101
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Li F, Wang P, Zhao C, Bao W, Qiu L. Cloning and characterization of PHGPx and its synergistic role with p53 in mediating stress in Penaeus monodon. FISH & SHELLFISH IMMUNOLOGY 2017; 71:380-392. [PMID: 29020605 DOI: 10.1016/j.fsi.2017.10.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 09/04/2017] [Accepted: 10/07/2017] [Indexed: 06/07/2023]
Abstract
Phospholipid-hydroperoxide glutathione peroxidase (PHGPx), a ubiquitous antioxidant enzyme in the glutathione peroxidase (GPx) family, plays multiple roles in different organisms. Here, a novel PHGPx (PmPHGPx) was identified from Penaeus monodon. The full-length PmPHGPx cDNA was 1885 bp in length with a 489-bp open reading frame (ORF) containing a selenocysteine codon, TGA177-179, and a selenocysteine insertion sequence in the 3'-UTR. The typical signature motifs of the GPx family were also detected in the PmPHGPx amino acid sequence. The PmPHGPx expression pattern showed tissue-specific variations, with the highest expression level in the heart and the lowest expression level in the muscle. To examine the relationship between Pmp53 and PmPHGPx, Pmp53 was successfully silenced with a dsRNA-p53 injection, and an obvious down-regulation in PmPHGPx expression was apparent. To clarify the functional roles of Pmp53 and PmPHGPx, their expression patterns were also assessed after pH-induced stress, salinity stress and heavy metal (Cu, Zn, and Cd) challenges. Similar trends in the expression profiles for PmPHGPx and Pmp53 were detected in both the gills and hepatopancreas in response to all stressors. Therefore, we conclude from the results that PmPHGPx acts synergistically and subsequently works cooperatively with Pmp53 toward mediating cell stress. This study improves our understanding of PmPHGPx and its synergistic role with Pmp53 in counteracting stressors in P. monodon.
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Affiliation(s)
- Fuxiang Li
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, PR China; College of Aqua-life Science and Technology, Shanghai Ocean University, Shanghai, PR China; Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture, Guangzhou, PR China
| | - Pengfei Wang
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, PR China; Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture, Guangzhou, PR China
| | - Chao Zhao
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, PR China; Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture, Guangzhou, PR China
| | | | - Lihua Qiu
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, PR China; Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture, Guangzhou, PR China; Key Laboratory of Aquatic Genomics, Ministry of Agriculture, CAFS, Beijing 100141, PR China.
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102
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Vigil-Stenman T, Ininbergs K, Bergman B, Ekman M. High abundance and expression of transposases in bacteria from the Baltic Sea. THE ISME JOURNAL 2017; 11:2611-2623. [PMID: 28731472 PMCID: PMC5649170 DOI: 10.1038/ismej.2017.114] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 05/23/2017] [Accepted: 06/01/2017] [Indexed: 02/06/2023]
Abstract
Transposases are mobile genetic elements suggested to have an important role in bacterial genome plasticity and host adaptation but their transcriptional activity in natural bacterial communities is largely unexplored. Here we analyzed metagenomes and -transcriptomes of size fractionated (0.1-0.8, 0.8-3.0 and 3.0-200 μm) bacterial communities from the brackish Baltic Sea, and adjacent marine waters. The Baltic Sea transposase levels, up to 1.7% of bacterial genes and 2% of bacterial transcripts, were considerably higher than in marine waters and similar to levels reported for extreme environments. Large variations in expression were found between transposase families and groups of bacteria, with a two-fold higher transcription in Cyanobacteria than in any other phylum. The community-level results were corroborated at the genus level by Synechococcus transposases reaching up to 5.2% of genes and 6.9% of transcripts, which is in contrast to marine Synechococcus that largely lack these genes. Levels peaked in Synechococcus from the largest size fraction, suggesting high frequencies of lateral gene transfer and high genome plasticity in colony-forming picocyanobacteria. Together, the results support an elevated rate of transposition-based genome change and adaptation in bacterial populations of the Baltic Sea, and possibly also of other highly dynamic estuarine waters.
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Affiliation(s)
- Theoden Vigil-Stenman
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Karolina Ininbergs
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Birgitta Bergman
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Martin Ekman
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
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103
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Horváth V, Merenciano M, González J. Revisiting the Relationship between Transposable Elements and the Eukaryotic Stress Response. Trends Genet 2017; 33:832-841. [DOI: 10.1016/j.tig.2017.08.007] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 08/02/2017] [Accepted: 08/31/2017] [Indexed: 10/18/2022]
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104
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Luchetti A, Plazzi F, Mantovani B. Evolution of Two Short Interspersed Elements in Callorhinchus milii (Chondrichthyes, Holocephali) and Related Elements in Sharks and the Coelacanth. Genome Biol Evol 2017; 9:3824762. [PMID: 28505260 PMCID: PMC5499810 DOI: 10.1093/gbe/evx094] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/11/2017] [Indexed: 12/11/2022] Open
Abstract
Short interspersed elements (SINEs) are non-autonomous retrotransposons. Although they usually show fast evolutionary rates, in some instances highly conserved domains (HCDs) have been observed in elements with otherwise divergent sequences and from distantly related species. Here, we document the life history of two HCD-SINE families in the elephant shark Callorhinchus milii, one specific to the holocephalan lineage (CmiSINEs) and another one (SacSINE1-CM) with homologous elements in sharks and the coelacanth (SacSINE1s, LmeSINE1s). The analyses of their relationships indicated that these elements share the same 3′-tail, which would have allowed both elements to rise to high copy number by exploiting the C. milii L2-2_CM long interspersed element (LINE) enzymes. Molecular clock analysis on SINE activity in C. milii genome evidenced two replication bursts occurring right after two major events in the holocephalan evolution: the end-Permian mass extinction and the radiation of modern Holocephali. Accordingly, the same analysis on the coelacanth homologous elements, LmeSINE1, identified a replication wave close to the split age of the two extant Latimeria species. The genomic distribution of the studied SINEs pointed out contrasting results: some elements were preferentially sorted out from gene regions, but accumulated in flanking regions, while others appear more conserved within genes. Moreover, data from the C. milii transcriptome suggest that these SINEs could be involved in miRNA biogenesis and may be targets for miRNA-based regulation.
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Affiliation(s)
- Andrea Luchetti
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali - Università di Bologna, Italy
| | - Federico Plazzi
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali - Università di Bologna, Italy
| | - Barbara Mantovani
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali - Università di Bologna, Italy
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105
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Jakšić AM, Kofler R, Schlötterer C. Regulation of transposable elements: Interplay between TE-encoded regulatory sequences and host-specific trans-acting factors in Drosophila melanogaster. Mol Ecol 2017; 26:5149-5159. [PMID: 28742942 DOI: 10.1111/mec.14259] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/14/2017] [Accepted: 07/17/2017] [Indexed: 12/18/2022]
Abstract
Transposable elements (TEs) are mobile genetic elements that can move around the genome, and their expression is one precondition for this mobility. Because the insertion of TEs in new genomic positions is largely deleterious, the molecular mechanisms for transcriptional suppression have been extensively studied. In contrast, very little is known about their primary transcriptional regulation. Here, we characterize the expression dynamics of TE families in Drosophila melanogaster across a broad temperature range (13-29°C). In 71% of the expressed TE families, the expression is modulated by temperature. We show that this temperature-dependent regulation is specific for TE families and strongly affected by the genetic background. We deduce that TEs carry family-specific regulatory sequences, which are targeted by host-specific trans-acting factors, such as transcription factors. Consistent with the widespread dominant inheritance of gene expression, we also find the prevailing dominance of TE family expression. We conclude that TE family expression across a range of temperatures is regulated by an interaction between TE family-specific regulatory elements and trans-acting factors of the host.
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Affiliation(s)
- Ana Marija Jakšić
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria.,Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Vienna, Austria
| | - Robert Kofler
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
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106
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Seidl MF, Thomma BPHJ. Transposable Elements Direct The Coevolution between Plants and Microbes. Trends Genet 2017; 33:842-851. [PMID: 28800915 DOI: 10.1016/j.tig.2017.07.003] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 06/24/2017] [Accepted: 07/14/2017] [Indexed: 12/31/2022]
Abstract
Transposable elements are powerful drivers of genome evolution in many eukaryotes. Although they are mostly considered as 'selfish' genetic elements, increasing evidence suggests that they contribute to genetic variability; particularly under stress conditions. Over the past few years, the role of transposable elements during host-microbe interactions has been recognised. It has been proposed that many pathogenic microbes have evolved a 'two-speed' genome with regions that show increased variability and that are enriched in transposable elements and pathogenicity-related genes. Plants similarly display structured genomes with transposable-element-rich regions that mediate accelerated evolution. Immune receptor genes typically reside in such regions. Various mechanisms have recently been identified through which transposable elements contribute to the coevolution between plants and their associated microbes.
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Affiliation(s)
- Michael F Seidl
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; Both authors contributed equally.
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; Both authors contributed equally.
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107
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Möller M, Stukenbrock EH. Evolution and genome architecture in fungal plant pathogens. Nat Rev Microbiol 2017; 15:756-771. [DOI: 10.1038/nrmicro.2017.76] [Citation(s) in RCA: 219] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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108
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Skeath JB, Wilson BA, Romero SE, Snee MJ, Zhu Y, Lacin H. The extracellular metalloprotease AdamTS-A anchors neural lineages in place within and preserves the architecture of the central nervous system. Development 2017; 144:3102-3113. [PMID: 28760813 DOI: 10.1242/dev.145854] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Accepted: 07/21/2017] [Indexed: 12/13/2022]
Abstract
The extracellular matrix (ECM) regulates cell migration and sculpts organ shape. AdamTS proteins are extracellular metalloproteases known to modify ECM proteins and promote cell migration, but demonstrated roles for AdamTS proteins in regulating CNS structure and ensuring cell lineages remain fixed in place have not been uncovered. Using forward genetic approaches in Drosophila, we find that reduction of AdamTS-A function induces both the mass exodus of neural lineages out of the CNS and drastic perturbations to CNS structure. Expressed and active in surface glia, AdamTS-A acts in parallel to perlecan and in opposition to viking/collagen IV and βPS-integrin to keep CNS lineages rooted in place and to preserve the structural integrity of the CNS. viking/collagen IV and βPS-integrin are known to promote tissue stiffness and oppose the function of perlecan, which reduces tissue stiffness. Our work supports a model in which AdamTS-A anchors cells in place and preserves CNS architecture by reducing tissue stiffness.
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Affiliation(s)
- James B Skeath
- Department of Genetics, Washington University School of Medicine, 4523 Clayton Avenue, St Louis, MO 63110, USA
| | - Beth A Wilson
- Department of Genetics, Washington University School of Medicine, 4523 Clayton Avenue, St Louis, MO 63110, USA
| | - Selena E Romero
- Department of Genetics, Washington University School of Medicine, 4523 Clayton Avenue, St Louis, MO 63110, USA
| | - Mark J Snee
- Department of Genetics, Washington University School of Medicine, 4523 Clayton Avenue, St Louis, MO 63110, USA
| | - Yi Zhu
- Department of Genetics, Washington University School of Medicine, 4523 Clayton Avenue, St Louis, MO 63110, USA
| | - Haluk Lacin
- Janelia Farm Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA
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109
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Balado M, Benzekri H, Labella AM, Claros MG, Manchado M, Borrego JJ, Osorio CR, Lemos ML. Genomic analysis of the marine fish pathogen Photobacterium damselae subsp. piscicida: Insertion sequences proliferation is associated with chromosomal reorganisations and rampant gene decay. INFECTION GENETICS AND EVOLUTION 2017; 54:221-229. [PMID: 28688976 DOI: 10.1016/j.meegid.2017.07.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 07/03/2017] [Accepted: 07/04/2017] [Indexed: 01/25/2023]
Abstract
Photobacterium damselae subsp. piscicida (Pdp) is an intracellular fish pathogen that causes photobacteriosis, a disease proven deadly in farmed fish worldwide. This work focuses on the analysis of genome sequences, chromosomes structure and gene contents of two strains from Sparus aurata (DI21) and Solea senegalensis (L091106-03H), isolated on the Spanish Atlantic coast. The comparative genomic analysis revealed that DI21 and L091106-03H share 98% of their genomes, including two virulence plasmids: pPHDP70 encoding siderophore piscibactin synthesis and pPHDP10 encoding the apoptotic toxin AIP56. Both genomes harbour a surprisingly large number of IS elements accounting for 12-17% of the total genome, representing an IS density of 0.15 elements per kb, one of the highest IS density values in a bacterial pathogen. This massive proliferation of ISs is responsible for the generation of a high number of pseudogenes that caused extensive loss of biological functions. Pseudogene formation is one of the main features of Pdp genome that explains most of the ecological and phenotypic differences with respect to its sibling subspecies P. damselae subsp. damselae and to other Vibrionaceae. Evidence was also found proving the existence of two chromosomal configurations depending on the origin of the strains: an European and an Asian/American types of genome organisation, reinforcing the idea of the existence of two geographically-linked clonal lineages in Pdp. In short, our study suggests that the host-dependent lifestyle of Pdp allowed massive IS proliferation and gene decay processes, which are major evolutionary forces in the shaping of the Pdp genome.
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Affiliation(s)
- Miguel Balado
- Departamento de Microbiología y Parasitología, Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Hicham Benzekri
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - Alejandro M Labella
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - M Gonzalo Claros
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - Manuel Manchado
- IFAPA Centro El Toruño, Junta de Andalucía, El Puerto de Santa María, Cádiz, Spain
| | - Juan J Borrego
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - Carlos R Osorio
- Departamento de Microbiología y Parasitología, Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.
| | - Manuel L Lemos
- Departamento de Microbiología y Parasitología, Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.
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110
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Saint-Leandre B, Clavereau I, Hua-Van A, Capy P. Transcriptional polymorphism ofpiRNA regulatory genes underlies themarineractivity inDrosophila simulanstestes. Mol Ecol 2017; 26:3715-3731. [DOI: 10.1111/mec.14145] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 12/28/2016] [Indexed: 02/03/2023]
Affiliation(s)
- Bastien Saint-Leandre
- Laboratoire Evolution, Génomes, Comportement, Ecologie CNRS; Univ. Paris-Sud, IRD; Université Paris-Saclay; Gif-sur-Yvette Cedex France
| | - Isabelle Clavereau
- Laboratoire Evolution, Génomes, Comportement, Ecologie CNRS; Univ. Paris-Sud, IRD; Université Paris-Saclay; Gif-sur-Yvette Cedex France
| | - Aurelie Hua-Van
- Laboratoire Evolution, Génomes, Comportement, Ecologie CNRS; Univ. Paris-Sud, IRD; Université Paris-Saclay; Gif-sur-Yvette Cedex France
| | - Pierre Capy
- Laboratoire Evolution, Génomes, Comportement, Ecologie CNRS; Univ. Paris-Sud, IRD; Université Paris-Saclay; Gif-sur-Yvette Cedex France
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111
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Schweizer F, Heidel-Fischer H, Vogel H, Reymond P. Arabidopsis glucosinolates trigger a contrasting transcriptomic response in a generalist and a specialist herbivore. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2017; 85:21-31. [PMID: 28455184 DOI: 10.1016/j.ibmb.2017.04.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 04/18/2017] [Accepted: 04/24/2017] [Indexed: 06/07/2023]
Abstract
Phytophagous insects have to deal with toxic defense compounds from their host plants. Although it is known that insects have evolved genes and mechanisms to detoxify plant allochemicals, how specialist and generalist precisely respond to specific secondary metabolites at the molecular level is less understood. Here we studied the larval performance and transcriptome of the generalist moth Heliothis virescens and the specialist butterfly Pieris brassicae feeding on Arabidopsis thaliana genotypes with different glucosinolate (GS) levels. H. virescens larvae gained significantly more weight on the GS-deficient mutant quadGS compared to wild-type (Col-0) plants. On the contrary, P. brassicae was unaffected by the presence of GS and performed equally well on both genotypes. Strikingly, there was a considerable differential gene expression in H. virescens larvae feeding on Col-0 compared to quadGS. In contrast, compared to H. virescens, P. brassicae displayed a much-reduced transcriptional activation when fed on both plant genotypes. Transcripts coding for putative detoxification enzymes were significantly upregulated in H. virescens, along with digestive enzymes and transposable elements. These data provide an unprecedented view on transcriptional changes that are specifically activated by GS and illustrate differential molecular responses that are linked to adaptation to diet in lepidopteran herbivores.
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Affiliation(s)
- Fabian Schweizer
- Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Hanna Heidel-Fischer
- Department of Entomology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Heiko Vogel
- Department of Entomology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany.
| | - Philippe Reymond
- Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland.
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112
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Hossain MS, Kawakatsu T, Kim KD, Zhang N, Nguyen CT, Khan SM, Batek JM, Joshi T, Schmutz J, Grimwood J, Schmitz RJ, Xu D, Jackson SA, Ecker JR, Stacey G. Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs. THE NEW PHYTOLOGIST 2017; 214:808-819. [PMID: 28106918 DOI: 10.1111/nph.14421] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 12/01/2016] [Indexed: 05/23/2023]
Abstract
Chromatin modifications, such as cytosine methylation of DNA, play a significant role in mediating gene expression in plants, which affects growth, development, and cell differentiation. As root hairs are single-cell extensions of the root epidermis and the primary organs for water uptake and nutrients, we sought to use root hairs as a single-cell model system to measure the impact of environmental stress. We measured changes in cytosine DNA methylation in single-cell root hairs as compared with multicellular stripped roots, as well as in response to heat stress. Differentially methylated regions (DMRs) in each methylation context showed very distinct methylation patterns between cell types and in response to heat stress. Intriguingly, at normal temperature, root hairs were more hypermethylated than were stripped roots. However, in response to heat stress, both root hairs and stripped roots showed hypomethylation in each context, especially in the CHH context. Moreover, expression analysis of mRNA from similar tissues and treatments identified some associations between DMRs, genes and transposons. Taken together, the data indicate that changes in DNA methylation are directly or indirectly associated with expression of genes and transposons within the context of either specific tissues/cells or stress (heat).
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Affiliation(s)
- Md Shakhawat Hossain
- Divisions of Plant Science and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Taiji Kawakatsu
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 30508602, Japan
| | - Kyung Do Kim
- Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA, 30602-6810, USA
| | - Ning Zhang
- Department of Computer Science, Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, 65211, USA
| | - Cuong T Nguyen
- Divisions of Plant Science and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Saad M Khan
- Department of Computer Science, Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, 65211, USA
| | - Josef M Batek
- Divisions of Plant Science and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Trupti Joshi
- Department of Computer Science, Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, 65211, USA
- Department of Molecular Microbiology and Immunology and Office of Research, School of Medicine, University of Missouri, Columbia, MO, 65211, USA
| | - Jeremy Schmutz
- HudsonAlpha Genome Sequencing Center, 601 Genome Way, Huntsville, AL, 35806, USA
| | - Jane Grimwood
- HudsonAlpha Genome Sequencing Center, 601 Genome Way, Huntsville, AL, 35806, USA
| | - Robert J Schmitz
- Department of Genetics, The University of Georgia, 120 East Green Street, Athens, GA, 30602, USA
| | - Dong Xu
- Department of Computer Science, Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, 65211, USA
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA, 30602-6810, USA
| | - Joseph R Ecker
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Gary Stacey
- Divisions of Plant Science and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
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113
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Borgognone A, Castanera R, Muguerza E, Pisabarro AG, Ramírez L. Somatic transposition and meiotically driven elimination of an active helitron family in Pleurotus ostreatus. DNA Res 2017; 24:103-115. [PMID: 28431016 PMCID: PMC5397611 DOI: 10.1093/dnares/dsw060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 12/14/2016] [Indexed: 01/31/2023] Open
Abstract
Helitrons constitute a superfamily of DNA transposons that were discovered in silico and are widespread in most eukaryotic genomes. They are postulated to mobilize through a "rolling-circle" mechanism, but the experimental evidence of their transposition has been described only recently. Here, we present the inheritance patterns of HELPO1 and HELPO2 helitron families in meiotically derived progeny of the basidiomycete Pleurotus ostreatus. We found distorted segregation patterns of HELPO2 helitrons that led to a strong under-representation of these elements in the progeny. Further investigation of HELPO2 flanking sites showed that gene conversion may contribute to the elimination of such repetitive elements in meiosis, favouring the presence of HELPO2 vacant loci. In addition, the analysis of HELPO2 content in a reconstructed pedigree of subclones maintained under different culture conditions revealed an event of helitron somatic transposition. Additional analyses of genome and transcriptome data indicated that P. ostreatus carries active RNAi machinery that could be involved in the control of transposable element proliferation. Our results provide the first evidence of helitron mobilization in the fungal kingdom and highlight the interaction between genome defence mechanisms and invasive DNA.
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Affiliation(s)
| | | | | | | | - Lucía Ramírez
- Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, Pamplona, Navarre, Spain
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114
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Kumar A, Castellano I, Patti FP, Delledonne M, Abdelgawad H, Beemster GTS, Asard H, Palumbo A, Buia MC. Molecular response of Sargassum vulgare to acidification at volcanic CO 2 vents: insights from de novo transcriptomic analysis. Mol Ecol 2017; 26:2276-2290. [PMID: 28133853 DOI: 10.1111/mec.14034] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 01/03/2017] [Accepted: 01/11/2017] [Indexed: 12/20/2022]
Abstract
Ocean acidification is an emerging problem that is expected to impact ocean species to varying degrees. Currently, little is known about its effect on molecular mechanisms induced in fleshy macroalgae. To elucidate genome wide responses to acidification, a transcriptome analysis was carried out on Sargassum vulgare populations growing under acidified conditions at volcanic CO2 vents and compared with populations in a control site. Several transcripts involved in a wide range of cellular and metabolic processes were differentially expressed. No drastic changes were observed in the carbon acquisition processes and RuBisCO level. Moreover, relatively few stress genes, including those for antioxidant enzymes and heat-shock proteins, were affected. Instead, increased expression of transcripts involved in energy metabolism, photosynthetic processes and ion homeostasis suggested that algae increased energy production to maintain ion homeostasis and other cellular processes. Also, an increased allocation of carbon to cell wall and carbon storage was observed. A number of genes encoding proteins involved in cellular signalling, information storage and processing and transposition were differentially expressed between the two conditions. The transcriptional changes of key enzymes were largely confirmed by enzymatic activity measurements. Altogether, the changes induced by acidification indicate an adaptation of growth and development of S. vulgare at the volcanic CO2 vents, suggesting that this fleshy alga exhibits a high plasticity to low pH and can adopt molecular strategies to grow also in future more acidified waters.
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Affiliation(s)
- Amit Kumar
- Department of Integrative Marine Ecology, Center of Villa Dohrn - Benthic Ecology, Stazione Zoologica Anton Dohrn, Ischia, Naples, Italy
| | - Immacolata Castellano
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Francesco Paolo Patti
- Department of Integrative Marine Ecology, Center of Villa Dohrn - Benthic Ecology, Stazione Zoologica Anton Dohrn, Ischia, Naples, Italy
| | | | - Hamada Abdelgawad
- Department of Biology, Integrated Molecular Plant Physiology Research Group (IMPRES), University of Antwerp, Antwerp, Belgium
| | - Gerrit T S Beemster
- Department of Biology, Integrated Molecular Plant Physiology Research Group (IMPRES), University of Antwerp, Antwerp, Belgium
| | - Han Asard
- Department of Biology, Integrated Molecular Plant Physiology Research Group (IMPRES), University of Antwerp, Antwerp, Belgium
| | - Anna Palumbo
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Maria Cristina Buia
- Department of Integrative Marine Ecology, Center of Villa Dohrn - Benthic Ecology, Stazione Zoologica Anton Dohrn, Ischia, Naples, Italy
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Puigvert M, Guarischi-Sousa R, Zuluaga P, Coll NS, Macho AP, Setubal JC, Valls M. Transcriptomes of Ralstonia solanacearum during Root Colonization of Solanum commersonii. FRONTIERS IN PLANT SCIENCE 2017; 8:370. [PMID: 28373879 PMCID: PMC5357869 DOI: 10.3389/fpls.2017.00370] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 03/02/2017] [Indexed: 05/03/2023]
Abstract
Bacterial wilt of potatoes-also called brown rot-is a devastating disease caused by the vascular pathogen Ralstonia solanacearum that leads to significant yield loss. As in other plant-pathogen interactions, the first contacts established between the bacterium and the plant largely condition the disease outcome. Here, we studied the transcriptome of R. solanacearum UY031 early after infection in two accessions of the wild potato Solanum commersonii showing contrasting resistance to bacterial wilt. Total RNAs obtained from asymptomatic infected roots were deep sequenced and for 4,609 out of the 4,778 annotated genes in strain UY031 were recovered. Only 2 genes were differentially-expressed between the resistant and the susceptible plant accessions, suggesting that the bacterial component plays a minor role in the establishment of disease. On the contrary, 422 genes were differentially expressed (DE) in planta compared to growth on a synthetic rich medium. Only 73 of these genes had been previously identified as DE in a transcriptome of R. solanacearum extracted from infected tomato xylem vessels. Virulence determinants such as the Type Three Secretion System (T3SS) and its effector proteins, motility structures, and reactive oxygen species (ROS) detoxifying enzymes were induced during infection of S. commersonii. On the contrary, metabolic activities were mostly repressed during early root colonization, with the notable exception of nitrogen metabolism, sulfate reduction and phosphate uptake. Several of the R. solanacearum genes identified as significantly up-regulated during infection had not been previously described as virulence factors. This is the first report describing the R. solanacearum transcriptome directly obtained from infected tissue and also the first to analyze bacterial gene expression in the roots, where plant infection takes place. We also demonstrate that the bacterial transcriptome in planta can be studied when pathogen numbers are low by sequencing transcripts from infected tissue avoiding prokaryotic RNA enrichment.
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Affiliation(s)
- Marina Puigvert
- Department of Genetics, University of BarcelonaBarcelona, Spain
- Centre for Research in Agricultural Genomics CSIC-IRTA, Autonomous University of BarcelonaBellaterra, Spain
| | | | - Paola Zuluaga
- Department of Genetics, University of BarcelonaBarcelona, Spain
- Centre for Research in Agricultural Genomics CSIC-IRTA, Autonomous University of BarcelonaBellaterra, Spain
| | - Núria S. Coll
- Centre for Research in Agricultural Genomics CSIC-IRTA, Autonomous University of BarcelonaBellaterra, Spain
| | - Alberto P. Macho
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences (CAS)Shanghai, China
| | - João C. Setubal
- Department of Biochemistry, University of São PauloSão Paulo, Brazil
| | - Marc Valls
- Department of Genetics, University of BarcelonaBarcelona, Spain
- Centre for Research in Agricultural Genomics CSIC-IRTA, Autonomous University of BarcelonaBellaterra, Spain
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116
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Integration site selection by retroviruses and transposable elements in eukaryotes. Nat Rev Genet 2017; 18:292-308. [PMID: 28286338 DOI: 10.1038/nrg.2017.7] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Transposable elements and retroviruses are found in most genomes, can be pathogenic and are widely used as gene-delivery and functional genomics tools. Exploring whether these genetic elements target specific genomic sites for integration and how this preference is achieved is crucial to our understanding of genome evolution, somatic genome plasticity in cancer and ageing, host-parasite interactions and genome engineering applications. High-throughput profiling of integration sites by next-generation sequencing, combined with large-scale genomic data mining and cellular or biochemical approaches, has revealed that the insertions are usually non-random. The DNA sequence, chromatin and nuclear context, and cellular proteins cooperate in guiding integration in eukaryotic genomes, leading to a remarkable diversity of insertion site distribution and evolutionary strategies.
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117
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Schumann U, Lee J, Kazan K, Ayliffe M, Wang MB. DNA-Demethylase Regulated Genes Show Methylation-Independent Spatiotemporal Expression Patterns. FRONTIERS IN PLANT SCIENCE 2017; 8:1449. [PMID: 28894455 PMCID: PMC5581395 DOI: 10.3389/fpls.2017.01449] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 08/04/2017] [Indexed: 05/12/2023]
Abstract
Recent research has indicated that a subset of defense-related genes is downregulated in the Arabidopsis DNA demethylase triple mutant rdd (ros1 dml2 dml3) resulting in increased susceptibility to the fungal pathogen Fusarium oxysporum. In rdd plants these downregulated genes contain hypermethylated transposable element sequences (TE) in their promoters, suggesting that this methylation represses gene expression in the mutant and that these sequences are actively demethylated in wild-type plants to maintain gene expression. In this study, the tissue-specific and pathogen-inducible expression patterns of rdd-downregulated genes were investigated and the individual role of ROS1, DML2, and DML3 demethylases in these spatiotemporal regulation patterns was determined. Large differences in defense gene expression were observed between pathogen-infected and uninfected tissues and between root and shoot tissues in both WT and rdd plants, however, only subtle changes in promoter TE methylation patterns occurred. Therefore, while TE hypermethylation caused decreased gene expression in rdd plants it did not dramatically effect spatiotemporal gene regulation, suggesting that this latter regulation is largely methylation independent. Analysis of ros1-3, dml2-1, and dml3-1 single gene mutant lines showed that promoter TE hypermethylation and defense-related gene repression was predominantly, but not exclusively, due to loss of ROS1 activity. These data demonstrate that DNA demethylation of TE sequences, largely by ROS1, promotes defense-related gene expression but does not control spatiotemporal expression in Arabidopsis. Summary: Ros1-mediated DNA demethylation of promoter transposable elements is essential for activation of defense-related gene expression in response to fungal infection in Arabidopsis thaliana.
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Affiliation(s)
- Ulrike Schumann
- CSIRO Agriculture and Food, CanberraACT, Australia
- *Correspondence: Ming-Bo Wang, Ulrike Schumann,
| | - Joanne Lee
- CSIRO Agriculture and Food, CanberraACT, Australia
| | - Kemal Kazan
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St. LuciaQLD, Australia
| | | | - Ming-Bo Wang
- CSIRO Agriculture and Food, CanberraACT, Australia
- *Correspondence: Ming-Bo Wang, Ulrike Schumann,
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Robillard É, Le Rouzic A, Zhang Z, Capy P, Hua-Van A. Experimental evolution reveals hyperparasitic interactions among transposable elements. Proc Natl Acad Sci U S A 2016; 113:14763-14768. [PMID: 27930288 PMCID: PMC5187678 DOI: 10.1073/pnas.1524143113] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Transposable elements (TEs) are repeated DNA sequences that can constitute a substantial part of genomes. Studying TEs' activity, interactions, and accumulation dynamics is thus of major interest to understand genome evolution. Here, we describe the transposition dynamics of cut-and-paste mariner elements during experimental (short- and longer-term) evolution in Drosophila melanogaster Flies with autonomous and nonautonomous mariner copies were introduced in populations containing no active mariner, and TE accumulation was tracked by quantitative PCR for up to 100 generations. Our results demonstrate that (i) active mariner elements are highly invasive and characterized by an elevated transposition rate, confirming their capacity to spread in populations, as predicted by the "selfish-DNA" mechanism; (ii) nonautonomous copies act as parasites of autonomous mariner elements by hijacking the transposition machinery produced by active mariner, which can be considered as a case of hyperparasitism; (iii) this behavior resulted in a failure of active copies to amplify which systematically drove the whole family to extinction in less than 100 generations. This study nicely illustrates how the presence of transposition-competitive variants can deeply impair TE dynamics and gives clues to the extraordinary diversity of TE evolutionary histories observed in genomes.
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Affiliation(s)
- Émilie Robillard
- Évolution, Génomes, Comportement, Écologie, CNRS, Institut de Recherche pour le Développement, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Arnaud Le Rouzic
- Évolution, Génomes, Comportement, Écologie, CNRS, Institut de Recherche pour le Développement, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Zheng Zhang
- Évolution, Génomes, Comportement, Écologie, CNRS, Institut de Recherche pour le Développement, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Pierre Capy
- Évolution, Génomes, Comportement, Écologie, CNRS, Institut de Recherche pour le Développement, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Aurélie Hua-Van
- Évolution, Génomes, Comportement, Écologie, CNRS, Institut de Recherche pour le Développement, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
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Ryan CP, Brownlie JC, Whyard S. Hsp90 and Physiological Stress Are Linked to Autonomous Transposon Mobility and Heritable Genetic Change in Nematodes. Genome Biol Evol 2016; 8:3794-3805. [PMID: 28082599 PMCID: PMC5521727 DOI: 10.1093/gbe/evw284] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2016] [Indexed: 12/21/2022] Open
Abstract
Transposable elements (TEs) have been recognized as potentially powerful drivers of genomic evolutionary change, but factors affecting their mobility and regulation remain poorly understood. Chaperones such as Hsp90 buffer environmental perturbations by regulating protein conformation, but are also part of the PIWI-interacting RNA pathway, which regulates genomic instability arising from mobile TEs in the germline. Stress-induced mutagenesis from TE movement could thus arise from functional trade-offs in the dual roles of Hsp90. We examined the functional constraints of Hsp90 and its role as a regulator of TE mobility by exposing nematodes (Caenorhabditis elegans and Caenorhabditis briggsae) to environmental stress, with and without RNAi-induced silencing of Hsp90. TE excision frequency increased with environmental stress intensity at multiple loci in several strains of each species. These effects were compounded by RNAi-induced knockdown of Hsp90. Mutation frequencies at the unc-22 marker gene in the offspring of animals exposed to environmental stress and Hsp90 RNAi mirrored excision frequency in response to these treatments. Our results support a role for Hsp90 in the suppression of TE mobility, and demonstrate that that the Hsp90 regulatory pathway can be overwhelmed with moderate environmental stress. By compromising genomic stability in germline cells, environmentally induced mutations arising from TE mobility and insertion can have permanent and heritable effects on both the phenotype and the genotype of subsequent generations.
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Affiliation(s)
- Calen P. Ryan
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Anthropology, Northwestern University, Evanston, IL
| | - Jeremy C. Brownlie
- School of Biomolecular and Physical Sciences, Griffith University, Brisbane, Queensland, Australia
| | - Steve Whyard
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
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Estoup A, Ravigné V, Hufbauer R, Vitalis R, Gautier M, Facon B. Is There a Genetic Paradox of Biological Invasion? ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2016. [DOI: 10.1146/annurev-ecolsys-121415-032116] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Arnaud Estoup
- Unité Mixte de Recherche Centre de Biologie pour la Gestion des Populations, Institut National de la Recherche Agronomique, 34988 Montferrier sur Lez, France;
| | - Virginie Ravigné
- Unité Mixte de Recherche Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, 97410 Saint-Pierre, La Réunion, France
| | - Ruth Hufbauer
- Department of Bioagricultural Science and Pest Management, Colorado State University, Fort Collins, Colorado 80523
| | - Renaud Vitalis
- Unité Mixte de Recherche Centre de Biologie pour la Gestion des Populations, Institut National de la Recherche Agronomique, 34988 Montferrier sur Lez, France;
| | - Mathieu Gautier
- Unité Mixte de Recherche Centre de Biologie pour la Gestion des Populations, Institut National de la Recherche Agronomique, 34988 Montferrier sur Lez, France;
| | - Benoit Facon
- Unité Mixte de Recherche Centre de Biologie pour la Gestion des Populations, Institut National de la Recherche Agronomique, 34988 Montferrier sur Lez, France;
- Unité Mixte de Recherche Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, 97410 Saint-Pierre, La Réunion, France
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121
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Kanhayuwa L, Coutts RHA. Short Interspersed Nuclear Element (SINE) Sequences in the Genome of the Human Pathogenic Fungus Aspergillus fumigatus Af293. PLoS One 2016; 11:e0163215. [PMID: 27736869 PMCID: PMC5063351 DOI: 10.1371/journal.pone.0163215] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 09/06/2016] [Indexed: 11/19/2022] Open
Abstract
Novel families of short interspersed nuclear element (SINE) sequences in the human pathogenic fungus Aspergillus fumigatus, clinical isolate Af293, were identified and categorised into tRNA-related and 5S rRNA-related SINEs. Eight predicted tRNA-related SINE families originating from different tRNAs, and nominated as AfuSINE2 sequences, contained target site duplications of short direct repeat sequences (4–14 bp) flanking the elements, an extended tRNA-unrelated region and typical features of RNA polymerase III promoter sequences. The elements ranged in size from 140–493 bp and were present in low copy number in the genome and five out of eight were actively transcribed. One putative tRNAArg-derived sequence, AfuSINE2-1a possessed a unique feature of repeated trinucleotide ACT residues at its 3’-terminus. This element was similar in sequence to the I-4_AO element found in A. oryzae and an I-1_AF long nuclear interspersed element-like sequence identified in A. fumigatus Af293. Families of 5S rRNA-related SINE sequences, nominated as AfuSINE3, were also identified and their 5'-5S rRNA-related regions show 50–65% and 60–75% similarity to respectively A. fumigatus 5S rRNAs and SINE3-1_AO found in A. oryzae. A. fumigatus Af293 contains five copies of AfuSINE3 sequences ranging in size from 259–343 bp and two out of five AfuSINE3 sequences were actively transcribed. Investigations on AfuSINE distribution in the fungal genome revealed that the elements are enriched in pericentromeric and subtelomeric regions and inserted within gene-rich regions. We also demonstrated that some, but not all, AfuSINE sequences are targeted by host RNA silencing mechanisms. Finally, we demonstrated that infection of the fungus with mycoviruses had no apparent effects on SINE activity.
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Affiliation(s)
- Lakkhana Kanhayuwa
- Division of Biology, Faculty of Natural Sciences, Imperial College London, Sir Alexander Fleming Building, Imperial College Road, London, United Kingdom
- * E-mail:
| | - Robert H. A. Coutts
- Division of Biology, Faculty of Natural Sciences, Imperial College London, Sir Alexander Fleming Building, Imperial College Road, London, United Kingdom
- School of Life and Medical Sciences, Department of Biological and Environmental Sciences, University of Hertfordshire, Hatfield, United Kingdom
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Dias LP, de Oliveira-Busatto LA, Bodanese-Zanettini MH. The differential expression of soybean [Glycine max (L.) Merrill] WRKY genes in response to water deficit. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 107:288-300. [PMID: 27343875 DOI: 10.1016/j.plaphy.2016.06.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 06/13/2016] [Accepted: 06/14/2016] [Indexed: 05/21/2023]
Abstract
Drought is today, and perhaps even more in the future, the main challenge for grain crops, resulting in a drastic yield reduction. Thus, it is of great interest to obtain soybean genotypes tolerant to water deficit. The drought tolerance trait is difficult to obtain through classical breeding due to its polygenic basis. In this context, genetic engineering is presented as a way to achieve this attribute. The ability to modulate the expression of many genes placed the transcription factors as promising biotechnological targets to develop stress tolerant cultivars. The WRKY proteins form a large family of transcription factors that are involved in important physiological and biochemical processes in plants, including the response to water deficit. In this study, the expression pattern determined by qPCR showed that, GmWRKY6, GmWRKY46, GmWRKY56, GmWRKY106 and GmWRKY149 genes are differentially expressed between a drought tolerant and a susceptible soybean genotype in water stress conditions. The in silico promoter and coexpression analysis indicate that these genes act in a stress physiological background.
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Affiliation(s)
- Letícia Pereira Dias
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), 91501-970, Porto Alegre, RS, Brazil.
| | - Luisa Abruzzi de Oliveira-Busatto
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), 91501-970, Porto Alegre, RS, Brazil.
| | - Maria Helena Bodanese-Zanettini
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), 91501-970, Porto Alegre, RS, Brazil.
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Craddock EM. Profuse evolutionary diversification and speciation on volcanic islands: transposon instability and amplification bursts explain the genetic paradox. Biol Direct 2016; 11:44. [PMID: 27600528 PMCID: PMC5012101 DOI: 10.1186/s13062-016-0146-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/26/2016] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Species-rich adaptive radiations arising from rare plant and animal colonizers are common on remote volcanic archipelagoes. However, they present a paradox. The severe genetic bottleneck of founder events and effects of inbreeding depression, coupled with the inherently stressful volcanic environment, would seem to predict reduced evolutionary potential and increased risk of extinction, rather than rapid adaptive divergence and speciation. Significantly, eukaryotic genomes harbor many families of transposable elements (TEs) that are mobilized by genome shock; these elements may be the primary drivers of genetic reorganization and speciation on volcanic islands. PRESENTATION OF THE HYPOTHESIS Here I propose that a central factor in the spectacular radiation and diversification of the endemic Hawaiian Drosophila and other terrestrial lineages on the Hawaiian and other oceanic islands has been repeated bursts of transposition of multiple TEs induced by the unique ecological features of volcanic habitats. Founder individuals and populations on remote volcanic islands experience significant levels of physiological and genomic stress as a consequence of both biotic and abiotic factors. This results in disruption of the usual epigenetic suppression of TEs, unleashing them to proliferate and spread, which in turn gives rise to novel genetic variation and remodels genomic regulatory circuits, facilitating rapid morphological, ecological and behavioral change, and adaptive radiation. TESTING THE HYPOTHESIS To obtain empirical support for the hypothesis, test organisms should be exposed to prolonged heat stress, high levels of carbon dioxide and other volcanic gases, along with inbreeding. Data from subsequent whole genome sequencing and bioinformatics screening for TE numbers and locations would then be compared with initial pre-exposure TE information for the test strains, a labor-intensive project. Several predicted outcomes arising from the hypothesis are discussed. Currently available data are consistent with the proposed concept of stress-induced TE mobilization as a trigger of evolutionary diversification and speciation on volcanic islands. IMPLICATIONS OF THE HYPOTHESIS The main implication is that both TEs and species should proliferate at a much higher rate on volcanic islands than elsewhere. Second, the evolvability of a lineage may correlate with the abundance and distribution of TEs in the genome. Successful colonizers of volcanic habitats with high genomic proportions of TEs may be best poised to found a speciose lineage that gives rise to a dramatic adaptive radiation. Colonizers that are depauperate in TEs are likely to be evolutionarily constrained and diversify little, if at all. REVIEWERS This article was reviewed by Dr. James Shapiro and Dr. Wolfgang Miller (nominated by Editorial Board member Dr. I. King Jordan).
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Affiliation(s)
- Elysse M Craddock
- School of Natural and Social Sciences, Purchase College, State University of New York, 735 Anderson Hill Road, Purchase, NY, 10577-1400, USA.
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Janoušek V, Laukaitis CM, Yanchukov A, Karn RC. The Role of Retrotransposons in Gene Family Expansions in the Human and Mouse Genomes. Genome Biol Evol 2016; 8:2632-50. [PMID: 27503295 PMCID: PMC5631067 DOI: 10.1093/gbe/evw192] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Retrotransposons comprise a large portion of mammalian genomes. They contribute to structural changes and more importantly to gene regulation. The expansion and diversification of gene families have been implicated as sources of evolutionary novelties. Given the roles retrotransposons play in genomes, their contribution to the evolution of gene families warrants further exploration. In this study, we found a significant association between two major retrotransposon classes, LINEs and LTRs, and lineage-specific gene family expansions in both the human and mouse genomes. The distribution and diversity differ between LINEs and LTRs, suggesting that each has a distinct involvement in gene family expansion. LTRs are associated with open chromatin sites surrounding the gene families, supporting their involvement in gene regulation, whereas LINEs may play a structural role promoting gene duplication. Our findings also suggest that gene family expansions, especially in the mouse genome, undergo two phases. The first phase is characterized by elevated deposition of LTRs and their utilization in reshaping gene regulatory networks. The second phase is characterized by rapid gene family expansion due to continuous accumulation of LINEs and it appears that, in some instances at least, this could become a runaway process. We provide an example in which this has happened and we present a simulation supporting the possibility of the runaway process. Altogether we provide evidence of the contribution of retrotransposons to the expansion and evolution of gene families. Our findings emphasize the putative importance of these elements in diversification and adaptation in the human and mouse lineages.
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Affiliation(s)
- Václav Janoušek
- Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic Institute of Vertebrate Biology, ASCR, Brno, Czech Republic
| | | | - Alexey Yanchukov
- Institute of Vertebrate Biology, ASCR, Brno, Czech Republic Department of Biology, Faculty of Arts and Sciences, Bülent Ecevit University, Zonguldak, Turkey
| | - Robert C Karn
- Department of Medicine, College of Medicine, University of Arizona
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126
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Wei B, Liu H, Liu X, Xiao Q, Wang Y, Zhang J, Hu Y, Liu Y, Yu G, Huang Y. Genome-wide characterization of non-reference transposons in crops suggests non-random insertion. BMC Genomics 2016; 17:536. [PMID: 27485608 PMCID: PMC4971691 DOI: 10.1186/s12864-016-2847-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 06/20/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Transposons (transposable elements or TEs) are DNA sequences that can change their position within the genome. A large number of TEs have been identified in reference genome of each crop(named accumulated TEs), which are the important part of genome. However, whether there existed TEs with different insert positions in resequenced crop accession genomes from those of reference genome (named non-reference transposable elements, non-ref TEs), and what the characteristics (such as the number, type and distribution) are. To identify and characterize crop non-ref TEs, we analyzed non-ref TEs in more than 125 accessions from rice (Oryza sativa), maize (Zea mays) and sorghum (Sorghum bicolor) using resequenced data with paired-end mapping methods. RESULTS We identified 13,066, 23,866 and 35,679 non-ref TEs in rice, maize and sorghum, respectively. Genome-wide characterization analysis shows that most of non-ref TEs were unique and non-ref TE classes shows different among rice, maize and sorghum. We found that non-ref TEs have a strong positive correlation with gene number and have a bias toward insertion near genes, but with a preference for avoiding coding regions in maize and sorghum. The genes affected by non-ref TE insertion were functionally enriched for stress response mechanisms in all three crops. CONCLUSIONS These observations suggest that transposon insertion is not a random event and it makes genomic diversity, which may affect the intraspecific adaption and evolution of crops.
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Affiliation(s)
- Bin Wei
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hanmei Liu
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Xin Liu
- Beijing Genome Institute and the Key Laboratory of Genomics of the Minister of Agriculture, Shenzhen, 518083, China
| | - Qianlin Xiao
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yongbin Wang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Junjie Zhang
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Yufeng Hu
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yinghong Liu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guowu Yu
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yubi Huang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China.
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Payen T, Murat C, Martin F. Reconstructing the evolutionary history of gypsy retrotransposons in the Périgord black truffle (Tuber melanosporum Vittad.). MYCORRHIZA 2016; 26:553-563. [PMID: 27025914 DOI: 10.1007/s00572-016-0692-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 03/21/2016] [Indexed: 06/05/2023]
Abstract
Truffles are ascomycete fungi belonging to genus Tuber, and they form ectomycorrhizal associations with trees and shrubs. Transposable elements constitute more than 50 % of the black Périgord truffle (Tuber melanosporum) genome, which are mainly class 1 gypsy retrotransposons, but their impact on its genome is unknown. The aims of this study are to investigate the diversity of gypsy retrotransposons in this species and their evolutionary history by analysing the reference genome and six resequenced genomes of different geographic accessions. Using the reverse transcriptase sequences, six different gypsy retrotransposon clades were identified. Tmt1 and Tmt6 are the most abundant transposable elements, representing 14 and 13 % of the T. melanosporum genome, respectively. Tmt6 showed a major burst of proliferation between 1 and 4 million years ago, but evidence of more recent transposition was observed. Except for Tmt2, the other clades tend to aggregate, and their mode of transposition excluded the master copy model. This suggests that each new copy has the same probability of transposing as other copies. This study provides a better view of the diversity and dynamic nature of gypsy retrotransposons in T. melanosporum. Even if the major gypsy retrotransposon bursts are old, some elements seem to have transposed recently, suggesting that they may continue to model the truffle genomes.
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Affiliation(s)
- Thibaut Payen
- UMR1136, "Interactions Arbres/Micro-organismes", INRA, Université de Lorraine, Laboratoire d'Excellence ARBRE, F-54280, Champenoux, France
| | - Claude Murat
- UMR1136, "Interactions Arbres/Micro-organismes", INRA, Université de Lorraine, Laboratoire d'Excellence ARBRE, F-54280, Champenoux, France.
| | - Francis Martin
- UMR1136, "Interactions Arbres/Micro-organismes", INRA, Université de Lorraine, Laboratoire d'Excellence ARBRE, F-54280, Champenoux, France
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128
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Hirsch CD, Springer NM. Transposable element influences on gene expression in plants. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:157-165. [PMID: 27235540 DOI: 10.1016/j.bbagrm.2016.05.010] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 05/17/2016] [Accepted: 05/18/2016] [Indexed: 01/29/2023]
Abstract
Transposable elements (TEs) comprise a major portion of many plant genomes and bursts of TE movements cause novel genomic variation within species. In order to maintain proper gene function, plant genomes have evolved a variety of mechanisms to tolerate the presence of TEs within or near genes. Here, we review our understanding of the interactions between TEs and gene expression in plants by assessing three ways that transposons can influence gene expression. First, there is growing evidence that TE insertions within introns or untranslated regions of genes are often tolerated and have minimal impact on expression level or splicing. However, there are examples in which TE insertions within genes can result in aberrant or novel transcripts. Second, TEs can provide novel alternative promoters, which can lead to new expression patterns or original coding potential of an alternate transcript. Third, TE insertions near genes can influence regulation of gene expression through a variety of mechanisms. For example, TEs may provide novel cis-acting regulatory sites behaving as enhancers or insert within existing enhancers to influence transcript production. Alternatively, TEs may change chromatin modifications in regions near genes, which in turn can influence gene expression levels. Together, the interactions of genes and TEs provide abundant evidence for the role of TEs in changing basic functions within plant genomes beyond acting as latent genomic elements or as simple insertional mutagens. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
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Affiliation(s)
- Cory D Hirsch
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Nathan M Springer
- Department of Plant Biology, University of Minnesota, Saint Paul, MN 55108, USA.
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129
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Verhoeven KJF, vonHoldt BM, Sork VL. Epigenetics in ecology and evolution: what we know and what we need to know. Mol Ecol 2016; 25:1631-8. [DOI: 10.1111/mec.13617] [Citation(s) in RCA: 183] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 03/11/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Koen J. F. Verhoeven
- Terrestrial Ecology Department; Netherlands Institute of Ecology (NIOO-KNAW); Droevendaalsesteeg 10 6708 PB Wageningen the Netherlands
| | | | - Victoria L. Sork
- Ecology & Evolutionary Biology; University of California; Los Angeles CA 90095 USA
- Institute of the Environment and Sustainability; University of California; Los Angeles CA 90095 USA
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130
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Janowitz Koch I, Clark MM, Thompson MJ, Deere-Machemer KA, Wang J, Duarte L, Gnanadesikan GE, McCoy EL, Rubbi L, Stahler DR, Pellegrini M, Ostrander EA, Wayne RK, Sinsheimer JS, vonHoldt BM. The concerted impact of domestication and transposon insertions on methylation patterns between dogs and grey wolves. Mol Ecol 2016; 25:1838-55. [PMID: 27112634 PMCID: PMC4849173 DOI: 10.1111/mec.13480] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 11/09/2015] [Accepted: 11/12/2015] [Indexed: 12/21/2022]
Abstract
The process of domestication can exert intense trait-targeted selection on genes and regulatory regions. Specifically, rapid shifts in the structure and sequence of genomic regulatory elements could provide an explanation for the extensive, and sometimes extreme, variation in phenotypic traits observed in domesticated species. Here, we explored methylation differences from >24 000 cytosines distributed across the genomes of the domesticated dog (Canis familiaris) and the grey wolf (Canis lupus). PCA and model-based cluster analyses identified two primary groups, domestic vs. wild canids. A scan for significantly differentially methylated sites (DMSs) revealed species-specific patterns at 68 sites after correcting for cell heterogeneity, with weak yet significant hypermethylation typical of purebred dogs when compared to wolves (59% and 58%, P < 0.05, respectively). Additionally, methylation patterns at eight genes significantly deviated from neutrality, with similar trends of hypermethylation in purebred dogs. The majority (>66%) of differentially methylated regions contained or were associated with repetitive elements, indicative of a genotype-mediated trend. However, DMSs were also often linked to functionally relevant genes (e.g. neurotransmitters). Finally, we utilized known genealogical relationships among Yellowstone wolves to survey transmission stability of methylation marks, from which we found a substantial fraction that demonstrated high heritability (both H(2) and h(2 ) > 0.99). These analyses provide a unique epigenetic insight into the molecular consequences of recent selection and radiation of our most ancient domesticated companion, the dog. These findings suggest selection has acted on methylation patterns, providing a new genomic perspective on phenotypic diversification in domesticated species.
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Affiliation(s)
- Ilana Janowitz Koch
- Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Michelle M Clark
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Michael J Thompson
- Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | | | - Jun Wang
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48085, USA
| | - Lionel Duarte
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | | | - Eskender L McCoy
- Yale School of Management, Yale University, New Haven, CT, 06511, USA
| | - Liudmilla Rubbi
- Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Daniel R Stahler
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, WY, 82190, USA
| | - Matteo Pellegrini
- Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Robert K Wayne
- Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Janet S Sinsheimer
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Human Genetics and Biomathematics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Bridgett M vonHoldt
- Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
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131
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Low Genetic Quality Alters Key Dimensions of the Mutational Spectrum. PLoS Biol 2016; 14:e1002419. [PMID: 27015430 PMCID: PMC4807879 DOI: 10.1371/journal.pbio.1002419] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 02/25/2016] [Indexed: 12/18/2022] Open
Abstract
Mutations affect individual health, population persistence, adaptation, diversification, and genome evolution. There is evidence that the mutation rate varies among genotypes, but the causes of this variation are poorly understood. Here, we link differences in genetic quality with variation in spontaneous mutation in a Drosophila mutation accumulation experiment. We find that chromosomes maintained in low-quality genetic backgrounds experience a higher rate of indel mutation and a lower rate of gene conversion in a manner consistent with condition-based differences in the mechanisms used to repair DNA double strand breaks. These aspects of the mutational spectrum were also associated with body mass, suggesting that the effect of genetic quality on DNA repair was mediated by overall condition, and providing a mechanistic explanation for the differences in mutational fitness decline among these genotypes. The rate and spectrum of substitutions was unaffected by genetic quality, but we find variation in the probability of substitutions and indels with respect to several aspects of local sequence context, particularly GC content, with implications for models of molecular evolution and genome scans for signs of selection. Our finding that the chances of mutation depend on genetic context and overall condition has important implications for how sequences evolve, the risk of extinction, and human health.
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Santos FAD, Marques DF, Terencio ML, Feldberg E, Rodrigues LRR. Cytogenetic variation of repetitive DNA elements in Hoplias malabaricus (Characiformes - Erythrinidae) from white, black and clear water rivers of the Amazon basin. Genet Mol Biol 2016; 39:40-8. [PMID: 27007897 PMCID: PMC4807386 DOI: 10.1590/1678-4685-gmb-2015-0099] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 08/02/2015] [Indexed: 11/22/2022] Open
Abstract
Hoplias malabaricus is a common fish species occurring in white, black and clear water rivers of the Amazon basin. Its large distribution across distinct aquatic environments can pose stressful conditions for dispersal and creates possibilities for the emergence of local adaptive profiles. We investigated the chromosomal localization of repetitive DNA markers (constitutive heterochromatin, rDNA and the transposable element REX-3) in populations from the Amazonas river (white water), the Negro river (black water) and the Tapajós river (clear water), in order to address the variation/association of cytogenomic features and environmental conditions. We found a conserved karyotypic macrostructure with a diploid number of 40 chromosomes (20 metacentrics + 20 submetacentrics) in all the samples. Heteromorphism in pair 14 was detected as evidence for the initial differentiation of an XX/XY system. Minor differences detected in the amount of repetitive DNA markers are interpreted as possible signatures of local adaptations to distinct aquatic environments.
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Affiliation(s)
- Fabíola Araújo Dos Santos
- Laboratório de Genética & Biodiversidade, Instituto de Ciências da Educação, Universidade Federal do Oeste do Pará, Santarém, PA, Brazil
| | - Diego Ferreira Marques
- Laboratório de Genética & Biodiversidade, Instituto de Ciências da Educação, Universidade Federal do Oeste do Pará, Santarém, PA, Brazil
| | - Maria Leandra Terencio
- Laboratório de Citogenética Animal, Instituto de Pesquisas da Amazônia, Manaus, AM, Brazil
| | - Eliana Feldberg
- Laboratório de Citogenética Animal, Instituto de Pesquisas da Amazônia, Manaus, AM, Brazil
| | - Luís Reginaldo R Rodrigues
- Laboratório de Genética & Biodiversidade, Instituto de Ciências da Educação, Universidade Federal do Oeste do Pará, Santarém, PA, Brazil
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133
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Canapa A, Barucca M, Biscotti MA, Forconi M, Olmo E. Transposons, Genome Size, and Evolutionary Insights in Animals. Cytogenet Genome Res 2016; 147:217-39. [PMID: 26967166 DOI: 10.1159/000444429] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/03/2015] [Indexed: 11/19/2022] Open
Abstract
The relationship between genome size and the percentage of transposons in 161 animal species evidenced that variations in genome size are linked to the amplification or the contraction of transposable elements. The activity of transposable elements could represent a response to environmental stressors. Indeed, although with different trends in protostomes and deuterostomes, comprehensive changes in genome size were recorded in concomitance with particular periods of evolutionary history or adaptations to specific environments. During evolution, genome size and the presence of transposable elements have influenced structural and functional parameters of genomes and cells. Changes of these parameters have had an impact on morphological and functional characteristics of the organism on which natural selection directly acts. Therefore, the current situation represents a balance between insertion and amplification of transposons and the mechanisms responsible for their deletion or for decreasing their activity. Among the latter, methylation and the silencing action of small RNAs likely represent the most frequent mechanisms.
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Affiliation(s)
- Adriana Canapa
- Dipartimento di Scienze della Vita e dell'Ambiente, Universitx00E0; Politecnica delle Marche, Ancona, Italy
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134
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Ni JZ, Kalinava N, Chen E, Huang A, Trinh T, Gu SG. A transgenerational role of the germline nuclear RNAi pathway in repressing heat stress-induced transcriptional activation in C. elegans. Epigenetics Chromatin 2016; 9:3. [PMID: 26779286 PMCID: PMC4714518 DOI: 10.1186/s13072-016-0052-x] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 01/05/2016] [Indexed: 02/07/2023] Open
Abstract
Background Environmental stress-induced transgenerational epigenetic effects have been observed in various model organisms and human. The capacity and mechanism of such phenomena are poorly understood. In C. elegans, siRNA mediates transgenerational gene
silencing through the germline nuclear RNAi pathway. This pathway is also required to maintain the germline immortality when C. elegans is under heat stress. However, the underlying molecular mechanism is unknown. In this study, we investigated the impact of heat stress on chromatin, transcription, and siRNAs at the whole-genome level, and whether any of the heat-induced effects is transgenerationally heritable in either the wild-type or the germline nuclear RNAi mutant animals. Results We performed 12-generation temperature-shift experiments using the wild-type C. elegans and a mutant strain that lacks the germline-specific nuclear Argonaute protein HRDE-1/WAGO-9. By examining the mRNA, small RNA, RNA polymerase II, and H3K9 trimethylation profiles at the whole-genome level, we revealed an epigenetic role of HRDE-1 in repressing heat stress-induced transcriptional activation of over 280 genes. Many of these genes are in or near LTR (long-terminal repeat) retrotransposons. Strikingly, for some of these genes, the heat stress-induced transcriptional activation in the hrde-1 mutant intensifies in the late generations under the heat stress and is heritable for at least two generations after the mutant animals are shifted back to lower temperature. hrde-1 mutation also leads to siRNA expression changes of many genes. This effect on siRNA is dependent on both the temperature and generation. Conclusions Our study demonstrated that a large number of the endogenous targets of the germline nuclear RNAi pathway in C. elegans are sensitive to heat-induced transcriptional activation. This effect at certain genomic loci including LTR retrotransposons is transgenerational. Germline nuclear RNAi antagonizes this temperature effect at the transcriptional level and therefore may play a key role in heat stress response in C. elegans. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0052-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Julie Zhouli Ni
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New Jersey, Piscataway, NJ 08854 USA
| | - Natallia Kalinava
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New Jersey, Piscataway, NJ 08854 USA
| | - Esteban Chen
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New Jersey, Piscataway, NJ 08854 USA
| | - Alex Huang
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New Jersey, Piscataway, NJ 08854 USA
| | - Thi Trinh
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New Jersey, Piscataway, NJ 08854 USA
| | - Sam Guoping Gu
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New Jersey, Piscataway, NJ 08854 USA ; Nelson Labs A125, 604 Allison Road, Piscataway, NJ 08854 USA
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135
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An R, Grewal PS. Comparative Analysis of Xenorhabdus koppenhoeferi Gene Expression during Symbiotic Persistence in the Host Nematode. PLoS One 2016; 11:e0145739. [PMID: 26745883 PMCID: PMC4706420 DOI: 10.1371/journal.pone.0145739] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 12/08/2015] [Indexed: 01/24/2023] Open
Abstract
Species of Xenorhabdus and Photorhabdus bacteria form mutualistic associations with Steinernema and Heterorhabditis nematodes, respectively and serve as model systems for studying microbe-animal symbioses. Here, we profiled gene expression of Xenorhabdus koppenhoeferi during their symbiotic persistence in the newly formed infective juveniles of the host nematode Steinernema scarabaei through the selective capture of transcribed sequences (SCOTS). The obtained gene expression profile was then compared with other nematode-bacteria partnerships represented by Steinernema carpocapsae-Xenorhabdus nematophila and Heterorhabditis bacteriophora-Photorhabdus temperata. A total of 29 distinct genes were identified to be up-regulated and 53 were down-regulated in X. koppenhoeferi while in S. scarabaei infective juveniles. Of the identified genes, 8 of the up-regulated and 14 of the down-regulated genes were similarly expressed in X. nematophila during persistence in its host nematode S. carpocapsae. However, only one from each of these up- and down-regulated genes was common to the mutualistic partnership between the bacterium P. temperata and the nematode H. bacteriophora. Interactive network analysis of the shared genes between X. koppenhoeferi and X. nematophila demonstrated that the up-regulated genes were mainly involved in bacterial survival and the down-regulated genes were more related to bacterial virulence and active growth. Disruption of two selected genes pta (coding phosphotransacetylase) and acnB (coding aconitate hydratase) in X. nematophila with shared expression signature with X. koppenhoeferi confirmed that these genes are important for bacterial persistence in the nematode host. The results of our comparative analyses show that the two Xenorhabdus species share a little more than a quarter of the transcriptional mechanisms during persistence in their nematode hosts but these features are quite different from those used by P. temperata bacteria in their nematode host H. bacteriophora.
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Affiliation(s)
- Ruisheng An
- Department of Entomology and Plant Pathology, University of Tennessee, 2505 E. J. Chapman Drive, Knoxville, TN, 37996, United States of America
| | - Parwinder S. Grewal
- Department of Entomology and Plant Pathology, University of Tennessee, 2505 E. J. Chapman Drive, Knoxville, TN, 37996, United States of America
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136
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Stamm C, Räsänen K, Burdon F, Altermatt F, Jokela J, Joss A, Ackermann M, Eggen R. Unravelling the Impacts of Micropollutants in Aquatic Ecosystems. ADV ECOL RES 2016. [DOI: 10.1016/bs.aecr.2016.07.002] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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137
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Rose NH, Seneca FO, Palumbi SR. Gene Networks in the Wild: Identifying Transcriptional Modules that Mediate Coral Resistance to Experimental Heat Stress. Genome Biol Evol 2015; 8:243-52. [PMID: 26710855 PMCID: PMC4758253 DOI: 10.1093/gbe/evv258] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Organisms respond to environmental variation partly through changes in gene expression, which underlie both homeostatic and acclimatory responses to environmental stress. In some cases, so many genes change in expression in response to different influences that understanding expression patterns for all these individual genes becomes difficult. To reduce this problem, we use a systems genetics approach to show that variation in the expression of thousands of genes of reef-building corals can be explained as variation in the expression of a small number of coexpressed “modules.” Modules were often enriched for specific cellular functions and varied predictably among individuals, experimental treatments, and physiological state. We describe two transcriptional modules for which expression levels immediately after heat stress predict bleaching a day later. One of these early “bleaching modules” is enriched for sequence-specific DNA-binding proteins, particularly E26 transformation-specific (ETS)-family transcription factors. The other module is enriched for extracellular matrix proteins. These classes of bleaching response genes are clear in the modular gene expression analysis we conduct but are much more difficult to discern in single gene analyses. Furthermore, the ETS-family module shows repeated differences in expression among coral colonies grown in the same common garden environment, suggesting a heritable genetic or epigenetic basis for these expression polymorphisms. This finding suggests that these corals harbor high levels of gene-network variation, which could facilitate rapid evolution in the face of environmental change.
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Affiliation(s)
- Noah H Rose
- Biology Department, Stanford University, Hopkins Marine Station
| | - Francois O Seneca
- Biology Department, Stanford University, Hopkins Marine Station Present address: Kewalo Marine Lab, University of Hawaii, Honolulu, HI
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138
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Wu Y, Aandahl RZ, Tanaka MM. Dynamics of bacterial insertion sequences: can transposition bursts help the elements persist? BMC Evol Biol 2015; 15:288. [PMID: 26690348 PMCID: PMC4687120 DOI: 10.1186/s12862-015-0560-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 12/06/2015] [Indexed: 01/22/2023] Open
Abstract
Background Currently there is no satisfactory explanation for why bacterial insertion sequences (ISs) widely occur across prokaryotes despite being mostly harmful to their host genomes. Rates of horizontal gene transfer are likely to be too low to maintain ISs within a population. IS-induced beneficial mutations may be important for both prevalence of ISs and microbial adaptation to changing environments but may be too rare to sustain IS elements in the long run. Environmental stress can induce elevated rates of IS transposition activities; such episodes are known as ‘transposition bursts’. By examining how selective forces and transposition events interact to influence IS dynamics, this study asks whether transposition bursts can lead to IS persistence. Results We show through a simulation model that ISs are gradually eliminated from a population even if IS transpositions occasionally cause advantageous mutations. With beneficial mutations, transposition bursts create variation in IS copy numbers and improve cell fitness on average. However, these benefits are not usually sufficient to overcome the negative selection against the elements, and transposition bursts amplify the mean fitness effect which, if negative, simply accelerates the extinction of ISs. If down regulation of transposition occurs, IS extinctions are reduced while ISs still generate variation amongst bacterial genomes. Conclusions Transposition bursts do not help ISs persist in a bacterial population in the long run because most burst-induced mutations are deleterious and therefore not favoured by natural selection. However, bursts do create more genetic variation through which occasional advantageous mutations can help organisms adapt. Regulation of IS transposition bursts and stronger positive selection of the elements interact to slow down the burst-induced extinction of ISs. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0560-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yue Wu
- School of Biotechnology & Biomolecular Sciences, University of New South Wales, Sydney, 2052, NSW, Australia. .,Evolution & Ecology Research Centre, University of New South Wales, Sydney, 2052, NSW, Australia. .,Present address: Telethon Kids Institute, University of Western Australia, Perth, 6008, WA, Australia.
| | - Richard Z Aandahl
- School of Biotechnology & Biomolecular Sciences, University of New South Wales, Sydney, 2052, NSW, Australia. .,Evolution & Ecology Research Centre, University of New South Wales, Sydney, 2052, NSW, Australia.
| | - Mark M Tanaka
- School of Biotechnology & Biomolecular Sciences, University of New South Wales, Sydney, 2052, NSW, Australia. .,Evolution & Ecology Research Centre, University of New South Wales, Sydney, 2052, NSW, Australia.
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139
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Filée J, Rouault JD, Harry M, Hua-Van A. Mariner transposons are sailing in the genome of the blood-sucking bug Rhodnius prolixus. BMC Genomics 2015; 16:1061. [PMID: 26666222 PMCID: PMC4678618 DOI: 10.1186/s12864-015-2060-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 10/10/2015] [Indexed: 11/30/2022] Open
Abstract
Background The Triatomine bug Rhodnius prolixus is a vector of Trypanosoma cruzi, which causes the Chagas disease in Latin America. R. prolixus can also transfer transposable elements horizontally across a wide range of species. We have taken advantage of the availability of the 700 Mbp complete genome sequence of R. prolixus to study the dynamics of invasion and persistence of transposable elements in this species. Results Using both library-based and de novo methods of transposon detection, we found less than 6 % of transposable elements in the R. prolixus genome, a relatively low percentage compared to other insect genomes with a similar genome size. DNA transposons are surprisingly abundant and elements belonging to the mariner family are by far the most preponderant components of the mobile part of this genome with 11,015 mariner transposons that could be clustered in 89 groups (75 % of the mobilome). Our analysis allowed the detection of a new mariner clade in the R. prolixus genome, that we called nosferatis. We demonstrated that a large diversity of mariner elements invaded the genome and expanded successfully over time via three main processes. (i) several families experienced recent and massive expansion, for example an explosive burst of a single mariner family led to the generation of more than 8000 copies. These recent expansion events explain the unusual prevalence of mariner transposons in the R. prolixus genome. Other families expanded via older bursts of transposition demonstrating the long lasting permissibility of mariner transposons in the R. prolixus genome. (ii) Many non-autonomous families generated by internal deletions were also identified. Interestingly, two non autonomous families were generated by atypical recombinations (5' part replacement with 3' part). (iii) at least 10 cases of horizontal transfers were found, supporting the idea that host/vector relationships played a pivotal role in the transmission and subsequent persistence of transposable elements in this genome. Conclusion These data provide a new insight into the evolution of transposons in the genomes of hematophagous insects and bring additional evidences that lateral exchanges of mobile genetics elements occur frequently in the R. prolixus genome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2060-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jonathan Filée
- Laboratoire Evolution, Génome, Comportement, Ecologie UMR9191 CNRS, IRD Université Paris-Sud, Gif-sur-Yvette, France.
| | - Jacques-Deric Rouault
- Laboratoire Evolution, Génome, Comportement, Ecologie UMR9191 CNRS, IRD Université Paris-Sud, Gif-sur-Yvette, France
| | - Myriam Harry
- Laboratoire Evolution, Génome, Comportement, Ecologie UMR9191 CNRS, IRD Université Paris-Sud, Gif-sur-Yvette, France.,UFR de Sciences, Université Paris Sud, Orsay, France
| | - Aurélie Hua-Van
- Laboratoire Evolution, Génome, Comportement, Ecologie UMR9191 CNRS, IRD Université Paris-Sud, Gif-sur-Yvette, France.,UFR de Sciences, Université Paris Sud, Orsay, France
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del Pozo JC, Ramirez-Parra E. Whole genome duplications in plants: an overview from Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:6991-7003. [PMID: 26417017 DOI: 10.1093/jxb/erv432] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Polyploidy is a common event in plants that involves the acquisition of more than two complete sets of chromosomes. Allopolyploidy originates from interspecies hybrids while autopolyploidy originates from intraspecies whole genome duplication (WGD) events. In spite of inconveniences derived from chromosomic rearrangement during polyploidization, natural plant polyploids species often exhibit improved growth vigour and adaptation to adverse environments, conferring evolutionary advantages. These advantages have also been incorporated into crop breeding programmes. Many tetraploid crops show increased stress tolerance, although the molecular mechanisms underlying these different adaptation abilities are poorly known. Understanding the physiological, cellular, and molecular mechanisms coupled to WGD, in both allo- and autopolyploidy, is a major challenge. Over the last few years, several studies, many of them in Arabidopsis, are shedding light on the basis of genetic, genomic, and epigenomic changes linked to WGD. In this review we summarize and discuss the latest advances made in Arabidopsis polyploidy, but also in other agronomic plant species.
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Affiliation(s)
- Juan Carlos del Pozo
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Elena Ramirez-Parra
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
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141
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Rahman R, Chirn GW, Kanodia A, Sytnikova YA, Brembs B, Bergman CM, Lau NC. Unique transposon landscapes are pervasive across Drosophila melanogaster genomes. Nucleic Acids Res 2015; 43:10655-72. [PMID: 26578579 PMCID: PMC4678822 DOI: 10.1093/nar/gkv1193] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 10/24/2015] [Indexed: 01/01/2023] Open
Abstract
To understand how transposon landscapes (TLs) vary across animal genomes, we describe a new method called the Transposon Insertion and Depletion AnaLyzer (TIDAL) and a database of >300 TLs in Drosophila melanogaster (TIDAL-Fly). Our analysis reveals pervasive TL diversity across cell lines and fly strains, even for identically named sub-strains from different laboratories such as the ISO1 strain used for the reference genome sequence. On average, >500 novel insertions exist in every lab strain, inbred strains of the Drosophila Genetic Reference Panel (DGRP), and fly isolates in the Drosophila Genome Nexus (DGN). A minority (<25%) of transposon families comprise the majority (>70%) of TL diversity across fly strains. A sharp contrast between insertion and depletion patterns indicates that many transposons are unique to the ISO1 reference genome sequence. Although TL diversity from fly strains reaches asymptotic limits with increasing sequencing depth, rampant TL diversity causes unsaturated detection of TLs in pools of flies. Finally, we show novel transposon insertions negatively correlate with Piwi-interacting RNA (piRNA) levels for most transposon families, except for the highly-abundant roo retrotransposon. Our study provides a useful resource for Drosophila geneticists to understand how transposons create extensive genomic diversity in fly cell lines and strains.
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Affiliation(s)
- Reazur Rahman
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, MA 02454, USA
| | - Gung-wei Chirn
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, MA 02454, USA
| | - Abhay Kanodia
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, MA 02454, USA
| | - Yuliya A Sytnikova
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, MA 02454, USA
| | - Björn Brembs
- Institute of Zoology, Universität Regensburg, Regensburg, Germany
| | - Casey M Bergman
- Faculty of Life Sciences, University of Manchester, Manchester M21 0RG, UK
| | - Nelson C Lau
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, MA 02454, USA
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142
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Jardim SS, Schuch AP, Pereira CM, Loreto ELS. Effects of heat and UV radiation on the mobilization of transposon mariner-Mos1. Cell Stress Chaperones 2015; 20:843-51. [PMID: 26092118 PMCID: PMC4529857 DOI: 10.1007/s12192-015-0611-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Revised: 06/03/2015] [Accepted: 06/09/2015] [Indexed: 01/04/2023] Open
Abstract
There are many complex interactions between transposable elements (TEs) and host genomes. Environmental changes that induce stressful conditions help to contribute for increasing complexity of these interactions. The transposon mariner-Mos1 increases its mobilization under mild heat stress. It has putative heat shock elements (HSEs), which are probably activated by heat shock factors (HSFs). Ultraviolet radiation (UVC) is a stressor that has been suggested as able to activate heat shock protein genes (Hsp). In this study, we test the hypothesis that if UVC induces Hsp expression, as heat does, it could also promote mariner-Mos1 transposition and mobilization. The Drosophila simulans white-peach is a mutant lineage that indicates the mariner-Mos1 transposition phenotypically through the formation of mosaic eyes. This lineage was exposed to UVC or mild heat stress (28 °C) in order to evaluate the induction of mariner-Mos1 expression by RT-qPCR, as well as the mariner-Mos1 mobilization activity based on the count number of red spots in the eyes. The effects of both treatments on the developmental time of flies and cell cycle progression were also investigated. Both the analysis of eyes and mariner-Mos1 gene expression indicate that UVC radiation has no effect in mariner-Mos1 transposition, although heat increases the expression and mobilization of this TE soon after the treatment. However, the expression of Hsp70 gene increased after 24 h of UVC exposure, suggesting different pathway of activation. These results showed that heat promotes mariner-Mos1 mobilization, although UVC does not induce the expression or mobilization of this TE.
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Affiliation(s)
- Sinara Santos Jardim
- />Postgraduate Program in Animal Biodiversity, University of Santa Maria, Santa Maria, RS Brazil
| | - André Passaglia Schuch
- />Postgraduate Program in Animal Biodiversity, University of Santa Maria, Santa Maria, RS Brazil
| | - Camila Moura Pereira
- />Postgraduate Program in Animal Biodiversity, University of Santa Maria, Santa Maria, RS Brazil
| | - Elgion Lucio Silva Loreto
- />Postgraduate Program in Animal Biodiversity, University of Santa Maria, Santa Maria, RS Brazil
- />Department of Biochemistry and Molecular Biology, University of Santa Maria, Ave. Roraima, 1000, Building 16-A, 3210, Santa Maria, RS 97105-900 Brazil
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143
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Cho WK, Lian S, Kim SM, Seo BY, Jung JK, Kim KH. Time-Course RNA-Seq Analysis Reveals Transcriptional Changes in Rice Plants Triggered by Rice stripe virus Infection. PLoS One 2015; 10:e0136736. [PMID: 26305329 PMCID: PMC4549299 DOI: 10.1371/journal.pone.0136736] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 08/04/2015] [Indexed: 12/31/2022] Open
Abstract
Rice stripe virus (RSV) has become a major pathogen of rice. To determine how the rice transcriptome is modified in response to RSV infection, we used RNA-Seq to perform a genome-wide gene expression analysis of a susceptible rice cultivar. The transcriptomes of RSV-infected samples were compared to those of mock-treated samples at 3, 7, and 15 days post-infection (dpi). From 8 to 11% of the genes were differentially expressed (>2-fold difference in expression) in RSV-infected vs. noninfected rice. Among them, 532 genes were differentially expressed at all three time points. Surprisingly, 37.6% of the 532 genes are related to transposons. Gene ontology enrichment analysis revealed that many chloroplast genes were down-regulated in infected plants at 3 and 15 dpi. Expression of genes associated with cell differentiation and flowering was significantly down-regulated in infected plants at 15 dpi. In contrast, most of the up-regulated genes in infected plants concern the cell wall, plasma membrane, and vacuole and are known to function in various metabolic pathways and stress responses. In addition, transcripts of diverse transcription factors gradually accumulated in infected plants with increasing infection time. We also confirmed that the expression of gene subsets (including NBS-LRR domain-containing genes, receptor-like kinase genes, and genes involving RNA silencing) was changed by RSV infection. Taken together, we demonstrated that down-regulation of genes related to photosynthesis and flowering was strongly associated with disease symptoms caused by RSV and that up-regulation of genes involved in metabolic pathways, stress responses, and transcription was related to host defense mechanisms.
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Affiliation(s)
- Won Kyong Cho
- Department of Agricultural Biotechnology and Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151–921, Republic of Korea
| | - Sen Lian
- Department of Agricultural Biotechnology and Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151–921, Republic of Korea
| | - Sang-Min Kim
- Department of Agricultural Biotechnology and Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151–921, Republic of Korea
| | - Bo Yoon Seo
- Crop Protection Division, National Academy of Agricultural Science, RDA, Suwon, 441–707, Republic of Korea
| | - Jin Kyo Jung
- Crop Environment Research Division, National Institute of Crop Science, RDA, Suwon, 441–857, Republic of Korea
| | - Kook-Hyung Kim
- Department of Agricultural Biotechnology and Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151–921, Republic of Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 151–921, Republic of Korea
- * E-mail:
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144
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Roncal J, Guyot R, Hamon P, Crouzillat D, Rigoreau M, Konan ON, Rakotomalala JJ, Nowak MD, Davis AP, de Kochko A. Active transposable elements recover species boundaries and geographic structure in Madagascan coffee species. Mol Genet Genomics 2015; 291:155-68. [PMID: 26231981 DOI: 10.1007/s00438-015-1098-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 07/21/2015] [Indexed: 01/10/2023]
Abstract
The completion of the genome assembly for the economically important coffee plant Coffea canephora (Rubiaceae) has allowed the use of bioinformatic tools to identify and characterize a diverse array of transposable elements (TEs), which can be used in evolutionary studies of the genus. An overview of the copy number and location within the C. canephora genome of four TEs is presented. These are tested for their use as molecular markers to unravel the evolutionary history of the Millotii Complex, a group of six wild coffee (Coffea) species native to Madagascar. Two TEs from the Gypsy superfamily successfully recovered some species boundaries and geographic structure among samples, whereas a TE from the Copia superfamily did not. Notably, species occurring in evergreen moist forests of eastern and southeastern Madagascar were divergent with respect to species in other habitats and regions. Our results suggest that the peak of transpositional activity of the Gypsy and Copia TEs occurred, respectively, before and after the speciation events of the tested Madagascan species. We conclude that the utilization of active TEs has considerable potential to unravel the evolutionary history and delimitation of closely related Coffea species. However, the selection of TE needs to be experimentally tested, since each element has its own evolutionary history. Different TEs with similar copy number in a given species can render different dendrograms; thus copy number is not a good selection criterion to attain phylogenetic resolution.
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Affiliation(s)
- Julissa Roncal
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John's, A1B 3X9, Canada. .,UMR DIADE, IRD, B.P. 64501, 34394, Cedex 5 Montpellier, France.
| | - Romain Guyot
- UMR IPME, IRD, B.P. 64501, 34394, Cedex 5 Montpellier, France
| | - Perla Hamon
- UMR DIADE, IRD, B.P. 64501, 34394, Cedex 5 Montpellier, France
| | - Dominique Crouzillat
- Nestlé R&D Tours, 101 AV. G. Eiffel, Notre Dame d'Oé, BP 49716, 37097, Tours, Cedex 2, France
| | - Michel Rigoreau
- Nestlé R&D Tours, 101 AV. G. Eiffel, Notre Dame d'Oé, BP 49716, 37097, Tours, Cedex 2, France
| | | | | | - Michael D Nowak
- Science for Life Laboratory, Stockholm University, Tomtebodavägen 23, 17165, Solna, Sweden
| | - Aaron P Davis
- Royal Botanic Gardens, Kew, Richmond, TW9 3AB, Surrey, UK
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145
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Morales ME, Servant G, Ade C, Roy-Enge AM. Altering Genomic Integrity: Heavy Metal Exposure Promotes Transposable Element-Mediated Damage. Biol Trace Elem Res 2015; 166:24-33. [PMID: 25774044 PMCID: PMC4696754 DOI: 10.1007/s12011-015-0298-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 03/03/2015] [Indexed: 12/13/2022]
Abstract
Maintenance of genomic integrity is critical for cellular homeostasis and survival. The active transposable elements (TEs) composed primarily of three mobile element lineages LINE-1, Alu, and SVA comprise approximately 30% of the mass of the human genome. For the past 2 decades, studies have shown that TEs significantly contribute to genetic instability and that TE-caused damages are associated with genetic diseases and cancer. Different environmental exposures, including several heavy metals, influence how TEs interact with its host genome increasing their negative impact. This mini-review provides some basic knowledge on TEs, their contribution to disease, and an overview of the current knowledge on how heavy metals influence TE-mediated damage.
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Affiliation(s)
- Maria E. Morales
- Department of Epidemiology and Tulane Cancer Center, SL-66, Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112
| | - Geraldine Servant
- Department of Epidemiology and Tulane Cancer Center, SL-66, Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112
| | - Catherine Ade
- Department of Cellular and Molecular Biology, Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112
| | - Astrid M. Roy-Enge
- Department of Epidemiology and Tulane Cancer Center, SL-66, Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112
- Corresponding author: Astrid M. Roy-Engel, Ph.D., Department of Epidemiology, Tulane Cancer Center, SL66, Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112. , Phone: (504) 988-6316, Fax: (504) 988-5516
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146
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Pyott DE, Molnar A. Going mobile: non-cell-autonomous small RNAs shape the genetic landscape of plants. PLANT BIOTECHNOLOGY JOURNAL 2015; 13:306-18. [PMID: 25756494 DOI: 10.1111/pbi.12353] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 01/16/2015] [Accepted: 01/20/2015] [Indexed: 05/09/2023]
Abstract
RNA silencing is a form of genetic regulation, which is conserved across eukaryotes and has wide ranging biological functions. Recently, there has been a growing appreciation for the importance of mobility in RNA silencing pathways, particularly in plants. Moreover, in addition to the importance for mobile RNA silencing in an evolutionary context, the potential for utilizing mobile short silencing RNAs in biotechnological applications is becoming apparent. This review aims to set current knowledge of this topic in a historical context and provides examples to illustrate the importance of mobile RNA silencing in both natural and artificially engineered systems in plants.
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Affiliation(s)
- Douglas E Pyott
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, UK
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147
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Changes of Osvaldo expression patterns in germline of male hybrids between the species Drosophila buzzatii and Drosophila koepferae. Mol Genet Genomics 2015; 290:1471-83. [PMID: 25711309 DOI: 10.1007/s00438-015-1012-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 02/15/2015] [Indexed: 01/08/2023]
Abstract
Hybridization between different genomes is a source of genomic instability, sometimes associated with transposable element (TE) mobilization. Previous work showed that hybridization between the species Drosophila buzzatii and Drosophila koepferae induced mobilization of different (TEs), the Osvaldo retrotransposon being the most unstable. However, we ignore the mechanisms involved in this transposition release in interspecific hybrids. In order to disentangle the mechanisms involved in this process, we performed Osvaldo expression studies in somatic and germinal tissues from hybrids and parental species. There was a trend towards increased Osvaldo expression in the somatic tissues of hybrid females and males, which was always significant in males compared to the parental species D. buzzatii but, not in females compared to maternal species D. koepferae. There were massive changes of Osvaldo expression in the testes, which varied depending on the hybrid generation and family. Moreover, Osvaldo hybridization signals, restricted to the apical and primary spermatocyte regions in parents, occupied broader region in the hybrids. In ovaries, there were no significant differences in Osvaldo expression rates between hybrids and the maternal species D. koepferae. The transcript location was restricted to ovarian nurse cells in both parents and hybrids, undetectable in some hybrids. This research highlights first, the existence of putative complex deregulation mechanisms different between sexes and cell types and second, disruption of Osvaldo activity particularly evident in testes from sterile hybrid males. Deeper studies of the total transcriptome in hybrids and parental species are necessary to gain a better knowledge of the TE deregulation pathways in hybrids.
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148
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Stapley J, Santure AW, Dennis SR. Transposable elements as agents of rapid adaptation may explain the genetic paradox of invasive species. Mol Ecol 2015; 24:2241-52. [PMID: 25611725 DOI: 10.1111/mec.13089] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 01/17/2015] [Accepted: 01/19/2015] [Indexed: 12/11/2022]
Abstract
Rapid adaptation of invasive species to novel habitats has puzzled evolutionary biologists for decades, especially as this often occurs in the face of limited genetic variability. Although some ecological traits common to invasive species have been identified, little is known about the possible genomic/genetic mechanisms that may underlie their success. A common scenario in many introductions is that small founder population sizes will often lead to reduced genetic diversity, but that invading populations experience large environmental perturbations, such as changes in habitat and environmental stress. Although sudden and intense stress is usually considered in a negative context, these perturbations may actually facilitate rapid adaptation by affecting genome structure, organization and function via interactions with transposable elements (TEs), especially in populations with low genetic diversity. Stress-induced changes in TE activity can alter gene action and can promote structural variation that may facilitate the rapid adaptation observed in new environments. We focus here on the adaptive potential of TEs in relation to invasive species and highlight their role as powerful mutational forces that can rapidly create genetic diversity. We hypothesize that activity of transposable elements can explain rapid adaptation despite low genetic variation (the genetic paradox of invasive species), and provide a framework under which this hypothesis can be tested using recently developed and emerging genomic technologies.
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Affiliation(s)
- Jessica Stapley
- Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield, S10 2TN, UK
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149
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The genomic proliferation of transposable elements in colonizing populations: Schistosoma mansoni in the new world. Genetica 2015; 143:287-98. [PMID: 25681233 DOI: 10.1007/s10709-015-9825-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Accepted: 02/02/2015] [Indexed: 10/24/2022]
Abstract
Transposable elements (TEs) are mobile genes with an inherent ability to move within and among genomes. Theory predicts that TEs proliferate extensively during physiological stress due to the breakdown of TE repression systems. We tested this hypothesis in Schistosoma mansoni, a widespread trematode parasite that causes the human disease schistosomiasis. According to phylogenetic analysis, S. mansoni invaded the new world during the last 500 years. We hypothesized that new world strains of S. mansoni would have more copies of TEs than old world strains due to the physiological stress associated with invasion of the new world. We quantified the copy number of six TEs (Saci-1, Saci-2 and Saci-3, Perere-1, Merlin-sm1, and SmTRC1) in the genome and the transcriptome of old world and new world strains of S. mansoni, using qPCR relative quantification. As predicted, the genomes of new world parasites contain significantly more copies of class I and class II TEs in both laboratory and field strains. However, such differences are not observed in the transcriptome suggesting that either TE silencing mechanisms have reactivated to control the expression of these elements or the presence of inactive truncated copies of TEs.
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150
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Carr M, Suga H. The holozoan Capsaspora owczarzaki possesses a diverse complement of active transposable element families. Genome Biol Evol 2015; 6:949-63. [PMID: 24696401 PMCID: PMC4007536 DOI: 10.1093/gbe/evu068] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Capsaspora owczarzaki, a protistan symbiont of the pulmonate snail Biomphalaria glabrata, is the centre of much interest in evolutionary biology due to its close relationship to Metazoa. The whole genome sequence of this protist has revealed new insights into the ancestral genome composition of Metazoa, in particular with regard to gene families involved in the evolution of multicellularity. The draft genome revealed the presence of 23 families of transposable element, made up from DNA transposon as well as long terminal repeat (LTR) and non-LTR retrotransposon families. The phylogenetic analyses presented here show that all of the transposable elements identified in the C. owczarzaki genome have orthologous families in Metazoa, indicating that the ancestral metazoan also had a rich diversity of elements. Molecular evolutionary analyses also show that the majority of families has recently been active within the Capsaspora genome. One family now appears to be inactive and a further five families show no evidence of current transposition. Most individual element copies are evolutionarily young; however, a small proportion of inserts appear to have persisted for longer in the genome. The families present in the genome show contrasting population histories and appear to be in different stages of their life cycles. Transcriptome data have been analyzed from multiple stages in the C. owczarzaki life cycle. Expression levels vary greatly both between families and between different stages of the life cycle, suggesting an unexpectedly complex level of transposable element regulation in a single celled organism.
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Affiliation(s)
- Martin Carr
- School of Applied Sciences, University of Huddersfield, West Yorkshire, United Kingdom
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