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Xu R, Ming Y, Li Y, Li S, Zhu W, Wang H, Guo J, Shi Z, Shu S, Xiong C, Cheng X, Wang L, You J, Wan D. Full-Length Transcriptomic Sequencing and Temporal Transcriptome Expression Profiling Analyses Offer Insights into Terpenoid Biosynthesis in Artemisia argyi. Molecules 2022; 27:molecules27185948. [PMID: 36144681 PMCID: PMC9501300 DOI: 10.3390/molecules27185948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 07/31/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
Artemisiae argyi Folium is a traditional herbal medicine used for moxibustion heat therapy in China. The volatile oils in A.argyi leaves are closely related to its medicinal value. Records suggest that the levels of these terpenoids components within the leaves vary as a function of harvest time, with June being the optimal time for A. argyi harvesting, owing to the high levels of active ingredients during this month. However, the molecular mechanisms governing terpenoid biosynthesis and the time-dependent changes in this activity remain unclear. In this study, GC–MS analysis revealed that volatile oil levels varied across four different harvest months (April, May, June, and July) in A. argyi leaves, and the primarily terpenoids components (including both monoterpenes and sesquiterpenes) reached peak levels in early June. Through single-molecule real-time (SMRT) sequencing, corrected by Illumina RNA-sequencing (RNA-Seq), 44 full-length transcripts potentially involved in terpenoid biosynthesis were identified in this study. Differentially expressed genes (DEGs) exhibiting time-dependent expression patterns were divided into 12 coexpression clusters. Integrated chemical and transcriptomic analyses revealed distinct time-specific transcriptomic patterns associated with terpenoid biosynthesis. Subsequent hierarchical clustering and correlation analyses ultimately identified six transcripts that were closely linked to the production of these two types of terpenoid within A. argyi leaves, revealing that the structural diversity of terpenoid is related to the generation of the diverse terpene skeletons by prenyltransferase (TPS) family of enzymes. These findings can guide further studies of the molecular mechanisms underlying the quality of A. argyi leaves, aiding in the selection of optimal timing for harvests of A. argyi.
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Affiliation(s)
- Ran Xu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China
- Correspondence: (R.X.); (J.Y.); (D.W.)
| | - Yue Ming
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China
| | - Yongchang Li
- College of Osteopathic Medicine, Kansas City University of Medicine and Biosciences, Joplin, MO 64804, USA
| | - Shaoting Li
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China
| | - Wenjun Zhu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China
| | - Hongxun Wang
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China
| | - Jie Guo
- Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi 445000, China
| | - Zhaohua Shi
- Key Laboratory of Chinese Medicine Resources and Compound Formula, Ministry of Education, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Shaohua Shu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Chao Xiong
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China
| | - Xiang Cheng
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China
| | - Limei Wang
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China
| | - Jingmao You
- Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi 445000, China
- Correspondence: (R.X.); (J.Y.); (D.W.)
| | - Dingrong Wan
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, China
- Correspondence: (R.X.); (J.Y.); (D.W.)
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Petereit J, Marsh JI, Bayer PE, Danilevicz MF, Thomas WJW, Batley J, Edwards D. Genetic and Genomic Resources for Soybean Breeding Research. PLANTS (BASEL, SWITZERLAND) 2022; 11:1181. [PMID: 35567182 PMCID: PMC9101001 DOI: 10.3390/plants11091181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/21/2022] [Accepted: 04/22/2022] [Indexed: 11/17/2022]
Abstract
Soybean (Glycine max) is a legume species of significant economic and nutritional value. The yield of soybean continues to increase with the breeding of improved varieties, and this is likely to continue with the application of advanced genetic and genomic approaches for breeding. Genome technologies continue to advance rapidly, with an increasing number of high-quality genome assemblies becoming available. With accumulating data from marker arrays and whole-genome resequencing, studying variations between individuals and populations is becoming increasingly accessible. Furthermore, the recent development of soybean pangenomes has highlighted the significant structural variation between individuals, together with knowledge of what has been selected for or lost during domestication and breeding, information that can be applied for the breeding of improved cultivars. Because of this, resources such as genome assemblies, SNP datasets, pangenomes and associated databases are becoming increasingly important for research underlying soybean crop improvement.
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Affiliation(s)
| | - Jacob I. Marsh
- School of Biological Sciences, The University of Western Australia, Perth, WA 6009, Australia; (J.P.); (J.I.M.); (P.E.B.); (M.F.D.); (W.J.W.T.); (J.B.)
| | | | | | | | | | - David Edwards
- School of Biological Sciences, The University of Western Australia, Perth, WA 6009, Australia; (J.P.); (J.I.M.); (P.E.B.); (M.F.D.); (W.J.W.T.); (J.B.)
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Xu H, Guo Y, Qiu L, Ran Y. Progress in Soybean Genetic Transformation Over the Last Decade. FRONTIERS IN PLANT SCIENCE 2022; 13:900318. [PMID: 35755694 PMCID: PMC9231586 DOI: 10.3389/fpls.2022.900318] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 05/11/2022] [Indexed: 05/13/2023]
Abstract
Soybean is one of the important food, feed, and biofuel crops in the world. Soybean genome modification by genetic transformation has been carried out for trait improvement for more than 4 decades. However, compared to other major crops such as rice, soybean is still recalcitrant to genetic transformation, and transgenic soybean production has been hampered by limitations such as low transformation efficiency and genotype specificity, and prolonged and tedious protocols. The primary goal in soybean transformation over the last decade is to achieve high efficiency and genotype flexibility. Soybean transformation has been improved by modifying tissue culture conditions such as selection of explant types, adjustment of culture medium components and choice of selection reagents, as well as better understanding the transformation mechanisms of specific approaches such as Agrobacterium infection. Transgenesis-based breeding of soybean varieties with new traits is now possible by development of improved protocols. In this review, we summarize the developments in soybean genetic transformation to date, especially focusing on the progress made using Agrobacterium-mediated methods and biolistic methods over the past decade. We also discuss current challenges and future directions.
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Affiliation(s)
- Hu Xu
- Tianjin Genovo Biotechnology Co., Ltd., Tianjin, China
| | - Yong Guo
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lijuan Qiu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Lijuan Qiu,
| | - Yidong Ran
- Tianjin Genovo Biotechnology Co., Ltd., Tianjin, China
- Yidong Ran,
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Rosso ML, Shang C, Song Q, Escamilla D, Gillenwater J, Zhang B. Development of Breeder-Friendly KASP Markers for Low Concentration of Kunitz Trypsin Inhibitor in Soybean Seeds. Int J Mol Sci 2021; 22:2675. [PMID: 33800919 PMCID: PMC7961957 DOI: 10.3390/ijms22052675] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 02/18/2021] [Accepted: 03/03/2021] [Indexed: 11/18/2022] Open
Abstract
Trypsin inhibitors (TI), a common anti-nutritional factor in soybean, prevent animals' protein digestibility reducing animal growth performance. No commercial soybean cultivars with low or null concentration of TI are available. The availability of a high throughput genotyping assay will be beneficial to incorporate the low TI trait into elite breeding lines. The aim of this study is to develop and validate a breeder friendly Kompetitive Allele Specific PCR (KASP) assay linked to low Kunitz trypsin inhibitor (KTI) in soybean seeds. A total of 200 F3:5 lines derived from PI 547656 (low KTI) X Glenn (normal KTI) were genotyped using the BARCSoySNP6K_v2 Beadchip. F3:4 and F3:5 lines were grown in Blacksburg and Orange, Virginia in three years, respectively, and were measured for KTI content using a quantitative HPLC method. We identified three SNP markers tightly linked to the major QTL associated to low KTI in the mapping population. Based on these SNPs, we developed and validated the KASP assays in a set of 93 diverse germplasm accessions. The marker Gm08_44814503 has 86% selection efficiency for the accessions with low KTI and could be used in marker assisted breeding to facilitate the incorporation of low KTI content in soybean seeds.
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Affiliation(s)
- M. Luciana Rosso
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA; (M.L.R.); (C.S.)
| | - Chao Shang
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA; (M.L.R.); (C.S.)
| | - Qijian Song
- Beltsville Agricultural Research Center, Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD 20705, USA;
| | - Diana Escamilla
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA;
| | - Jay Gillenwater
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, USA;
| | - Bo Zhang
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA; (M.L.R.); (C.S.)
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Fan YL, Zhang XH, Zhong LJ, Wang XY, Jin LS, Lyu SH. One-step generation of composite soybean plants with transgenic roots by Agrobacterium rhizogenes-mediated transformation. BMC PLANT BIOLOGY 2020; 20:208. [PMID: 32397958 PMCID: PMC7333419 DOI: 10.1186/s12870-020-02421-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 04/29/2020] [Indexed: 05/22/2023]
Abstract
BACKGROUND Agrobacterium rhizogenes-mediated (ARM) transformation is a highly efficient technique for generating composite plants composed of transgenic roots and wild-type shoot, providing a powerful tool for studying root biology. The ARM transformation has been established in many plant species, including soybean. However, traditional transformation of soybean, transformation efficiency is low. Additionally, the hairy roots were induced in a medium, and then the generated composite plants were transplanted into another medium for growth. This two-step operation is not only time-consuming, but aggravates contamination risk in the study of plant-microbe interactions. RESULTS Here, we report a one-step ARM transformation method with higher transformation efficiency for generating composite soybean plants. Both the induction of hairy roots and continuous growth of the composite plants were conducted in a single growth medium. The primary root of a 7-day-old seedling was decapitated with a slanted cut, the residual hypocotyl (maintained 0.7-1 cm apical portion) was inoculated with A. rhizogenes harboring the gene construct of interest. Subsequently, the infected seedling was planted into a pot with wet sterile vermiculite. Almost 100% of the infected seedlings could produce transgenic positive roots 16 days post-inoculation in 7 tested genotypes. Importantly, the transgenic hairy roots in each composite plant are about three times more than those of the traditional ARM transformation, indicating that the one-step method is simpler in operation and higher efficiency in transformation. The reliability of the one-step method was verified by CRISPR/Cas9 system to knockout the soybean Rfg1, which restricts nodulation in Williams 82 (Nod-) by Sinorhizobium fredii USDA193. Furthermore, we applied this method to analyze the function of Arabidopsis YAO promoter in soybean. The activity of YAO promoter was detected in whole roots and stronger in the root tips. We also extended the protocol to tomato. CONCLUSIONS We established a one-step ARM transformation method, which is more convenient in operation and higher efficiency (almost 100%) in transformation for generating composite soybean plants. This method has been validated in promoter functional analysis and rhizobia-legume interactions. We anticipate a broad application of this method to analyze root-related events in tomato and other plant species besides soybean.
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Affiliation(s)
- Ying-lun Fan
- College of Agriculture, Liaocheng University, Liaocheng, 252000 China
| | - Xing-hui Zhang
- College of Agriculture, Liaocheng University, Liaocheng, 252000 China
| | - Li-jing Zhong
- College of Agriculture, Liaocheng University, Liaocheng, 252000 China
| | - Xiu-yuan Wang
- College of Agriculture, Liaocheng University, Liaocheng, 252000 China
| | - Liang-shen Jin
- College of Agriculture, Liaocheng University, Liaocheng, 252000 China
| | - Shan-hua Lyu
- College of Agriculture, Liaocheng University, Liaocheng, 252000 China
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Lin L, Cai W, Du Z, Zhang W, Xu Q, Sun W, Chen M. Establishing a System for Functional Characterization of Full-Length cDNAs of Camellia sinensis. Int J Mol Sci 2019; 20:ijms20235929. [PMID: 31775391 PMCID: PMC6929147 DOI: 10.3390/ijms20235929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 11/15/2019] [Accepted: 11/21/2019] [Indexed: 11/17/2022] Open
Abstract
Tea (Camellia sinensis) is enriched with bioactive secondary metabolites, and is one of the most popular nonalcoholic beverages globally. Two tea reference genomes have been reported; however, the functional analysis of tea genes has lagged, mainly due to tea’s recalcitrance to genetic transformation and the absence of alternative high throughput heterologous expression systems. A full-length cDNA collection with a streamlined cloning system is needed in this economically important woody crop species. RNAs were isolated from nine different vegetative tea tissues, pooled, then used to construct a normalized full-length cDNA library. The titer of unamplified and amplified cDNA library was 6.89 × 106 and 1.8 × 1010 cfu/mL, respectively; the library recombinant rate was 87.2%. Preliminary characterization demonstrated that this collection can complement existing tea reference genomes and facilitate rare gene discovery. In addition, to streamline tea cDNA cloning and functional analysis, a binary vector (pBIG2113SF) was reengineered, seven tea cDNAs isolated from this library were successfully cloned into this vector, then transformed into Arabidopsis. One FL-cDNA, which encodes a putative P1B-type ATPase 5 (CsHMA5), was characterized further as a proof of concept. We demonstrated that overexpression of CsHMA5 in Arabidopsis resulted in copper hyposensitivity. Thus, our data demonstrated that this represents an efficient system for rare gene discovery and functional characterization of tea genes. The integration of a tea FL-cDNA collection with efficient cloning and a heterologous expression system would facilitate functional annotation and characterization of tea genes.
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Affiliation(s)
- Lin Lin
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Horticultural Plant Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.L.); (W.C.); (Z.D.); (Q.X.)
| | - Weiwei Cai
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Horticultural Plant Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.L.); (W.C.); (Z.D.); (Q.X.)
| | - Zhenghua Du
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Horticultural Plant Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.L.); (W.C.); (Z.D.); (Q.X.)
| | - Wenjing Zhang
- Anxi College of Tea Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Quanming Xu
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Horticultural Plant Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.L.); (W.C.); (Z.D.); (Q.X.)
| | - Weijiang Sun
- Anxi College of Tea Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (W.S.); (M.C.); Tel.: +86-13705067139 (W.S.); +86-18860109236 (M.C.)
| | - Mingjie Chen
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Horticultural Plant Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.L.); (W.C.); (Z.D.); (Q.X.)
- Correspondence: (W.S.); (M.C.); Tel.: +86-13705067139 (W.S.); +86-18860109236 (M.C.)
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Wang J, Deng Y, Zhou Y, Liu D, Yu H, Zhou Y, Lv J, Ou L, Li X, Ma Y, Dai X, Liu F, Zou X, Ouyang B, Li F. Full-length mRNA sequencing and gene expression profiling reveal broad involvement of natural antisense transcript gene pairs in pepper development and response to stresses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:763-783. [PMID: 31009127 DOI: 10.1111/tpj.14351] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 03/18/2019] [Accepted: 03/27/2019] [Indexed: 06/09/2023]
Abstract
Pepper is an important vegetable with great economic value and unique biological features. In the past few years, significant development has been made toward understanding the huge complex pepper genome; however, pepper functional genomics has not been well studied. To better understand the pepper gene structure and pepper gene regulation, we conducted full-length mRNA sequencing by PacBio sequencing and obtained 57 862 high-quality full-length mRNA sequences derived from 18 362 previously annotated and 5769 newly detected genes. New gene models were built that combined the full-length mRNA sequences and corrected approximately 500 fragmented gene models from previous annotations. Based on the full-length mRNA, we identified 4114 and 5880 pepper genes forming natural antisense transcript (NAT) genes in-cis and in-trans, respectively. Most of these genes accumulate small RNAs in their overlapping regions. By analyzing these NAT gene expression patterns in our transcriptome data, we identified many NAT pairs responsive to a variety of biological processes in pepper. Pepper formate dehydrogenase 1 (FDH1), which is required for R-gene-mediated disease resistance, may be regulated by nat-siRNAs and participate in a positive feedback loop in salicylic acid biosynthesis during resistance responses. Several cis-NAT pairs and subgroups of trans-NAT genes were responsive to pepper pericarp and placenta development, which may play roles in capsanthin and capsaicin biosynthesis. Using a comparative genomics approach, the evolutionary mechanisms of cis-NATs were investigated, and we found that an increase in intergenic sequences accounted for the loss of most cis-NATs, while transposon insertion contributed to the formation of most new cis-NATs. OPEN RESEARCH BADGES: This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at http://bigd.big.ac.cn/gsa Accession number, CRA001412.
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Affiliation(s)
- Jubin Wang
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, HB, China
| | - Yingtian Deng
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, HB, China
| | - Yingjia Zhou
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, HB, China
| | - Dan Liu
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, HB, China
| | - Huiyang Yu
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, HB, China
| | - Yuhong Zhou
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, HB, China
| | - Junheng Lv
- Hunan Institute of Vegetable Research, Academy of Agricultural Sciences of Hunan Province, Changsha, HN, China
| | - Lijun Ou
- Hunan Institute of Vegetable Research, Academy of Agricultural Sciences of Hunan Province, Changsha, HN, China
| | - Xuefeng Li
- Hunan Institute of Vegetable Research, Academy of Agricultural Sciences of Hunan Province, Changsha, HN, China
| | - Yanqing Ma
- Hunan Institute of Vegetable Research, Academy of Agricultural Sciences of Hunan Province, Changsha, HN, China
| | - Xiongze Dai
- Hunan Institute of Vegetable Research, Academy of Agricultural Sciences of Hunan Province, Changsha, HN, China
| | - Feng Liu
- Hunan Institute of Vegetable Research, Academy of Agricultural Sciences of Hunan Province, Changsha, HN, China
| | - Xuexiao Zou
- Hunan Institute of Vegetable Research, Academy of Agricultural Sciences of Hunan Province, Changsha, HN, China
| | - Bo Ouyang
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, HB, China
| | - Feng Li
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, HB, China
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Sakamoto K, Ogiwara N, Kaji T, Sugimoto Y, Ueno M, Sonoda M, Matsui A, Ishida J, Tanaka M, Totoki Y, Shinozaki K, Seki M. Transcriptome analysis of soybean (Glycine max) root genes differentially expressed in rhizobial, arbuscular mycorrhizal, and dual symbiosis. JOURNAL OF PLANT RESEARCH 2019; 132:541-568. [PMID: 31165947 DOI: 10.1007/s10265-019-01117-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 05/25/2019] [Indexed: 05/11/2023]
Abstract
Soybean (Glycine max) roots establish associations with nodule-inducing rhizobia and arbuscular mycorrhizal (AM) fungi. Both rhizobia and AM fungi have been shown to affect the activity of and colonization by the other, and their interactions can be detected within host plants. Here, we report the transcription profiles of genes differentially expressed in soybean roots in the presence of rhizobial, AM, or rhizobial-AM dual symbiosis, compared with those in control (uninoculated) roots. Following inoculation, soybean plants were grown in a glasshouse for 6 weeks; thereafter their root transcriptomes were analyzed using an oligo DNA microarray. Among the four treatments, the root nodule number and host plant growth were highest in plants with dual symbiosis. We observed that the expression of 187, 441, and 548 host genes was up-regulated and 119, 1,439, and 1,298 host genes were down-regulated during rhizobial, AM, and dual symbiosis, respectively. The expression of 34 host genes was up-regulated in each of the three symbioses. These 34 genes encoded several membrane transporters, type 1 metallothionein, and transcription factors in the MYB and bHLH families. We identified 56 host genes that were specifically up-regulated during dual symbiosis. These genes encoded several nodulin proteins, phenylpropanoid metabolism-related proteins, and carbonic anhydrase. The nodulin genes up-regulated by the AM fungal colonization probably led to the observed increases in root nodule number and host plant growth. Some other nodulin genes were down-regulated specifically during AM symbiosis. Based on the results above, we suggest that the contribution of AM fungal colonization is crucial to biological N2-fixation and host growth in soybean with rhizobial-AM dual symbiosis.
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Affiliation(s)
- Kazunori Sakamoto
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan.
| | - Natsuko Ogiwara
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan
| | - Tomomitsu Kaji
- JA ZEN-NOH Research and Development Center, 4-18-1 Higashiyawata, Hiratsuka, Kanagawa, 254-0016, Japan
| | - Yurie Sugimoto
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan
| | - Mitsuru Ueno
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan
| | - Masatoshi Sonoda
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan
| | - Akihiro Matsui
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Junko Ishida
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Maho Tanaka
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Yasushi Totoki
- Division of Cancer Genomics, National Cancer Center Research Institute, Chuo-ku, Tokyo, 104-0045, Japan
| | - Kazuo Shinozaki
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Motoaki Seki
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, 244-0813, Japan
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Ishikawa S, Ono Y, Ohtake N, Sueyoshi K, Tanabata S, Ohyama T. Transcriptome and Metabolome Analyses Reveal That Nitrate Strongly Promotes Nitrogen and Carbon Metabolism in Soybean Roots, but Tends to Repress It in Nodules. PLANTS 2018; 7:plants7020032. [PMID: 29649183 PMCID: PMC6027490 DOI: 10.3390/plants7020032] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 04/04/2018] [Accepted: 04/09/2018] [Indexed: 11/25/2022]
Abstract
Leguminous plants form root nodules with rhizobia that fix atmospheric dinitrogen (N2) for the nitrogen (N) nutrient. Combined nitrogen sources, particular nitrate, severely repress nodule growth and nitrogen fixation activity in soybeans (Glycine max [L.] Merr.). A microarray-based transcriptome analysis and the metabolome analysis were carried out for the roots and nodules of hydroponically grown soybean plants treated with 5 mM of nitrate for 24 h and compared with control without nitrate. Gene expression ratios of nitrate vs. the control were highly enhanced for those probesets related to nitrate transport and assimilation and carbon metabolism in the roots, but much less so in the nodules, except for the nitrate transport and asparagine synthetase. From the metabolome analysis, the concentration ratios of metabolites for the nitrate treatment vs. the control indicated that most of the amino acids, phosphorous-compounds and organic acids in roots were increased about twofold in the roots, whereas in the nodules most of the concentrations of the amino acids, P-compounds and organic acids were decreased while asparagine increased exceptionally. These results may support the hypothesis that nitrate primarily promotes nitrogen and carbon metabolism in the roots, but mainly represses this metabolism in the nodules.
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Affiliation(s)
- Shinji Ishikawa
- Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan.
| | - Yuki Ono
- Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan.
| | - Norikuni Ohtake
- Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan.
| | - Kuni Sueyoshi
- Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan.
| | - Sayuri Tanabata
- Faculty of Agriculture, Ibaraki University, Ibaraki 300-0332, Japan.
| | - Takuji Ohyama
- Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan.
- Faculty of Applied Biosciences, Tokyo University of Agriculture, Tokyo 156-8502, Japan.
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Yuan SL, Li R, Chen HF, Zhang CJ, Chen LM, Hao QN, Chen SL, Shan ZH, Yang ZL, Zhang XJ, Qiu DZ, Zhou XA. RNA-Seq analysis of nodule development at five different developmental stages of soybean (Glycine max) inoculated with Bradyrhizobium japonicum strain 113-2. Sci Rep 2017; 7:42248. [PMID: 28169364 PMCID: PMC5294573 DOI: 10.1038/srep42248] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 01/08/2017] [Indexed: 12/15/2022] Open
Abstract
Nodule development directly affects nitrogen fixation efficiency during soybean growth. Although abundant genome-based information related to nodule development has been released and some studies have reported the molecular mechanisms that regulate nodule development, information on the way nodule genes operate in nodule development at different developmental stages of soybean is limited. In this report, notably different nodulation phenotypes in soybean roots inoculated with Bradyrhizobium japonicum strain 113-2 at five developmental stages (branching stage, flowering stage, fruiting stage, pod stage and harvest stage) were shown, and the expression of nodule genes at these five stages was assessed quantitatively using RNA-Seq. Ten comparisons were made between these developmental periods, and their differentially expressed genes were analysed. Some important genes were identified, primarily encoding symbiotic nitrogen fixation-related proteins, cysteine proteases, cystatins and cysteine-rich proteins, as well as proteins involving plant-pathogen interactions. There were no significant shifts in the distribution of most GO functional annotation terms and KEGG pathway enrichment terms between these five development stages. A cystatin Glyma18g12240 was firstly identified from our RNA-seq, and was likely to promote nodulation and delay nodule senescence. This study provides molecular material for further investigations into the mechanisms of nitrogen fixation at different soybean developmental stages.
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Affiliation(s)
- Song L. Yuan
- Key Laboratory of Oil Crop Biology, Ministry of Agriculture, Wuhan 430062, China
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, China
| | - Rong Li
- Key Laboratory of Oil Crop Biology, Ministry of Agriculture, Wuhan 430062, China
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, China
| | - Hai F. Chen
- Key Laboratory of Oil Crop Biology, Ministry of Agriculture, Wuhan 430062, China
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, China
| | - Chan J. Zhang
- Key Laboratory of Oil Crop Biology, Ministry of Agriculture, Wuhan 430062, China
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, China
| | - Li M. Chen
- Key Laboratory of Oil Crop Biology, Ministry of Agriculture, Wuhan 430062, China
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, China
| | - Qing N. Hao
- Key Laboratory of Oil Crop Biology, Ministry of Agriculture, Wuhan 430062, China
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, China
| | - Shui L. Chen
- Key Laboratory of Oil Crop Biology, Ministry of Agriculture, Wuhan 430062, China
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, China
| | - Zhi H. Shan
- Key Laboratory of Oil Crop Biology, Ministry of Agriculture, Wuhan 430062, China
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, China
| | - Zhong L. Yang
- Key Laboratory of Oil Crop Biology, Ministry of Agriculture, Wuhan 430062, China
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, China
| | - Xiao J. Zhang
- Key Laboratory of Oil Crop Biology, Ministry of Agriculture, Wuhan 430062, China
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, China
| | - De Z. Qiu
- Key Laboratory of Oil Crop Biology, Ministry of Agriculture, Wuhan 430062, China
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, China
| | - Xin A. Zhou
- Key Laboratory of Oil Crop Biology, Ministry of Agriculture, Wuhan 430062, China
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, China
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11
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Hirade Y, Kotoku N, Terasaka K, Saijo-Hamano Y, Fukumoto A, Mizukami H. Identification and functional analysis of 2-hydroxyflavanone C-glucosyltransferase in soybean (Glycine max). FEBS Lett 2015; 589:1778-86. [PMID: 25979175 DOI: 10.1016/j.febslet.2015.05.010] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 04/28/2015] [Accepted: 05/01/2015] [Indexed: 11/21/2022]
Abstract
C-Glucosyltransferase is an enzyme that mediates carbon-carbon bond formation to generate C-glucoside metabolites. Although it has been identified in several plant species, the catalytic amino acid residues required for C-glucosylation activity remain obscure. Here, we identified a 2-hydroxyflavanone C-glucosyltransferase (UGT708D1) in soybean. We found that three residues, His20, Asp85, and Arg292, of UGT708D1 were located at the predicted active site and evolutionarily conserved. The substitution of Asp85 or Arg292 with alanine destroyed C-glucosyltransferase activity, whereas the substitution of His20 with alanine abolished C-glucosyltransferase activity but enabled O-glucosyltransferase activity. The catalytic mechanism is discussed on the basis of the findings.
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Affiliation(s)
- Yoshihiro Hirade
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamada-oka, Suita City, Osaka 565-0871, Japan.
| | - Naoyuki Kotoku
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamada-oka, Suita City, Osaka 565-0871, Japan
| | - Kazuyoshi Terasaka
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya City, Aichi 467-8603, Japan
| | - Yumiko Saijo-Hamano
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamada-oka, Suita City, Osaka 565-0871, Japan
| | - Akemi Fukumoto
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamada-oka, Suita City, Osaka 565-0871, Japan
| | - Hajime Mizukami
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya City, Aichi 467-8603, Japan; The Kochi Prefectural Makino Botanical Garden, 4200-6 Godaisan, Kochi City, Kochi 781-8125, Japan
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12
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Qian G, Ping J, Zhang Z, Xu D. Sequencing and comparative genomics analysis in Senecio scandens Buch.-Ham. Ex D. Don, based on full-length cDNA library. BIOTECHNOL BIOTEC EQ 2014; 28:805-812. [PMID: 26740776 PMCID: PMC4684062 DOI: 10.1080/13102818.2014.956461] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 03/10/2014] [Indexed: 11/23/2022] Open
Abstract
Senecio scandens Buch.-Ham. ex D. Don, an important antibacterial source of Chinese traditional medicine, has a widespread distribution in a few ecological habitats of China. We generated a full-length complementary DNA (cDNA) library from a sample of elite individuals with superior antibacterial properties, with satisfactory parameters such as library storage (4.30 × 106 CFU), efficiency of titre (1.30 × 106 CFU/mL), transformation efficiency (96.35%), full-length ratio (64.00%) and redundancy ratio (3.28%). The BLASTN search revealed the facile formation of counterparts between the experimental sample and Arabidopsis thaliana in view of high-homology cDNA sequence (90.79%) with e-values <1e - 50. Sequence similarities to known proteins indicate that the entire sequences of the full-length cDNA clones consist of the major of functional genes identified by a large set of microarray data from the present experimental material. For other Compositae species, a large set of full-length cDNA clones reported in the present article will serve as a useful resource to facilitate further research on the transferability of expressed sequence tag-derived simple sequence repeats (EST-SSR) development, comparative genomics and novel transcript profiles.
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Affiliation(s)
- Gang Qian
- Department of Cell Biology and Genetics, Zunyi Medical College, Zunyi, Guizhou, P.R. China
| | - Junjiao Ping
- Department of Cell Biology and Genetics, Zunyi Medical College, Zunyi, Guizhou, P.R. China
| | - Zhen Zhang
- Department of Cell Biology and Genetics, Zunyi Medical College, Zunyi, Guizhou, P.R. China
| | - Delin Xu
- Department of Cell Biology and Genetics, Zunyi Medical College, Zunyi, Guizhou, P.R. China
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13
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Qian G, Ping J, Lu J, Zhang Z, Wang L, Xu D. Construction of Full-Length cDNA Library and Development of EST-Derived Simple Sequence Repeat (EST-SSR) Markers in Senecio scandens. Biochem Genet 2014; 52:494-508. [DOI: 10.1007/s10528-014-9662-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2013] [Accepted: 06/10/2014] [Indexed: 11/28/2022]
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Yu J, Zhang Z, Wei J, Ling Y, Xu W, Su Z. SFGD: a comprehensive platform for mining functional information from soybean transcriptome data and its use in identifying acyl-lipid metabolism pathways. BMC Genomics 2014; 15:271. [PMID: 24712981 PMCID: PMC4051163 DOI: 10.1186/1471-2164-15-271] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2013] [Accepted: 03/31/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Soybean (Glycine max L.) is one of the world's most important leguminous crops producing high-quality protein and oil. Increasing the relative oil concentration in soybean seeds is many researchers' goal, but a complete analysis platform of functional annotation for the genes involved in the soybean acyl-lipid pathway is still lacking. Following the success of soybean whole-genome sequencing, functional annotation has become a major challenge for the scientific community. Whole-genome transcriptome analysis is a powerful way to predict genes with biological functions. It is essential to build a comprehensive analysis platform for integrating soybean whole-genome sequencing data, the available transcriptome data and protein information. This platform could also be used to identify acyl-lipid metabolism pathways. DESCRIPTION In this study, we describe our construction of the Soybean Functional Genomics Database (SFGD) using Generic Genome Browser (Gbrowse) as the core platform. We integrated microarray expression profiling with 255 samples from 14 groups' experiments and mRNA-seq data with 30 samples from four groups' experiments, including spatial and temporal transcriptome data for different soybean development stages and environmental stresses. The SFGD includes a gene co-expression regulatory network containing 23,267 genes and 1873 miRNA-target pairs, and a group of acyl-lipid pathways containing 221 enzymes and more than 1550 genes. The SFGD also provides some key analysis tools, i.e. BLAST search, expression pattern search and cis-element significance analysis, as well as gene ontology information search and single nucleotide polymorphism display. CONCLUSION The SFGD is a comprehensive database integrating genome and transcriptome data, and also for soybean acyl-lipid metabolism pathways. It provides useful toolboxes for biologists to improve the accuracy and robustness of soybean functional genomics analysis, further improving understanding of gene regulatory networks for effective crop improvement. The SFGD is publically accessible at http://bioinformatics.cau.edu.cn/SFGD/, with all data available for downloading.
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Affiliation(s)
- Juan Yu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Zhenhai Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jiangang Wei
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yi Ling
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Wenying Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Zhen Su
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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15
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High-throughput sequencing and de novo assembly of Brassica oleracea var. Capitata L. for transcriptome analysis. PLoS One 2014; 9:e92087. [PMID: 24682075 PMCID: PMC3969326 DOI: 10.1371/journal.pone.0092087] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 02/18/2014] [Indexed: 12/28/2022] Open
Abstract
Background The cabbage, Brassica oleracea var. capitata L., has a distinguishable phenotype within the genus Brassica. Despite the economic and genetic importance of cabbage, there is little genomic data for cabbage, and most studies of Brassica are focused on other species or other B. oleracea subspecies. The lack of genomic data for cabbage, a non-model organism, hinders research on its molecular biology. Hence, the construction of reliable transcriptomic data based on high-throughput sequencing technologies is needed to enhance our understanding of cabbage and provide genomic information for future work. Methodology/Principal Findings We constructed cDNAs from total RNA isolated from the roots, leaves, flowers, seedlings, and calcium-limited seedling tissues of two cabbage genotypes: 102043 and 107140. We sequenced a total of six different samples using the Illumina HiSeq platform, producing 40.5 Gbp of sequence data comprising 401,454,986 short reads. We assembled 205,046 transcripts (≥ 200 bp) using the Velvet and Oases assembler and predicted 53,562 loci from the transcripts. We annotated 35,274 of the loci with 55,916 plant peptides in the Phytozome database. The average length of the annotated loci was 1,419 bp. We confirmed the reliability of the sequencing assembly using reverse-transcriptase PCR to identify tissue-specific gene candidates among the annotated loci. Conclusion Our study provides valuable transcriptome sequence data for B. oleracea var. capitata L., offering a new resource for studying B. oleracea and closely related species. Our transcriptomic sequences will enhance the quality of gene annotation and functional analysis of the cabbage genome and serve as a material basis for future genomic research on cabbage. The sequencing data from this study can be used to develop molecular markers and to identify the extreme differences among the phenotypes of different species in the genus Brassica.
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Fukami-Kobayashi K, Nakamura Y, Tamura T, Kobayashi M. SABRE2: A Database Connecting Plant EST/Full-Length cDNA Clones with Arabidopsis Information. ACTA ACUST UNITED AC 2014; 55:e5. [DOI: 10.1093/pcp/pct177] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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17
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Gao X, Jia R, Wang M, Zhu D, Chen S, Lin M, Yin Z, Wang Y, Chen X, Cheng A. Construction and identification of a cDNA library for use in the yeast two-hybrid system from duck embryonic fibroblast cells post-infected with duck enteritis virus. Mol Biol Rep 2013; 41:467-75. [PMID: 24293127 DOI: 10.1007/s11033-013-2881-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 11/21/2013] [Indexed: 12/30/2022]
Abstract
To explore and isolate genes related to duck embryonic fibroblast cells (DEFs) post-infected with duck enteritis virus (DEV), a cDNA library was established using SMART (Switching Mechanism At 5' end of the RNA Transcript) technique coupling with a homologous recombination method. The cells were harvested and total RNA was extracted at 48 h post infection. Then the mRNAs were purified and reverse transcribed to first-strand cDNAs using oligo (dT) primers (CDS III). Subsequently, long distance-PCR was performed, the double-stranded cDNAs were purified, and a transformation assay was carried out in that order. Eventually, a high qualitative library was successfully established according to an evaluation on quality. The transformation efficiency was about 2.33 × 10(6) transformants/4.34 μg pGADT7-Rec (>1.0 × 10(6)). The cell density of the library was 1.75 × 10(9) cells/mL (>2 × 10(7) cells/mL). The titer of the primary cDNA library and amplified cDNA library was 6.75 × 10(5) and 2.33 × 10(7) CFU/mL respectively. The numbers for the primary cDNA library and amplified cDNA library were 1.01 × 10(7) and 1.14 × 10(9), respectively, and the recombinant rate was 97.14 %. The sequence results of 27 randomly picked independent clones revealed the insert ranged from 0.323 to 2.017 kb with an average insert size of 0.807 kb. Full-length transcripts of DEV-CHv LORF3, UL26 and UL35 genes were acquired through sequence similarity analysis from the non-redundant nucleic acid or protein database. Five polyA sites were identified in the DEV-CHv genome. Also, a new transcript of 668 bp was found between the IRS gene and US1 gene of the DEV-CHv genome. Thus, we concluded that the constructed cDNA library will be a useful tool in proteomic analysis of interactions between the DEV and host DEFs, and discovery of biomarkers studies on the mechanism of DEV and subsequently exploitation original vaccines and antiviral drugs to prevent or cure diseases.
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Affiliation(s)
- Xinghong Gao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China,
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Mochida K, Uehara-Yamaguchi Y, Takahashi F, Yoshida T, Sakurai T, Shinozaki K. Large-scale collection and analysis of full-length cDNAs from Brachypodium distachyon and integration with Pooideae sequence resources. PLoS One 2013; 8:e75265. [PMID: 24130698 PMCID: PMC3793998 DOI: 10.1371/journal.pone.0075265] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 08/14/2013] [Indexed: 01/09/2023] Open
Abstract
A comprehensive collection of full-length cDNAs is essential for correct structural gene annotation and functional analyses of genes. We constructed a mixed full-length cDNA library from 21 different tissues of Brachypodium distachyon Bd21, and obtained 78,163 high quality expressed sequence tags (ESTs) from both ends of ca. 40,000 clones (including 16,079 contigs). We updated gene structure annotations of Brachypodium genes based on full-length cDNA sequences in comparison with the latest publicly available annotations. About 10,000 non-redundant gene models were supported by full-length cDNAs; ca. 6,000 showed some transcription unit modifications. We also found ca. 580 novel gene models, including 362 newly identified in Bd21. Using the updated transcription start sites, we searched a total of 580 plant cis-motifs in the −3 kb promoter regions and determined a genome-wide Brachypodium promoter architecture. Furthermore, we integrated the Brachypodium full-length cDNAs and updated gene structures with available sequence resources in wheat and barley in a web-accessible database, the RIKEN Brachypodium FL cDNA database. The database represents a “one-stop” information resource for all genomic information in the Pooideae, facilitating functional analysis of genes in this model grass plant and seamless knowledge transfer to the Triticeae crops.
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Affiliation(s)
- Keiichi Mochida
- Biomass Research Platform Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan
- Kihara Institute for Biological Research, Yokohama City University, Totsuka-ku, Yokohama, Kanagawa, Japan
- * E-mail:
| | - Yukiko Uehara-Yamaguchi
- Biomass Research Platform Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Fuminori Takahashi
- Biomass Research Platform Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Takuhiro Yoshida
- Integrated Genome Informatics Research Unit, RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Tetsuya Sakurai
- Integrated Genome Informatics Research Unit, RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Kazuo Shinozaki
- Biomass Research Platform Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan
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Sakurai T, Mochida K, Yoshida T, Akiyama K, Ishitani M, Seki M, Shinozaki K. Genome-wide discovery and information resource development of DNA polymorphisms in cassava. PLoS One 2013; 8:e74056. [PMID: 24040164 PMCID: PMC3770675 DOI: 10.1371/journal.pone.0074056] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 07/29/2013] [Indexed: 01/06/2023] Open
Abstract
Cassava (Manihot esculenta Crantz) is an important crop that provides food security and income generation in many tropical countries, and is known for its adaptability to various environmental conditions. Its draft genome sequence and many expressed sequence tags are now publicly available, allowing the development of cassava polymorphism information. Here, we describe the genome-wide discovery of cassava DNA polymorphisms. Using the alignment of predicted transcribed sequences from the cassava draft genome sequence and ESTs from GenBank, we discovered 10,546 single-nucleotide polymorphisms and 647 insertions and deletions. To facilitate molecular marker development for cassava, we designed 9,316 PCR primer pairs to amplify the genomic region around each DNA polymorphism. Of the discovered SNPs, 62.7% occurred in protein-coding regions. Disease-resistance genes were found to have a significantly higher ratio of nonsynonymous-to-synonymous substitutions. We identified 24 read-through (changes of a stop codon to a coding codon) and 38 premature stop (changes of a coding codon to a stop codon) single-nucleotide polymorphisms, and found that the 5 gene ontology terms in biological process were significantly different in genes with read-through single-nucleotide polymorphisms compared with all cassava genes. All data on the discovered DNA polymorphisms were organized into the Cassava Online Archive database, which is available at http://cassava.psc.riken.jp/.
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Affiliation(s)
- Tetsuya Sakurai
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Keiichi Mochida
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan
- RIKEN Biomass Engineering Program, Tsurumi-ku, Yokohama, Kanagawa, Japan
- Kihara Institute for Biological Research, Yokohama City University, Totsuka-ku, Yokohama, Kanagawa, Japan
| | - Takuhiro Yoshida
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Kenji Akiyama
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Manabu Ishitani
- Agrobiodiversity Research Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Motoaki Seki
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan
- Kihara Institute for Biological Research, Yokohama City University, Totsuka-ku, Yokohama, Kanagawa, Japan
| | - Kazuo Shinozaki
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan
- RIKEN Biomass Engineering Program, Tsurumi-ku, Yokohama, Kanagawa, Japan
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Mercati F, Riccardi P, Leebens-Mack J, Abenavoli MR, Falavigna A, Sunseri F. Single nucleotide polymorphism isolated from a novel EST dataset in garden asparagus (Asparagus officinalis L.). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2013; 203-204:115-23. [PMID: 23415335 DOI: 10.1016/j.plantsci.2013.01.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 01/07/2013] [Accepted: 01/09/2013] [Indexed: 05/03/2023]
Abstract
Single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSR) are abundant and evenly distributed co-dominant molecular markers in plant genomes. SSRs are valuable for marker assisted breeding and positional cloning of genes associated traits of interest. Although several high throughput platforms have been developed to identify SNP and SSR markers for analysis of segregant plant populations, breeding in garden asparagus (Asparagus officinalis L.) has been limited by a low content of such markers. In this study massively parallel GS-FLX pyro-sequencing technology (454 Life Sciences) has been used to sequence and compare transcriptome from two genotypes: a rust tolerant male (1770) and a susceptible female (G190). A total of 122,963 and 99,368 sequence reads, with an average length of 245.7bp, have been recovered from accessions 1770 and 190 respectively. A computational pipeline has been used to predict and visually inspect putative SNPs and SSR sequences. Analysis of Gene Ontology (GO) slim annotation assignments for all assembled uniscripts indicated that the 24,403 assemblies represent genes from a broad array of functions. Further, over 1800 putative SNPs and 1000 SSRs were detected. One hundred forty-four SNPs together with 60 selected SSRs were validated and used to develop a preliminary genetic map by using a large BC(1) population, derived from 1770 and G190. The abundance of SNPs and SSRs provides a foundation for the development of saturated genetic maps and their utilization in assisted asparagus breeding programs.
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Affiliation(s)
- Francesco Mercati
- Dipartimento di AGRARIA, Università Mediterranea di Reggio Calabria, Salita Melissari, 89124 Reggio Calabria (RC), Italy
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Benko-Iseppon AM, Nepomuceno AL, Abdelnoor RV. GENOSOJA - The Brazilian Soybean Genome Consortium: High throughput omics and beyond. Genet Mol Biol 2012; 35:i-iv. [PMID: 22802722 PMCID: PMC3392889 DOI: 10.1590/s1415-47572012000200001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- Ana M Benko-Iseppon
- Laboratório de Genética e Biotecnologia Vegetal, Departamento de Genética, Universidade Federal de Pernambuco, Recife, PE, Brazil
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do Nascimento LC, Costa GGL, Binneck E, Pereira GAG, Carazzolle MF. A web-based bioinformatics interface applied to the GENOSOJA Project: Databases and pipelines. Genet Mol Biol 2012; 35:203-11. [PMID: 22802706 PMCID: PMC3392873 DOI: 10.1590/s1415-47572012000200002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The Genosoja consortium is an initiative to integrate different omics research approaches carried out in Brazil. Basically, the aim of the project is to improve the plant by identifying genes involved in responses against stresses that affect domestic production, like drought stress and Asian Rust fungal disease. To do so, the project generated several types of sequence data using different methodologies, most of them sequenced by next generation sequencers. The initial stage of the project is highly dependent on bioinformatics analysis, providing suitable tools and integrated databases. In this work, we describe the main features of the Genosoja web database, including the pipelines to analyze some kinds of data (ESTs, SuperSAGE, microRNAs, subtractive cDNA libraries), as well as web interfaces to access information about soybean gene annotation and expression.
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Affiliation(s)
- Leandro Costa do Nascimento
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Gustavo Gilson Lacerda Costa
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Eliseu Binneck
- Empresa Brasileira de Pesquisa Agropecuária, Londrina, PR, Brazil
| | - Gonçalo Amarante Guimarães Pereira
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Marcelo Falsarella Carazzolle
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
- Centro Nacional de Processamento de Alto Desempenho em São Paulo, Universidade Estadual de Campinas, Campinas, SP, Brazil
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Sayama T, Ono E, Takagi K, Takada Y, Horikawa M, Nakamoto Y, Hirose A, Sasama H, Ohashi M, Hasegawa H, Terakawa T, Kikuchi A, Kato S, Tatsuzaki N, Tsukamoto C, Ishimoto M. The Sg-1 glycosyltransferase locus regulates structural diversity of triterpenoid saponins of soybean. THE PLANT CELL 2012; 24:2123-38. [PMID: 22611180 PMCID: PMC3442591 DOI: 10.1105/tpc.111.095174] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2011] [Revised: 04/20/2012] [Accepted: 04/30/2012] [Indexed: 05/18/2023]
Abstract
Triterpene saponins are a diverse group of biologically functional products in plants. Saponins usually are glycosylated, which gives rise to a wide diversity of structures and functions. In the group A saponins of soybean (Glycine max), differences in the terminal sugar species located on the C-22 sugar chain of an aglycone core, soyasapogenol A, were observed to be under genetic control. Further genetic analyses and mapping revealed that the structural diversity of glycosylation was determined by multiple alleles of a single locus, Sg-1, and led to identification of a UDP-sugar-dependent glycosyltransferase gene (Glyma07g38460). Although their sequences are highly similar and both glycosylate the nonacetylated saponin A0-αg, the Sg-1(a) allele encodes the xylosyltransferase UGT73F4, whereas Sg-1(b) encodes the glucosyltransferase UGT73F2. Homology models and site-directed mutagenesis analyses showed that Ser-138 in Sg-1(a) and Gly-138 in Sg-1(b) proteins are crucial residues for their respective sugar donor specificities. Transgenic complementation tests followed by recombinant enzyme assays in vitro demonstrated that sg-1(0) is a loss-of-function allele of Sg-1. Considering that the terminal sugar species in the group A saponins are responsible for the strong bitterness and astringent aftertastes of soybean seeds, our findings herein provide useful tools to improve commercial properties of soybean products.
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Affiliation(s)
- Takashi Sayama
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Eiichiro Ono
- Institute for Plant Science, Suntory Business Expert Ltd., Shimamoto, Mishima, Osaka 618-8503, Japan
| | - Kyoko Takagi
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Yoshitake Takada
- National Agricultural Research Center for Western Region, Zentsuji, Kagawa 765-8508, Japan
| | - Manabu Horikawa
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Shimamoto, Mishima, Osaka 618-8503, Japan
| | - Yumi Nakamoto
- National Agricultural Research Center for Hokkaido Region, Toyohira, Sapporo, Hokkaido 062-8555, Japan
| | - Aya Hirose
- National Agricultural Research Center for Hokkaido Region, Toyohira, Sapporo, Hokkaido 062-8555, Japan
| | - Hiroko Sasama
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Mihoko Ohashi
- National Agricultural Research Center for Hokkaido Region, Toyohira, Sapporo, Hokkaido 062-8555, Japan
| | | | | | - Akio Kikuchi
- National Agricultural Research Center for Tohoku Region, Kariwano, Daisen, Akita 019-2112, Japan
| | - Shin Kato
- National Agricultural Research Center for Tohoku Region, Kariwano, Daisen, Akita 019-2112, Japan
| | - Nana Tatsuzaki
- Graduate School of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan
| | - Chigen Tsukamoto
- Graduate School of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan
| | - Masao Ishimoto
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
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Sha AH, Li C, Yan XH, Shan ZH, Zhou XA, Jiang ML, Mao H, Chen B, Wan X, Wei WH. Large-scale sequencing of normalized full-length cDNA library of soybean seed at different developmental stages and analysis of the gene expression profiles based on ESTs. Mol Biol Rep 2012; 39:2867-74. [PMID: 21667246 DOI: 10.1007/s11033-011-1046-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Accepted: 06/04/2011] [Indexed: 12/15/2022]
Abstract
Although GenBank has now covered over 1,400,000 expressed sequence tags (ESTs) from soybean, most ESTs available to the public have been derived from tissues or environmental conditions rather than developing seeds. It is absolutely necessary for annotating the molecular mechanisms of soybean seed development to analyze completely the gene expression profiles of its immature seed at various stages. Here we have constructed a full-length-enriched cDNA library comprised of a total of 45,408 cDNA clones which cover various stages of soybean seed development. Furthermore, we have sequenced from 5' ends of these clones, 36,656 ESTs were obtained in the present study. These EST sequences could be categorized into 27,982 unigenes, including 22,867 contigs and 5,115 singletons, among which 27,931 could be mapped onto soybean 20 chromosome sequences. Comparative genomic analysis with other plants has revealed that these unigenes include lots of candidate genes specific to dicot, legume and soybean. Approximately 1,789 of these unigenes currently show no homology to known soybean sequences, suggesting that many represent mRNAs specifically expressed in seeds. Novel abundant genes involved in the oil synthesis have been found in this study, may serve as a valuable resource for soybean seed improvement.
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Affiliation(s)
- Ai-Hua Sha
- Institute of Oil Crops, Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
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Yamada T, Takagi K, Ishimoto M. Recent advances in soybean transformation and their application to molecular breeding and genomic analysis. BREEDING SCIENCE 2012; 61:480-94. [PMID: 23136488 PMCID: PMC3406787 DOI: 10.1270/jsbbs.61.480] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Accepted: 11/02/2011] [Indexed: 05/07/2023]
Abstract
Herbicide-resistant transgenic soybean plants hold a leading market share in the USA and other countries, but soybean has been regarded as recalcitrant to transformation for many years. The cumulative and, at times, exponential advances in genetic manipulation have made possible further choices for soybean transformation. The most widely and routinely used transformation systems are cotyledonary node-Agrobacterium-mediated transformation and somatic embryo-particle-bombardment-mediated transformation. These ready systems enable us to improve seed qualities and agronomic characteristics by transgenic approaches. In addition, with the accumulation of soybean genomic resources, convenient or promising approaches will be requisite for the determination and use of gene function in soybean. In this article, we describe recent advances in and problems of soybean transformation, and survey the current transgenic approaches for applied and basic research in Japan.
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Affiliation(s)
- Tetsuya Yamada
- Research Faculty of Agriculture, Hokkaido University, Kita 9 Nishi 9, Kita, Sapporo, Hokkaido 060-8589, Japan
| | - Kyoko Takagi
- Soybean Applied Genomics Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Masao Ishimoto
- Soybean Applied Genomics Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
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26
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Hashiguchi M, Abe J, Aoki T, Anai T, Suzuki A, Akashi R. The National BioResource Project (NBRP) Lotus and Glycine in Japan. BREEDING SCIENCE 2012; 61:453-61. [PMID: 23136485 PMCID: PMC3406794 DOI: 10.1270/jsbbs.61.453] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Accepted: 10/30/2011] [Indexed: 05/21/2023]
Abstract
The objective of the National BioResource Project (NBRP) in Japan is to collect, conserve and distribute biological materials for life sciences research. The project consists of twenty-eight bioresources, including animal, plant, microorganism and DNA resources. NBRP Lotus and Glycine aims to support the development of legume research through the collection, conservation, and distribution of these bioresources. Lotus japonicus is a perennial legume that grows naturally throughout Japan and is widely used as a model plant for legumes because of such advantages as its small genome size and short life cycle. Soybean (Glycine max) has been cultivated as an important crop since ancient times, and numerous research programs have generated a large amount of basic research information and valuable bioresources for this crop. We have also developed a "LegumeBase" a specialized database for the genera Lotus and Glycine, and are maintaining this database as a part of the NBRP. In this paper we will provide an overview of the resources available from the NBRP Lotus and Glycine database site, called "LegumeBase".
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Affiliation(s)
- Masatsugu Hashiguchi
- Frontier Science Research Center, University of Miyazaki, 1-1 Gakuen Kibanadai Nishi, Miyazaki 889-2192, Japan
| | - Jun Abe
- Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita, Sapporo, Hokkaido 060-8589, Japan
| | - Toshio Aoki
- Department of Applied Biological Sciences, Nihon University, Fujisawa, Kanagawa 252-0880, Japan
| | - Toyoaki Anai
- Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga 840-8502, Japan
| | - Akihiro Suzuki
- Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga 840-8502, Japan
| | - Ryo Akashi
- Frontier Science Research Center, University of Miyazaki, 1-1 Gakuen Kibanadai Nishi, Miyazaki 889-2192, Japan
- Corresponding author (e-mail: )
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27
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Hayashi M, Saeki Y, Haga M, Harada K, Kouchi H, Umehara Y. Rj (rj) genes involved in nitrogen-fixing root nodule formation in soybean. BREEDING SCIENCE 2012; 61:544-53. [PMID: 23136493 PMCID: PMC3406786 DOI: 10.1270/jsbbs.61.544] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 08/18/2011] [Indexed: 05/06/2023]
Abstract
It has long been known that formation of symbiotic root nodules in soybean (Glycine max (L.) Merr.) is controlled by several host genes referred to as Rj (rj) genes, but molecular cloning of these genes has been hampered by soybean's complicated genome structure and large genome size. Progress in molecular identification of legume genes involved in root nodule symbiosis have been mostly achieved by using two model legumes, Lotus japonicus and Medicago truncatula, that have relatively simple and small genomes and are capable of molecular transfection. However, recent development of resources for soybean molecular genetic research, such as genome sequencing, large EST databases, and high-density linkage maps, have enabled us to isolate several Rj genes. This progress has been achieved in connection with systematic utilization of the information obtained from molecular genetics of the model legumes. In this review, we summarize the current status of knowledge of host-controlled nodulation in soybean based on information from recent studies on Rj genes, and discuss the future research prospects.
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Affiliation(s)
- Masaki Hayashi
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
- Corresponding author (e-mail: )
| | - Yuichi Saeki
- Faculty of Agriculture, Miyazaki University, 1-1 Gakuen Kibanadai-Nishi, Miyazaki, Miyazaki 889-2192, Japan
| | - Michiyo Haga
- Fukushima Prefecture Ken-chu Agriculture and Forestry Office, 1-1-1 Hayama, Koriyama, Fukushima 963-8540, Japan
| | - Kyuya Harada
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Hiroshi Kouchi
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Yosuke Umehara
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
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28
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Katayose Y, Kanamori H, Shimomura M, Ohyanagi H, Ikawa H, Minami H, Shibata M, Ito T, Kurita K, Ito K, Tsubokura Y, Kaga A, Wu J, Matsumoto T, Harada K, Sasaki T. DaizuBase, an integrated soybean genome database including BAC-based physical maps. BREEDING SCIENCE 2012; 61:661-4. [PMID: 23136506 PMCID: PMC3406781 DOI: 10.1270/jsbbs.61.661] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 12/09/2011] [Indexed: 05/07/2023]
Abstract
Soybean [Glycine max (L) Merrill] is one of the most important leguminous crops and ranks fourth after to rice, wheat and maize in terms of world crop production. Soybean contains abundant protein and oil, which makes it a major source of nutritious food, livestock feed and industrial products. In Japan, soybean is also an important source of traditional staples such as tofu, natto, miso and soy sauce. The soybean genome was determined in 2010. With its enormous size, physical mapping and genome sequencing are the most effective approaches towards understanding the structure and function of the soybean genome. We constructed bacterial artificial chromosome (BAC) libraries from the Japanese soybean cultivar, Enrei. The end-sequences of approximately 100,000 BAC clones were analyzed and used for construction of a BAC-based physical map of the genome. BLAST analysis between Enrei BAC-end sequences and the Williams82 genome was carried out to increase the saturation of the map. This physical map will be used to characterize the genome structure of Japanese soybean cultivars, to develop methods for the isolation of agronomically important genes and to facilitate comparative soybean genome research. The current status of physical mapping of the soybean genome and construction of database are presented.
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Affiliation(s)
- Yuichi Katayose
- National Institute of Agrobiological Sciences, 1-2 Ohwashi, Tsukuba, Ibaraki 305-8634, Japan
- Corresponding author (e-mail: )
| | - Hiroyuki Kanamori
- National Institute of Agrobiological Sciences, 1-2 Ohwashi, Tsukuba, Ibaraki 305-8634, Japan
- STAFF Institute, 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki 305-0854, Japan
| | - Michihiko Shimomura
- Mitsubishi Space Software Co. Ltd., Takezono, Tsukuba, Ibaraki 305-0032, Japan
| | - Hajime Ohyanagi
- Mitsubishi Space Software Co. Ltd., Takezono, Tsukuba, Ibaraki 305-0032, Japan
| | - Hiroshi Ikawa
- STAFF Institute, 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki 305-0854, Japan
| | - Hiroshi Minami
- STAFF Institute, 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki 305-0854, Japan
| | - Michie Shibata
- National Institute of Agrobiological Sciences, 1-2 Ohwashi, Tsukuba, Ibaraki 305-8634, Japan
- STAFF Institute, 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki 305-0854, Japan
| | - Tomoko Ito
- STAFF Institute, 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki 305-0854, Japan
| | - Kanako Kurita
- National Institute of Agrobiological Sciences, 1-2 Ohwashi, Tsukuba, Ibaraki 305-8634, Japan
- STAFF Institute, 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki 305-0854, Japan
| | - Kazue Ito
- National Institute of Agrobiological Sciences, 1-2 Ohwashi, Tsukuba, Ibaraki 305-8634, Japan
- STAFF Institute, 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki 305-0854, Japan
| | - Yasutaka Tsubokura
- National Institute of Agrobiological Sciences, 1-2 Ohwashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Akito Kaga
- National Institute of Agrobiological Sciences, 1-2 Ohwashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Jianzhong Wu
- National Institute of Agrobiological Sciences, 1-2 Ohwashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Takashi Matsumoto
- National Institute of Agrobiological Sciences, 1-2 Ohwashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Kyuya Harada
- National Institute of Agrobiological Sciences, 1-2 Ohwashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Takuji Sasaki
- National Institute of Agrobiological Sciences, 1-2 Ohwashi, Tsukuba, Ibaraki 305-8634, Japan
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29
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Mochida K, Shinozaki K. Advances in omics and bioinformatics tools for systems analyses of plant functions. PLANT & CELL PHYSIOLOGY 2011; 52:2017-38. [PMID: 22156726 PMCID: PMC3233218 DOI: 10.1093/pcp/pcr153] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Omics and bioinformatics are essential to understanding the molecular systems that underlie various plant functions. Recent game-changing sequencing technologies have revitalized sequencing approaches in genomics and have produced opportunities for various emerging analytical applications. Driven by technological advances, several new omics layers such as the interactome, epigenome and hormonome have emerged. Furthermore, in several plant species, the development of omics resources has progressed to address particular biological properties of individual species. Integration of knowledge from omics-based research is an emerging issue as researchers seek to identify significance, gain biological insights and promote translational research. From these perspectives, we provide this review of the emerging aspects of plant systems research based on omics and bioinformatics analyses together with their associated resources and technological advances.
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Affiliation(s)
- Keiichi Mochida
- RIKEN Biomass Engineering Program, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan.
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30
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Mochida K, Shinozaki K. Advances in omics and bioinformatics tools for systems analyses of plant functions. PLANT & CELL PHYSIOLOGY 2011. [PMID: 22156726 DOI: 10.1093/pcp/pc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Omics and bioinformatics are essential to understanding the molecular systems that underlie various plant functions. Recent game-changing sequencing technologies have revitalized sequencing approaches in genomics and have produced opportunities for various emerging analytical applications. Driven by technological advances, several new omics layers such as the interactome, epigenome and hormonome have emerged. Furthermore, in several plant species, the development of omics resources has progressed to address particular biological properties of individual species. Integration of knowledge from omics-based research is an emerging issue as researchers seek to identify significance, gain biological insights and promote translational research. From these perspectives, we provide this review of the emerging aspects of plant systems research based on omics and bioinformatics analyses together with their associated resources and technological advances.
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Affiliation(s)
- Keiichi Mochida
- RIKEN Biomass Engineering Program, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan.
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31
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Blair MW, Fernandez AC, Ishitani M, Moreta D, Seki M, Ayling S, Shinozaki K. Construction and EST sequencing of full-length, drought stress cDNA libraries for common beans (Phaseolus vulgaris L.). BMC PLANT BIOLOGY 2011; 11:171. [PMID: 22118559 PMCID: PMC3240127 DOI: 10.1186/1471-2229-11-171] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Accepted: 11/25/2011] [Indexed: 05/07/2023]
Abstract
BACKGROUND Common bean is an important legume crop with only a moderate number of short expressed sequence tags (ESTs) made with traditional methods. The goal of this research was to use full-length cDNA technology to develop ESTs that would overlap with the beginning of open reading frames and therefore be useful for gene annotation of genomic sequences. The library was also constructed to represent genes expressed under drought, low soil phosphorus and high soil aluminum toxicity. We also undertook comparisons of the full-length cDNA library to two previous non-full clone EST sets for common bean. RESULTS Two full-length cDNA libraries were constructed: one for the drought tolerant Mesoamerican genotype BAT477 and the other one for the acid-soil tolerant Andean genotype G19833 which has been selected for genome sequencing. Plants were grown in three soil types using deep rooting cylinders subjected to drought and non-drought stress and tissues were collected from both roots and above ground parts. A total of 20,000 clones were selected robotically, half from each library. Then, nearly 10,000 clones from the G19833 library were sequenced with an average read length of 850 nucleotides. A total of 4,219 unigenes were identified consisting of 2,981 contigs and 1,238 singletons. These were functionally annotated with gene ontology terms and placed into KEGG pathways. Compared to other EST sequencing efforts in common bean, about half of the sequences were novel or represented the 5' ends of known genes. CONCLUSIONS The present full-length cDNA libraries add to the technological toolbox available for common bean and our sequencing of these clones substantially increases the number of unique EST sequences available for the common bean genome. All of this should be useful for both functional gene annotation, analysis of splice site variants and intron/exon boundary determination by comparison to soybean genes or with common bean whole-genome sequences. In addition the library has a large number of transcription factors and will be interesting for discovery and validation of drought or abiotic stress related genes in common bean.
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Affiliation(s)
- Matthew W Blair
- Bean Program and Biotechnology Unit, International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
| | - Andrea C Fernandez
- Bean Program and Biotechnology Unit, International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
| | - Manabu Ishitani
- Bean Program and Biotechnology Unit, International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
| | - Danilo Moreta
- Bean Program and Biotechnology Unit, International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
| | - Motoaki Seki
- Plant Genomic Network Research Team and Director, RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Sarah Ayling
- Bean Program and Biotechnology Unit, International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
| | - Kazuo Shinozaki
- Plant Genomic Network Research Team and Director, RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
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Takagi K, Nishizawa K, Hirose A, Kita A, Ishimoto M. Manipulation of saponin biosynthesis by RNA interference-mediated silencing of β-amyrin synthase gene expression in soybean. PLANT CELL REPORTS 2011; 30:1835-46. [PMID: 21630021 DOI: 10.1007/s00299-011-1091-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Revised: 05/18/2011] [Accepted: 05/18/2011] [Indexed: 05/28/2023]
Abstract
Soybean seeds contain substantial amount of diverse triterpenoid saponins that influence the seed quality, although little is known about the physiologic functions of saponins in plants. We now describe the modification of saponin biosynthesis by RNA interference (RNAi)-mediated gene silencing targeted to β-amyrin synthase, a key enzyme in the synthesis of a common aglycon of soybean saponins. We identified two putative β-amyrin synthase genes in soybean that manifested distinct expression patterns with regard to developmental stage and tissue specificity. Given that one of these genes, GmBAS1, was expressed at a much higher level than the other (GmBAS2) in various tissues including the developing seeds, we constructed two RNAi vectors that encode self-complementary hairpin RNAs corresponding to the distinct regions of GmBAS1 under the control of a seed-specific promoter derived from the soybean gene for the α' subunit of the seed storage protein β-conglycinin. These vectors were introduced independently into soybean. Six independent transgenic lines exhibited a stable reduction in seed saponin content, with the extent of saponin deficiency correlating with the β-amyrin synthase mRNA depletion. Although some transgenic lines produced seeds almost devoid of saponins, no abnormality in their growth was apparent and the antioxidant activity of their seeds was similar to that of control seeds. These results suggest that saponins are not required for seed development and survival, and that soybean seeds may therefore be amenable to the modification of triterpenoid saponin content and composition through molecular biologic approaches.
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Affiliation(s)
- Kyoko Takagi
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
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33
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Alekseeva A, Savin S, Tishkov V. NAD (+) -dependent Formate Dehydrogenase from Plants. Acta Naturae 2011; 3:38-54. [PMID: 22649703 PMCID: PMC3347622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
NAD(+)-dependent formate dehydrogenase (FDH, EC 1.2.1.2) widely occurs in nature. FDH consists of two identical subunits and contains neither prosthetic groups nor metal ions. This type of FDH was found in different microorganisms (including pathogenic ones), such as bacteria, yeasts, fungi, and plants. As opposed to microbiological FDHs functioning in cytoplasm, plant FDHs localize in mitochondria. Formate dehydrogenase activity was first discovered as early as in 1921 in plant; however, until the past decade FDHs from plants had been considerably less studied than the enzymes from microorganisms. This review summarizes the recent results on studying the physiological role, properties, structure, and protein engineering of plant formate dehydrogenases.
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Affiliation(s)
- A.A. Alekseeva
- Chemistry Department, Lomonosov Moscow State University
- Innovations and High Technologies MSU Ltd
- Bach Institute of Biochemistry, Russian Academy of Sciences
| | - S.S. Savin
- Innovations and High Technologies MSU Ltd
- Bach Institute of Biochemistry, Russian Academy of Sciences
| | - V.I. Tishkov
- Chemistry Department, Lomonosov Moscow State University
- Innovations and High Technologies MSU Ltd
- Bach Institute of Biochemistry, Russian Academy of Sciences
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34
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Agrawal GK, Bourguignon J, Rolland N, Ephritikhine G, Ferro M, Jaquinod M, Alexiou KG, Chardot T, Chakraborty N, Jolivet P, Doonan JH, Rakwal R. Plant organelle proteomics: collaborating for optimal cell function. MASS SPECTROMETRY REVIEWS 2011; 30:772-853. [PMID: 21038434 DOI: 10.1002/mas.20301] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2009] [Revised: 02/02/2010] [Accepted: 02/02/2010] [Indexed: 05/10/2023]
Abstract
Organelle proteomics describes the study of proteins present in organelle at a particular instance during the whole period of their life cycle in a cell. Organelles are specialized membrane bound structures within a cell that function by interacting with cytosolic and luminal soluble proteins making the protein composition of each organelle dynamic. Depending on organism, the total number of organelles within a cell varies, indicating their evolution with respect to protein number and function. For example, one of the striking differences between plant and animal cells is the plastids in plants. Organelles have their own proteins, and few organelles like mitochondria and chloroplast have their own genome to synthesize proteins for specific function and also require nuclear-encoded proteins. Enormous work has been performed on animal organelle proteomics. However, plant organelle proteomics has seen limited work mainly due to: (i) inter-plant and inter-tissue complexity, (ii) difficulties in isolation of subcellular compartments, and (iii) their enrichment and purity. Despite these concerns, the field of organelle proteomics is growing in plants, such as Arabidopsis, rice and maize. The available data are beginning to help better understand organelles and their distinct and/or overlapping functions in different plant tissues, organs or cell types, and more importantly, how protein components of organelles behave during development and with surrounding environments. Studies on organelles have provided a few good reviews, but none of them are comprehensive. Here, we present a comprehensive review on plant organelle proteomics starting from the significance of organelle in cells, to organelle isolation, to protein identification and to biology and beyond. To put together such a systematic, in-depth review and to translate acquired knowledge in a proper and adequate form, we join minds to provide discussion and viewpoints on the collaborative nature of organelles in cell, their proper function and evolution.
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Affiliation(s)
- Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), P.O. Box 13265, Sanepa, Kathmandu, Nepal.
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Nanjo Y, Maruyama K, Yasue H, Yamaguchi-Shinozaki K, Shinozaki K, Komatsu S. Transcriptional responses to flooding stress in roots including hypocotyl of soybean seedlings. PLANT MOLECULAR BIOLOGY 2011; 77:129-44. [PMID: 21656040 DOI: 10.1007/s11103-011-9799-4] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Accepted: 05/27/2011] [Indexed: 05/25/2023]
Abstract
To understand the transcriptional responses to flooding stress in roots including hypocotyl of soybean seedlings, genome-wide changes in gene expression were analyzed using a soybean microarray chip containing 42,034 60-mer oligonucleotide probes. More than 6,000 of flooding-responsive genes in the roots including hypocotyl of soybean seedlings were identified. The transcriptional analysis showed that genes related to photosynthesis, glycolysis, Ser-Gly-Cys group amino acid synthesis, regulation of transcription, ubiquitin-mediated protein degradation and cell death were significantly up-regulated by flooding. Meanwhile, genes related to cell wall synthesis, secondary metabolism, metabolite transport, cell organization, chromatin structure synthesis, and degradation of aspartate family amino acid were significantly down-regulated. Comparison of the responses with other plants showed that genes encoding pyrophosphate dependent phosphofructokinase were down-regulated in flooded soybean seedlings, however, those in tolerant plants were up-regulated. Additionally, genes related to RNA processing and initiation of protein synthesis were not up-regulated in soybean, however, those in tolerant plants were up-regulated. Furthermore, we found that flooding-specific up-regulation of genes encoding small proteins which might have roles in acclimation to flooding. These results suggest that functional disorder of acclimative responses to flooding through transcriptional and post-transcriptional regulations is involved in occurring flooding injury to soybean seedlings.
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Affiliation(s)
- Yohei Nanjo
- National Institute of Crop Science, Tsukuba 305-8518, Japan
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Abe H, Narusaka Y, Sasaki I, Hatakeyama K, Shin-I S, Narusaka M, Fukami-Kobayashi K, Matsumoto S, Kobayashi M. Development of full-length cDNAs from Chinese cabbage (Brassica rapa Subsp. pekinensis) and identification of marker genes for defence response. DNA Res 2011; 18:277-89. [PMID: 21745830 PMCID: PMC3158467 DOI: 10.1093/dnares/dsr018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2011] [Accepted: 05/25/2011] [Indexed: 11/13/2022] Open
Abstract
Arabidopsis belongs to the Brassicaceae family and plays an important role as a model plant for which researchers have developed fine-tuned genome resources. Genome sequencing projects have been initiated for other members of the Brassicaceae family. Among these projects, research on Chinese cabbage (Brassica rapa subsp. pekinensis) started early because of strong interest in this species. Here, we report the development of a library of Chinese cabbage full-length cDNA clones, the RIKEN BRC B. rapa full-length cDNA (BBRAF) resource, to accelerate research on Brassica species. We sequenced 10 000 BBRAF clones and confirmed 5476 independent clones. Most of these cDNAs showed high homology to Arabidopsis genes, but we also obtained more than 200 cDNA clones that lacked any sequence homology to Arabidopsis genes. We also successfully identified several possible candidate marker genes for plant defence responses from our analysis of the expression of the Brassica counterparts of Arabidopsis marker genes in response to salicylic acid and jasmonic acid. We compared gene expression of these markers in several Chinese cabbage cultivars. Our BBRAF cDNA resource will be publicly available from the RIKEN Bioresource Center and will help researchers to transfer Arabidopsis-related knowledge to Brassica crops.
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Affiliation(s)
- Hiroshi Abe
- Experimental Plant Division, Department of Biological Systems, RIKEN BioResource Center, Koyadai, Tsukuba, Ibaraki, Japan.
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KE T, DONG CH, MAO H, ZHAO YZ, LIU HY, LIU SY. Construction of a Normalized Full-Length cDNA Library of Sesame Developing Seed by DSN and SMART™. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/s1671-2927(11)60087-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Clepet C, Joobeur T, Zheng Y, Jublot D, Huang M, Truniger V, Boualem A, Hernandez-Gonzalez ME, Dolcet-Sanjuan R, Portnoy V, Mascarell-Creus A, Caño-Delgado AI, Katzir N, Bendahmane A, Giovannoni JJ, Aranda MA, Garcia-Mas J, Fei Z. Analysis of expressed sequence tags generated from full-length enriched cDNA libraries of melon. BMC Genomics 2011; 12:252. [PMID: 21599934 PMCID: PMC3118787 DOI: 10.1186/1471-2164-12-252] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Accepted: 05/20/2011] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Melon (Cucumis melo), an economically important vegetable crop, belongs to the Cucurbitaceae family which includes several other important crops such as watermelon, cucumber, and pumpkin. It has served as a model system for sex determination and vascular biology studies. However, genomic resources currently available for melon are limited. RESULT We constructed eleven full-length enriched and four standard cDNA libraries from fruits, flowers, leaves, roots, cotyledons, and calluses of four different melon genotypes, and generated 71,577 and 22,179 ESTs from full-length enriched and standard cDNA libraries, respectively. These ESTs, together with ~35,000 ESTs available in public domains, were assembled into 24,444 unigenes, which were extensively annotated by comparing their sequences to different protein and functional domain databases, assigning them Gene Ontology (GO) terms, and mapping them onto metabolic pathways. Comparative analysis of melon unigenes and other plant genomes revealed that 75% to 85% of melon unigenes had homologs in other dicot plants, while approximately 70% had homologs in monocot plants. The analysis also identified 6,972 gene families that were conserved across dicot and monocot plants, and 181, 1,192, and 220 gene families specific to fleshy fruit-bearing plants, the Cucurbitaceae family, and melon, respectively. Digital expression analysis identified a total of 175 tissue-specific genes, which provides a valuable gene sequence resource for future genomics and functional studies. Furthermore, we identified 4,068 simple sequence repeats (SSRs) and 3,073 single nucleotide polymorphisms (SNPs) in the melon EST collection. Finally, we obtained a total of 1,382 melon full-length transcripts through the analysis of full-length enriched cDNA clones that were sequenced from both ends. Analysis of these full-length transcripts indicated that sizes of melon 5' and 3' UTRs were similar to those of tomato, but longer than many other dicot plants. Codon usages of melon full-length transcripts were largely similar to those of Arabidopsis coding sequences. CONCLUSION The collection of melon ESTs generated from full-length enriched and standard cDNA libraries is expected to play significant roles in annotating the melon genome. The ESTs and associated analysis results will be useful resources for gene discovery, functional analysis, marker-assisted breeding of melon and closely related species, comparative genomic studies and for gaining insights into gene expression patterns.
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Affiliation(s)
- Christian Clepet
- URGV Plant Genomics, Unité de Recherche en Génomique Végétale, UMR1165 ERL8196 INRA-UEVE-CNRS. 2, Rue Gaston Crémieux, 91057 Evry, France
| | - Tarek Joobeur
- Molecular and Cellular Imaging Center, The Ohio State University, OARDC, 1680 Madison Ave, Wooster, OH 44691, USA
- Seminis Vegetable Seeds, 37437 State Highway 16 Woodland, CA 95695, USA
| | - Yi Zheng
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Delphine Jublot
- URGV Plant Genomics, Unité de Recherche en Génomique Végétale, UMR1165 ERL8196 INRA-UEVE-CNRS. 2, Rue Gaston Crémieux, 91057 Evry, France
| | - Mingyun Huang
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Veronica Truniger
- Centro de Edafología y Biología Aplicada del Segura (CEBAS), Consejo Superior de Investigaciones Científicas (CSIC), Apdo. Correos 164, 30100 Espinardo, Murcia, Spain
| | - Adnane Boualem
- URGV Plant Genomics, Unité de Recherche en Génomique Végétale, UMR1165 ERL8196 INRA-UEVE-CNRS. 2, Rue Gaston Crémieux, 91057 Evry, France
| | | | - Ramon Dolcet-Sanjuan
- IRTA, Center for Research in Agricultural Genomics CSIC-IRTA-UAB, Campus UAB, Edifici CRAG, 08193 Bellaterra (Barcelona), Spain
| | - Vitaly Portnoy
- Department of Vegetable Research, Agricultural Research Organization, Newe Ya'ar Research Center, P.O. Box 1021, Ramat Yishay, 30095, Israel
| | - Albert Mascarell-Creus
- Department de Genètica Molecular, Center for Research in Agricultural Genomics CSIC-IRTA-UAB, Campus UAB, Edifici CRAG, 08193 Bellaterra (Barcelona), Spain
| | - Ana I Caño-Delgado
- Department de Genètica Molecular, Center for Research in Agricultural Genomics CSIC-IRTA-UAB, Campus UAB, Edifici CRAG, 08193 Bellaterra (Barcelona), Spain
| | - Nurit Katzir
- Department of Vegetable Research, Agricultural Research Organization, Newe Ya'ar Research Center, P.O. Box 1021, Ramat Yishay, 30095, Israel
| | - Abdelhafid Bendahmane
- URGV Plant Genomics, Unité de Recherche en Génomique Végétale, UMR1165 ERL8196 INRA-UEVE-CNRS. 2, Rue Gaston Crémieux, 91057 Evry, France
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh Saudi Arabia
| | - James J Giovannoni
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
- USDA Robert W. Holley Center for Agriculture and Health, Tower Road, Ithaca, NY 14853, USA
| | - Miguel A Aranda
- Centro de Edafología y Biología Aplicada del Segura (CEBAS), Consejo Superior de Investigaciones Científicas (CSIC), Apdo. Correos 164, 30100 Espinardo, Murcia, Spain
| | - Jordi Garcia-Mas
- IRTA, Center for Research in Agricultural Genomics CSIC-IRTA-UAB, Campus UAB, Edifici CRAG, 08193 Bellaterra (Barcelona), Spain
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
- USDA Robert W. Holley Center for Agriculture and Health, Tower Road, Ithaca, NY 14853, USA
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Matsumoto T, Tanaka T, Sakai H, Amano N, Kanamori H, Kurita K, Kikuta A, Kamiya K, Yamamoto M, Ikawa H, Fujii N, Hori K, Itoh T, Sato K. Comprehensive sequence analysis of 24,783 barley full-length cDNAs derived from 12 clone libraries. PLANT PHYSIOLOGY 2011; 156:20-8. [PMID: 21415278 PMCID: PMC3091036 DOI: 10.1104/pp.110.171579] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 03/16/2011] [Indexed: 05/18/2023]
Abstract
Full-length cDNA (FLcDNA) libraries consisting of 172,000 clones were constructed from a two-row malting barley cultivar (Hordeum vulgare 'Haruna Nijo') under normal and stressed conditions. After sequencing the clones from both ends and clustering the sequences, a total of 24,783 complete sequences were produced. By removing duplicates between these and publicly available sequences, 22,651 representative sequences were obtained: 17,773 were novel barley FLcDNAs, and 1,699 were barley specific. Highly conserved genes were found in the barley FLcDNA sequences for 721 of 881 rice (Oryza sativa) trait genes with 50% or greater identity. These FLcDNA resources from our Haruna Nijo cDNA libraries and the full-length sequences of representative clones will improve our understanding of the biological functions of genes in barley, which is the cereal crop with the fourth highest production in the world, and will provide a powerful tool for annotating the barley genome sequences that will become available in the near future.
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Affiliation(s)
- Takashi Matsumoto
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan.
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Zhang JZ, Ai XY, Sun LM, Zhang DL, Guo WW, Deng XX, Hu CG. Transcriptome profile analysis of flowering molecular processes of early flowering trifoliate orange mutant and the wild-type [Poncirus trifoliata (L.) Raf.] by massively parallel signature sequencing. BMC Genomics 2011; 12:63. [PMID: 21269450 PMCID: PMC3039610 DOI: 10.1186/1471-2164-12-63] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Accepted: 01/26/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND After several years in the juvenile phase, trees undergo flowering transition to become mature (florally competent) trees. This transition depends on the balanced expression of a complex network of genes that is regulated by both endogenous and environmental factors. However, relatively little is known about the molecular processes regulating flowering transition in woody plants compared with herbaceous plants. RESULTS Comparative transcript profiling of spring shoots after self-pruning was performed on a spontaneously early flowering trifoliate orange mutant (precocious trifoliate orange, Poncirus trifoliata) with a short juvenile phase and the wild-type (WT) tree by using massively parallel signature sequencing (MPSS). A total of 16,564,500 and 16,235,952 high quality reads were obtained for the WT and the mutant (MT), respectively. Interpretation of the MPSS signatures revealed that the total number of transcribed genes in the MT (31,468) was larger than in the WT (29,864), suggesting that newly initiated transcription occurs in the MT. Further comparison of the transcripts revealed that 2735 genes had more than twofold expression difference in the MT compared with the WT. In addition, we identified 110 citrus flowering-time genes homologous with known elements of flowering-time pathways through sequencing and bioinformatics analysis. These genes are highly conserved in citrus and other species, suggesting that the functions of the related proteins in controlling reproductive development may be conserved as well. CONCLUSION Our results provide a foundation for comparative gene expression studies between WT and precocious trifoliate orange. Additionally, a number of candidate genes required for the early flowering process of precocious trifoliate orange were identified. These results provide new insight into the molecular processes regulating flowering time in citrus.
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Affiliation(s)
- Jin-Zhi Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Xiao-Yan Ai
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Lei-Ming Sun
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, PR China
| | | | - Wen-Wu Guo
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, PR China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Xiu-Xin Deng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, PR China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Chun-Gen Hu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, PR China
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Kondou Y, Higuchi M, Ichikawa T, Matsui M. Application of full-length cDNA resources to gain-of-function technology for characterization of plant gene function. Methods Mol Biol 2011; 729:183-97. [PMID: 21365491 DOI: 10.1007/978-1-61779-065-2_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Generation and characterization of mutants are important for the investigation of gene function. Gain-of-function technology is one of the most useful approaches for the systematic production of mutant resources. Full-length cDNAs have been collected from various plant species and have become important resources for functional genomics. We have developed a novel gain-of-function technology for the identification of gene function using a full-length cDNA library, and this system has been named as FOX hunting system (Full-length cDNA Over-eXpressing gene hunting system). In this system, full-length cDNAs are randomly expressed in Arabidopsis. We also generated rice FOX Arabidopsis lines in which full-length cDNAs from rice were expressed in Arabidopsis, and we demonstrated that gene function derived from heterologous organisms can be analyzed systematically using the FOX hunting approach. In this protocol, we describe the process of generating Arabidopsis mutants expressing rice full-length cDNA libraries and the methods of identifying genes from the isolated mutants.
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Understanding Vegetative Desiccation Tolerance Using Integrated Functional Genomics Approaches Within a Comparative Evolutionary Framework. PLANT DESICCATION TOLERANCE 2011. [DOI: 10.1007/978-3-642-19106-0_15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Delseny M, Han B, Hsing YI. High throughput DNA sequencing: The new sequencing revolution. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2010; 179:407-22. [PMID: 21802600 DOI: 10.1016/j.plantsci.2010.07.019] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2010] [Revised: 07/23/2010] [Accepted: 07/26/2010] [Indexed: 05/02/2023]
Abstract
Improvements in technology have rapidly changed the field of DNA sequencing. These improvements are boosted by bio-medical research. Plant science has benefited from this breakthrough, and a number of plant genomes are now available, new biological questions can be approached and new breeding strategies can be designed. The first part of this review aims to briefly describe the principles of the new sequencing methods, many of which are already used in plant laboratories. The second part summarizes the state of plant genome sequencing and illustrates the achievements in the last few years. Although already impressive, these results represent only the beginning of a new genomic era in plant science. Finally we describe some of the exciting discoveries in the structure and evolution of plant genomes made possible by genome sequencing in terms of biodiversity, genome expression and epigenetic regulations. All of these findings have already influenced plant breeding and biodiversity protection. Finally we discuss current trends, challenges and perspectives.
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Affiliation(s)
- Michel Delseny
- Laboratoire Génome et Développement des Plantes, UMR5096 CNRS-IRD-UP, University of Perpignan, 58 av. Paul Alduy, 66860 Perpignan, France.
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Tran LSP, Mochida K. Functional genomics of soybean for improvement of productivity in adverse conditions. Funct Integr Genomics 2010; 10:447-62. [PMID: 20582712 DOI: 10.1007/s10142-010-0178-z] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Revised: 06/01/2010] [Accepted: 06/16/2010] [Indexed: 01/07/2023]
Abstract
Global soybean production is frequently impacted by various stresses, including both abiotic and biotic stresses. To develop soybean plants with enhanced tolerance to different stressors, functional genomics of soybean and a comprehensive understanding of available biotechnological resources and approaches are essential. In this review, we will discuss recent advances in soybean functional genomics which provide unprecedented opportunities to understand global patterns of gene expression, gene regulatory networks, various physiological, biochemical, and metabolic pathways as well as their association with the development of specific phenotypes. Soybean functional genomics, therefore, will ultimately enable us to develop new soybean varieties with improved productivity under adverse conditions by genetic engineering.
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Natarajan P, Kanagasabapathy D, Gunadayalan G, Panchalingam J, Shree N, Sugantham PA, Singh KK, Madasamy P. Gene discovery from Jatropha curcas by sequencing of ESTs from normalized and full-length enriched cDNA library from developing seeds. BMC Genomics 2010; 11:606. [PMID: 20979643 PMCID: PMC3091748 DOI: 10.1186/1471-2164-11-606] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2010] [Accepted: 10/27/2010] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Jatropha curcas L. is promoted as an important non-edible biodiesel crop worldwide. Jatropha oil, which is a triacylglycerol, can be directly blended with petro-diesel or transesterified with methanol and used as biodiesel. Genetic improvement in jatropha is needed to increase the seed yield, oil content, drought and pest resistance, and to modify oil composition so that it becomes a technically and economically preferred source for biodiesel production. However, genetic improvement efforts in jatropha could not take advantage of genetic engineering methods due to lack of cloned genes from this species. To overcome this hurdle, the current gene discovery project was initiated with an objective of isolating as many functional genes as possible from J. curcas by large scale sequencing of expressed sequence tags (ESTs). RESULTS A normalized and full-length enriched cDNA library was constructed from developing seeds of J. curcas. The cDNA library contained about 1 × 10(6) clones and average insert size of the clones was 2.1 kb. Totally 12,084 ESTs were sequenced to average high quality read length of 576 bp. Contig analysis revealed 2258 contigs and 4751 singletons. Contig size ranged from 2-23 and there were 7333 ESTs in the contigs. This resulted in 7009 unigenes which were annotated by BLASTX. It showed 3982 unigenes with significant similarity to known genes and 2836 unigenes with significant similarity to genes of unknown, hypothetical and putative proteins. The remaining 191 unigenes which did not show similarity with any genes in the public database may encode for unique genes. Functional classification revealed unigenes related to broad range of cellular, molecular and biological functions. Among the 7009 unigenes, 6233 unigenes were identified to be potential full-length genes. CONCLUSIONS The high quality normalized cDNA library was constructed from developing seeds of J. curcas for the first time and 7009 unigenes coding for diverse biological functions including oil biosynthesis were identified. These genes will serve as invaluable genetic resource for crop improvement in jatropha to make it an ideal and profitable crop for biodiesel production.
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Affiliation(s)
- Purushothaman Natarajan
- Genomics Laboratory, Department of Genetic Engineering, SRM University, Chennai, Tamil Nadu, 603 203, India
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Agrawal GK, Jwa NS, Lebrun MH, Job D, Rakwal R. Plant secretome: unlocking secrets of the secreted proteins. Proteomics 2010; 10:799-827. [PMID: 19953550 DOI: 10.1002/pmic.200900514] [Citation(s) in RCA: 197] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Plant secretomics is a newly emerging area of the plant proteomics field. It basically describes the global study of secreted proteins into the extracellular space of plant cell or tissue at any given time and under certain conditions through various secretory mechanisms. A combination of biochemical, proteomics and bioinformatics approaches has been developed to isolate, identify and profile secreted proteins using complementary in vitro suspension-cultured cells and in planta systems. Developed inventories of secreted proteins under normal, biotic and abiotic conditions revealed several different types of novel secreted proteins, including the leaderless secretory proteins (LSPs). On average, LSPs can account for more than 50% of the total identified secretome, supporting, as in other eukaryotes, the existence of novel secretory mechanisms independent of the classical endoplasmic reticulum-Golgi secretory pathway, and suggesting that this non-classical mechanism of protein expression is, for as yet unknown reasons, more massively used than in other eukaryotic systems. Plants LSPs, which seem to be potentially involved in the defense/stress responses, might have dual (extracellular and/or intracellular) roles as most of them have established intracellular functions, yet presently unknown extracellular functions. Evidence is emerging on the role of glycosylation in the apical sorting and trafficking of secretory proteins. These initial secretome studies in plants have considerably advanced our understanding on secretion of different types of proteins and their underlying mechanisms, and opened a door for comparative analyses of plant secretomes with those of other organisms. In this first review on plant secretomics, we summarize and discuss the secretome definition, the applied approaches for unlocking secrets of the secreted proteins in the extracellular fluid, the possible functional significance and secretory mechanisms of LSPs, as well as glycosylation of secreted proteins and challenges involved ahead. Further improvements in existing and developing strategies and techniques will continue to drive forward plant secretomics research to building comprehensive and confident data sets of secreted proteins. This will lead to an increased understanding on how cells couple the concerted action of secreted protein networks to their internal and external environments.
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Amano N, Tanaka T, Numa H, Sakai H, Itoh T. Efficient plant gene identification based on interspecies mapping of full-length cDNAs. DNA Res 2010; 17:271-9. [PMID: 20668003 PMCID: PMC2955710 DOI: 10.1093/dnares/dsq017] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
We present an annotation pipeline that accurately predicts exon–intron structures and protein-coding sequences (CDSs) on the basis of full-length cDNAs (FLcDNAs). This annotation pipeline was used to identify genes in 10 plant genomes. In particular, we show that interspecies mapping of FLcDNAs to genomes is of great value in fully utilizing FLcDNA resources whose availability is limited to several species. Because low sequence conservation at 5′- and 3′-ends of FLcDNAs between different species tends to result in truncated CDSs, we developed an improved algorithm to identify complete CDSs by the extension of both ends of truncated CDSs. Interspecies mapping of 71 801 monocot FLcDNAs to the Oryza sativa genome led to the detection of 22 142 protein-coding regions. Moreover, in comparing two mapping programs and three ab initio prediction programs, we found that our pipeline was more capable of identifying complete CDSs. As demonstrated by monocot interspecies mapping, in which nucleotide identity between FLcDNAs and the genome was ∼80%, the resultant inferred CDSs were sufficiently accurate. Finally, we applied both inter- and intraspecies mapping to 10 monocot and dicot genomes and identified genes in 210 551 loci. Interspecies mapping of FLcDNAs is expected to effectively predict genes and CDSs in newly sequenced genomes.
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Affiliation(s)
- Naoki Amano
- Bioinformatics Research Unit, Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
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Peng Z, Lu T, Li L, Liu X, Gao Z, Hu T, Yang X, Feng Q, Guan J, Weng Q, Fan D, Zhu C, Lu Y, Han B, Jiang Z. Genome-wide characterization of the biggest grass, bamboo, based on 10,608 putative full-length cDNA sequences. BMC PLANT BIOLOGY 2010; 10:116. [PMID: 20565830 PMCID: PMC3017805 DOI: 10.1186/1471-2229-10-116] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Accepted: 06/18/2010] [Indexed: 05/04/2023]
Abstract
BACKGROUND With the availability of rice and sorghum genome sequences and ongoing efforts to sequence genomes of other cereal and energy crops, the grass family (Poaceae) has become a model system for comparative genomics and for better understanding gene and genome evolution that underlies phenotypic and ecological divergence of plants. While the genomic resources have accumulated rapidly for almost all major lineages of grasses, bamboo remains the only large subfamily of Poaceae with little genomic information available in databases, which seriously hampers our ability to take a full advantage of the wealth of grass genomic data for effective comparative studies. RESULTS Here we report the cloning and sequencing of 10,608 putative full length cDNAs (FL-cDNAs) primarily from Moso bamboo, Phyllostachys heterocycla cv. pubescens, a large woody bamboo with the highest ecological and economic values of all bamboos. This represents the third largest FL-cDNA collection to date of all plant species, and provides the first insight into the gene and genome structures of bamboos. We developed a Moso bamboo genomic resource database that so far contained the sequences of 10,608 putative FL-cDNAs and nearly 38,000 expressed sequence tags (ESTs) generated in this study. CONCLUSION Analysis of FL-cDNA sequences show that bamboo diverged from its close relatives such as rice, wheat, and barley through an adaptive radiation. A comparative analysis of the lignin biosynthesis pathway between bamboo and rice suggested that genes encoding caffeoyl-CoA O-methyltransferase may serve as targets for genetic manipulation of lignin content to reduce pollutants generated from bamboo pulping.
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Affiliation(s)
- Zhenhua Peng
- Chinese Academy of Forestry, Wanshou Shan, Beijing 100091, PR China
- International Network for Bamboo and Rattan, 8 Fu Tong Dong Da Jie, Chaoyang District, Beijing 100102, PR China
| | - Tingting Lu
- National Center for Gene Research & Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, PR China
| | - Lubin Li
- Chinese Academy of Forestry, Wanshou Shan, Beijing 100091, PR China
| | - Xiaohui Liu
- National Center for Gene Research & Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, PR China
| | - Zhimin Gao
- International Network for Bamboo and Rattan, 8 Fu Tong Dong Da Jie, Chaoyang District, Beijing 100102, PR China
| | - Tao Hu
- Chinese Academy of Forestry, Wanshou Shan, Beijing 100091, PR China
| | - Xuewen Yang
- International Network for Bamboo and Rattan, 8 Fu Tong Dong Da Jie, Chaoyang District, Beijing 100102, PR China
| | - Qi Feng
- National Center for Gene Research & Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, PR China
| | - Jianping Guan
- National Center for Gene Research & Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, PR China
| | - Qijun Weng
- National Center for Gene Research & Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, PR China
| | - Danlin Fan
- National Center for Gene Research & Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, PR China
| | - Chuanrang Zhu
- National Center for Gene Research & Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, PR China
| | - Ying Lu
- National Center for Gene Research & Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, PR China
| | - Bin Han
- National Center for Gene Research & Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, PR China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, PR China
| | - Zehui Jiang
- Chinese Academy of Forestry, Wanshou Shan, Beijing 100091, PR China
- International Network for Bamboo and Rattan, 8 Fu Tong Dong Da Jie, Chaoyang District, Beijing 100102, PR China
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Nouri MZ, Komatsu S. Comparative analysis of soybean plasma membrane proteins under osmotic stress using gel-based and LC MS/MS-based proteomics approaches. Proteomics 2010; 10:1930-45. [PMID: 20209511 DOI: 10.1002/pmic.200900632] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2009] [Accepted: 02/15/2010] [Indexed: 11/12/2022]
Abstract
To study the soybean plasma membrane proteome under osmotic stress, two methods were used: a gel-based and a LC MS/MS-based proteomics method. Two-day-old seedlings were subjected to 10% PEG for 2 days. Plasma membranes were purified from seedlings using a two-phase partitioning method and their purity was verified by measuring ATPase activity. Using the gel-based proteomics, four and eight protein spots were identified as up- and downregulated, respectively, whereas in the nanoLC MS/MS approach, 11 and 75 proteins were identified as up- and downregulated, respectively, under PEG treatment. Out of osmotic stress responsive proteins, most of the transporter proteins and all proteins with high number of transmembrane helices as well as low-abundance proteins could be identified by the LC MS/MS-based method. Three homologues of plasma membrane H(+)-ATPase, which are transporter proteins involved in ion efflux, were upregulated under osmotic stress. Gene expression of this protein was increased after 12 h of stress exposure. Among the identified proteins, seven proteins were mutual in two proteomics techniques, in which calnexin was the highly upregulated protein. Accumulation of calnexin in plasma membrane was confirmed by immunoblot analysis. These results suggest that under hyperosmotic conditions, calnexin accumulates in the plasma membrane and ion efflux accelerates by upregulation of plasma membrane H(+)-ATPase protein.
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Affiliation(s)
- Mohammad-Zaman Nouri
- Graduate School of Life and Environmental Science, University of Tsukuba, Tsukuba, Japan
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Mochida K, Shinozaki K. Genomics and bioinformatics resources for crop improvement. PLANT & CELL PHYSIOLOGY 2010; 51:497-523. [PMID: 20208064 PMCID: PMC2852516 DOI: 10.1093/pcp/pcq027] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2010] [Accepted: 03/01/2010] [Indexed: 05/19/2023]
Abstract
Recent remarkable innovations in platforms for omics-based research and application development provide crucial resources to promote research in model and applied plant species. A combinatorial approach using multiple omics platforms and integration of their outcomes is now an effective strategy for clarifying molecular systems integral to improving plant productivity. Furthermore, promotion of comparative genomics among model and applied plants allows us to grasp the biological properties of each species and to accelerate gene discovery and functional analyses of genes. Bioinformatics platforms and their associated databases are also essential for the effective design of approaches making the best use of genomic resources, including resource integration. We review recent advances in research platforms and resources in plant omics together with related databases and advances in technology.
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