An allele test by crossing Hongyundou with another resistant cultivar revealed that the resistance gene is in the Co-1 locus (therefore named Co-1HY). The physical distance between this locus and the two flanking markers was 46 kb, and this region included four candidate genes, namely, Phvul.001G243500, Phvul.001G243600, Phvul.001G243700 and Phvul.001G243800. These candidate genes encoded serine/threonine-protein kinases. Expression analysis of the four candidate genes in the resistant and susceptible cultivars under control condition and inoculated treatment revealed that all the four candidate genes are expressed at significantly higher levels in the resistant genotype than in susceptible genotype. Phvul.001G243600 and Phvul.001G243700 are expressed nearly 15-fold and 90-fold higher in the resistant genotype than in the susceptible parent before inoculation, respectively. Four candidate genes will provide useful information for further research into the resistance mechanism of anthracnose in common bean. The closely linked flanking markers identified here may be useful for transferring the resistance allele Co-1HY from Hongyundou to elite anthracnose susceptible common bean lines.
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Affiliation(s)
- Mingli Chen
- Key Laboratory of Crop Germplasm Resources and Utilization, Ministry of Agriculture; The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, the Chinese Academy of Agricultural Sciences, Beijing, China
- Tobacco Research Institute, Chinese Academy of Agricultural Science, Qingdao, Shandong, China
| | - Jing Wu
- Key Laboratory of Crop Germplasm Resources and Utilization, Ministry of Agriculture; The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, the Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lanfen Wang
- Key Laboratory of Crop Germplasm Resources and Utilization, Ministry of Agriculture; The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, the Chinese Academy of Agricultural Sciences, Beijing, China
| | - Nitin Mantri
- RMIT University, School of Science, Melbourne, Victoria, Australia
| | - Xiaoyan Zhang
- Qingdao Academy of Agricultural Sciences, Shandong, China
| | - Zhendong Zhu
- Key Laboratory of Crop Germplasm Resources and Utilization, Ministry of Agriculture; The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, the Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shumin Wang
- Key Laboratory of Crop Germplasm Resources and Utilization, Ministry of Agriculture; The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, the Chinese Academy of Agricultural Sciences, Beijing, China
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26
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Zarafeta D, Moschidi D, Ladoukakis E, Gavrilov S, Chrysina ED, Chatziioannou A, Kublanov I, Skretas G, Kolisis FN. Metagenomic mining for thermostable esterolytic enzymes uncovers a new family of bacterial esterases. Sci Rep 2016; 6:38886. [PMID: 27991516 PMCID: PMC5171882 DOI: 10.1038/srep38886] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 11/14/2016] [Indexed: 11/09/2022] Open
Abstract
Biocatalysts exerting activity against ester bonds have a broad range of applications in modern biotechnology. Here, we have identified a new esterolytic enzyme by screening a metagenomic sample collected from a hot spring in Kamchatka, Russia. Biochemical characterization of the new esterase, termed EstDZ2, revealed that it is highly active against medium chain fatty acid esters at temperatures between 25 and 60 °C and at pH values 7-8. The new enzyme is moderately thermostable with a half-life of more than six hours at 60 °C, but exhibits exquisite stability against high concentrations of organic solvents. Phylogenetic analysis indicated that EstDZ2 is likely an Acetothermia enzyme that belongs to a new family of bacterial esterases, for which we propose the index XV. One distinctive feature of this new family, is the presence of a conserved GHSAG catalytic motif. Multiple sequence alignment, coupled with computational modelling of the three-dimensional structure of EstDZ2, revealed that the enzyme lacks the largest part of the "cap" domain, whose extended structure is characteristic for the closely related Family IV esterases. Thus, EstDZ2 appears to be distinct from known related esterolytic enzymes, both in terms of sequence characteristics, as well as in terms of three-dimensional structure.
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Affiliation(s)
- Dimitra Zarafeta
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Danai Moschidi
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Efthymios Ladoukakis
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Sergey Gavrilov
- Winogradsky Institute of Microbiology, Research Center for Biotechnology Russian Academy of Sciences, Moscow, Russian Federation
| | - Evangelia D. Chrysina
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Aristotelis Chatziioannou
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Ilya Kublanov
- Winogradsky Institute of Microbiology, Research Center for Biotechnology Russian Academy of Sciences, Moscow, Russian Federation
| | - Georgios Skretas
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Fragiskos N. Kolisis
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
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27
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Behringer MG, Hall DW. Selection on Position of Nonsense Codons in Introns. Genetics 2016; 204:1239-1248. [PMID: 27630196 PMCID: PMC5105854 DOI: 10.1534/genetics.116.189894] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 09/09/2016] [Indexed: 02/04/2023] Open
Abstract
Introns occasionally remain in mature messenger RNAs (mRNAs) due to splicing errors and the translated, aberrant proteins that result represent a metabolic cost and may have other deleterious consequences. The nonsense-mediated decay (NMD) pathway degrades aberrant mRNAs, which it recognizes by the presence of an in-frame premature termination codon (PTC). We investigated whether selection has shaped the location of PTCs in introns to reduce waste and facilitate NMD. We found across seven model organisms, that in both first and last introns, PTCs occur earlier in introns than expected by chance, suggesting that selection favors earlier position. This pattern is more pronounced in species with larger effective population sizes. The pattern does not hold for last introns in the two mammal species, however, perhaps because in these species NMD is not initiated from 3'-terminal introns. We conclude that there is compelling evidence that the location of PTCs is shaped by selection for reduced waste and efficient degradation of aberrant mRNAs.
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Affiliation(s)
- Megan G Behringer
- Department of Genetics, University of Georgia, Athens, Georgia 30602
| | - David W Hall
- Department of Genetics, University of Georgia, Athens, Georgia 30602
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28
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Su J, Pang C, Wei H, Li L, Liang B, Wang C, Song M, Wang H, Zhao S, Jia X, Mao G, Huang L, Geng D, Wang C, Fan S, Yu S. Identification of favorable SNP alleles and candidate genes for traits related to early maturity via GWAS in upland cotton. BMC Genomics 2016; 17:687. [PMID: 27576450 PMCID: PMC5006539 DOI: 10.1186/s12864-016-2875-z] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 07/05/2016] [Indexed: 11/17/2022] Open
Abstract
Background Early maturity is one of the most important and complex agronomic traits in upland cotton (Gossypium hirsutum L). To dissect the genetic architecture of this agronomically important trait, a population consisting of 355 upland cotton germplasm accessions was genotyped using the specific-locus amplified fragment sequencing (SLAF-seq) approach, of which a subset of 185 lines representative of the diversity among the accessions was phenotypically characterized for six early maturity traits in four environments. A genome-wide association study (GWAS) was conducted using the generalized linear model (GLM) and mixed linear model (MLM). Results A total of 81,675 SNPs in 355 upland cotton accessions were discovered using SLAF-seq and were subsequently used in GWAS. Thirteen significant associations between eight SNP loci and five early maturity traits were successfully identified using the GLM and MLM; two of the 13 associations were common between the models. By computing phenotypic effect values for the associations detected at each locus, 11 highly favorable SNP alleles were identified for five early maturity traits. Moreover, dosage pyramiding effects of the highly favorable SNP alleles and significant linear correlations between the numbers of highly favorable alleles and the phenotypic values of the target traits were identified. Most importantly, a major locus (rs13562854) on chromosome Dt3 and a potential candidate gene (CotAD_01947) for early maturity were detected. Conclusions This study identified highly favorable SNP alleles and candidate genes associated with early maturity traits in upland cotton. The results demonstrate that GWAS is a powerful tool for dissecting complex traits and identifying candidate genes. The highly favorable SNP alleles and candidate genes for early maturity traits identified in this study should be show high potential for improvement of early maturity in future cotton breeding programs. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2875-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Junji Su
- College of Agronomy, Northwest A&F University, Yangling, China.,State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.,Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, Xinjiang, China
| | - Chaoyou Pang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Libei Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Bing Liang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Caixiang Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Meizhen Song
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Hantao Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Shuqi Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiaoyun Jia
- College of Agronomy, Northwest A&F University, Yangling, China.,State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Guangzhi Mao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Long Huang
- Bioinformatics Division, Biomarker Technologies Corporation, Beijing, China
| | - Dandan Geng
- Bioinformatics Division, Biomarker Technologies Corporation, Beijing, China
| | - Chengshe Wang
- College of Agronomy, Northwest A&F University, Yangling, China.
| | - Shuli Fan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
| | - Shuxun Yu
- College of Agronomy, Northwest A&F University, Yangling, China. .,State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
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29
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Bashir Z, Shafique S, Ahmad A, Shafique S, Yasin NA, Ashraf Y, Ibrahim A, Akram W, Noreen S. Tomato Plant Proteins Actively Responding to Fungal Applications and Their Role in Cell Physiology. Front Physiol 2016; 7:257. [PMID: 27445848 PMCID: PMC4927627 DOI: 10.3389/fphys.2016.00257] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 06/11/2016] [Indexed: 11/13/2022] Open
Abstract
The pattern of protein induction in tomato plants has been investigated after the applications of pathogenic and non-pathogenic fungal species. Moreover, particular roles of the most active protein against biological applications were also determined using chromatographic techniques. Alternaria alternata and Penicillium oxalicum were applied as a pathogenic and non-pathogenic fungal species, respectively. Protein profile analysis revealed that a five protein species (i.e., protein 1, 6, 10, 12, and 13) possessed completely coupled interaction with non-pathogenic inducer application (P. oxalicum). However, three protein species (i.e., 10, 12, and 14) recorded a strong positive interaction with both fungal species. Protein 14 exhibited the maximum interaction with fungal applications, and its role in plant metabolism was studied after its identification as protein Q9M1W6. It was determined that protein Q1M1W6 was involved in guaiacyl lignin biosynthesis, and its inhibition increased the coumarin contents in tomato plants. Moreover, it was also observed that the protein Q9M1W6 takes significant part in the biosynthesis of jasmonic acid and Indole acetic acid contents, which are defense and growth factors of tomato plants. The study will help investigators to design fundamental rules of plant proteins affecting cell physiology under the influence of external fungal applications.
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Affiliation(s)
- Zoobia Bashir
- Department of Physics, University of the PunjabLahore, Pakistan
| | - Sobiya Shafique
- Institute of Agricultural Sciences, University of the PunjabLahore, Pakistan
| | - Aqeel Ahmad
- Institute of Agricultural Sciences, University of the PunjabLahore, Pakistan
- Institute for Medicinal Plants, College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Shazia Shafique
- Institute of Agricultural Sciences, University of the PunjabLahore, Pakistan
| | - Nasim A. Yasin
- Institute of Agricultural Sciences, University of the PunjabLahore, Pakistan
| | - Yaseen Ashraf
- Institute of Agricultural Sciences, University of the PunjabLahore, Pakistan
| | - Asma Ibrahim
- Institute of Agricultural Sciences, University of the PunjabLahore, Pakistan
| | - Waheed Akram
- Institute of Agricultural Sciences, University of the PunjabLahore, Pakistan
- Institute for Medicinal Plants, College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
- Institute of Molecular Biology and Biotechnology, University of LahoreLahore, Pakistan
| | - Sibgha Noreen
- Institute of Pure and Applied Biology, Bahauddin Zakariya UniversityMultan, Pakistan
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30
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Aflitos SA, Severing E, Sanchez-Perez G, Peters S, de Jong H, de Ridder D. Cnidaria: fast, reference-free clustering of raw and assembled genome and transcriptome NGS data. BMC Bioinformatics 2015; 16:352. [PMID: 26525298 PMCID: PMC4630969 DOI: 10.1186/s12859-015-0806-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Accepted: 10/29/2015] [Indexed: 12/05/2022] Open
Abstract
Background Identification of biological specimens is a requirement for a range of applications. Reference-free methods analyse unprocessed sequencing data without relying on prior knowledge, but generally do not scale to arbitrarily large genomes and arbitrarily large phylogenetic distances. Results We present Cnidaria, a practical tool for clustering genomic and transcriptomic data with no limitation on genome size or phylogenetic distances. We successfully simultaneously clustered 169 genomic and transcriptomic datasets from 4 kingdoms, achieving 100 % identification accuracy at supra-species level and 78 % accuracy at the species level. Conclusion CNIDARIA allows for fast, resource-efficient comparison and identification of both raw and assembled genome and transcriptome data. This can help answer both fundamental (e.g. in phylogeny, ecological diversity analysis) and practical questions (e.g. sequencing quality control, primer design). Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0806-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Saulo Alves Aflitos
- Applied Bioinformatics, Plant Research International, Wageningen, The Netherlands. .,Bioinformatics Group, Department of Plant Sciences, Wageningen University, Wageningen, The Netherlands.
| | - Edouard Severing
- Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands.
| | - Gabino Sanchez-Perez
- Applied Bioinformatics, Plant Research International, Wageningen, The Netherlands. .,Bioinformatics Group, Department of Plant Sciences, Wageningen University, Wageningen, The Netherlands.
| | - Sander Peters
- Applied Bioinformatics, Plant Research International, Wageningen, The Netherlands.
| | - Hans de Jong
- Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands.
| | - Dick de Ridder
- Bioinformatics Group, Department of Plant Sciences, Wageningen University, Wageningen, The Netherlands.
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31
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Tong Y, Su P, Zhao Y, Zhang M, Wang X, Liu Y, Zhang X, Gao W, Huang L. Molecular Cloning and Characterization of DXS and DXR Genes in the Terpenoid Biosynthetic Pathway of Tripterygium wilfordii. Int J Mol Sci 2015; 16:25516-35. [PMID: 26512659 PMCID: PMC4632813 DOI: 10.3390/ijms161025516] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 10/08/2015] [Accepted: 10/13/2015] [Indexed: 11/18/2022] Open
Abstract
1-Deoxy-d-xylulose-5-phosphate synthase (DXS) and 1-deoxy-d-xylulose-5-phosphate reductoisomerase (DXR) genes are the key enzyme genes of terpenoid biosynthesis but still unknown in Tripterygium wilfordii Hook. f. Here, three full-length cDNA encoding DXS1, DXS2 and DXR were cloned from suspension cells of T. wilfordii with ORF sizes of 2154 bp (TwDXS1, GenBank accession no.KM879187), 2148 bp (TwDXS2, GenBank accession no.KM879186), 1410 bp (TwDXR, GenBank accession no.KM879185). And, the TwDXS1, TwDXS2 and TwDXR were characterized by color complementation in lycopene accumulating strains of Escherichia coli, which indicated that they encoded functional proteins and promoted lycopene pathway flux. TwDXS1 and TwDXS2 are constitutively expressed in the roots, stems and leaves and the expression level showed an order of roots > stems > leaves. After the suspension cells were induced by methyl jasmonate, the mRNA expression level of TwDXS1, TwDXS2, and TwDXR increased, and triptophenolide was rapidly accumulated to 149.52 µg·g−1, a 5.88-fold increase compared with the control. So the TwDXS1, TwDXS2, and TwDXR could be important genes involved in terpenoid biosynthesis in Tripterygium wilfordii Hook. f.
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Affiliation(s)
- Yuru Tong
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China.
| | - Ping Su
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China.
| | - Yujun Zhao
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China.
| | - Meng Zhang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China.
| | - Xiujuan Wang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China.
| | - Yujia Liu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China.
| | - Xianan Zhang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China.
| | - Wei Gao
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China.
| | - Luqi Huang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
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32
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Sekhwal MK, Li P, Lam I, Wang X, Cloutier S, You FM. Disease Resistance Gene Analogs (RGAs) in Plants. Int J Mol Sci 2015; 16:19248-90. [PMID: 26287177 PMCID: PMC4581296 DOI: 10.3390/ijms160819248] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 08/01/2015] [Accepted: 08/06/2015] [Indexed: 12/12/2022] Open
Abstract
Plants have developed effective mechanisms to recognize and respond to infections caused by pathogens. Plant resistance gene analogs (RGAs), as resistance (R) gene candidates, have conserved domains and motifs that play specific roles in pathogens' resistance. Well-known RGAs are nucleotide binding site leucine rich repeats, receptor like kinases, and receptor like proteins. Others include pentatricopeptide repeats and apoplastic peroxidases. RGAs can be detected using bioinformatics tools based on their conserved structural features. Thousands of RGAs have been identified from sequenced plant genomes. High-density genome-wide RGA genetic maps are useful for designing diagnostic markers and identifying quantitative trait loci (QTL) or markers associated with plant disease resistance. This review focuses on recent advances in structures and mechanisms of RGAs, and their identification from sequenced genomes using bioinformatics tools. Applications in enhancing fine mapping and cloning of plant disease resistance genes are also discussed.
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Affiliation(s)
- Manoj Kumar Sekhwal
- Cereal Research Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada.
| | - Pingchuan Li
- Cereal Research Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada.
| | - Irene Lam
- Cereal Research Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada.
| | - Xiue Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University, Nanjing 210095, China.
| | - Sylvie Cloutier
- Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada.
| | - Frank M You
- Cereal Research Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada.
- Plant Science Department, University of Manitoba, Winnipeg, MB R3T 2N6, Canada.
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33
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Cao H. Genome-Wide Analysis of Oleosin Gene Family in 22 Tree Species: An Accelerator for Metabolic Engineering of BioFuel Crops and Agrigenomics Industrial Applications? OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2015; 19:521-41. [PMID: 26258573 DOI: 10.1089/omi.2015.0073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Trees contribute to enormous plant oil reserves because many trees contain 50%-80% of oil (triacylglycerols, TAGs) in the fruits and kernels. TAGs accumulate in subcellular structures called oil bodies/droplets, in which TAGs are covered by low-molecular-mass hydrophobic proteins called oleosins (OLEs). The OLEs/TAGs ratio determines the size and shape of intracellular oil bodies. There is a lack of comprehensive sequence analysis and structural information of OLEs among diverse trees. The objectives of this study were to identify OLEs from 22 tree species (e.g., tung tree, tea-oil tree, castor bean), perform genome-wide analysis of OLEs, classify OLEs, identify conserved sequence motifs and amino acid residues, and predict secondary and three-dimensional structures in tree OLEs and OLE subfamilies. Data mining identified 65 OLEs with perfect conservation of the "proline knot" motif (PX5SPX3P) from 19 trees. These OLEs contained >40% hydrophobic amino acid residues. They displayed similar properties and amino acid composition. Genome-wide phylogenetic analysis and multiple sequence alignment demonstrated that these proteins could be classified into five OLE subfamilies. There were distinct patterns of sequence conservation among the OLE subfamilies and within individual tree species. Computational modeling indicated that OLEs were composed of at least three α-helixes connected with short coils without any β-strand and that they exhibited distinct 3D structures and ligand binding sites. These analyses provide fundamental information in the similarity and specificity of diverse OLE isoforms within the same subfamily and among the different species, which should facilitate studying the structure-function relationship and identify critical amino acid residues in OLEs for metabolic engineering of tree TAGs.
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Affiliation(s)
- Heping Cao
- U.S. Department of Agriculture, Agricultural Research Service, Southern Regional Research Center , New Orleans, Louisiana
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Chromosomal organizations of major repeat families on potato (Solanum tuberosum) and further exploring in its sequenced genome. Mol Genet Genomics 2014; 289:1307-19. [PMID: 25106953 DOI: 10.1007/s00438-014-0891-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Accepted: 07/18/2014] [Indexed: 10/24/2022]
Abstract
One of the most powerful technologies in unraveling the organization of a eukaryotic plant genome is high-resolution Fluorescent in situ hybridization of repeats and single copy DNA sequences on pachytene chromosomes. This technology allows the integration of physical mapping information with chromosomal positions, including centromeres, telomeres, nucleolar-organizing region, and euchromatin and heterochromatin. In this report, we established chromosomal positions of different repeat fractions of the potato genomic DNA (Cot100, Cot500 and Cot1000) on the chromosomes. We also analysed various repeat elements that are unique to potato including the moderately repetitive P5 and REP2 elements, where the REP2 is part of a larger Gypsy-type LTR retrotransposon and cover most chromosome regions, with some brighter fluorescing spots in the heterochromatin. The most abundant tandem repeat is the potato genomic repeat 1 that covers subtelomeric regions of most chromosome arms. Extensive multiple alignments of these repetitive sequences in the assembled RH89-039-16 potato BACs and the draft assembly of the DM1-3 516 R44 genome shed light on the conservation of these repeats within the potato genome. The consensus sequences thus obtained revealed the native complete transposable elements from which they were derived.
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Park JI, Ahmed NU, Jung HJ, Arasan SKT, Chung MY, Cho YG, Watanabe M, Nou IS. Identification and characterization of LIM gene family in Brassica rapa. BMC Genomics 2014; 15:641. [PMID: 25086651 PMCID: PMC4246497 DOI: 10.1186/1471-2164-15-641] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 07/24/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND LIM (Lin-11, Isl-1 and Mec-3 domains) genes have been reported to trigger the formation of actin bundles, a major higher-order cytoskeletal assembly, in higher plants; however, the stress resistance related functions of these genes are still not well known. In this study, we collected 22 LIM genes designated as Brassica rapa LIM (BrLIM) from the Brassica database, analyzed the sequences, compared them with LIM genes of other plants and analyzed their expression after applying biotic and abiotic stresses in Chinese cabbage. RESULTS Upon sequence analysis these genes were confirmed as LIM genes and found to have a high degree of homology with LIM genes of other species. These genes showed distinct clusters when compared to other recognized LIM proteins upon phylogenetic analysis. Additionally, organ specific expression of these genes was observed in Chinese cabbage plants, with BrPLIM2a, b, c, BrDAR1, BrPLIM2e, f and g only being expressed in flower buds. Furthermore, the expression of these genes (except for BrDAR1 and BrPLIM2e) was high in the early flowering stages. The remaining genes were expressed in almost all organs tested. All BrDAR genes showed higher expression in flower buds compared to other organs. These organ specific expressions were clearly correlated with the phylogenetic grouping. In addition, BrWLIM2c and BrDAR4 responded to Fusarium oxysporum f. sp. conglutinans infection, while commonly two BrDARs and eight BrLIMs responded to cold, ABA and pH (pH5, pH7 and pH9) stress treatments in Chinese cabbage plants. CONCLUSION Taken together, the results of this study indicate that BrLIM and BrDAR genes may be involved in resistance against biotic and abiotic stresses in Brassica.
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Affiliation(s)
| | | | | | | | | | | | | | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, 255 Jungangno, Suncheon, Jeonnam 540-950, Republic of Korea.
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Kordyukova MY, Polzikov MA, Shishova KV, Zatsepina OV. Analysis of protein partners of the human nucleolar protein SURF6 in HeLa cells by a GST pull-down assay. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2014. [DOI: 10.1134/s1068162014040062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Qu G, Fetterer R, Leng L, Du X, Zarlenga D, Shen Z, Han W, Bucala R, Tuo W. Ostertagia ostertagi macrophage migration inhibitory factor is present in all developmental stages and may cross-regulate host functions through interaction with the host receptor. Int J Parasitol 2014; 44:355-67. [PMID: 24583184 DOI: 10.1016/j.ijpara.2014.01.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 12/31/2013] [Accepted: 01/06/2014] [Indexed: 01/04/2023]
Abstract
Macrophage migration inhibitory factor (MIF) of Ostertagia ostertagi, an abomasal parasite of cattle, was characterised in the present study. Phylogenetic analysis identified at least three O. ostertagi MIFs (Oos-MIFs), each encoded by a distinct transcript: Oos-MIF-1.1, Oos-MIF-1.2 and Oos-MIF-2. Oos-MIF-2 is only distantly related to Oos-MIF-1s, but has higher sequence similarity with the Caenorhabditis elegans MIF2. Oos-MIF-1.1 and Oos-MIF-1.2 are similar (93%) and thus collectively referred to as Oos-MIF-1 when characterised with immunoassays. Recombinant Oos-MIF-1.1 (rOos-MIF-1.1) is catalytically active as a tautomerase. A mutation (rOos-MIF-1.1P1G) or duplication of Pro1 residue (rOos-MIF-1.1P1+P) resulted in reduced oligomerisation and loss of tautomerase activity. The tautomerase activity of rOos-MIF-1.1 was only partially inhibited by ISO-1 but was abrogated by a rOos-MIF-1.1-specific antibody. Oos-MIF-1 was detected in all developmental stages of O. ostertagi, with higher levels in the adult stage; it was also detected in adult worm excretory/secretory product. Oos-MIF-1 was localised to the hypodermis/muscle, reproductive tract and intestine, but not to the cuticle. rOos-MIF-1.1, but not rOos-MIF-1.1P1G, was able to specifically bind to human CD74, a MIF cell surface receptor, with an affinity comparable with human MIF. Immunostaining indicated that macrophages were able to internalise rOos-MIF-1.1, further supporting receptor-mediated transportation. Herein we also show that rOos-MIF-1.1 inhibited migration of bovine macrophages and restored glucocorticoid-suppressed, lipopolysaccharide-induced TNF-α and IL-8 in human and/or bovine macrophages. Given its dual role in self-regulation and molecular mimicry, this secreted parasite protein warrants investigation as a vaccine candidate against O. ostertagi infections in cattle.
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Affiliation(s)
- Guanggang Qu
- Animal Parasitic Diseases Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705, USA; Shangdong Binzhou Academy of Animal Science and Veterinary Medicine, Binzhou City, Shandong 256600, China
| | - Raymond Fetterer
- Animal Parasitic Diseases Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Lin Leng
- Department of Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Xin Du
- Department of Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Dante Zarlenga
- Animal Parasitic Diseases Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Zhiqiang Shen
- Shangdong Binzhou Academy of Animal Science and Veterinary Medicine, Binzhou City, Shandong 256600, China
| | - Wenyu Han
- College of Veterinary Medicine and Animal Science, Jilin University, Changchun, China
| | - Richard Bucala
- Department of Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Wenbin Tuo
- Animal Parasitic Diseases Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705, USA.
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Cao H, Zhang L, Tan X, Long H, Shockey JM. Identification, classification and differential expression of oleosin genes in tung tree (Vernicia fordii). PLoS One 2014; 9:e88409. [PMID: 24516650 PMCID: PMC3916434 DOI: 10.1371/journal.pone.0088409] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 01/06/2014] [Indexed: 11/19/2022] Open
Abstract
Triacylglycerols (TAG) are the major molecules of energy storage in eukaryotes. TAG are packed in subcellular structures called oil bodies or lipid droplets. Oleosins (OLE) are the major proteins in plant oil bodies. Multiple isoforms of OLE are present in plants such as tung tree (Vernicia fordii), whose seeds are rich in novel TAG with a wide range of industrial applications. The objectives of this study were to identify OLE genes, classify OLE proteins and analyze OLE gene expression in tung trees. We identified five tung tree OLE genes coding for small hydrophobic proteins. Genome-wide phylogenetic analysis and multiple sequence alignment demonstrated that the five tung OLE genes represented the five OLE subfamilies and all contained the "proline knot" motif (PX5SPX3P) shared among 65 OLE from 19 tree species, including the sequenced genomes of Prunus persica (peach), Populus trichocarpa (poplar), Ricinus communis (castor bean), Theobroma cacao (cacao) and Vitis vinifera (grapevine). Tung OLE1, OLE2 and OLE3 belong to the S type and OLE4 and OLE5 belong to the SM type of Arabidopsis OLE. TaqMan and SYBR Green qPCR methods were used to study the differential expression of OLE genes in tung tree tissues. Expression results demonstrated that 1) All five OLE genes were expressed in developing tung seeds, leaves and flowers; 2) OLE mRNA levels were much higher in seeds than leaves or flowers; 3) OLE1, OLE2 and OLE3 genes were expressed in tung seeds at much higher levels than OLE4 and OLE5 genes; 4) OLE mRNA levels rapidly increased during seed development; and 5) OLE gene expression was well-coordinated with tung oil accumulation in the seeds. These results suggest that tung OLE genes 1-3 probably play major roles in tung oil accumulation and/or oil body development. Therefore, they might be preferred targets for tung oil engineering in transgenic plants.
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Affiliation(s)
- Heping Cao
- U.S. Department of Agriculture, Agricultural Research Service, Southern Regional Research Center, Commodity Utilization Research Unit, New Orleans, Louisiana, United States of America
- * E-mail:
| | - Lin Zhang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan Province, People's Republic of China
| | - Xiaofeng Tan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan Province, People's Republic of China
| | - Hongxu Long
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan Province, People's Republic of China
| | - Jay M. Shockey
- U.S. Department of Agriculture, Agricultural Research Service, Southern Regional Research Center, Commodity Utilization Research Unit, New Orleans, Louisiana, United States of America
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Grob S, Schmid MW, Luedtke NW, Wicker T, Grossniklaus U. Characterization of chromosomal architecture in Arabidopsis by chromosome conformation capture. Genome Biol 2013; 14:R129. [PMID: 24267747 PMCID: PMC4053840 DOI: 10.1186/gb-2013-14-11-r129] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 11/24/2013] [Indexed: 12/22/2022] Open
Abstract
Background The packaging of long chromatin fibers in the nucleus poses a major challenge, as it must fulfill both physical and functional requirements. Until recently, insights into the chromosomal architecture of plants were mainly provided by cytogenetic studies. Complementary to these analyses, chromosome conformation capture technologies promise to refine and improve our view on chromosomal architecture and to provide a more generalized description of nuclear organization. Results Employing circular chromosome conformation capture, this study describes chromosomal architecture in Arabidopsis nuclei from a genome-wide perspective. Surprisingly, the linear organization of chromosomes is reflected in the genome-wide interactome. In addition, we study the interplay of the interactome and epigenetic marks and report that the heterochromatic knob on the short arm of chromosome 4 maintains a pericentromere-like interaction profile and interactome despite its euchromatic surrounding. Conclusion Despite the extreme condensation that is necessary to pack the chromosomes into the nucleus, the Arabidopsis genome appears to be packed in a predictive manner, according to the following criteria: heterochromatin and euchromatin represent two distinct interactomes; interactions between chromosomes correlate with the linear position on the chromosome arm; and distal chromosome regions have a higher potential to interact with other chromosomes.
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Benoit M, Layat E, Tourmente S, Probst AV. Heterochromatin dynamics during developmental transitions in Arabidopsis - a focus on ribosomal DNA loci. Gene 2013; 526:39-45. [PMID: 23410919 DOI: 10.1016/j.gene.2013.01.060] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 01/16/2013] [Accepted: 01/23/2013] [Indexed: 01/01/2023]
Abstract
The Arabidopsis chromosomes contain conspicuous heterochromatin domains comprising the repetitive 45S and 5S ribosomal DNA loci as well as centromeric and pericentromeric repeats that organize into chromocenters during interphase. During developmental phase transitions such as seed maturation, germination, seedling growth and flowering that require large-scale reprogramming of gene expression patterns, the organization of repetitive sequences into chromocenters dynamically changes. Here we illustrate recent studies that shed light on the heterochromatin dynamics in cotyledons, the first aerial tissues preformed in the embryo, and in true leaves. We will summarize available data for the 5S rDNA repeat loci, in particular their chromatin organization and expression dynamics during the first days of post-germination development, and discuss how the plant accommodates 5S rRNA transcription during large-scale chromatin reorganization events.
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Affiliation(s)
- Matthias Benoit
- Génétique, Reproduction et Développement, UMR CNRS 6293, Clermont Université, INSERM U1103, 24 Avenue des Landais, BP 80026, 63171 Aubière Cedex, France.
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Yao Y, Dai W. Shugoshins function as a guardian for chromosomal stability in nuclear division. Cell Cycle 2012; 11:2631-42. [PMID: 22732496 PMCID: PMC3850027 DOI: 10.4161/cc.20633] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 05/04/2012] [Indexed: 11/19/2022] Open
Abstract
Accurate chromosome segregation during mitosis and meiosis is regulated and secured by several distinctly different yet intricately connected regulatory mechanisms. As chromosomal instability is a hallmark of a majority of tumors as well as a cause of infertility for germ cells, extensive research in the past has focused on the identification and characterization of molecular components that are crucial for faithful chromosome segregation during cell division. Shugoshins, including Sgo1 and Sgo2, are evolutionarily conserved proteins that function to protect sister chromatid cohesion, thus ensuring chromosomal stability during mitosis and meiosis in eukaryotes. Recent studies reveal that Shugoshins in higher animals play an essential role not only in protecting centromeric cohesion of sister chromatids and assisting bi-orientation attachment at the kinetochores, but also in safeguarding centriole cohesion/engagement during early mitosis. Many molecular components have been identified that play essential roles in modulating/mediating Sgo functions. This review primarily summarizes recent advances on the mechanisms of action of Shugoshins in suppressing chromosomal instability during nuclear division in eukaryotic organisms.
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Affiliation(s)
- Yixin Yao
- Departments of Environmental Medicine and Pharmacology; New York University School of Medicine; Tuxedo, NY USA
| | - Wei Dai
- Departments of Environmental Medicine and Pharmacology; New York University School of Medicine; Tuxedo, NY USA
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Reinders A, Sivitz AB, Ward JM. Evolution of plant sucrose uptake transporters. FRONTIERS IN PLANT SCIENCE 2012; 3:22. [PMID: 22639641 PMCID: PMC3355574 DOI: 10.3389/fpls.2012.00022] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 01/20/2012] [Indexed: 05/18/2023]
Abstract
In angiosperms, sucrose uptake transporters (SUTs) have important functions especially in vascular tissue. Here we explore the evolutionary origins of SUTs by analysis of angiosperm SUTs and homologous transporters in a vascular early land plant, Selaginella moellendorffii, and a non-vascular plant, the bryophyte Physcomitrella patens, the charophyte algae Chlorokybus atmosphyticus, several red algae and fission yeast, Schizosaccharomyces pombe. Plant SUTs cluster into three types by phylogenetic analysis. Previous studies using angiosperms had shown that types I and II are localized to the plasma membrane while type III SUTs are associated with vacuolar membrane. SUT homologs were not found in the chlorophyte algae Chlamydomonas reinhardtii and Volvox carterii. However, the characean algae Chlorokybus atmosphyticus contains a SUT homolog (CaSUT1) and phylogenetic analysis indicated that it is basal to all other streptophyte SUTs analyzed. SUTs are present in both red algae and S. pombe but they are less related to plant SUTs than CaSUT1. Both Selaginella and Physcomitrella encode type II and III SUTs suggesting that both plasma membrane and vacuolar sucrose transporter activities were present in early land plants. It is likely that SUT transporters are important for scavenging sucrose from the environment and intracellular compartments in charophyte and non-vascular plants. Type I SUTs were only found in eudicots and we conclude that they evolved from type III SUTs, possibly through loss of a vacuolar targeting sequence. Eudicots utilize type I SUTs for phloem (vascular tissue) loading while monocots use type II SUTs for phloem loading. We show that HvSUT1 from barley, a type II SUT, reverted the growth defect of the Arabidopsis atsuc2 (type I) mutant. This indicates that type I and II SUTs evolved similar (and interchangeable) phloem loading transporter capabilities independently.
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Affiliation(s)
- Anke Reinders
- Department of Plant Biology, University of MinnesotaSt. Paul, MN, USA
| | - Alicia B. Sivitz
- Department of Biological Sciences, Dartmouth CollegeHanover, NH, USA
| | - John M. Ward
- Department of Plant Biology, University of MinnesotaSt. Paul, MN, USA
- *Correspondence: John M. Ward, Department of Plant Biology, University of Minnesota, 250 Biological Sciences Center, 1445 Gortner Avenue, St. Paul, MN 55108, USA. e-mail:
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Cottage A, Edwards YJ, Elgar G. SAND, a new protein family: from nucleic acid to protein structure and function prediction. Comp Funct Genomics 2010; 2:226-35. [PMID: 18628914 PMCID: PMC2447211 DOI: 10.1002/cfg.93] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2001] [Accepted: 06/21/2001] [Indexed: 11/09/2022] Open
Abstract
As a result of genome, EST and cDNA sequencing projects, there are huge numbers of predicted and/or partially characterised protein sequences compared with a relatively small number of proteins with experimentally determined function and structure. Thus, there is a considerable attention focused on the accurate prediction of gene function and structure from sequence by using bioinformatics. In the course of our analysis of genomic sequence from Fugu rubripes, we identified a novel gene, SAND, with significant sequence identity to hypothetical proteins predicted in Saccharomyces cerevisiae, Schizosaccharomyces pombe, Caenorhabditis elegans, a Drosophila melanogaster gene, and mouse and human cDNAs. Here we identify a further SAND homologue in human and Arabidopsis thaliana by use of standard computational tools. We describe the genomic organisation of SAND in these evolutionarily divergent species and identify sequence homologues from EST database searches confirming the expression of SAND in over 20 different eukaryotes. We confirm the expression of two different SAND paralogues in mammals and determine expression of one SAND in other vertebrates and eukaryotes. Furthermore, we predict structural properties of SAND, and characterise conserved sequence motifs in this protein family.
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Affiliation(s)
- A Cottage
- UK Human Genome mapping Project Resource Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SB, UK
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Nah G, Jeffrey Chen Z. Tandem duplication of the FLC locus and the origin of a new gene in Arabidopsis related species and their functional implications in allopolyploids. THE NEW PHYTOLOGIST 2010; 186:228-38. [PMID: 20100201 DOI: 10.1111/j.1469-8137.2009.03164.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Flowering time is an important adaptive trait and varies among Arabidopsis thaliana and its related species, including allopolyploids that are formed between A. thaliana and Arabidopsis arenosa. FLOWERING LOCUS C (FLC) inhibits early flowering in A. thaliana. A previous study showed that late-flowering A. arenosa contained two or more FLC alleles that were differentially expressed in Arabidopsis allotetraploids, but the genomic organization and evolution of FLC locus were unknown. Comparative sequence and evolutionary analyses were performed in FLC-containing genomic regions in A. thaliana, A. arenosa and Arabidopsis lyrata, and expression of FLC loci and alleles was examined in Arabidopsis allopolyploids. The FLC locus was tandemly duplicated in A. lyrata and triplicated in A. arenosa, and the tandem duplication event occurred after divergence from A. thaliana. Although FLC duplicates were highly conserved, their upstream sequences rapidly diverged. The third FLC copy in A. arenosa acquired a new splicing site through a point mutation in the intron and generated the new exon followed by an early stop codon, resulting in a novel MADS box gene. Flowering time variation in Arabidopsis allopolyploids is probably related to the expression diversity and/or copy number of multiple FLC loci. Moreover, exonization of intronic sequence is a mechanism for the origin of new genes.
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FIDEL-a retrovirus-like retrotransposon and its distinct evolutionary histories in the A- and B-genome components of cultivated peanut. Chromosome Res 2010; 18:227-46. [PMID: 20127167 PMCID: PMC2844528 DOI: 10.1007/s10577-009-9109-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2009] [Accepted: 12/16/2009] [Indexed: 12/26/2022]
Abstract
In this paper, we describe a Ty3-gypsy retrotransposon from allotetraploid peanut (Arachis hypogaea) and its putative diploid ancestors Arachis duranensis (A-genome) and Arachis ipaënsis (B-genome). The consensus sequence is 11,223 bp. The element, named FIDEL (Fairly long Inter-Dispersed Euchromatic LTR retrotransposon), is more frequent in the A- than in the B-genome, with copy numbers of about 3,000 (±950, A. duranensis), 820 (±480, A. ipaënsis), and 3,900 (±1,500, A. hypogaea) per haploid genome. Phylogenetic analysis of reverse transcriptase sequences showed distinct evolution of FIDEL in the ancestor species. Fluorescent in situ hybridization revealed disperse distribution in euchromatin and absence from centromeres, telomeric regions, and the nucleolar organizer region. Using paired sequences from bacterial artificial chromosomes, we showed that elements appear less likely to insert near conserved ancestral genes than near the fast evolving disease resistance gene homologs. Within the Ty3-gypsy elements, FIDEL is most closely related with the Athila/Calypso group of retrovirus-like retrotransposons. Putative transmembrane domains were identified, supporting the presence of a vestigial envelope gene. The results emphasize the importance of FIDEL in the evolution and divergence of different Arachis genomes and also may serve as an example of the role of retrotransposons in the evolution of legume genomes in general.
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Filichkin SA, Priest HD, Givan SA, Shen R, Bryant DW, Fox SE, Wong WK, Mockler TC. Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome Res 2009; 20:45-58. [PMID: 19858364 DOI: 10.1101/gr.093302.109] [Citation(s) in RCA: 669] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Alternative splicing can enhance transcriptome plasticity and proteome diversity. In plants, alternative splicing can be manifested at different developmental stages, and is frequently associated with specific tissue types or environmental conditions such as abiotic stress. We mapped the Arabidopsis transcriptome at single-base resolution using the Illumina platform for ultrahigh-throughput RNA sequencing (RNA-seq). Deep transcriptome sequencing confirmed a majority of annotated introns and identified thousands of novel alternatively spliced mRNA isoforms. Our analysis suggests that at least approximately 42% of intron-containing genes in Arabidopsis are alternatively spliced; this is significantly higher than previous estimates based on cDNA/expressed sequence tag sequencing. Random validation confirmed that novel splice isoforms empirically predicted by RNA-seq can be detected in vivo. Novel introns detected by RNA-seq were substantially enriched in nonconsensus terminal dinucleotide splice signals. Alternative isoforms with premature termination codons (PTCs) comprised the majority of alternatively spliced transcripts. Using an example of an essential circadian clock gene, we show that intron retention can generate relatively abundant PTC(+) isoforms and that this specific event is highly conserved among diverse plant species. Alternatively spliced PTC(+) isoforms can be potentially targeted for degradation by the nonsense mediated mRNA decay (NMD) surveillance machinery or regulate the level of functional transcripts by the mechanism of regulated unproductive splicing and translation (RUST). We demonstrate that the relative ratios of the PTC(+) and reference isoforms for several key regulatory genes can be considerably shifted under abiotic stress treatments. Taken together, our results suggest that like in animals, NMD and RUST may be widespread in plants and may play important roles in regulating gene expression.
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Affiliation(s)
- Sergei A Filichkin
- Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331, USA
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Wichadakul D, McDermott J, Samudrala R. Prediction and integration of regulatory and protein-protein interactions. Methods Mol Biol 2009; 541:101-43. [PMID: 19381527 DOI: 10.1007/978-1-59745-243-4_6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Knowledge of transcriptional regulatory interactions (TRIs) is essential for exploring functional genomics and systems biology in any organism. While several results from genome-wide analysis of transcriptional regulatory networks are available, they are limited to model organisms such as yeast ( 1 ) and worm ( 2 ). Beyond these networks, experiments on TRIs study only individual genes and proteins of specific interest. In this chapter, we present a method for the integration of various data sets to predict TRIs for 54 organisms in the Bioverse ( 3 ). We describe how to compile and handle various formats and identifiers of data sets from different sources and how to predict TRIs using a homology-based approach, utilizing the compiled data sets. Integrated data sets include experimentally verified TRIs, binding sites of transcription factors, promoter sequences, protein subcellular localization, and protein families. Predicted TRIs expand the networks of gene regulation for a large number of organisms. The integration of experimentally verified and predicted TRIs with other known protein-protein interactions (PPIs) gives insight into specific pathways, network motifs, and the topological dynamics of an integrated network with gene expression under different conditions, essential for exploring functional genomics and systems biology.
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Danilova TV, Birchler JA. Integrated cytogenetic map of mitotic metaphase chromosome 9 of maize: resolution, sensitivity, and banding paint development. Chromosoma 2008; 117:345-56. [PMID: 18317793 DOI: 10.1007/s00412-008-0151-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2007] [Revised: 02/04/2008] [Accepted: 02/05/2008] [Indexed: 11/28/2022]
Abstract
To study the correlation of the sequence positions on the physical DNA finger print contig (FPC) map and cytogenetic maps of pachytene and somatic maize chromosomes, sequences located along the chromosome 9 FPC map approximately every 10 Mb were selected to place on maize chromosomes using fluorescent in situ hybridization (FISH). The probes were produced as pooled polymerase chain reaction products based on sequences of genetic markers or repeat-free portions of mapped bacterial artificial chromosome (BAC) clones. Fifteen probes were visualized on chromosome 9. The cytological positions of most sequences correspond on the pachytene, somatic, and FPC maps except some probes at the pericentromeric regions. Because of unequal condensation of mitotic metaphase chromosomes, being lower at pericentromeric regions and higher in the arms, probe positions are displaced to the distal ends of both arms. The axial resolution of FISH on somatic chromosome 9 varied from 3.3 to 8.2 Mb, which is 12-30 times lower than on pachytene chromosomes. The probe collection can be used as chromosomal landmarks or as a "banding paint" for the physical mapping of sequences including transgenes and BAC clones and for studying chromosomal rearrangements.
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Affiliation(s)
- Tatiana V Danilova
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, MO 65211, USA
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Heterosis for biomass-related traits in Arabidopsis investigated by quantitative trait loci analysis of the triple testcross design with recombinant inbred lines. Genetics 2008; 177:1839-50. [PMID: 18039885 DOI: 10.1534/genetics.107.077628] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Arabidopsis thaliana has emerged as a leading model species in plant genetics and functional genomics including research on the genetic causes of heterosis. We applied a triple testcross (TTC) design and a novel biometrical approach to identify and characterize quantitative trait loci (QTL) for heterosis of five biomass-related traits by (i) estimating the number, genomic positions, and genetic effects of heterotic QTL, (ii) characterizing their mode of gene action, and (iii) testing for presence of epistatic effects by a genomewide scan and marker x marker interactions. In total, 234 recombinant inbred lines (RILs) of Arabidopsis hybrid C24 x Col-0 were crossed to both parental lines and their F1 and analyzed with 110 single-nucleotide polymorphism (SNP) markers. QTL analyses were conducted using linear transformations Z1, Z2, and Z3 calculated from the adjusted entry means of TTC progenies. With Z1, we detected 12 QTL displaying augmented additive effects. With Z2, we mapped six QTL for augmented dominance effects. A one-dimensional genome scan with Z3 revealed two genomic regions with significantly negative dominance x additive epistatic effects. Two-way analyses of variance between marker pairs revealed nine digenic epistatic interactions: six reflecting dominance x dominance effects with variable sign and three reflecting additive x additive effects with positive sign. We conclude that heterosis for biomass-related traits in Arabidopsis has a polygenic basis with overdominance and/or epistasis being presumably the main types of gene action.
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Locational distribution of gene functional classes in Arabidopsis thaliana. BMC Bioinformatics 2007; 8:112. [PMID: 17397552 PMCID: PMC1855069 DOI: 10.1186/1471-2105-8-112] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2006] [Accepted: 03/30/2007] [Indexed: 11/10/2022] Open
Abstract
Background We are interested in understanding the locational distribution of genes and their functions in genomes, as this distribution has both functional and evolutionary significance. Gene locational distribution is known to be affected by various evolutionary processes, with tandem duplication thought to be the main process producing clustering of homologous sequences. Recent research has found clustering of protein structural families in the human genome, even when genes identified as tandem duplicates have been removed from the data. However, this previous research was hindered as they were unable to analyse small sample sizes. This is a challenge for bioinformatics as more specific functional classes have fewer examples and conventional statistical analyses of these small data sets often produces unsatisfactory results. Results We have developed a novel bioinformatics method based on Monte Carlo methods and Greenwood's spacing statistic for the computational analysis of the distribution of individual functional classes of genes (from GO). We used this to make the first comprehensive statistical analysis of the relationship between gene functional class and location on a genome. Analysis of the distribution of all genes except tandem duplicates on the five chromosomes of A. thaliana reveals that the distribution on chromosomes I, II, IV and V is clustered at P = 0.001. Many functional classes are clustered, with the degree of clustering within an individual class generally consistent across all five chromosomes. A novel and surprising result was that the locational distribution of some functional classes were significantly more evenly spaced than would be expected by chance. Conclusion Analysis of the A. thaliana genome reveals evidence of unexplained order in the locational distribution of genes. The same general analysis method can be applied to any genome, and indeed any sequential data involving classes.
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