1
|
Iwai R, Uchida S, Yamaguchi S, Nagata D, Koga A, Hayashi S, Yamamoto S, Miyasaka H. Effects of LPS from Rhodobacter sphaeroides, a Purple Non-Sulfur Bacterium (PNSB), on the Gene Expression of Rice Root. Microorganisms 2023; 11:1676. [PMID: 37512850 PMCID: PMC10383378 DOI: 10.3390/microorganisms11071676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/18/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
The effects of lipopolysaccharide (LPS) from Rhodobacter sphaeroides, a purple non-sulfur bacterium (PNSB), on the gene expression of the root of rice (Oryza sativa) were investigated by next generation sequencing (NGS) RNA-seq analysis. The rice seeds were germinated on agar plates containing 10 pg/mL of LPS from Rhodobacter sphaeroides NBRC 12203 (type culture). Three days after germination, RNA samples were extracted from the roots and analyzed by RNA-seq. The effects of dead (killed) PNSB cells of R. sphaeroides NBRC 12203T at the concentration of 101 cfu/mL (ca. 50 pg cell dry weight/mL) were also examined. Clean reads of NGS were mapped to rice genome (number of transcript ID: 44785), and differentially expressed genes were analyzed by DEGs. As a result of DEG analysis, 300 and 128 genes, and 86 and 8 genes were significantly up- and down-regulated by LPS and dead cells of PNSB, respectively. The plot of logFC (fold change) values of the up-regulated genes of LPS and PNSB dead cells showed a significant positive relationship (r2 = 0.6333, p < 0.0001), indicating that most of the effects of dead cell were attributed to those of LPS. Many genes related to tolerance against biotic (fungal and bacterial pathogens) and abiotic (cold, drought, and high salinity) stresses were up-regulated, and the most strikingly up-regulated genes were those involved in the jasmonate signaling pathway, and the genes of chalcone synthase isozymes, indicating that PNSB induced defense response against biotic and abiotic stresses via the jasmonate signaling pathway, despite the non-pathogenicity of PNSB.
Collapse
Affiliation(s)
- Ranko Iwai
- Department of Applied Life Science, Sojo University, 4-22-1 Ikeda, Nishiku, Kumamoto 860-0082, Japan
| | - Shunta Uchida
- Department of Applied Life Science, Sojo University, 4-22-1 Ikeda, Nishiku, Kumamoto 860-0082, Japan
| | - Sayaka Yamaguchi
- Department of Applied Life Science, Sojo University, 4-22-1 Ikeda, Nishiku, Kumamoto 860-0082, Japan
| | - Daiki Nagata
- Department of Applied Life Science, Sojo University, 4-22-1 Ikeda, Nishiku, Kumamoto 860-0082, Japan
| | - Aoi Koga
- Ciamo Co., Ltd., G-2F Sojo University, 4-22-1 Ikeda, Nishiku, Kumamoto 860-0082, Japan
| | - Shuhei Hayashi
- Department of Applied Life Science, Sojo University, 4-22-1 Ikeda, Nishiku, Kumamoto 860-0082, Japan
| | - Shinjiro Yamamoto
- Department of Applied Life Science, Sojo University, 4-22-1 Ikeda, Nishiku, Kumamoto 860-0082, Japan
| | - Hitoshi Miyasaka
- Department of Applied Life Science, Sojo University, 4-22-1 Ikeda, Nishiku, Kumamoto 860-0082, Japan
| |
Collapse
|
2
|
Balzano L, Alezones J, Diez García N. Identification of maize kernel resistance proteins against Aspergillus flavus by a statistical approach: A predictive model of resistance capacity. BIONATURA 2021. [DOI: 10.21931/rb/2021.06.02.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Although kernel infection by Aspergillus flavus and pre-harvest aflatoxin contamination of Zea mays grain is a significant crop production problem, not only in Venezuela but also around the world, little progress has been made in identifying proteins and metabolic pathways associated with this pathogen resistance. Usually, a protein with a two-fold expression between control and condition is considered a biomarker of some phenomena, but we think it is essential to evaluate its contribution to resistance. That is why we decided to determine the behavior's resistance capacity in terms of expression levels of an identified protein of maize kernels infected with A. flavus by using a multivariate approach. In this work, we identify 47 of 66 differentially expressed spots with a remarkable contribution to resistance against the fungus Aspergillus flavus. We finally test this approach to know if it can be used as a predictive resistance model and probe it by including theoretical and experimental protein expression profiles of other inoculated maize lines.
Collapse
Affiliation(s)
- Leandro Balzano
- University of Florida. Department of Microbiology and Cell Science. Gainesville, United States
| | - Jesús Alezones
- Fundación para la Investigación Agrícola DANAC. Carretera San Javier-Guarataro. Estado Yaracuy. Venezuela
| | - Nardy Diez García
- Centro de Investigación Biotecnológicas del Ecuador (CIBE), Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil, Ecuador
| |
Collapse
|
3
|
The Role of Stress-Responsive Transcription Factors in Modulating Abiotic Stress Tolerance in Plants. AGRONOMY-BASEL 2020. [DOI: 10.3390/agronomy10060788] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Abiotic stresses, such as drought, high temperature, and salinity, affect plant growth and productivity. Furthermore, global climate change may increase the frequency and severity of abiotic stresses, suggesting that development of varieties with improved stress tolerance is critical for future sustainable crop production. Improving stress tolerance requires a detailed understanding of the hormone signaling and transcriptional pathways involved in stress responses. Abscisic acid (ABA) and jasmonic acid (JA) are key stress-response hormones in plants, and some stress-responsive transcription factors such as ABFs and MYCs function as direct components of ABA and JA signaling, playing a pivotal role in plant tolerance to abiotic stress. In addition, extensive studies have identified other stress-responsive transcription factors belonging to the NAC, AP2/ERF, MYB, and WRKY families that mediate plant response and tolerance to abiotic stress. These suggest that transcriptional regulation of stress-responsive genes is an essential step to determine the mechanisms underlying plant stress responses and tolerance to abiotic stress, and that these transcription factors may be important targets for development of crops with enhanced abiotic stress tolerance. In this review, we briefly describe the mechanisms underlying plant abiotic stress responses, focusing on ABA and JA metabolism and signaling pathways. We then summarize the diverse array of transcription factors involved in plant responses to abiotic stress, while noting their potential applications for improvement of stress tolerance.
Collapse
|
4
|
Forestan C, Farinati S, Zambelli F, Pavesi G, Rossi V, Varotto S. Epigenetic signatures of stress adaptation and flowering regulation in response to extended drought and recovery in Zea mays. PLANT, CELL & ENVIRONMENT 2020; 43:55-75. [PMID: 31677283 DOI: 10.1111/pce.13660] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 09/03/2019] [Accepted: 09/23/2019] [Indexed: 05/22/2023]
Abstract
During their lifespan, plants respond to a multitude of stressful factors. Dynamic changes in chromatin and concomitant transcriptional variations control stress response and adaptation, with epigenetic memory mechanisms integrating environmental conditions and appropriate developmental programs over the time. Here we analyzed transcriptome and genome-wide histone modifications of maize plants subjected to a mild and prolonged drought stress just before the flowering transition. Stress was followed by a complete recovery period to evaluate drought memory mechanisms. Three categories of stress-memory genes were identified: i) "transcriptional memory" genes, with stable transcriptional changes persisting after the recovery; ii) "epigenetic memory candidate" genes in which stress-induced chromatin changes persist longer than the stimulus, in absence of transcriptional changes; iii) "delayed memory" genes, not immediately affected by the stress, but perceiving and storing stress signal for a delayed response. This last memory mechanism is described for the first time in drought response. In addition, applied drought stress altered floral patterning, possibly by affecting expression and chromatin of flowering regulatory genes. Altogether, we provided a genome-wide map of the coordination between genes and chromatin marks utilized by plants to adapt to a stressful environment, describing how this serves as a backbone for setting stress memory.
Collapse
Affiliation(s)
- Cristian Forestan
- Department of Agronomy Animals Food Natural Resources and Environment (DAFNAE), University of Padova, Viale dell'Università 16, 35020, Legnaro, Italy
| | - Silvia Farinati
- Department of Agronomy Animals Food Natural Resources and Environment (DAFNAE), University of Padova, Viale dell'Università 16, 35020, Legnaro, Italy
| | - Federico Zambelli
- Department of Biosciences, University of Milan, Via Celoria 26, 20133, Milan, Italy
| | - Giulio Pavesi
- Department of Biosciences, University of Milan, Via Celoria 26, 20133, Milan, Italy
| | - Vincenzo Rossi
- CREA - Centro di Cerealicoltura e Colture Industriali (CREA-CI), Via Stezzano 24, 24126, Bergamo, Italy
| | - Serena Varotto
- Department of Agronomy Animals Food Natural Resources and Environment (DAFNAE), University of Padova, Viale dell'Università 16, 35020, Legnaro, Italy
| |
Collapse
|
5
|
Mmadi MA, Dossa K, Wang L, Zhou R, Wang Y, Cisse N, Sy MO, Zhang X. Functional Characterization of the Versatile MYB Gene Family Uncovered Their Important Roles in Plant Development and Responses to Drought and Waterlogging in Sesame. Genes (Basel) 2017; 8:genes8120362. [PMID: 29231869 PMCID: PMC5748680 DOI: 10.3390/genes8120362] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 11/22/2017] [Accepted: 11/29/2017] [Indexed: 12/02/2022] Open
Abstract
The MYB gene family constitutes one of the largest transcription factors (TFs) modulating various biological processes in plants. Although genome-wide analysis of this gene family has been carried out in some species, only three MYB members have been functionally characterized heretofore in sesame (Sesamum indicum L.). Here, we identified a relatively high number (287) of sesame MYB genes (SIMYBs) with an uncommon overrepresentation of the 1R-subfamily. A total of 95% of SIMYBs was mapped unevenly onto the 16 linkage groups of the sesame genome with 55 SIMYBs tandemly duplicated. In addition, molecular characterization, gene structure, and evolutionary relationships of SIMYBs were established. Based on the close relationship between sesame and Arabidopsis thaliana, we uncovered that the functions of SIMYBs are highly diverse. A total of 65% of SIMYBs were commonly detected in five tissues, suggesting that they represent key TFs modulating sesame growth and development. Moreover, we found that SIMYBs regulate sesame responses to drought and waterlogging, which highlights the potential of SIMYBs towards improving stress tolerance in sesame. This work presents a comprehensive picture of the MYB gene family in sesame and paves the way for further functional validation of the members of this versatile gene family.
Collapse
Affiliation(s)
- Marie Ali Mmadi
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China.
- Centre d'Etudes Régional pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS), BP 3320, Thiès, Senegal.
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, 107000 Dakar, Senegal.
| | - Komivi Dossa
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China.
- Centre d'Etudes Régional pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS), BP 3320, Thiès, Senegal.
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, 107000 Dakar, Senegal.
| | - Linhai Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China.
| | - Rong Zhou
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China.
| | - Yanyan Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China.
| | - Ndiaga Cisse
- Centre d'Etudes Régional pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS), BP 3320, Thiès, Senegal.
| | - Mame Oureye Sy
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, 107000 Dakar, Senegal.
| | - Xiurong Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China.
| |
Collapse
|
6
|
Zhang X, Liu X, Zhang D, Tang H, Sun B, Li C, Hao L, Liu C, Li Y, Shi Y, Xie X, Song Y, Wang T, Li Y. Genome-wide identification of gene expression in contrasting maize inbred lines under field drought conditions reveals the significance of transcription factors in drought tolerance. PLoS One 2017; 12:e0179477. [PMID: 28700592 PMCID: PMC5507481 DOI: 10.1371/journal.pone.0179477] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 05/31/2017] [Indexed: 11/19/2022] Open
Abstract
Drought is a major threat to maize growth and production. Understanding the molecular regulation network of drought tolerance in maize is of great importance. In this study, two maize inbred lines with contrasting drought tolerance were tested in the field under natural soil drought and well-watered conditions. In addition, the transcriptomes of their leaves was analyzed by RNA-Seq. In total, 555 and 2,558 genes were detected to specifically respond to drought in the tolerant and the sensitive line, respectively, with a more positive regulation tendency in the tolerant genotype. Furthermore, 4,700, 4,748, 4,403 and 4,288 genes showed differential expression between the two lines under moderate drought, severe drought and their well-watered controls, respectively. Transcription factors were enriched in both genotypic differentially expressed genes and specifically responsive genes of the tolerant line. It was speculated that the genotype-specific response of 20 transcription factors in the tolerance line and the sustained genotypically differential expression of 22 transcription factors might enhance tolerance to drought in maize. Our results provide new insight into maize drought tolerance-related regulation systems and provide gene resources for subsequent studies and drought tolerance improvement.
Collapse
Affiliation(s)
- Xiaojing Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuyang Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dengfeng Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huaijun Tang
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Baocheng Sun
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Chunhui Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Luyang Hao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Cheng Liu
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Yongxiang Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunsu Shi
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoqing Xie
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Yanchun Song
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tianyu Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yu Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
7
|
Li T, Sun Y, Ruan Y, Xu L, Hu Y, Hao Z, Zhang X, Li H, Wang Y, Yang L, Chen B. Potential role of D-myo-inositol-3-phosphate synthase and 14-3-3 genes in the crosstalk between Zea mays and Rhizophagus intraradices under drought stress. MYCORRHIZA 2016; 26:879-893. [PMID: 27456042 DOI: 10.1007/s00572-016-0723-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 07/12/2016] [Indexed: 05/16/2023]
Abstract
Arbuscular mycorrhizal (AM) symbiosis is known to stimulate plant drought tolerance. However, the mechanisms underlying the synergistic responses of the symbiotic partners to drought stress are largely unknown. A split-root experiment was designed to investigate the molecular interactions between a host plant and an AM fungus (AMF) under drought stress. In the two-compartment cultivation system, an entire or only a half root system of a maize plant was inoculated with an AMF, Rhizophagus intraradices, in the presence of localized or systemic drought treatment. Plant physiological parameters including growth, water status, and phosphorus concentration, and the expression of drought tolerance-related genes in both roots and R. intraradices were recorded. Although mycorrhizal inoculation in either one or both compartments systemically decreased abscisic acid (ABA) content in the whole root system subjected to systemic or local drought stress, we observed local and/or systemic AM effects on root physiological traits and the expression of functional genes in both roots and R. intraradices. Interestingly, the simultaneous increase in the expression of plant genes encoding D-myo-inositol-3-phosphate synthase (IPS) and 14-3-3-like protein GF14 (14-3GF), which were responsible for ABA signal transduction, was found to be involved in the activation of 14-3-3 protein and aquaporins (GintAQPF1 and GintAQPF2) in R. intraradices. These findings suggest that coexpression of IPS and 14-3GF is responsible for the crosstalk between maize and R. intraradices under drought stress, and potentially induces the synergistic actions of the symbiotic partners in enhancing plant drought tolerance.
Collapse
Affiliation(s)
- Tao Li
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Yuqing Sun
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Yuan Ruan
- Department of Botany, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | - Lijiiao Xu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Yajun Hu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - Zhipeng Hao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Xin Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Hong Li
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Youshan Wang
- Institute of Plant Nutrition and Resources, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Liguo Yang
- Beijing Agricultural Machinery Experiment Appraisal Popularization Station, Beijing, 100079, China
| | - Baodong Chen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
| |
Collapse
|
8
|
Opitz N, Marcon C, Paschold A, Malik WA, Lithio A, Brandt R, Piepho HP, Nettleton D, Hochholdinger F. Extensive tissue-specific transcriptomic plasticity in maize primary roots upon water deficit. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:1095-107. [PMID: 26463995 PMCID: PMC4753846 DOI: 10.1093/jxb/erv453] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Water deficit is the most important environmental constraint severely limiting global crop growth and productivity. This study investigated early transcriptome changes in maize (Zea mays L.) primary root tissues in response to moderate water deficit conditions by RNA-Sequencing. Differential gene expression analyses revealed a high degree of plasticity of the water deficit response. The activity status of genes (active/inactive) was determined by a Bayesian hierarchical model. In total, 70% of expressed genes were constitutively active in all tissues. In contrast, <3% (50 genes) of water deficit-responsive genes (1915) were consistently regulated in all tissues, while >75% (1501 genes) were specifically regulated in a single root tissue. Water deficit-responsive genes were most numerous in the cortex of the mature root zone and in the elongation zone. The most prominent functional categories among differentially expressed genes in all tissues were 'transcriptional regulation' and 'hormone metabolism', indicating global reprogramming of cellular metabolism as an adaptation to water deficit. Additionally, the most significant transcriptomic changes in the root tip were associated with cell wall reorganization, leading to continued root growth despite water deficit conditions. This study provides insight into tissue-specific water deficit responses and will be a resource for future genetic analyses and breeding strategies to develop more drought-tolerant maize cultivars.
Collapse
Affiliation(s)
- Nina Opitz
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, D-53113 Bonn, Germany
| | - Caroline Marcon
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, D-53113 Bonn, Germany
| | - Anja Paschold
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, D-53113 Bonn, Germany
| | - Waqas Ahmed Malik
- Institute for Crop Science, Biostatistics Unit, University of Hohenheim, D-70599 Stuttgart, Germany
| | - Andrew Lithio
- Department of Statistics, Iowa State University, Ames, IA 50011-1210, USA
| | - Ronny Brandt
- Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
| | - Hans-Peter Piepho
- Institute for Crop Science, Biostatistics Unit, University of Hohenheim, D-70599 Stuttgart, Germany
| | - Dan Nettleton
- Department of Statistics, Iowa State University, Ames, IA 50011-1210, USA
| | - Frank Hochholdinger
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, D-53113 Bonn, Germany
| |
Collapse
|
9
|
Kebede H, Payton P, Pham HTM, Allen RD, Wright RJ. Toward Coalescing Gene Expression and Function with QTLs of Water-Deficit Stress in Cotton. INTERNATIONAL JOURNAL OF PLANT GENOMICS 2015; 2015:892716. [PMID: 26167172 PMCID: PMC4488579 DOI: 10.1155/2015/892716] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 05/08/2015] [Accepted: 05/13/2015] [Indexed: 05/08/2023]
Abstract
Cotton exhibits moderately high vegetative tolerance to water-deficit stress but lint production is restricted by the available rainfed and irrigation capacity. We have described the impact of water-deficit stress on the genetic and metabolic control of fiber quality and production. Here we examine the association of tentative consensus sequences (TCs) derived from various cotton tissues under irrigated and water-limited conditions with stress-responsive QTLs. Three thousand sixteen mapped sequence-tagged-sites were used as anchored targets to examine sequence homology with 15,784 TCs to test the hypothesis that putative stress-responsive genes will map within QTLs associated with stress-related phenotypic variation more frequently than with other genomic regions not associated with these QTLs. Approximately 1,906 of 15,784 TCs were mapped to the consensus map. About 35% of the annotated TCs that mapped within QTL regions were genes involved in an abiotic stress response. By comparison, only 14.5% of the annotated TCs mapped outside these QTLs were classified as abiotic stress genes. A simple binomial probability calculation of this degree of bias being observed if QTL and non-QTL regions are equally likely to contain stress genes was P (x ≥ 85) = 7.99 × 10(-15). These results suggest that the QTL regions have a higher propensity to contain stress genes.
Collapse
Affiliation(s)
- Hirut Kebede
- USDA-ARS Crop Genetics Research Unit, Stoneville, MS 38776, USA
| | - Paxton Payton
- USDA-ARS Cropping Systems Research Laboratory, Lubbock, TX 79415, USA
| | - Hanh Thi My Pham
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409, USA
| | - Randy D. Allen
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 73401, USA
| | - Robert J. Wright
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409, USA
- *Robert J. Wright:
| |
Collapse
|
10
|
Nishiyama MY, Ferreira SS, Tang PZ, Becker S, Pörtner-Taliana A, Souza GM. Full-length enriched cDNA libraries and ORFeome analysis of sugarcane hybrid and ancestor genotypes. PLoS One 2014; 9:e107351. [PMID: 25222706 PMCID: PMC4164538 DOI: 10.1371/journal.pone.0107351] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 08/14/2014] [Indexed: 11/18/2022] Open
Abstract
Sugarcane is a major crop used for food and bioenergy production. Modern cultivars are hybrids derived from crosses between Saccharum officinarum and Saccharum spontaneum. Hybrid cultivars combine favorable characteristics from ancestral species and contain a genome that is highly polyploid and aneuploid, containing 100–130 chromosomes. These complex genomes represent a huge challenge for molecular studies and for the development of biotechnological tools that can facilitate sugarcane improvement. Here, we describe full-length enriched cDNA libraries for Saccharum officinarum, Saccharum spontaneum, and one hybrid genotype (SP803280) and analyze the set of open reading frames (ORFs) in their genomes (i.e., their ORFeomes). We found 38,195 (19%) sugarcane-specific transcripts that did not match transcripts from other databases. Less than 1.6% of all transcripts were ancestor-specific (i.e., not expressed in SP803280). We also found 78,008 putative new sugarcane transcripts that were absent in the largest sugarcane expressed sequence tag database (SUCEST). Functional annotation showed a high frequency of protein kinases and stress-related proteins. We also detected natural antisense transcript expression, which mapped to 94% of all plant KEGG pathways; however, each genotype showed different pathways enriched in antisense transcripts. Our data appeared to cover 53.2% (17,563 genes) and 46.8% (937 transcription factors) of all sugarcane full-length genes and transcription factors, respectively. This work represents a significant advancement in defining the sugarcane ORFeome and will be useful for protein characterization, single nucleotide polymorphism and splicing variant identification, evolutionary and comparative studies, and sugarcane genome assembly and annotation.
Collapse
Affiliation(s)
| | | | - Pei-Zhong Tang
- ThermoFisher Scientific, Carlsbad, California, United States of America
| | - Scott Becker
- ThermoFisher Scientific, Carlsbad, California, United States of America
| | | | - Glaucia Mendes Souza
- Departamento de Bioquímica, Universidade de São Paulo, São Paulo, SP, Brazil
- * E-mail:
| |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
Opitz N, Paschold A, Marcon C, Malik WA, Lanz C, Piepho HP, Hochholdinger F. Transcriptomic complexity in young maize primary roots in response to low water potentials. BMC Genomics 2014; 15:741. [PMID: 25174417 PMCID: PMC4174653 DOI: 10.1186/1471-2164-15-741] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 08/22/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Widespread and more frequently occurring drought conditions are a consequence of global warming and increase the demand for tolerant crop varieties to feed the growing world population. A better understanding of the molecular mechanisms underlying the water deficit response of crops will enable targeted breeding strategies to develop robust cultivars. RESULTS In the present study, the transcriptional response of maize (Zea mays L.) primary roots to low water potentials was monitored by RNA sequencing (RNA-Seq) experiments. After 6 h and 24 h of mild (-0.2 MPa) and severe (-0.8 MPa) water deficit conditions, the primary root transcriptomes of seedlings grown under water deficit and control conditions were compared. The number of responsive genes was dependent on and increased with intensification of water deficit treatment. After short-term mild and severe water deficit 249 and 3,000 genes were differentially expressed, respectively. After a 24 h treatment the number of affected genes increased to 7,267 and 12,838 for mild and severe water deficit, respectively, including more than 80% of the short-term responsive genes. About half of the differentially expressed genes were up-regulated and maximal fold-changes increased with treatment intensity to more than 300-fold. A consensus set of 53 genes was differentially regulated independently of the nature of deficit treatment. Characterization revealed an overrepresentation of the Gene Ontology (GO) categories "oxidoreductase activity" and "heme binding" among regulated genes connecting the water deficit response to ROS metabolism. CONCLUSION This study gives a comprehensive insight in water deficit responsive genes in young maize primary roots and provides a set of candidate genes that merit further genetic analyses in the future.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Frank Hochholdinger
- Institute of Crop Science and Resource Conservation (INRES), Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany.
| |
Collapse
|
13
|
Zhu YN, Shi DQ, Ruan MB, Zhang LL, Meng ZH, Liu J, Yang WC. Transcriptome analysis reveals crosstalk of responsive genes to multiple abiotic stresses in cotton (Gossypium hirsutum L.). PLoS One 2013; 8:e80218. [PMID: 24224045 PMCID: PMC3818253 DOI: 10.1371/journal.pone.0080218] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2013] [Accepted: 09/28/2013] [Indexed: 12/15/2022] Open
Abstract
Abiotic stress is a major environmental factor that limits cotton growth and yield, moreover, this problem has become more and more serious recently, as multiple stresses often occur simultaneously due to the global climate change and environmental pollution. In this study, we sought to identify genes involved in diverse stresses including abscisic acid (ABA), cold, drought, salinity and alkalinity by comparative microarray analysis. Our result showed that 5790, 3067, 5608, 778 and 6148 transcripts, were differentially expressed in cotton seedlings under treatment of ABA (1 μM ABA), cold (4°C), drought (200 mM mannitol), salinity (200 mM NaCl) and alkalinity (pH=11) respectively. Among the induced or suppressed genes, 126 transcripts were shared by all of the five kinds of abiotic stresses, with 64 up-regulated and 62 down-regulated. These common members are grouped as stress signal transduction, transcription factors (TFs), stress response/defense proteins, metabolism, transport facilitation, as well as cell wall/structure, according to the function annotation. We also noticed that large proportion of significant differentially expressed genes specifically regulated in response to different stress. Nine of the common transcripts of multiple stresses were selected for further validation with quantitative real time RT-PCR (qRT-PCR). Furthermore, several well characterized TF families, for example, WRKY, MYB, NAC, AP2/ERF and zinc finger were shown to be involved in different stresses. As an original report using comparative microarray to analyze transcriptome of cotton under five abiotic stresses, valuable information about functional genes and related pathways of anti-stress, and/or stress tolerance in cotton seedlings was unveiled in our result. Besides this, some important common factors were focused for detailed identification and characterization. According to our analysis, it suggested that there was crosstalk of responsive genes or pathways to multiple abiotic or even biotic stresses, in cotton. These candidate genes will be worthy of functional study under diverse stresses.
Collapse
Affiliation(s)
- Ya-Na Zhu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Dong-Qiao Shi
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- * E-mail: (WCY); (DQS)
| | - Meng-Bin Ruan
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Li-Li Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Zhao-Hong Meng
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jie Liu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Wei-Cai Yang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- * E-mail: (WCY); (DQS)
| |
Collapse
|
14
|
Thamil Arasan SK, Park JI, Ahmed NU, Jung HJ, Hur Y, Kang KK, Lim YP, Nou IS. Characterization and expression analysis of dirigent family genes related to stresses in Brassica. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2013; 67:144-53. [PMID: 23562798 DOI: 10.1016/j.plaphy.2013.02.030] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 02/28/2013] [Indexed: 05/04/2023]
Abstract
The dirigent (DIR) genes are playing a vital role in enhancing stress resistance in different crop plants. In this study, we collected 29 DIR like genes, two from a Brassica rapa cv. Osome full length cDNA library and 27 from the B. rapa database designated as B. rapa Dirigent (BrDIR) like genes. Sequence analysis and a comparison study of these genes confirmed that seven were dirigent and the remaining 22 were dirigent like genes. Expression analysis revealed an organ specific expression of these genes. BrDIR2 showed differential responses after Fusarium oxysporum f.sp. conglutinans infection in cabbage. Four Brassica oleracea dirigent like genes highly homologous to BrDIR2 also showed similar responses in cabbage plants infected with this fungus. Moreover, several BrDIR like genes showed significant responses after water, ABA and cold stress treatments in Chinese cabbage. Under water stress, most responsive genes showed the highest expression at 24 h, at which time the acid soluble lignin content of samples under the same stress condition were also highest, indicating a possible relationship between BrDIR like genes and lignin content. Taken together, our results indicate a protective role of BrDIR genes against biotic and abiotic stresses in Brassica.
Collapse
Affiliation(s)
- Senthil Kumar Thamil Arasan
- Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam 540-742, Republic of Korea
| | - Jong-In Park
- Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam 540-742, Republic of Korea
| | - Nasar Uddin Ahmed
- Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam 540-742, Republic of Korea
| | - Hee-Jeong Jung
- Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam 540-742, Republic of Korea
| | - Yoonkang Hur
- Department of Biology, Chungnam National University, 96 Daehangno, Gung-dong, Yuseong-gu, Daejeon 305-764, Republic of Korea
| | - Kwon-Kyoo Kang
- Department of Horticulture, Hankyong National University, 327 Chungangno, Anseong, Kyonggi 456-749, Republic of Korea
| | - Yong-Pyo Lim
- Department of Horticulture, Chungnam National University, 96 Daehangno, Gung-dong, Yuseong-gu, Daejeon 305-764, Republic of Korea
| | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam 540-742, Republic of Korea.
| |
Collapse
|
15
|
Sakai H, Lee SS, Tanaka T, Numa H, Kim J, Kawahara Y, Wakimoto H, Yang CC, Iwamoto M, Abe T, Yamada Y, Muto A, Inokuchi H, Ikemura T, Matsumoto T, Sasaki T, Itoh T. Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics. PLANT & CELL PHYSIOLOGY 2013; 54:e6. [PMID: 23299411 PMCID: PMC3583025 DOI: 10.1093/pcp/pcs183] [Citation(s) in RCA: 446] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The Rice Annotation Project Database (RAP-DB, http://rapdb.dna.affrc.go.jp/) has been providing a comprehensive set of gene annotations for the genome sequence of rice, Oryza sativa (japonica group) cv. Nipponbare. Since the first release in 2005, RAP-DB has been updated several times along with the genome assembly updates. Here, we present our newest RAP-DB based on the latest genome assembly, Os-Nipponbare-Reference-IRGSP-1.0 (IRGSP-1.0), which was released in 2011. We detected 37,869 loci by mapping transcript and protein sequences of 150 monocot species. To provide plant researchers with highly reliable and up to date rice gene annotations, we have been incorporating literature-based manually curated data, and 1,626 loci currently incorporate literature-based annotation data, including commonly used gene names or gene symbols. Transcriptional activities are shown at the nucleotide level by mapping RNA-Seq reads derived from 27 samples. We also mapped the Illumina reads of a Japanese leading japonica cultivar, Koshihikari, and a Chinese indica cultivar, Guangluai-4, to the genome and show alignments together with the single nucleotide polymorphisms (SNPs) and gene functional annotations through a newly developed browser, Short-Read Assembly Browser (S-RAB). We have developed two satellite databases, Plant Gene Family Database (PGFD) and Integrative Database of Cereal Gene Phylogeny (IDCGP), which display gene family and homologous gene relationships among diverse plant species. RAP-DB and the satellite databases offer simple and user-friendly web interfaces, enabling plant and genome researchers to access the data easily and facilitating a broad range of plant research topics.
Collapse
Affiliation(s)
- Hiroaki Sakai
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602 Japan
| | - Sung Shin Lee
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602 Japan
| | - Tsuyoshi Tanaka
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602 Japan
| | - Hisataka Numa
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602 Japan
| | - Jungsok Kim
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602 Japan
| | - Yoshihiro Kawahara
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602 Japan
| | - Hironobu Wakimoto
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602 Japan
- Application Solution Department, Hitachi Government & Public Corporation System Engineering, Ltd., Koto-ku, Tokyo, 135-8633 Japan
| | - Ching-chia Yang
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602 Japan
- Present address: Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, 277-8564 Japan
| | - Masao Iwamoto
- Division of Plant Sciences, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602 Japan
| | - Takashi Abe
- Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, 526-0829 Japan
- Graduate School of Science and Technology, Niigata University, Niigata, 950-2181 Japan
| | - Yuko Yamada
- Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, 526-0829 Japan
| | - Akira Muto
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori, 036-8561 Japan
| | - Hachiro Inokuchi
- Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, 526-0829 Japan
| | - Toshimichi Ikemura
- Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, 526-0829 Japan
| | - Takashi Matsumoto
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602 Japan
| | - Takuji Sasaki
- Tokyo University of Agriculture, Setagaya-ku, Tokyo, 156-8502 Japan
| | - Takeshi Itoh
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602 Japan
- *Corresponding author: E-mail, ; Fax, +81-29-838-7065
| |
Collapse
|
16
|
Begcy K, Mariano ED, Gentile A, Lembke CG, Zingaretti SM, Souza GM, Menossi M. A novel stress-induced sugarcane gene confers tolerance to drought, salt and oxidative stress in transgenic tobacco plants. PLoS One 2012; 7:e44697. [PMID: 22984543 PMCID: PMC3439409 DOI: 10.1371/journal.pone.0044697] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 08/09/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Drought is a major abiotic stress that affects crop productivity worldwide. Sugarcane can withstand periods of water scarcity during the final stage of culm maturation, during which sucrose accumulation occurs. Meanwhile, prolonged periods of drought can cause severe plant losses. METHODOLOGY/PRINCIPAL FINDINGS In a previous study, we evaluated the transcriptome of drought-stressed plants to better understand sugarcane responses to drought. Among the up-regulated genes was Scdr1 (sugarcane drought-responsive 1). The aim of the research reported here was to characterize this gene. Scdr1 encodes a putative protein containing 248 amino acids with a large number of proline (19%) and cysteine (13%) residues. Phylogenetic analysis showed that ScDR1is in a clade with homologs from other monocotyledonous plants, separate from those of dicotyledonous plants. The expression of Scdr1 in different varieties of sugarcane plants has not shown a clear association with drought tolerance. CONCLUSIONS/SIGNIFICANCE The overexpression of Scdr1 in transgenic tobacco plants increased their tolerance to drought, salinity and oxidative stress, as demonstrated by increased photosynthesis, water content, biomass, germination rate, chlorophyll content and reduced accumulation of ROS. Physiological parameters, such as transpiration rate (E), net photosynthesis (A), stomatal conductance (gs) and internal leaf CO(2) concentration, were less affected by abiotic stresses in transgenic Scdr1 plants compared with wild-type plants. Overall, our results indicated that Scdr1 conferred tolerance to multiple abiotic stresses, highlighting the potential of this gene for biotechnological applications.
Collapse
Affiliation(s)
- Kevin Begcy
- Laboratório de Genoma Funcional, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
| | - Eduardo D. Mariano
- Laboratório de Genoma Funcional, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
| | - Agustina Gentile
- Laboratório de Genoma Funcional, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
| | - Carolina G. Lembke
- Laboratório de Transdução de Sinal, Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Sonia Marli Zingaretti
- Unidade de Biotecnologia, Universidade de Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | - Glaucia M. Souza
- Laboratório de Transdução de Sinal, Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Marcelo Menossi
- Laboratório de Genoma Funcional, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
| |
Collapse
|
17
|
Xia Z, Liu Q, Wu J, Ding J. ZmRFP1, the putative ortholog of SDIR1, encodes a RING-H2 E3 ubiquitin ligase and responds to drought stress in an ABA-dependent manner in maize. Gene 2012; 495:146-53. [DOI: 10.1016/j.gene.2011.12.028] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2011] [Revised: 12/12/2011] [Accepted: 12/15/2011] [Indexed: 01/06/2023]
|
18
|
Lu HF, Dong HT, Sun CB, Qing DJ, Li N, Wu ZK, Wang ZQ, Li YZ. The panorama of physiological responses and gene expression of whole plant of maize inbred line YQ7-96 at the three-leaf stage under water deficit and re-watering. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:943-58. [PMID: 21735236 DOI: 10.1007/s00122-011-1638-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Accepted: 06/13/2011] [Indexed: 05/08/2023]
Abstract
Changes in water potential, growth elongation, photosynthesis of three-leaf-old seedlings of maize inbred line YQ7-96 under water deficit (WD) for 0.5, 1 and 2 h and re-watering (RW) for 24 h were characterized. Gene expression was analyzed using cDNA microarray covering 11,855 maize unigenes. As for whole maize plant, the expression of WD-regulated genes was characterized by up-regulation. The expression of WD-regulated genes was categorized into eight different patterns, respectively, in leaves and roots. Newly found and WD-affected cellular processes were metabolic process, amino acid and derivative metabolic process and cell death. A great number of the analyzed genes were found to be regulated specifically by RW and commonly by both WD and RW, respectively, in leaves. It is therefore concluded that (1) whole maize plant tolerance to WD, as well as growth recovery from WD, depends at least in part on transcriptional coordination between leaves and roots; (2) WD exerts effects on the maize, especially on basal metabolism; (3) WD could probably affect CO(2) uptake and partitioning, and transport of fixed carbons; (4) WD could likely influence nuclear activity and genome stability; and (5) maize growth recovery from WD is likely involved in some specific signaling pathways related to RW-specific responsive genes.
Collapse
Affiliation(s)
- Hai-Feng Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, College of Life Science and Technology, Guangxi University, Nanning, 530005, Guangxi, People's Republic of China
| | | | | | | | | | | | | | | |
Collapse
|
19
|
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.
Collapse
Affiliation(s)
- Hiroshi Abe
- Experimental Plant Division, Department of Biological Systems, RIKEN BioResource Center, Koyadai, Tsukuba, Ibaraki, Japan.
| | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Délano-Frier JP, Avilés-Arnaut H, Casarrubias-Castillo K, Casique-Arroyo G, Castrillón-Arbeláez PA, Herrera-Estrella L, Massange-Sánchez J, Martínez-Gallardo NA, Parra-Cota FI, Vargas-Ortiz E, Estrada-Hernández MG. Transcriptomic analysis of grain amaranth (Amaranthus hypochondriacus) using 454 pyrosequencing: comparison with A. tuberculatus, expression profiling in stems and in response to biotic and abiotic stress. BMC Genomics 2011; 12:363. [PMID: 21752295 PMCID: PMC3146458 DOI: 10.1186/1471-2164-12-363] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Accepted: 07/13/2011] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Amaranthus hypochondriacus, a grain amaranth, is a C4 plant noted by its ability to tolerate stressful conditions and produce highly nutritious seeds. These possess an optimal amino acid balance and constitute a rich source of health-promoting peptides. Although several recent studies, mostly involving subtractive hybridization strategies, have contributed to increase the relatively low number of grain amaranth expressed sequence tags (ESTs), transcriptomic information of this species remains limited, particularly regarding tissue-specific and biotic stress-related genes. Thus, a large scale transcriptome analysis was performed to generate stem- and (a)biotic stress-responsive gene expression profiles in grain amaranth. RESULTS A total of 2,700,168 raw reads were obtained from six 454 pyrosequencing runs, which were assembled into 21,207 high quality sequences (20,408 isotigs + 799 contigs). The average sequence length was 1,064 bp and 930 bp for isotigs and contigs, respectively. Only 5,113 singletons were recovered after quality control. Contigs/isotigs were further incorporated into 15,667 isogroups. All unique sequences were queried against the nr, TAIR, UniRef100, UniRef50 and Amaranthaceae EST databases for annotation. Functional GO annotation was performed with all contigs/isotigs that produced significant hits with the TAIR database. Only 8,260 sequences were found to be homologous when the transcriptomes of A. tuberculatus and A. hypochondriacus were compared, most of which were associated with basic house-keeping processes. Digital expression analysis identified 1,971 differentially expressed genes in response to at least one of four stress treatments tested. These included several multiple-stress-inducible genes that could represent potential candidates for use in the engineering of stress-resistant plants. The transcriptomic data generated from pigmented stems shared similarity with findings reported in developing stems of Arabidopsis and black cottonwood (Populus trichocarpa). CONCLUSIONS This study represents the first large-scale transcriptomic analysis of A. hypochondriacus, considered to be a highly nutritious and stress-tolerant crop. Numerous genes were found to be induced in response to (a)biotic stress, many of which could further the understanding of the mechanisms that contribute to multiple stress-resistance in plants, a trait that has potential biotechnological applications in agriculture.
Collapse
Affiliation(s)
- John P Délano-Frier
- Unidad de Biotecnología e Ingeniería Genética de Plantas, (Cinvestav-Unidad Irapuato) Km 9.6 del Libramiento Norte Carretera Irapuato-León. Apartado Postal 629, C.P. 36821, Irapuato, Gto., México
| | - Hamlet Avilés-Arnaut
- Unidad de Biotecnología e Ingeniería Genética de Plantas, (Cinvestav-Unidad Irapuato) Km 9.6 del Libramiento Norte Carretera Irapuato-León. Apartado Postal 629, C.P. 36821, Irapuato, Gto., México
| | - Kena Casarrubias-Castillo
- Unidad de Biotecnología e Ingeniería Genética de Plantas, (Cinvestav-Unidad Irapuato) Km 9.6 del Libramiento Norte Carretera Irapuato-León. Apartado Postal 629, C.P. 36821, Irapuato, Gto., México
| | - Gabriela Casique-Arroyo
- Unidad de Biotecnología e Ingeniería Genética de Plantas, (Cinvestav-Unidad Irapuato) Km 9.6 del Libramiento Norte Carretera Irapuato-León. Apartado Postal 629, C.P. 36821, Irapuato, Gto., México
| | - Paula A Castrillón-Arbeláez
- Unidad de Biotecnología e Ingeniería Genética de Plantas, (Cinvestav-Unidad Irapuato) Km 9.6 del Libramiento Norte Carretera Irapuato-León. Apartado Postal 629, C.P. 36821, Irapuato, Gto., México
| | - Luis Herrera-Estrella
- Laboratorio Nacional de Génomica para la Biodiversidad, Km 9.6 del Libramiento Norte Carretera Irapuato-León. Apartado Postal 629, C.P. 36821, Irapuato, Gto., México
| | - Julio Massange-Sánchez
- Unidad de Biotecnología e Ingeniería Genética de Plantas, (Cinvestav-Unidad Irapuato) Km 9.6 del Libramiento Norte Carretera Irapuato-León. Apartado Postal 629, C.P. 36821, Irapuato, Gto., México
| | - Norma A Martínez-Gallardo
- Unidad de Biotecnología e Ingeniería Genética de Plantas, (Cinvestav-Unidad Irapuato) Km 9.6 del Libramiento Norte Carretera Irapuato-León. Apartado Postal 629, C.P. 36821, Irapuato, Gto., México
| | - Fannie I Parra-Cota
- Unidad de Biotecnología e Ingeniería Genética de Plantas, (Cinvestav-Unidad Irapuato) Km 9.6 del Libramiento Norte Carretera Irapuato-León. Apartado Postal 629, C.P. 36821, Irapuato, Gto., México
| | - Erandi Vargas-Ortiz
- Unidad de Biotecnología e Ingeniería Genética de Plantas, (Cinvestav-Unidad Irapuato) Km 9.6 del Libramiento Norte Carretera Irapuato-León. Apartado Postal 629, C.P. 36821, Irapuato, Gto., México
| | - María G Estrada-Hernández
- Unidad de Biotecnología e Ingeniería Genética de Plantas, (Cinvestav-Unidad Irapuato) Km 9.6 del Libramiento Norte Carretera Irapuato-León. Apartado Postal 629, C.P. 36821, Irapuato, Gto., México
- Department of Entomology, College of Agricultural Sciences. Penn State University, University Park, PA 16802, USA
| |
Collapse
|
21
|
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.
Collapse
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
| |
Collapse
|
22
|
Lopes MS, Araus JL, van Heerden PDR, Foyer CH. Enhancing drought tolerance in C(4) crops. JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:3135-53. [PMID: 21511912 DOI: 10.1093/jxb/err105] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Adaptation to abiotic stresses is a quantitative trait controlled by many different genes. Enhancing the tolerance of crop plants to abiotic stresses such as drought has therefore proved to be somewhat elusive in terms of plant breeding. While many C(4) species have significant agronomic importance, most of the research effort on improving drought tolerance has focused on maize. Ideally, drought tolerance has to be achieved without penalties in yield potential. Possibilities for success in this regard are highlighted by studies on maize hybrids performed over the last 70 years that have demonstrated that yield potential and enhanced stress tolerance are associated traits. However, while our understanding of the molecular mechanisms that enable plants to tolerate drought has increased considerably in recent years, there have been relatively few applications of DNA marker technologies in practical C(4) breeding programmes for improved stress tolerance. Moreover, until recently, targeted approaches to drought tolerance have concentrated largely on shoot parameters, particularly those associated with photosynthesis and stay green phenotypes, rather than on root traits such as soil moisture capture for transpiration, root architecture, and improvement of effective use of water. These root traits are now increasingly considered as important targets for yield improvement in C(4) plants under drought stress. Similarly, the molecular mechanisms underpinning heterosis have considerable potential for exploitation in enhancing drought stress tolerance. While current evidence points to the crucial importance of root traits in drought tolerance in C(4) plants, shoot traits may also be important in maintaining high yields during drought.
Collapse
Affiliation(s)
- Marta S Lopes
- International Maize and Wheat Improvement (CIMMYT), Km. 45, Carretera Mexico-Veracruz, El Batan, Texcoco, CP 56130 Mexico
| | | | | | | |
Collapse
|
23
|
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.
Collapse
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
| |
Collapse
|
24
|
Payton P, Kottapalli KR, Kebede H, Mahan JR, Wright RJ, Allen RD. Examining the drought stress transcriptome in cotton leaf and root tissue. Biotechnol Lett 2010; 33:821-8. [DOI: 10.1007/s10529-010-0499-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Accepted: 12/08/2010] [Indexed: 10/18/2022]
|
25
|
Xie Z, Wang C, Wang K, Wang S, Li X, Zhang Z, Ma W, Yan Y. Molecular characterization of the celiac disease epitope domains in α-gliadin genes in Aegilops tauschii and hexaploid wheats (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 121:1239-51. [PMID: 20556595 DOI: 10.1007/s00122-010-1384-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2010] [Accepted: 06/03/2010] [Indexed: 05/24/2023]
Abstract
Nineteen novel full-ORF α-gliadin genes and 32 pseudogenes containing at least one stop codon were cloned and sequenced from three Aegilops tauschii accessions (T15, T43 and T26) and two bread wheat cultivars (Gaocheng 8901 and Zhongyou 9507). Analysis of three typical α-gliadin genes (Gli-At4, Gli-G1 and Gli-Z4) revealed some InDels and a considerable number of SNPs among them. Most of the pseudogenes were resulted from C to T change, leading to the generation of TAG or TAA in-frame stop codon. The putative proteins of both Gli-At3 and Gli-Z7 genes contained an extra cysteine residue in the unique domain II. Analysis of toxic epitodes among 19 deduced α-gliadins demonstrated that 14 of these contained 1-5 T cell stimulatory toxic epitopes while the other 5 did not contain any toxic epitopes. The glutamine residues in two specific ployglutamine domains ranged from 7 to 27, indicating a high variation in length. According to the numbers of 4 T cell stimulatory toxic epitopes and glutamine residues in the two ployglutamine domains among the 19 α-gliadin genes, 2 were assigned to chromosome 6A, 5 to chromosome 6B and 12 to chromosome 6D. These results were consistent with those from wheat cv. Chinese Spring nulli-tetrasomic and phylogenetic analysis. Secondary structure prediction showed that all α-gliadins had high content of β-strands and most of the α-helixes and β-strands were present in two unique domains. Phylogenetic analysis demonstrated that α-gliadin genes had a high homology with γ-gliadin, B-hordein, and LMW-GS genes and they diverged at approximate 39 MYA. Finally, the five α-gliadin genes were successfully expressed in E. coli, and their expression amount reached to the maximum after 4 h induced by IPTG, indicating that the α-gliadin genes can express in a high level under the control of T(7) promoter.
Collapse
MESH Headings
- Amino Acid Sequence
- Base Sequence
- Celiac Disease/genetics
- Celiac Disease/immunology
- Chromosome Mapping
- Cloning, Molecular
- DNA, Plant/genetics
- Epitopes, T-Lymphocyte/chemistry
- Epitopes, T-Lymphocyte/genetics
- Epitopes, T-Lymphocyte/immunology
- Escherichia coli
- Genes, Plant/genetics
- Genes, Plant/immunology
- Gliadin/chemistry
- Gliadin/genetics
- Gliadin/immunology
- Humans
- INDEL Mutation
- Open Reading Frames
- Peptides
- Phylogeny
- Polymorphism, Single Nucleotide
- Protein Structure, Secondary
- Pseudogenes
- Sequence Alignment
- Sequence Analysis, DNA
- Triticum/genetics
- Triticum/immunology
Collapse
Affiliation(s)
- Zhenze Xie
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, Beijing, China
| | | | | | | | | | | | | | | |
Collapse
|
26
|
Ling Y, Du Z, Zhang Z, Su Z. ProFITS of maize: a database of protein families involved in the transduction of signalling in the maize genome. BMC Genomics 2010; 11:580. [PMID: 20955618 PMCID: PMC3091727 DOI: 10.1186/1471-2164-11-580] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Accepted: 10/19/2010] [Indexed: 11/13/2022] Open
Abstract
Background Maize (Zea mays ssp. mays L.) is an important model for plant basic and applied research. In 2009, the B73 maize genome sequencing made a great step forward, using clone by clone strategy; however, functional annotation and gene classification of the maize genome are still limited. Thus, a well-annotated datasets and informative database will be important for further research discoveries. Signal transduction is a fundamental biological process in living cells, and many protein families participate in this process in sensing, amplifying and responding to various extracellular or internal stimuli. Therefore, it is a good starting point to integrate information on the maize functional genes involved in signal transduction. Results Here we introduce a comprehensive database 'ProFITS' (Protein Families Involved in the Transduction of Signalling), which endeavours to identify and classify protein kinases/phosphatases, transcription factors and ubiquitin-proteasome-system related genes in the B73 maize genome. Users can explore gene models, corresponding transcripts and FLcDNAs using the three abovementioned protein hierarchical categories, and visualize them using an AJAX-based genome browser (JBrowse) or Generic Genome Browser (GBrowse). Functional annotations such as GO annotation, protein signatures, protein best-hits in the Arabidopsis and rice genome are provided. In addition, pre-calculated transcription factor binding sites of each gene are generated and mutant information is incorporated into ProFITS. In short, ProFITS provides a user-friendly web interface for studies in signal transduction process in maize. Conclusion ProFITS, which utilizes both the B73 maize genome and full length cDNA (FLcDNA) datasets, provides users a comprehensive platform of maize annotation with specific focus on the categorization of families involved in the signal transduction process. ProFITS is designed as a user-friendly web interface and it is valuable for experimental researchers. It is freely available now to all users at http://bioinfo.cau.edu.cn/ProFITS.
Collapse
Affiliation(s)
- Yi Ling
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | | | | | | |
Collapse
|
27
|
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.
Collapse
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
| | | | | | | | | |
Collapse
|
28
|
Cao Z, Jia Z, Liu Y, Wang M, Zhao J, Zheng J, Wang G. Constitutive expression of ZmsHSP in Arabidopsis enhances their cytokinin sensitivity. Mol Biol Rep 2010; 37:1089-97. [PMID: 19821154 DOI: 10.1007/s11033-009-9848-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2009] [Accepted: 09/28/2009] [Indexed: 01/15/2023]
Abstract
A small HSP gene, ZmsHSP, was isolated from Zea mays. Sequence analysis revealed that the open reading frame of ZmsHSP was 477 bp and that it encodes a protein composed of 159 amino acid residues with a calculated molecular mass of 18.17 kD and a predicated isoelectric point (pI) of 5.63. ZmsHSP contains a CS domain (p23-like domain) and shares similarity with the HSP90 co-chaperone p23. The expression level of ZmsHSP was different among various tissues with the highest expression in leaves and the lowest in silks. Results also showed that the expression of ZmsHSP in maize was significantly up-regulated by dehydration. Transgenic Arabidopsis plants overexpressing ZmsHSP under the control of the CaMV 35S promoter had lower endogenous cytokinin content and showed more sensitivity to cytokinin during the germination and early seedling stage than wild-type plants, suggesting that ZmsHSP might has a function in cytokinin response in Zea mays.
Collapse
Affiliation(s)
- Zuping Cao
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100094, China
| | | | | | | | | | | | | |
Collapse
|
29
|
Aoki K, Yano K, Suzuki A, Kawamura S, Sakurai N, Suda K, Kurabayashi A, Suzuki T, Tsugane T, Watanabe M, Ooga K, Torii M, Narita T, Shin-I T, Kohara Y, Yamamoto N, Takahashi H, Watanabe Y, Egusa M, Kodama M, Ichinose Y, Kikuchi M, Fukushima S, Okabe A, Arie T, Sato Y, Yazawa K, Satoh S, Omura T, Ezura H, Shibata D. Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomics. BMC Genomics 2010. [PMID: 20350329 DOI: 10.1186/1471‐2164‐11‐210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Solanaceae family includes several economically important vegetable crops. The tomato (Solanum lycopersicum) is regarded as a model plant of the Solanaceae family. Recently, a number of tomato resources have been developed in parallel with the ongoing tomato genome sequencing project. In particular, a miniature cultivar, Micro-Tom, is regarded as a model system in tomato genomics, and a number of genomics resources in the Micro-Tom-background, such as ESTs and mutagenized lines, have been established by an international alliance. RESULTS To accelerate the progress in tomato genomics, we developed a collection of fully-sequenced 13,227 Micro-Tom full-length cDNAs. By checking redundant sequences, coding sequences, and chimeric sequences, a set of 11,502 non-redundant full-length cDNAs (nrFLcDNAs) was generated. Analysis of untranslated regions demonstrated that tomato has longer 5'- and 3'-untranslated regions than most other plants but rice. Classification of functions of proteins predicted from the coding sequences demonstrated that nrFLcDNAs covered a broad range of functions. A comparison of nrFLcDNAs with genes of sixteen plants facilitated the identification of tomato genes that are not found in other plants, most of which did not have known protein domains. Mapping of the nrFLcDNAs onto currently available tomato genome sequences facilitated prediction of exon-intron structure. Introns of tomato genes were longer than those of Arabidopsis and rice. According to a comparison of exon sequences between the nrFLcDNAs and the tomato genome sequences, the frequency of nucleotide mismatch in exons between Micro-Tom and the genome-sequencing cultivar (Heinz 1706) was estimated to be 0.061%. CONCLUSION The collection of Micro-Tom nrFLcDNAs generated in this study will serve as a valuable genomic tool for plant biologists to bridge the gap between basic and applied studies. The nrFLcDNA sequences will help annotation of the tomato whole-genome sequence and aid in tomato functional genomics and molecular breeding. Full-length cDNA sequences and their annotations are provided in the database KaFTom http://www.pgb.kazusa.or.jp/kaftom/ via the website of the National Bioresource Project Tomato http://tomato.nbrp.jp.
Collapse
Affiliation(s)
- Koh Aoki
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Japan.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Aoki K, Yano K, Suzuki A, Kawamura S, Sakurai N, Suda K, Kurabayashi A, Suzuki T, Tsugane T, Watanabe M, Ooga K, Torii M, Narita T, Shin-I T, Kohara Y, Yamamoto N, Takahashi H, Watanabe Y, Egusa M, Kodama M, Ichinose Y, Kikuchi M, Fukushima S, Okabe A, Arie T, Sato Y, Yazawa K, Satoh S, Omura T, Ezura H, Shibata D. Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomics. BMC Genomics 2010; 11:210. [PMID: 20350329 PMCID: PMC2859864 DOI: 10.1186/1471-2164-11-210] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2009] [Accepted: 03/30/2010] [Indexed: 11/18/2022] Open
Abstract
Background The Solanaceae family includes several economically important vegetable crops. The tomato (Solanum lycopersicum) is regarded as a model plant of the Solanaceae family. Recently, a number of tomato resources have been developed in parallel with the ongoing tomato genome sequencing project. In particular, a miniature cultivar, Micro-Tom, is regarded as a model system in tomato genomics, and a number of genomics resources in the Micro-Tom-background, such as ESTs and mutagenized lines, have been established by an international alliance. Results To accelerate the progress in tomato genomics, we developed a collection of fully-sequenced 13,227 Micro-Tom full-length cDNAs. By checking redundant sequences, coding sequences, and chimeric sequences, a set of 11,502 non-redundant full-length cDNAs (nrFLcDNAs) was generated. Analysis of untranslated regions demonstrated that tomato has longer 5'- and 3'-untranslated regions than most other plants but rice. Classification of functions of proteins predicted from the coding sequences demonstrated that nrFLcDNAs covered a broad range of functions. A comparison of nrFLcDNAs with genes of sixteen plants facilitated the identification of tomato genes that are not found in other plants, most of which did not have known protein domains. Mapping of the nrFLcDNAs onto currently available tomato genome sequences facilitated prediction of exon-intron structure. Introns of tomato genes were longer than those of Arabidopsis and rice. According to a comparison of exon sequences between the nrFLcDNAs and the tomato genome sequences, the frequency of nucleotide mismatch in exons between Micro-Tom and the genome-sequencing cultivar (Heinz 1706) was estimated to be 0.061%. Conclusion The collection of Micro-Tom nrFLcDNAs generated in this study will serve as a valuable genomic tool for plant biologists to bridge the gap between basic and applied studies. The nrFLcDNA sequences will help annotation of the tomato whole-genome sequence and aid in tomato functional genomics and molecular breeding. Full-length cDNA sequences and their annotations are provided in the database KaFTom http://www.pgb.kazusa.or.jp/kaftom/ via the website of the National Bioresource Project Tomato http://tomato.nbrp.jp.
Collapse
Affiliation(s)
- Koh Aoki
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Japan.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Zhao YH, Möller M, Yang JB, Liu TS, Zhao JF, Dong LN, Zhang JP, Li CY, Wang GY, Li DZ. Extended expression of B-class MADS-box genes in the paleoherb Asarum caudigerum. PLANTA 2010; 231:265-276. [PMID: 19904556 PMCID: PMC7088318 DOI: 10.1007/s00425-009-1048-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2009] [Accepted: 10/23/2009] [Indexed: 05/28/2023]
Abstract
Asarum caudigerum (Aristolochiaceae) is a paleoherb species that is important for research in origin and evolution of angiosperm flowers due to its basal position in the angiosperm phylogeny. In this study, a subtracted floral cDNA library from floral buds of A. caudigerum was constructed and cDNA arrays by suppression subtractive hybridization were generated. cDNAs of floral buds at different stages before flower opening and of leaves at the seedling stage were used. The macroarray analyses of expression profiles of isolated floral genes showed that 157 genes out of the 612 unique ESTs tested revealed higher transcript abundance in the floral buds and uppermost leaves. Among them, 78 genes were determined to be differentially expressed in the perianth, 62 in the stamens, and 100 genes in the carpels. Quantitative real-time PCR of selected genes validated the macroarray results. Remarkably, APETALA3 (AP3) B-class genes isolated from A. caudigerum were upregulated in the perianth, stamens and carpels, implying that the expression domain of B-class genes in this basal angiosperm was broader than those in their eudicot counterparts.
Collapse
Affiliation(s)
- Yin-He Zhao
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, 650204 Kunming, China
- College of Agronomy and Key Laboratory for Plant Pathology of Yunnan Province, Yunnan Agricultural University, 650201 Kunming, China
| | - Michael Möller
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR Scotland, UK
| | - Jun-Bo Yang
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, 650204 Kunming, China
| | - Ting-Song Liu
- State Key Laboratory of Agrobiotechnology, China Agricultural University, 100094 Beijing, China
| | - Jin-Feng Zhao
- State Key Laboratory of Agrobiotechnology, China Agricultural University, 100094 Beijing, China
| | - Li-Na Dong
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, 650204 Kunming, China
| | - Jin-Peng Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Zhongguancun Nandajie 12, 100081 Beijing, China
| | - Cheng-Yun Li
- College of Agronomy and Key Laboratory for Plant Pathology of Yunnan Province, Yunnan Agricultural University, 650201 Kunming, China
| | - Guo-Ying Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Zhongguancun Nandajie 12, 100081 Beijing, China
| | - De-Zhu Li
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, 650204 Kunming, China
| |
Collapse
|
32
|
Sequencing, mapping, and analysis of 27,455 maize full-length cDNAs. PLoS Genet 2009; 5:e1000740. [PMID: 19936069 PMCID: PMC2774520 DOI: 10.1371/journal.pgen.1000740] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Accepted: 10/24/2009] [Indexed: 11/29/2022] Open
Abstract
Full-length cDNA (FLcDNA) sequencing establishes the precise primary structure of individual gene transcripts. From two libraries representing 27 B73 tissues and abiotic stress treatments, 27,455 high-quality FLcDNAs were sequenced. The average transcript length was 1.44 kb including 218 bases and 321 bases of 5′ and 3′ UTR, respectively, with 8.6% of the FLcDNAs encoding predicted proteins of fewer than 100 amino acids. Approximately 94% of the FLcDNAs were stringently mapped to the maize genome. Although nearly two-thirds of this genome is composed of transposable elements (TEs), only 5.6% of the FLcDNAs contained TE sequences in coding or UTR regions. Approximately 7.2% of the FLcDNAs are putative transcription factors, suggesting that rare transcripts are well-enriched in our FLcDNA set. Protein similarity searching identified 1,737 maize transcripts not present in rice, sorghum, Arabidopsis, or poplar annotated genes. A strict FLcDNA assembly generated 24,467 non-redundant sequences, of which 88% have non-maize protein matches. The FLcDNAs were also assembled with 41,759 FLcDNAs in GenBank from other projects, where semi-strict parameters were used to identify 13,368 potentially unique non-redundant sequences from this project. The libraries, ESTs, and FLcDNA sequences produced from this project are publicly available. The annotated EST and FLcDNA assemblies are available through the maize FLcDNA web resource (www.maizecdna.org). To complement the completion of sequencing the maize B73 genome, we sequenced 27,455 full-length cDNAs (FLcDNA) from two maize B73 libraries representing the gene transcripts from most tissues and common abiotic stress conditions. The FLcDNAs are beneficial in determining the exon/intron structure of genes by aligning them to the sequenced genome; 94% of our FLcDNAs aligned to the maize genome. The 27,455 FLcDNAs were compared to gene sequences for rice, sorghum, Arabidopsis, and poplar; 22,874 were found in all four sets, and 1,737 were unique to maize. Two-thirds of the maize genome is composed of a type of repetitive sequence called “transposable elements”; only 5.6% of the FLcDNA sequence contained any segment homologous to these repeats. In addition to our set, there are three other sets of maize FLcDNAs for a total of 69,306 gene transcripts, where many of them are from different maize lines (i.e. FLcDNAs often have only slight differences reflecting divergence). We assembled these together using parameters that would allow most alleles and recently diverged gene transcripts to align together, resulting in 46,739 unique gene transcripts.
Collapse
|
33
|
Hayano-Kanashiro C, Calderón-Vázquez C, Ibarra-Laclette E, Herrera-Estrella L, Simpson J. Analysis of gene expression and physiological responses in three Mexican maize landraces under drought stress and recovery irrigation. PLoS One 2009; 4:e7531. [PMID: 19888455 PMCID: PMC2766256 DOI: 10.1371/journal.pone.0007531] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2009] [Accepted: 09/18/2009] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Drought is one of the major constraints for plant productivity worldwide. Different mechanisms of drought-tolerance have been reported for several plant species including maize. However, the differences in global gene expression between drought-tolerant and susceptible genotypes and their relationship to physiological adaptations to drought are largely unknown. The study of the differences in global gene expression between tolerant and susceptible genotypes could provide important information to design more efficient breeding programs to produce maize varieties better adapted to water limiting conditions. METHODOLOGY/PRINCIPAL FINDINGS Changes in physiological responses and gene expression patterns were studied under drought stress and recovery in three Mexican maize landraces which included two drought tolerant (Cajete criollo and Michoacán 21) and one susceptible (85-2) genotypes. Photosynthesis, stomatal conductance, soil and leaf water potentials were monitored throughout the experiment and microarray analysis was carried out on transcripts obtained at 10 and 17 days following application of stress and after recovery irrigation. The two tolerant genotypes show more drastic changes in global gene expression which correlate with different physiological mechanisms of adaptation to drought. Differences in the kinetics and number of up- and down-regulated genes were observed between the tolerant and susceptible maize genotypes, as well as differences between the two tolerant genotypes. Interestingly, the most dramatic differences between the tolerant and susceptible genotypes were observed during recovery irrigation, suggesting that the tolerant genotypes activate mechanisms that allow more efficient recovery after a severe drought. CONCLUSIONS/SIGNIFICANCE A correlation between levels of photosynthesis and transcription under stress was observed and differences in the number, type and expression levels of transcription factor families were also identified under drought and recovery between the three maize landraces. Gene expression analysis suggests that the drought tolerant landraces have a greater capacity to rapidly modulate more genes under drought and recovery in comparison to the susceptible landrace. Modulation of a greater number of differentially expressed genes of different TF gene families is an important characteristic of the tolerant genotypes. Finally, important differences were also noted between the tolerant landraces that underlie different mechanisms of achieving tolerance.
Collapse
Affiliation(s)
- Corina Hayano-Kanashiro
- Centro de Investigación y Estudios Avanzados, Departamento de Ingeniería Genética de Plantas, Libramiento Norte Carretera Irapuato-León, Irapuato, Guanajuato, Mexico
| | - Carlos Calderón-Vázquez
- Centro de Investigación y Estudios Avanzados, Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Libramiento Norte Carretera Irapuato-León, Irapuato, Guanajuato, Mexico
| | - Enrique Ibarra-Laclette
- Centro de Investigación y Estudios Avanzados, Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Libramiento Norte Carretera Irapuato-León, Irapuato, Guanajuato, Mexico
| | - Luis Herrera-Estrella
- Centro de Investigación y Estudios Avanzados, Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Libramiento Norte Carretera Irapuato-León, Irapuato, Guanajuato, Mexico
| | - June Simpson
- Centro de Investigación y Estudios Avanzados, Departamento de Ingeniería Genética de Plantas, Libramiento Norte Carretera Irapuato-León, Irapuato, Guanajuato, Mexico
| |
Collapse
|
34
|
Li Y, Sun C, Huang Z, Pan J, Wang L, Fan X. Mechanisms of Progressive Water Deficit Tolerance and Growth Recovery of Chinese Maize Foundation Genotypes Huangzao 4 and Chang 7-2, Which are Proposed on the Basis of Comparison of Physiological and Transcriptomic Responses. ACTA ACUST UNITED AC 2009; 50:2092-111. [DOI: 10.1093/pcp/pcp145] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
35
|
Differential gene expression analysis of maize leaf at heading stage in response to water-deficit stress. Biosci Rep 2009; 28:125-34. [PMID: 18422487 DOI: 10.1042/bsr20070023] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The whole-genomic gene-expression changes of maize (Zea mays L.) plants in response to water-deficit stress at the heading stage have not been previously studied. The present work utilized a maize oligonucleotide array ('57K', approximately 57000 sequences; http://www.maizearray.org/) representing more than 30000 unique genes, to profile transcriptome changes in maize leaves subjected to 1d (day) and 7d water-deficit stress. After 1d and 7d water-stress treatment, 195 and 1008 differential genes were identified respectively. One-third of 1d-water-stress-induced genes had known or putative functions in various cellular signalling pathways, indicating that signal-transduction-related genes play important roles in the early responses of maize leaves to water stress. The 7d-stress-regulated genes were involved in a broad range of cellular and biochemical activities. The most notable genes may function in compatible osmolyte metabolism, particularly in proline, sucrose, trehalose and raffinose metabolism in the leaves. The present study provided a valuable starting point for further elucidation of molecular mechanisms in the drought tolerance of maize plants.
Collapse
|
36
|
DENG XF, FU FL, NI N, LI WC. Differential Gene Expression in Response to Drought Stress in Maize Seedling. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/s1671-2927(08)60277-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
37
|
Mochida K, Yoshida T, Sakurai T, Ogihara Y, Shinozaki K. TriFLDB: a database of clustered full-length coding sequences from Triticeae with applications to comparative grass genomics. PLANT PHYSIOLOGY 2009; 150:1135-46. [PMID: 19448038 PMCID: PMC2705016 DOI: 10.1104/pp.109.138214] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2009] [Accepted: 05/08/2009] [Indexed: 05/19/2023]
Abstract
The Triticeae Full-Length CDS Database (TriFLDB) contains available information regarding full-length coding sequences (CDSs) of the Triticeae crops wheat (Triticum aestivum) and barley (Hordeum vulgare) and includes functional annotations and comparative genomics features. TriFLDB provides a search interface using keywords for gene function and related Gene Ontology terms and a similarity search for DNA and deduced translated amino acid sequences to access annotations of Triticeae full-length CDS (TriFLCDS) entries. Annotations consist of similarity search results against several sequence databases and domain structure predictions by InterProScan. The deduced amino acid sequences in TriFLDB are grouped with the proteome datasets for Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), and sorghum (Sorghum bicolor) by hierarchical clustering in stepwise thresholds of sequence identity, providing hierarchical clustering results based on full-length protein sequences. The database also provides sequence similarity results based on comparative mapping of TriFLCDSs onto the rice and sorghum genome sequences, which together with current annotations can be used to predict gene structures for TriFLCDS entries. To provide the possible genetic locations of full-length CDSs, TriFLCDS entries are also assigned to the genetically mapped cDNA sequences of barley and diploid wheat, which are currently accommodated in the Triticeae Mapped EST Database. These relational data are searchable from the search interfaces of both databases. The current TriFLDB contains 15,871 full-length CDSs from barley and wheat and includes putative full-length cDNAs for barley and wheat, which are publicly accessible. This informative content provides an informatics gateway for Triticeae genomics and grass comparative genomics. TriFLDB is publicly available at http://TriFLDB.psc.riken.jp/.
Collapse
|
38
|
Zamora A, Sun Q, Hamblin MT, Aquadro CF, Kresovich S. Positively selected disease response orthologous gene sets in the cereals identified using Sorghum bicolor L. Moench expression profiles and comparative genomics. Mol Biol Evol 2009; 26:2015-30. [PMID: 19506000 DOI: 10.1093/molbev/msp114] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Disease response genes (DRGs) diverge under recurrent positive selection as a result of a molecular arms race between hosts and pathogens. Most of these studies were conducted in animals, and few defense genes have been shown to evolve adaptively in plants. To test for adaptation in the molecules mediating disease resistance in the cereals, we first combined information from the expression pattern of Sorghum bicolor genes and from divergence to the full genome of rice to identify candidate DRGs. We then used evolutionary analyses of orthologous gene sets from several grass species, to determine whether the DRGs show signals of positive selection and the residues targeted. We found 140 divergent genes upregulated under biotic stress in S. bicolor by evaluating the relative abundance of expressed sequence tags in different libraries and comparing them with rice genes. For 10 of these genes, we found sets of orthologs including sequences from rice and three other cereals; six genes showed a pattern of substitution that was consistent with positive selection. Three of these genes, a thaumatin, a peroxidase, and a barley mlo homolog, are known antifungal proteins. The other three genes with evidence of positive selection were a MCM-1 agamous deficiens SRF- (MADS) box transcription factor, an eIF5 translation initiation factor, and a gene of unknown function but with evidence of expression during stress. Permutation analyses, using different ortholog and paralog sequences, consistently identified five positively selected codons in the peroxidase, a member of a cluster of genes and a large gene family. We mapped the positively selected residues onto the structure of the peroxidase and thaumatin and found that all sites are on the surface of these proteins and several are close to biochemically determined active sites. Identifying new positively selected plant disease resistance genes and the critical amino acid sites provides a basis for functional studies that may increase our understanding of their underlying molecular mechanisms of action. Additionally, it may lead to the identification of individuals having variation at functionally important sites, as well as eventually using this information in the rational design and engineering of proteins involved in plant disease resistance.
Collapse
Affiliation(s)
- Alejandro Zamora
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA.
| | | | | | | | | |
Collapse
|
39
|
Alexandrov NN, Brover VV, Freidin S, Troukhan ME, Tatarinova TV, Zhang H, Swaller TJ, Lu YP, Bouck J, Flavell RB, Feldmann KA. Insights into corn genes derived from large-scale cDNA sequencing. PLANT MOLECULAR BIOLOGY 2009; 69:179-94. [PMID: 18937034 PMCID: PMC2709227 DOI: 10.1007/s11103-008-9415-4] [Citation(s) in RCA: 149] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2008] [Accepted: 10/01/2008] [Indexed: 05/19/2023]
Abstract
We present a large portion of the transcriptome of Zea mays, including ESTs representing 484,032 cDNA clones from 53 libraries and 36,565 fully sequenced cDNA clones, out of which 31,552 clones are non-redundant. These and other previously sequenced transcripts have been aligned with available genome sequences and have provided new insights into the characteristics of gene structures and promoters within this major crop species. We found that although the average number of introns per gene is about the same in corn and Arabidopsis, corn genes have more alternatively spliced isoforms. Examination of the nucleotide composition of coding regions reveals that corn genes, as well as genes of other Poaceae (Grass family), can be divided into two classes according to the GC content at the third position in the amino acid encoding codons. Many of the transcripts that have lower GC content at the third position have dicot homologs but the high GC content transcripts tend to be more specific to the grasses. The high GC content class is also enriched with intronless genes. Together this suggests that an identifiable class of genes in plants is associated with the Poaceae divergence. Furthermore, because many of these genes appear to be derived from ancestral genes that do not contain introns, this evolutionary divergence may be the result of horizontal gene transfer from species not only with different codon usage but possibly that did not have introns, perhaps outside of the plant kingdom. By comparing the cDNAs described herein with the non-redundant set of corn mRNAs in GenBank, we estimate that there are about 50,000 different protein coding genes in Zea. All of the sequence data from this study have been submitted to DDBJ/GenBank/EMBL under accession numbers EU940701-EU977132 (FLI cDNA) and FK944382-FL482108 (EST).
Collapse
|
40
|
Umezawa T, Sakurai T, Totoki Y, Toyoda A, Seki M, Ishiwata A, Akiyama K, Kurotani A, Yoshida T, Mochida K, Kasuga M, Todaka D, Maruyama K, Nakashima K, Enju A, Mizukado S, Ahmed S, Yoshiwara K, Harada K, Tsubokura Y, Hayashi M, Sato S, Anai T, Ishimoto M, Funatsuki H, Teraishi M, Osaki M, Shinano T, Akashi R, Sakaki Y, Yamaguchi-Shinozaki K, Shinozaki K. Sequencing and analysis of approximately 40,000 soybean cDNA clones from a full-length-enriched cDNA library. DNA Res 2008; 15:333-46. [PMID: 18927222 PMCID: PMC2608845 DOI: 10.1093/dnares/dsn024] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Accepted: 09/10/2008] [Indexed: 11/14/2022] Open
Abstract
A large collection of full-length cDNAs is essential for the correct annotation of genomic sequences and for the functional analysis of genes and their products. We obtained a total of 39,936 soybean cDNA clones (GMFL01 and GMFL02 clone sets) in a full-length-enriched cDNA library which was constructed from soybean plants that were grown under various developmental and environmental conditions. Sequencing from 5' and 3' ends of the clones generated 68 661 expressed sequence tags (ESTs). The EST sequences were clustered into 22,674 scaffolds involving 2580 full-length sequences. In addition, we sequenced 4712 full-length cDNAs. After removing overlaps, we obtained 6570 new full-length sequences of soybean cDNAs so far. Our data indicated that 87.7% of the soybean cDNA clones contain complete coding sequences in addition to 5'- and 3'-untranslated regions. All of the obtained data confirmed that our collection of soybean full-length cDNAs covers a wide variety of genes. Comparative analysis between the derived sequences from soybean and Arabidopsis, rice or other legumes data revealed that some specific genes were involved in our collection and a large part of them could be annotated to unknown functions. A large set of soybean full-length cDNA clones reported in this study will serve as a useful resource for gene discovery from soybean and will also aid a precise annotation of the soybean genome.
Collapse
Affiliation(s)
- Taishi Umezawa
- Gene Discovery Research Team, RIKEN Plant Science Center, Koyadai 3-1-1, Tsukuba, Ibaraki 305-0074, Japan
| | - Tetsuya Sakurai
- Integrated Genome Informatics Research Unit, RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Yasushi Totoki
- Genome Annotation and Comparative Analysis Team, RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Atsushi Toyoda
- Sequence Technology Team, RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Atsushi Ishiwata
- Integrated Genome Informatics Research Unit, RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Kenji Akiyama
- Integrated Genome Informatics Research Unit, RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Atsushi Kurotani
- Integrated Genome Informatics Research Unit, RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Takuhiro Yoshida
- Integrated Genome Informatics Research Unit, RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Keiichi Mochida
- Gene Discovery Research Group, RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Mie Kasuga
- Biological Resources Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Daisuke Todaka
- Biological Resources Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
- Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kyonoshin Maruyama
- Biological Resources Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Kazuo Nakashima
- Biological Resources Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Akiko Enju
- Plant Genomic Network Research Team, RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Saho Mizukado
- Gene Discovery Research Team, RIKEN Plant Science Center, Koyadai 3-1-1, Tsukuba, Ibaraki 305-0074, Japan
| | - Selina Ahmed
- Biological Resources Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Kyoko Yoshiwara
- Biological Resources Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Kyuya Harada
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Yasutaka Tsubokura
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Masaki Hayashi
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Shusei Sato
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Toyoaki Anai
- Department of Applied Biological Sciences, Faculty of Agriculture, Saga University, Honjo 840-8502, Saga, Japan
| | - Masao Ishimoto
- National Agricultural Research Center for Hokkaido Region, 1 Hitsujigaoka, Sapporo, Hokkaido 062-8555, Japan
| | - Hideyuki Funatsuki
- National Agricultural Research Center for Hokkaido Region, 1 Hitsujigaoka, Sapporo, Hokkaido 062-8555, Japan
| | | | - Mitsuru Osaki
- Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Takuro Shinano
- National Agricultural Research Center for Hokkaido Region, 1 Hitsujigaoka, Sapporo, Hokkaido 062-8555, Japan
| | - Ryo Akashi
- Division of BioResource, Frontier Science Research Center, University of Miyazaki, Miyazaki 889-2192, Japan
| | - Yoshiyuki Sakaki
- Genome Annotation and Comparative Analysis Team, RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- Sequence Technology Team, RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Kazuko Yamaguchi-Shinozaki
- Biological Resources Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
- Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kazuo Shinozaki
- Gene Discovery Research Team, RIKEN Plant Science Center, Koyadai 3-1-1, Tsukuba, Ibaraki 305-0074, Japan
| |
Collapse
|
41
|
Taji T, Sakurai T, Mochida K, Ishiwata A, Kurotani A, Totoki Y, Toyoda A, Sakaki Y, Seki M, Ono H, Sakata Y, Tanaka S, Shinozaki K. Large-scale collection and annotation of full-length enriched cDNAs from a model halophyte, Thellungiella halophila. BMC PLANT BIOLOGY 2008; 8:115. [PMID: 19014467 PMCID: PMC2621223 DOI: 10.1186/1471-2229-8-115] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2008] [Accepted: 11/12/2008] [Indexed: 05/15/2023]
Abstract
BACKGROUND Thellungiella halophila (also known as Thellungiella salsuginea) is a model halophyte with a small plant size, short life cycle, and small genome. It easily undergoes genetic transformation by the floral dipping method used with its close relative, Arabidopsis thaliana. Thellungiella genes exhibit high sequence identity (approximately 90% at the cDNA level) with Arabidopsis genes. Furthermore, Thellungiella not only shows tolerance to extreme salinity stress, but also to chilling, freezing, and ozone stress, supporting the use of Thellungiella as a good genomic resource in studies of abiotic stress tolerance. RESULTS We constructed a full-length enriched Thellungiella (Shan Dong ecotype) cDNA library from various tissues and whole plants subjected to environmental stresses, including high salinity, chilling, freezing, and abscisic acid treatment. We randomly selected about 20,000 clones and sequenced them from both ends to obtain a total of 35 171 sequences. CAP3 software was used to assemble the sequences and cluster them into 9569 nonredundant cDNA groups. We named these cDNAs "RTFL" (RIKEN Thellungiella Full-Length) cDNAs. Information on functional domains and Gene Ontology (GO) terms for the RTFL cDNAs were obtained using InterPro. The 8289 genes assigned to InterPro IDs were classified according to the GO terms using Plant GO Slim. Categorical comparison between the whole Arabidopsis genome and Thellungiella genes showing low identity to Arabidopsis genes revealed that the population of Thellungiella transport genes is approximately 1.5 times the size of the corresponding Arabidopsis genes. This suggests that these genes regulate a unique ion transportation system in Thellungiella. CONCLUSION As the number of Thellungiella halophila (Thellungiella salsuginea) expressed sequence tags (ESTs) was 9388 in July 2008, the number of ESTs has increased to approximately four times the original value as a result of this effort. Our sequences will thus contribute to correct future annotation of the Thellungiella genome sequence. The full-length enriched cDNA clones will enable the construction of overexpressing mutant plants by introduction of the cDNAs driven by a constitutive promoter, the complementation of Thellungiella mutants, and the determination of promoter regions in the Thellungiella genome.
Collapse
Affiliation(s)
- Teruaki Taji
- Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
- Laboratory of Plant Molecular Biology, RIKEN Tsukuba Institute, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Tetsuya Sakurai
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Keiichi Mochida
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Atsushi Ishiwata
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Atsushi Kurotani
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yasushi Totoki
- RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- MetaSystems Research Team, RIKEN Advanced Science Institute, Yokohama, 230-0045, Japan
| | - Atsushi Toyoda
- RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yoshiyuki Sakaki
- RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Motoaki Seki
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Hirokazu Ono
- Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Yoichi Sakata
- Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Shigeo Tanaka
- Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Kazuo Shinozaki
- Laboratory of Plant Molecular Biology, RIKEN Tsukuba Institute, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| |
Collapse
|
42
|
De-Paula VS, Razzera G, Medeiros L, Miyamoto CA, Almeida MS, Kurtenbach E, Almeida FCL, Valente AP. Evolutionary relationship between defensins in the Poaceae family strengthened by the characterization of new sugarcane defensins. PLANT MOLECULAR BIOLOGY 2008; 68:321-335. [PMID: 18618271 DOI: 10.1007/s11103-008-9372-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2008] [Accepted: 06/28/2008] [Indexed: 05/26/2023]
Abstract
Plant defensins are small (45-54 amino acids), highly basic, cysteine-rich peptides structurally related to defensins of other organisms, including insects and mammals. Small putative proteins (MW < 10 kDa) containing eight cysteines were screened based on the sugarcane expressed sequence tag (EST) database. We selected ORFs that exhibited 25-100% similarity in primary sequence with other defensins in the NCBI database and that contained eight cysteines. This similarity is sufficient for folding prediction, but not enough for biological activity inference. Six putative defensins (Sd1-6) were selected, and activity assays showed that recombinant Sd1, Sd3 and Sd5 are active against fungi, but not against bacteria. Structural characterization, based on circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy showed that the structures of these Sds were compatible with alpha/beta proteins, a feature expected for plant defensins. Phylogenetic analysis revealed that sugarcane defensins could clearly be grouped within defensins from Poaceae family and Andropogoneae tribe. Our work demonstrates that defensins show strong conservation in the Poaceae family and may indicate that the same conservation occurs in other families. We suggest that evolutionary relationships within plant families can be used as a procedure to predict and annotate new defensins in genomes and group them in evolutionary classes to help in the investigation of their biological function.
Collapse
Affiliation(s)
- V S De-Paula
- Centro Nacional de Ressonância Magnética Nuclear, Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Av. Brigadeiro Trompowski, s/n, CCS Bloco E sala 10, Rio de Janeiro, RJ, Brazil
| | | | | | | | | | | | | | | |
Collapse
|
43
|
Fernandes J, Morrow DJ, Casati P, Walbot V. Distinctive transcriptome responses to adverse environmental conditions in Zea mays L. PLANT BIOTECHNOLOGY JOURNAL 2008; 6:782-98. [PMID: 18643947 DOI: 10.1111/j.1467-7652.2008.00360.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Maize seedling transcriptome responses to six abiotic perturbations (heat, cold, darkness, desiccation, salt, ultraviolet-B) were analysed. Approximately 7800 transcripts were expressed in one or more treatments compared with light-grown seedlings plus juvenile leaves from field-grown plants. Approximately 5200 transcripts were expressed in one or more treatments and absent in light-grown seedlings. Approximately 2000 transcripts were unique to one treatment. Salt and heat elicited the largest number of transcript changes; however, salt resulted in mostly a decreased abundance of transcripts, whereas heat shock resulted in mostly an increased abundance of transcripts. A total of 384 transcripts were common to all stress treatments and not expressed in light-grown seedlings; 146 transcripts were present in light-grown seedlings and absent from all stress treatments. A complex pattern of overlapping transcripts between treatments was found, and a significant pattern of congruence in the direction of transcript change between pairs of treatments was uncovered. From the analysis, it appears that the scope of gene expression changes is determined by the challenge, indicating specificity in perception and response. Nonetheless, transcripts regulated by multiple responses are generally affected in the same manner, indicating common or converging regulatory networks. The data are available for additional analysis through a searchable database.
Collapse
Affiliation(s)
- John Fernandes
- Department of Biology, 385 Serra Mall, Stanford University, Stanford, CA 94305-5020, USA
| | | | | | | |
Collapse
|
44
|
Coll A, Nadal A, Palaudelmàs M, Messeguer J, Melé E, Puigdomènech P, Pla M. Lack of repeatable differential expression patterns between MON810 and comparable commercial varieties of maize. PLANT MOLECULAR BIOLOGY 2008; 68:105-17. [PMID: 18604604 DOI: 10.1007/s11103-008-9355-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2008] [Accepted: 05/21/2008] [Indexed: 05/09/2023]
Abstract
The introduction of genetically modified organisms (GMO) in many countries follows strict regulations to assure that only products that have been safety tested in relation to human health and the environment are marketed. Thus, GMOs must be authorized before use. By complementing more targeted approaches, profiling methods can assess possible unintended effects of transformation. We used microarrays to compare the transcriptome profiles of widely commercialized maize MON810 varieties and their non-GM near-isogenic counterparts. The expression profiles of MON810 seedlings are more similar to those of their corresponding near-isogenic varieties than are the profiles of other lines produced by conventional breeding. However, differential expression of approximately 1.7 and approximately 0.1% of transcripts was identified in two variety pairs (AristisBt/Aristis and PR33P67/PR33P66) that had similar cryIA(b) mRNA levels, demonstrating that commercial varieties of the same event have different similarity levels to their near-isogenic counterparts without the transgene (note that these two pairs also show phenotypic differences). In the tissues, developmental stage and varieties analyzed, we could not identify any gene differentially expressed in all variety-pairs. However, a small set of sequences were differentially expressed in various pairs. Their relation to the transgenesis was not proven, although this is likely to be modulated by the genetic background of each variety.
Collapse
Affiliation(s)
- Anna Coll
- Institut de Tecnologia Agroalimentària, Universitat de Girona, Campus Montilivi, EPS-I, Girona, Spain
| | | | | | | | | | | | | |
Collapse
|
45
|
Wisniewski M, Bassett C, Norelli J, Macarisin D, Artlip T, Gasic K, Korban S. Expressed sequence tag analysis of the response of apple (Malus x domestica'Royal Gala') to low temperature and water deficit. PHYSIOLOGIA PLANTARUM 2008; 133:298-317. [PMID: 18298416 DOI: 10.1111/j.1399-3054.2008.01063.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Leaf, bark, xylem and root tissues were used to make nine cDNA libraries from non-stressed (control) 'Royal Gala' apple trees, and from 'Royal Gala' trees exposed to either low temperature (5 degrees C for 24 h) or water deficit (45% of saturated pot mass for 2 weeks). Over 22 600 clones from the nine libraries were subjected to 5' single-pass sequencing, clustered and annotated using blastx. The number of clusters in the libraries ranged from 170 to 1430. Regarding annotation of the sequences, blastx analysis indicated that within the libraries 65-72% of the clones had a high similarity to known function genes, 6-15% had no functional assignment and 15-26% were completely novel. The expressed sequence tags were combined into three classes (control, low-temperature and water deficit) and the annotated genes in each class were placed into 1 of 10 different functional categories. The percentage of genes falling into each category was then calculated. This analysis indicated a distinct downregulation of genes involved in general metabolism and photosynthesis, while a significant increase in defense/stress-related genes, protein metabolism and energy was observed. In particular, there was a three-fold increase in the number of stress genes observed in the water deficit libraries indicating a major shift in gene expression in response to a chronic stress. The number of stress genes in response to low temperature, although elevated, was much less than the water deficit libraries perhaps reflecting the shorter (24 h) exposure to stress. Genes with greater than five clones in any specific library were identified and, based on the number of clones obtained, the fold increase or decrease in expression in the libraries was calculated and verified by semiquantitative polymerase chain reaction. Genes, of particular note, that code for the following proteins were overexpressed in the low-temperature libraries: dehydrin and metallothionein-like proteins, ubiquitin proteins, a dormancy-associated protein, a plasma membrane intrinsic protein and an RNA-binding protein. Genes that were upregulated in the water deficit libraries fell mainly into the functional categories of stress (heat shock proteins, dehydrins) and photosynthesis. With few exceptions, the overall differences in downregulated genes were nominal compared with differences in upregulated genes. The results of this apple study are similar to other global studies of plant response to stress but offer a more detailed analysis of specific tissue response (bark vs xylem vs leaf vs root) and a comparison between an acute stress (24-h exposure to low temperature) and a chronic stress (2 weeks of water deficit).
Collapse
Affiliation(s)
- Michael Wisniewski
- United States Department of Agriculture - Agricultural Research Service (USDA-ARS), Appalachian Fruit Research Station, 2217 Wiltshire Road, Kearneysville, WV 25430, USA.
| | | | | | | | | | | | | |
Collapse
|
46
|
Ralph SG, Chun HJE, Cooper D, Kirkpatrick R, Kolosova N, Gunter L, Tuskan GA, Douglas CJ, Holt RA, Jones SJM, Marra MA, Bohlmann J. Analysis of 4,664 high-quality sequence-finished poplar full-length cDNA clones and their utility for the discovery of genes responding to insect feeding. BMC Genomics 2008; 9:57. [PMID: 18230180 PMCID: PMC2270264 DOI: 10.1186/1471-2164-9-57] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2007] [Accepted: 01/29/2008] [Indexed: 11/30/2022] Open
Abstract
Background The genus Populus includes poplars, aspens and cottonwoods, which will be collectively referred to as poplars hereafter unless otherwise specified. Poplars are the dominant tree species in many forest ecosystems in the Northern Hemisphere and are of substantial economic value in plantation forestry. Poplar has been established as a model system for genomics studies of growth, development, and adaptation of woody perennial plants including secondary xylem formation, dormancy, adaptation to local environments, and biotic interactions. Results As part of the poplar genome sequencing project and the development of genomic resources for poplar, we have generated a full-length (FL)-cDNA collection using the biotinylated CAP trapper method. We constructed four FLcDNA libraries using RNA from xylem, phloem and cambium, and green shoot tips and leaves from the P. trichocarpa Nisqually-1 genotype, as well as insect-attacked leaves of the P. trichocarpa × P. deltoides hybrid. Following careful selection of candidate cDNA clones, we used a combined strategy of paired end reads and primer walking to generate a set of 4,664 high-accuracy, sequence-verified FLcDNAs, which clustered into 3,990 putative unique genes. Mapping FLcDNAs to the poplar genome sequence combined with BLAST comparisons to previously predicted protein coding sequences in the poplar genome identified 39 FLcDNAs that likely localize to gaps in the current genome sequence assembly. Another 173 FLcDNAs mapped to the genome sequence but were not included among the previously predicted genes in the poplar genome. Comparative sequence analysis against Arabidopsis thaliana and other species in the non-redundant database of GenBank revealed that 11.5% of the poplar FLcDNAs display no significant sequence similarity to other plant proteins. By mapping the poplar FLcDNAs against transcriptome data previously obtained with a 15.5 K cDNA microarray, we identified 153 FLcDNA clones for genes that were differentially expressed in poplar leaves attacked by forest tent caterpillars. Conclusion This study has generated a high-quality FLcDNA resource for poplar and the third largest FLcDNA collection published to date for any plant species. We successfully used the FLcDNA sequences to reassess gene prediction in the poplar genome sequence, perform comparative sequence annotation, and identify differentially expressed transcripts associated with defense against insects. The FLcDNA sequences will be essential to the ongoing curation and annotation of the poplar genome, in particular for targeting gaps in the current genome assembly and further improvement of gene predictions. The physical FLcDNA clones will serve as useful reagents for functional genomics research in areas such as analysis of gene functions in defense against insects and perennial growth. Sequences from this study have been deposited in NCBI GenBank under the accession numbers EF144175 to EF148838.
Collapse
Affiliation(s)
- Steven G Ralph
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Sakurai T, Plata G, Rodríguez-Zapata F, Seki M, Salcedo A, Toyoda A, Ishiwata A, Tohme J, Sakaki Y, Shinozaki K, Ishitani M. Sequencing analysis of 20,000 full-length cDNA clones from cassava reveals lineage specific expansions in gene families related to stress response. BMC PLANT BIOLOGY 2007; 7:66. [PMID: 18096061 PMCID: PMC2245942 DOI: 10.1186/1471-2229-7-66] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2007] [Accepted: 12/20/2007] [Indexed: 05/18/2023]
Abstract
BACKGROUND Cassava, an allotetraploid known for its remarkable tolerance to abiotic stresses is an important source of energy for humans and animals and a raw material for many industrial processes. A full-length cDNA library of cassava plants under normal, heat, drought, aluminum and post harvest physiological deterioration conditions was built; 19968 clones were sequence-characterized using expressed sequence tags (ESTs). RESULTS The ESTs were assembled into 6355 contigs and 9026 singletons that were further grouped into 10577 scaffolds; we found 4621 new cassava sequences and 1521 sequences with no significant similarity to plant protein databases. Transcripts of 7796 distinct genes were captured and we were able to assign a functional classification to 78% of them while finding more than half of the enzymes annotated in metabolic pathways in Arabidopsis. The annotation of sequences that were not paired to transcripts of other species included many stress-related functional categories showing that our library is enriched with stress-induced genes. Finally, we detected 230 putative gene duplications that include key enzymes in reactive oxygen species signaling pathways and could play a role in cassava stress response features. CONCLUSION The cassava full-length cDNA library here presented contains transcripts of genes involved in stress response as well as genes important for different areas of cassava research. This library will be an important resource for gene discovery, characterization and cloning; in the near future it will aid the annotation of the cassava genome.
Collapse
Affiliation(s)
- Tetsuya Sakurai
- Metabolomics Research Group, RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Germán Plata
- Agrobiodiversity and Biotechnology Project, International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
| | - Fausto Rodríguez-Zapata
- Agrobiodiversity and Biotechnology Project, International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
| | - Motoaki Seki
- Plant Functional Genomics Research Group, RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Andrés Salcedo
- Agrobiodiversity and Biotechnology Project, International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
| | - Atsushi Toyoda
- Genome Core Technology Facilities, RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Atsushi Ishiwata
- Metabolomics Research Group, RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Joe Tohme
- Agrobiodiversity and Biotechnology Project, International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
| | - Yoshiyuki Sakaki
- Genome Core Technology Facilities, RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Kazuo Shinozaki
- Plant Functional Genomics Research Group, RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Manabu Ishitani
- Agrobiodiversity and Biotechnology Project, International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
| |
Collapse
|
48
|
Zhuang Y, Ren G, Yue G, Li Z, Qu X, Hou G, Zhu Y, Zhang J. Effects of water-deficit stress on the transcriptomes of developing immature ear and tassel in maize. PLANT CELL REPORTS 2007; 26:2137-47. [PMID: 17668218 DOI: 10.1007/s00299-007-0419-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2007] [Revised: 07/14/2007] [Accepted: 07/16/2007] [Indexed: 05/16/2023]
Abstract
Water-deficit stress during meiosis is one of the most serious threats to crop production. To elucidate the mechanisms of the response to water-deficit stress in the reproductive organs of maize, we have characterized the changes in transcription that occur during meiosis in the tassels and floret formation in the ears following water deficit stress. We used oligo microarray analysis, which included 57,452 transcripts representing more than 30,000 identifiable unique maize genes, and combined this with reverse Northern blot analysis. After 7 days of stress, immature tassels and ears differed considerably in their transcriptional responses, and the majority of changes were organ specific. In the tassels, 1,513 transcripts were differentially expressed (by threefold or greater) with 62% of these being upregulated by water stress. In the ears, 202 transcripts were differentially expressed with 95% being upregulated by water stress. Most of these transcripts have not been previously reported to be associated with water stress. Only 74 of these transcripts were co-regulated in the two organs. The stress-regulated transcripts are involved in a broad range of cellular and biochemical activities. The most notable may function in carbohydrate metabolism, particular in sucrose, trehalose and raffinose metabolism, and in cell wall metabolism in the tassels. Collectively, these data suggest that the transcripts differentially expressed during reproductive organic development may represent candidate genes for dissecting molecular mechanism of this important biological process in response to water-deficit stress.
Collapse
Affiliation(s)
- Yunlong Zhuang
- School of Life Science, Shandong University, Jinan, Shandong, China
| | | | | | | | | | | | | | | |
Collapse
|
49
|
Irsigler AST, Costa MDL, Zhang P, Reis PAB, Dewey RE, Boston RS, Fontes EPB. Expression profiling on soybean leaves reveals integration of ER- and osmotic-stress pathways. BMC Genomics 2007; 8:431. [PMID: 18036212 PMCID: PMC2242807 DOI: 10.1186/1471-2164-8-431] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2007] [Accepted: 11/23/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Despite the potential of the endoplasmic reticulum (ER) stress response to accommodate adaptive pathways, its integration with other environmental-induced responses is poorly understood in plants. We have previously demonstrated that the ER-stress sensor binding protein (BiP) from soybean exhibits an unusual response to drought. The members of the soybean BiP gene family are differentially regulated by osmotic stress and soybean BiP confers tolerance to drought. While these results may reflect crosstalk between the osmotic and ER-stress signaling pathways, the lack of mutants, transcriptional response profiles to stresses and genome sequence information of this relevant crop has limited our attempts to identify integrated networks between osmotic and ER stress-induced adaptive responses. As a fundamental step towards this goal, we performed global expression profiling on soybean leaves exposed to polyethylene glycol treatment (osmotic stress) or to ER stress inducers. RESULTS The up-regulated stress-specific changes unmasked the major branches of the ER-stress response, which include enhancing protein folding and degradation in the ER, as well as specific osmotically regulated changes linked to cellular responses induced by dehydration. However, a small proportion (5.5%) of total up-regulated genes represented a shared response that seemed to integrate the two signaling pathways. These co-regulated genes were considered downstream targets based on similar induction kinetics and a synergistic response to the combination of osmotic- and ER-stress-inducing treatments. Genes in this integrated pathway with the strongest synergistic induction encoded proteins with diverse roles, such as plant-specific development and cell death (DCD) domain-containing proteins, an ubiquitin-associated (UBA) protein homolog and NAC domain-containing proteins. This integrated pathway diverged further from characterized specific branches of ER-stress as downstream targets were inversely regulated by osmotic stress. CONCLUSION The present ER-stress- and osmotic-stress-induced transcriptional studies demonstrate a clear predominance of stimulus-specific positive changes over shared responses on soybean leaves. This scenario indicates that polyethylene glycol (PEG)-induced cellular dehydration and ER stress elicited very different up-regulated responses within a 10-h stress treatment regime. In addition to identifying ER-stress and osmotic-stress-specific responses in soybean (Glycine max), our global expression-profiling analyses provided a list of candidate regulatory components, which may integrate the osmotic-stress and ER-stress signaling pathways in plants.
Collapse
Affiliation(s)
- André ST Irsigler
- Departamento de Bioquímica e Biologia Molecular, BIOAGRO, Universidade Federal de Viçosa, 36571.000 Viçosa, Minas Gerais, Brazil
- Molecular Core Facility, Department of Biology, Florida State University, Tallahassee, FL 32306-4370, USA
| | - Maximiller DL Costa
- Departamento de Bioquímica e Biologia Molecular, BIOAGRO, Universidade Federal de Viçosa, 36571.000 Viçosa, Minas Gerais, Brazil
| | - Ping Zhang
- Department of Crop Science, North Carolina State University, Raleigh, NC 27695, USA
| | - Pedro AB Reis
- Departamento de Bioquímica e Biologia Molecular, BIOAGRO, Universidade Federal de Viçosa, 36571.000 Viçosa, Minas Gerais, Brazil
| | - Ralph E Dewey
- Department of Crop Science, North Carolina State University, Raleigh, NC 27695, USA
| | - Rebecca S Boston
- Department of Plant Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Elizabeth PB Fontes
- Departamento de Bioquímica e Biologia Molecular, BIOAGRO, Universidade Federal de Viçosa, 36571.000 Viçosa, Minas Gerais, Brazil
| |
Collapse
|
50
|
Jin Y, Wang M, Fu J, Xuan N, Zhu Y, Lian Y, Jia Z, Zheng J, Wang G. Phylogenetic and expression analysis of ZnF-AN1 genes in plants. Genomics 2007; 90:265-75. [PMID: 17524611 DOI: 10.1016/j.ygeno.2007.03.019] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2007] [Revised: 03/23/2007] [Accepted: 03/27/2007] [Indexed: 11/24/2022]
Abstract
In plants, ZnF-AN1 genes are part of a multigene family with 13 members in Arabidopsis thaliana, 19 members in Populus trichocarpa, 17 members in Oryza sativa, at least 11 members in Zea mays, and 2 members in Chlamydomonas reinhardtii. All ZnF-AN1 genes contain the ZnF-AN1 domain. According to the phylogenetic analysis of the ZnF-AN1 domain, we divided plant ZnF-AN1 genes into two types. The coding sequences of most type I members do not possess any introns, while most type II members do possess intron(s). Through Northern blot analysis of maize members and digital Northern analysis of Arabidopsis members, we found that most ZnF-AN1 genes are involved in responses to abiotic stresses. The evolutionary analysis indicated that the expansion rate of type I was higher than that of type II. After expansion, some ZnF-AN1 genes may have gained new functions, some may have lost their functions, and some were specialized to perform their functions in stress-specific or tissue-specific modes. In addition, we propose an evolutionary model of type II ZnF-AN1 genes in plants.
Collapse
Affiliation(s)
- Ying Jin
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100094, China
| | | | | | | | | | | | | | | | | |
Collapse
|