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Arnaiz A, Martinez M, Gonzalez-Melendi P, Grbic V, Diaz I, Santamaria ME. Plant Defenses Against Pests Driven by a Bidirectional Promoter. FRONTIERS IN PLANT SCIENCE 2019; 10:930. [PMID: 31379907 PMCID: PMC6652247 DOI: 10.3389/fpls.2019.00930] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 07/02/2019] [Indexed: 05/06/2023]
Abstract
The plant defense responses to pests results in the synchronized change of a complex network of interconnected genes and signaling pathways. An essential part of this process is mediated by the binding of transcription factors to the specific responsive cis-elements within in the promoters of phytophagous-responsive genes. In this work, it is reported the identification and characterization of a bidirectional promoter that simultaneously co-regulate two divergent genes, At5g10300 and At5g10290, upon arthropod feeding. Computational analysis identified the presence of cis-elements within the intergenic region between two loci, mainly from the DOF but also from the AP2/ERF, Golden 2-like and bHLH families. The function of the bidirectional promoter was analyzed using two enhanced variants of the GFP and CherryFP reporter genes, in both orientations, in transient tobacco and stably transformed Arabidopsis plants. Promoter activity was tested in response to feeding of Tetranychus urticae and Pieris brassicae, as well as wounding, flagellin and chitin treatments. Using RT-qPCR assays and confocal microscopy, it was shown that all treatments resulted in the induction of both reporter genes. Furthermore, our findings revealed the asymmetric character of the promoter with stronger activity in the forward than in the reverse orientation. This study provides an example of a bidirectional promoter with a strong potential to be used in plant biotechnology in pest control that requires stacking of the defense genes.
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Affiliation(s)
- Ana Arnaiz
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid, Spain
| | - Manuel Martinez
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Pablo Gonzalez-Melendi
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Vojislava Grbic
- Department of Biology, The University of Western Ontario, London, ON, Canada
| | - Isabel Diaz
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - M. Estrella Santamaria
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid, Spain
- *Correspondence: M. Estrella Santamaria,
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Sunil M, Hariharan N, Dixit S, Choudhary B, Srinivasan S. Differential genomic arrangements in Caryophyllales through deep transcriptome sequencing of A. hypochondriacus. PLoS One 2017; 12:e0180528. [PMID: 28786999 PMCID: PMC5546567 DOI: 10.1371/journal.pone.0180528] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 06/17/2017] [Indexed: 12/28/2022] Open
Abstract
Genome duplication event in edible dicots under the orders Rosid and Asterid, common during the oligocene period, is missing for species under the order Caryophyllales. Despite this, grain amaranths not only survived this period but display many desirable traits missing in species under rosids and asterids. For example, grain amaranths display traits like C4 photosynthesis, high-lysine seeds, high-yield, drought resistance, tolerance to infection and resilience to stress. It is, therefore, of interest to look for minor genome rearrangements with potential functional implications that are unique to grain amaranths. Here, by deep sequencing and assembly of 16 transcriptomes (86.8 billion bases) we have interrogated differential genome rearrangement unique to Amaranthus hypochondriacus with potential links to these phenotypes. We have predicted 125,581 non-redundant transcripts including 44,529 protein coding transcripts identified based on homology to known proteins and 13,529 predicted as novel/amaranth specific coding transcripts. Of the protein coding de novo assembled transcripts, we have identified 1810 chimeric transcripts. More than 30% and 19% of the gene pairs within the chimeric transcripts are found within the same loci in the genomes of A. hypochondriacus and Beta vulgaris respectively and are considered real positives. Interestingly, one of the chimeric transcripts comprises two important genes, namely DHDPS1, a key enzyme implicated in the biosynthesis of lysine, and alpha-glucosidase, an enzyme involved in sucrose catabolism, in close proximity to each other separated by a distance of 612 bases in the genome of A. hypochondriacus in a convergent configuration. We have experimentally validated that transcripts of these two genes are also overlapping in the 3' UTR with their expression negatively correlated from bud to mature seed, suggesting a potential link between the high seed lysine trait and unique genome organization.
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Affiliation(s)
- Meeta Sunil
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, Karnataka, India
- Manipal University, Manipal, Karnataka, India
| | - Nivedita Hariharan
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, Karnataka, India
| | - Shubham Dixit
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, Karnataka, India
| | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, Karnataka, India
| | - Subhashini Srinivasan
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, Karnataka, India
- * E-mail:
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Meersseman C, Letaief R, Léjard V, Rebours E, Guillocheau G, Esquerré D, Djari A, Chamberlain A, Vander Jagt C, Klopp C, Boussaha M, Renand G, Maftah A, Petit D, Rocha D. Genetic variability of the activity of bidirectional promoters: a pilot study in bovine muscle. DNA Res 2017; 24:221-233. [PMID: 28338730 PMCID: PMC5499805 DOI: 10.1093/dnares/dsx004] [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: 09/02/2016] [Accepted: 01/24/2017] [Indexed: 11/25/2022] Open
Abstract
Bidirectional promoters are regulatory regions co-regulating the expression of two neighbouring genes organized in a head-to-head orientation. In recent years, these regulatory regions have been studied in many organisms; however, no investigation to date has been done to analyse the genetic variation of the activity of this type of promoter regions. In our study, we conducted an investigation to first identify bidirectional promoters sharing genes expressed in bovine Longissimus thoracis and then to find genetic variants affecting the activity of some of these bidirectional promoters. Combining bovine gene information and expression data obtained using RNA-Seq, we identified 120 putative bidirectional promoters active in bovine muscle. We experimentally validated in vitro 16 of these bidirectional promoters. Finally, using gene expression and whole-genome genotyping data, we explored the variability of the activity in muscle of the identified bidirectional promoters and discovered genetic variants affecting their activity. We found that the expression level of 77 genes is correlated with the activity of 12 bidirectional promoters. We also identified 57 single nucleotide polymorphisms associated with the activity of 5 bidirectional promoters. To our knowledge, our study is the first analysis in any species of the genetic variability of the activity of bidirectional promoters.
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Affiliation(s)
- Cédric Meersseman
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.,GMA, INRA, Université de Limoges, 87060 Limoges, France
| | - Rabia Letaief
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Véronique Léjard
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Emmanuelle Rebours
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Gabriel Guillocheau
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Diane Esquerré
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, 31326 Castanet Tolosan, France
| | - Anis Djari
- SIGENAE, UR 875, INRA, 31362 Castanet-Tolosan, France
| | - Amanda Chamberlain
- Dairy Futures Cooperative Research Centre, AgriBio, Bundoora, Victoria, Australia.,AgriBio, Department of Economic Development, Jobs, Transport & Resources, Victoria, Australia
| | - Christy Vander Jagt
- Dairy Futures Cooperative Research Centre, AgriBio, Bundoora, Victoria, Australia.,AgriBio, Department of Economic Development, Jobs, Transport & Resources, Victoria, Australia
| | | | - Mekki Boussaha
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Gilles Renand
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | | | - Daniel Petit
- GMA, INRA, Université de Limoges, 87060 Limoges, France
| | - Dominique Rocha
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
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Sen S, Dutta SK. A potent bidirectional promoter from the monocot cereal Eleusine coracana. PHYTOCHEMISTRY 2016; 129:24-35. [PMID: 27460530 DOI: 10.1016/j.phytochem.2016.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 04/12/2016] [Accepted: 07/15/2016] [Indexed: 06/06/2023]
Abstract
Ragi bifunctional α-amylase-trypsin inhibitor (RBI) of Eleusine coracana (L.) Gaertn. (finger millet) simultaneously inhibits α-amylase and trypsin. In continuation of previous work on the cloning, expression and characterization of RBI, a bidirectional promoter from finger millet was explored on the basis of experimental observations. Two trypsin inhibitors were identified while purifying RBI from a trypsin-Sepharose column eluent. Using an FPLC gel filtration column, these three inhibitors were purified to homogeneity and subjected to MALDI-TOF-TOF-MS/MS analysis and N-terminal sequencing. Both ragi trypsin inhibitors (RTIs) showed the same N-terminal sequence and considerable sequence similarity to RBI, indicating the presence of a multigene protease inhibitor family in finger millet. To gain insight into the evolution of these genes, the upstream region of RBI was explored by Genome Walking. Interestingly, on sequencing, a genome walking product of ∼1 Kb showed presence of an N-terminal RBI specific primer sequence twice but in opposite directions and leaving an intervening region of ∼0.9 Kb. The intervening region was presumed to represent an E. coracana bidirectional promoter (EcBDP), intuitively having a divergent RBI-RTI gene pair at two sides. For assaying the bidirectionality of promoter activity, a dual reporter GUS-GFP vector construct was made for plant expression containing the reporter genes at two ends of EcBDP, which was used to transform Agrobacterium tumefaciens LBA 4404. Transient plant transformation by recombinant Agrobacterium cells was carried out in onion scale epidermal cells and finger millet seedling leaves. Simultaneous expression of GUS and GFP under EcBDP established it as a potent natural bidirectional promoter from monocot origin, thereby potentially having vast application in cereal gene manipulations. In addition, inducibility of the EcBDP by either abscisic acid or cold treatment, as determined by transient transformation in onion, would substantiate more precise control of gene expression to mitigate the effects of adverse environmental conditions.
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Affiliation(s)
- Saswati Sen
- Drug Development/Diagnostics and Biotechnology Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata, 700 032, India.
| | - Samir Kr Dutta
- Drug Development/Diagnostics and Biotechnology Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata, 700 032, India
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Xie T, Fu LY, Yang QY, Xiong H, Xu H, Ma BG, Zhang HY. Spatial features for Escherichia coli genome organization. BMC Genomics 2015; 16:37. [PMID: 25652224 PMCID: PMC4326437 DOI: 10.1186/s12864-015-1258-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Accepted: 01/19/2015] [Indexed: 12/21/2022] Open
Abstract
Background In bacterial genomes, the compactly encoded genes and operons are well organized, with genes in the same biological pathway or operons in the same regulon close to each other on the genome sequence. In addition, the linearly close genes have a higher probability of co-expression and their protein products tend to form protein–protein interactions. However, the organization features of bacterial genomes in a three-dimensional space remain elusive. The DNA interaction data of Escherichia coli, measured by the genome conformation capture (GCC) technique, have recently become available, which allowed us to investigate the spatial features of bacterial genome organization. Results By renormalizing the GCC data, we compared the interaction frequency of operon pairs in the same regulon with that of random operon pairs. The results showed that arrangements of operons in the E. coli genome tend to minimize the spatial distance between operons in the same regulon. A similar global organization feature exists for genes in biological pathways of E. coli. In addition, the genes close to each other spatially (even if they are far from each other on the genome sequence) tend to be co-expressed and form protein–protein interactions. These results provided new insights into the organization principles of bacterial genomes and support the notion of transcription factory. Conclusions This study revealed the organization features of Escherichia coli genomic functional units in the 3D space and furthered our understanding of the link between the three-dimensional structure of chromosomes and biological function. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1258-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ting Xie
- National Key Laboratory of Crop Genetic Improvement, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China.
| | - Liang-Yu Fu
- National Key Laboratory of Crop Genetic Improvement, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China.
| | - Qing-Yong Yang
- National Key Laboratory of Crop Genetic Improvement, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China.
| | - Heng Xiong
- National Key Laboratory of Crop Genetic Improvement, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China.
| | - Hongrui Xu
- National Key Laboratory of Crop Genetic Improvement, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China.
| | - Bin-Guang Ma
- National Key Laboratory of Crop Genetic Improvement, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China.
| | - Hong-Yu Zhang
- National Key Laboratory of Crop Genetic Improvement, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China.
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Dhadi SR, Deshpande A, Driscoll K, Ramakrishna W. Major cis-regulatory elements for rice bidirectional promoter activity reside in the 5'-untranslated regions. Gene 2013; 526:400-10. [PMID: 23756196 DOI: 10.1016/j.gene.2013.05.060] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 05/28/2013] [Indexed: 10/26/2022]
Abstract
Bidirectional promoters are defined as those that regulate adjacent genes organized in a divergent fashion (head to head orientation) and separated by <1 kb. In order to dissect bidirectional promoter activity in a model plant, deletion analysis was performed for seven rice promoters using promoter-reporter gene constructs, which identified three promoters to be bidirectional. Regulatory elements located in or close to the 5'-untranslated regions (UTR) of one of the genes (divergent gene pair) were found to be responsible for their bidirectional activity. DNA footprinting analysis identified unique protein binding sites in these promoters. Deletion/alteration of these motifs resulted in significant loss of expression of the reporter genes on either side of the promoter. Changes in the motifs at both the positions resulted in a remarkable decrease in bidirectional activity of the reporter genes flanking the promoter. Based on our results, we propose a novel mechanism for the bidirectionality of rice bidirectional promoters.
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Affiliation(s)
- Surendar Reddy Dhadi
- Department of Biological Sciences, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA
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Liu T, Zeng J, Xia K, Fan T, Li Y, Wang Y, Xu X, Zhang M. Evolutionary expansion and functional diversification of oligopeptide transporter gene family in rice. RICE (NEW YORK, N.Y.) 2012; 5:12. [PMID: 27234238 PMCID: PMC5520842 DOI: 10.1186/1939-8433-5-12] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 06/22/2012] [Indexed: 05/10/2023]
Abstract
BACKGROUND Oligopeptide transporters (OPTs) play important roles in the mobilization of organic nitrogenous compounds and usually associate with tissues that show signs of rapid protein hydrolysis, such as germinating seeds and senescing leaves. This study is to investigate rice OPT genes. RESULTS A total of sixteen OsOPT genes (Os for Oryza sative L.) were identified in the rice genome, which were then classified into six sections that belong to two subfamilies (the PT and YSL subfamily). The major mechanisms for evolutionary expansion of the sixteen genes during the rice genome evolution include segmental and tandem duplication. Calculation of the duplication event dates indicated that the sixteen genes originated from nine original OsOPT genes, and the duplication events could be classified into three evolutionary stages. The first evolutionary stage occurred approximately 50 million years ago (Mya) and involved the evolution of four new genes. The second evolutionary stage was approximately 20 Mya and was marked by the appearance of two new genes, and the third evolutionary stage was approximately 9 Mya when two new genes evolved. Mining of the expression database and RT-PCR analysis indicated that the expression of most duplicated OsOPT genes showed high tissue specificities. Diverse expression patterns for the sixteen genes were evaluated using both semi-quantitative RT-PCR and the MPSS data. Expression levels of some OsOPT genes were regulated by abiotic and biotic stresses suggesting the potential involvement of these gene products in rice stress adaptation. Five OsOPT gene mutants showed abnormal development and growth, the primary analysis of five OsOPT gene mutants suggested that they may be necessary for rice development. CONCLUSIONS These results suggested that rice-specific OsOPT genes might be potentially useful in improving rice.
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Affiliation(s)
- Tao Liu
- Key Laboratory of South China Agricultural Plant Genetics and Breeding, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 People's Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing, 100049 People's Republic of China
| | - Jiqing Zeng
- Key Laboratory of South China Agricultural Plant Genetics and Breeding, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 People's Republic of China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 People's Republic of China
| | - Kuaifei Xia
- Key Laboratory of South China Agricultural Plant Genetics and Breeding, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 People's Republic of China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 People's Republic of China
| | - Tian Fan
- Key Laboratory of South China Agricultural Plant Genetics and Breeding, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 People's Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing, 100049 People's Republic of China
| | - Yuge Li
- Key Laboratory of South China Agricultural Plant Genetics and Breeding, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 People's Republic of China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 People's Republic of China
| | - Yaqin Wang
- Guangdong Key Lab of Biotechnology for Plant Development, College of Life Science, South China Normal University, Guangzhou, 510631 People's Republic of China
| | - Xinlan Xu
- Key Laboratory of South China Agricultural Plant Genetics and Breeding, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 People's Republic of China
| | - Mingyong Zhang
- Key Laboratory of South China Agricultural Plant Genetics and Breeding, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 People's Republic of China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 People's Republic of China
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Krom N, Ramakrishna W. Retrotransposon insertions in rice gene pairs associated with reduced conservation of gene pairs in grass genomes. Genomics 2012; 99:308-14. [PMID: 22414560 DOI: 10.1016/j.ygeno.2012.02.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Revised: 02/15/2012] [Accepted: 02/24/2012] [Indexed: 12/26/2022]
Abstract
Small-scale changes in gene order and orientation are common in plant genomes, even across relatively short evolutionary distances. We investigated the association of retrotransposons in and near rice gene pairs with gene pair conservation, inversion, rearrangement, and deletion in sorghum, maize, and Brachypodium. Copia and Gypsy LTR-retrotransposon insertions were found to be primarily associated with reduced frequency of gene pair conservation and an increase in both gene pair rearrangement and gene deletions. SINEs are associated with gene pair rearrangement, while LINEs are associated with gene deletions. Despite being more frequently associated with retrotransposons than convergent and tandem pairs, divergent gene pairs showed the least effects from that association. In contrast, convergent pairs were least frequently associated with retrotransposons yet showed the greatest effects. Insertions between genes were associated with the greatest effects on gene pair arrangement, while insertions flanking gene pairs had significant effects only on divergent pairs.
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Affiliation(s)
- Nicholas Krom
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, USA
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