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Paul M, Tanskanen J, Jääskeläinen M, Chang W, Dalal A, Moshelion M, Schulman AH. Drought and recovery in barley: key gene networks and retrotransposon response. FRONTIERS IN PLANT SCIENCE 2023; 14:1193284. [PMID: 37377802 PMCID: PMC10291200 DOI: 10.3389/fpls.2023.1193284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/09/2023] [Indexed: 06/29/2023]
Abstract
Introduction During drought, plants close their stomata at a critical soil water content (SWC), together with making diverse physiological, developmental, and biochemical responses. Methods Using precision-phenotyping lysimeters, we imposed pre-flowering drought on four barley varieties (Arvo, Golden Promise, Hankkija 673, and Morex) and followed their physiological responses. For Golden Promise, we carried out RNA-seq on leaf transcripts before and during drought and during recovery, also examining retrotransposon BARE1expression. Transcriptional data were subjected to network analysis. Results The varieties differed by their critical SWC (ϴcrit), Hankkija 673 responding at the highest and Golden Promise at the lowest. Pathways connected to drought and salinity response were strongly upregulated during drought; pathways connected to growth and development were strongly downregulated. During recovery, growth and development pathways were upregulated; altogether, 117 networked genes involved in ubiquitin-mediated autophagy were downregulated. Discussion The differential response to SWC suggests adaptation to distinct rainfall patterns. We identified several strongly differentially expressed genes not earlier associated with drought response in barley. BARE1 transcription is strongly transcriptionally upregulated by drought and downregulated during recovery unequally between the investigated cultivars. The downregulation of networked autophagy genes suggests a role for autophagy in drought response; its importance to resilience should be further investigated.
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Affiliation(s)
- Maitry Paul
- HiLIFE Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Viikki Plant Science Centre (ViPS), University of Helsinki, Helsinki, Finland
| | - Jaakko Tanskanen
- HiLIFE Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Viikki Plant Science Centre (ViPS), University of Helsinki, Helsinki, Finland
- Production Systems, Natural Resources Institute Finland (LUKE), Helsinki, Finland
| | - Marko Jääskeläinen
- HiLIFE Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Viikki Plant Science Centre (ViPS), University of Helsinki, Helsinki, Finland
| | - Wei Chang
- HiLIFE Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Viikki Plant Science Centre (ViPS), University of Helsinki, Helsinki, Finland
| | - Ahan Dalal
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Menachem Moshelion
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Alan H. Schulman
- HiLIFE Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Viikki Plant Science Centre (ViPS), University of Helsinki, Helsinki, Finland
- Production Systems, Natural Resources Institute Finland (LUKE), Helsinki, Finland
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Abstract
Transposons were once thought to be junk repetitive DNA in the genome. However, their importance gradually became apparent as it became clear that they regulate gene expression, which is essential for organisms to survive, and that they are important factors in the driving force of evolution. Since there are multiple transposons in the genomes of all organisms, transposons have likely been activated and increased in copy number throughout their long history. This review focuses on environmental stress as a factor in transposon activation, paying particular attention to transposons in plants that are activated by environmental stresses. It is now known that plants respond to environmental stress in various ways, and correspondingly, many transposons respond to stress. The relationship between environmental stress and transposons is reviewed, including the mechanisms of their activation and the effects of transposon activation on host plants.
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Hong Y, Wang Z, Li M, Su Y, Wang T. First Multi-Organ Full-Length Transcriptome of Tree Fern Alsophila spinulosa Highlights the Stress-Resistant and Light-Adapted Genes. Front Genet 2022; 12:784546. [PMID: 35186007 PMCID: PMC8854977 DOI: 10.3389/fgene.2021.784546] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/22/2021] [Indexed: 11/13/2022] Open
Abstract
Alsophila spinulosa, a relict tree fern, is a valuable plant for investigating environmental adaptations. Its genetic resources, however, are scarce. We used the PacBio and Illumina platforms to sequence the polyadenylated RNA of A. spinulosa root, rachis, and pinna, yielding 125,758, 89,107, and 89,332 unigenes, respectively. Combining the unigenes from three organs yielded a non-redundant reference transcriptome with 278,357 unigenes and N50 of 4141 bp, which were further reconstructed into 38,470 UniTransModels. According to functional annotation, pentatricopeptide repeat genes and retrotransposon-encoded polyprotein genes are the most abundant unigenes. Clean reads mapping to the full-length transcriptome is used to assess the expression of unigenes. The stress-induced ASR genes are highly expressed in all three organs, which is validated by qRT-PCR. The organ-specific upregulated genes are enriched for pathways involved in stress response, secondary metabolites, and photosynthesis. Genes for five types of photoreceptors, CRY signaling pathway, ABA biosynthesis and transduction pathway, and stomatal movement-related ion channel/transporter are profiled using the high-quality unigenes. The gene expression pattern coincides with the previously identified stomatal characteristics of fern. This study is the first multi-organ full-length transcriptome report of a tree fern species, the abundant genetic resources and comprehensive analysis of A. spinulosa, which provides the groundwork for future tree fern research.
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Affiliation(s)
- Yongfeng Hong
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhen Wang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Minghui Li
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Research Institute of Sun Yat-sen University in Shenzhen, Shenzhen, China
- *Correspondence: Yingjuan Su, ; Ting Wang,
| | - Ting Wang
- Research Institute of Sun Yat-sen University in Shenzhen, Shenzhen, China
- College of Life Sciences, South China Agricultural University, Guangzhou, China
- *Correspondence: Yingjuan Su, ; Ting Wang,
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Orłowska R, Pachota KA, Dynkowska WM, Niedziela A, Bednarek PT. Androgenic-Induced Transposable Elements Dependent Sequence Variation in Barley. Int J Mol Sci 2021; 22:ijms22136783. [PMID: 34202586 PMCID: PMC8268840 DOI: 10.3390/ijms22136783] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/14/2021] [Accepted: 06/22/2021] [Indexed: 01/10/2023] Open
Abstract
A plant genome usually encompasses different families of transposable elements (TEs) that may constitute up to 85% of nuclear DNA. Under stressful conditions, some of them may activate, leading to sequence variation. In vitro plant regeneration may induce either phenotypic or genetic and epigenetic changes. While DNA methylation alternations might be related, i.e., to the Yang cycle problems, DNA pattern changes, especially DNA demethylation, may activate TEs that could result in point mutations in DNA sequence changes. Thus, TEs have the highest input into sequence variation (SV). A set of barley regenerants were derived via in vitro anther culture. High Performance Liquid Chromatography (RP-HPLC), used to study the global DNA methylation of donor plants and their regenerants, showed that the level of DNA methylation increased in regenerants by 1.45% compared to the donors. The Methyl-Sensitive Transposon Display (MSTD) based on methylation-sensitive Amplified Fragment Length Polymorphism (metAFLP) approach demonstrated that, depending on the selected elements belonging to the TEs family analyzed, varying levels of sequence variation were evaluated. DNA sequence contexts may have a different impact on SV generated by distinct mobile elements belonged to various TE families. Based on the presented study, some of the selected mobile elements contribute differently to TE-related SV. The surrounding context of the TEs DNA sequence is possibly important here, and the study explained some part of SV related to those contexts.
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Setiawan AB, Teo CH, Kikuchi S, Sassa H, Kato K, Koba T. Chromosomal Locations of a Non-LTR Retrotransposon, Menolird18, in Cucumis melo and Cucumis sativus, and Its Implication on Genome Evolution of Cucumis Species. Cytogenet Genome Res 2020; 160:554-564. [DOI: 10.1159/000511119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 07/07/2020] [Indexed: 11/19/2022] Open
Abstract
Mobile elements are major regulators of genome evolution through their effects on genome size and chromosome structure in higher organisms. Non-long terminal repeat (non-LTR) retrotransposons, one of the subclasses of transposons, are specifically inserted into repetitive DNA sequences. While studies on the insertion of non-LTR retrotransposons into ribosomal RNA genes and other repetitive DNA sequences have been reported in the animal kingdom, studies in the plant kingdom are limited. Here, using FISH, we confirmed that <i>Menolird18</i>, a member of LINE (long interspersed nuclear element) in non-LTR retrotransposons and found in <i>Cucumis melo</i>, was inserted into ITS and ETS (internal and external transcribed spacers) regions of 18S rDNA in melon and cucumber. Beside the 18S rDNA regions, <i>Menolird18</i> was also detected in all centromeric regions of melon, while it was located at pericentromeric and sub-telomeric regions in cucumber. The fact that FISH signals of <i>Menolird18</i> were found in centromeric and rDNA regions of mitotic chromosomes suggests that <i>Menolird18</i> is a rDNA and centromere-specific non-LTR retrotransposon in melon. Our findings are the first report on a non-LTR retrotransposon that is highly conserved in 2 different plant species, melon and cucumber. The clear distinction of chromosomal localization of <i>Menolird18</i> in melon and cucumber implies that it might have been involved in the evolutionary processes of the melon (<i>C. melo</i>) and cucumber (<i>C. sativus</i>) genomes.
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Turzhanova A, Khapilina ON, Tumenbayeva A, Shevtsov V, Raiser O, Kalendar R. Genetic diversity of Alternaria species associated with black point in wheat grains. PeerJ 2020; 8:e9097. [PMID: 32411537 PMCID: PMC7207207 DOI: 10.7717/peerj.9097] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 04/09/2020] [Indexed: 12/12/2022] Open
Abstract
The genus Alternaria is a widely distributed major plant pathogen that can act as a saprophyte in plant debris. Fungi of this genus frequently infect cereal crops and cause such diseases as black point and wheat leaf blight, which decrease the yield and quality of cereal products. A total of 25 Alternaria sp. isolates were collected from germ grains of various wheat cultivars from different geographic regions in Kazakhstan. We investigated the genetic relationships of the main Alternaria species related to black point disease of wheat in Kazakhstan, using the inter-primer binding site (iPBS) DNA profiling technique. We used 25 retrotransposon-based iPBS primers to identify the differences among and within Alternaria species populations, and analyzed the variation using clustering (UPGMA) and statistical approaches (AMOVA). Isolates of Alternaria species clustered into two main genetic groups, with species of A.alternata and A.tennuissima forming one cluster, and isolates of A. infectoria forming another. The genetic diversity found using retrotransposon profiles was strongly correlated with geographic data. Overall, the iPBS fingerprinting technique is highly informative and useful for the evaluation of genetic diversity and relationships of Alternaria species.
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Affiliation(s)
| | | | | | | | - Olesya Raiser
- National Center for Biotechnology, Nur-Sultan, Kazakhstan
| | - Ruslan Kalendar
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Uusimaa, Finland
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Li C, Tang J, Hu Z, Wang J, Yu T, Yi H, Cao M. A novel maize dwarf mutant generated by Ty1-copia LTR-retrotransposon insertion in Brachytic2 after spaceflight. PLANT CELL REPORTS 2020; 39:393-408. [PMID: 31834482 DOI: 10.1007/s00299-019-02498-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 12/02/2019] [Indexed: 05/12/2023]
Abstract
Retrotransposon insertion in Brachytic2 generated a new incomplete recessive dwarf allele after spaceflight can moderately reduce plant height in heterozygous and potentially improve maize yield. Plant height and ear height are two important agronomic traits in maize breeding. In this study, two dwarf mutants short internode length1 (sil1) and short internode length2 (sil2) were obtained from two of 398 spaceflighted seeds of inbred line 18-599. The decrease in longitudinal cell number and cell length led to the shortened internodes of sil1 and sil2. A Ty1-copia LTR-retrotransposon, termed ZmRE-1, inserted in the fifth exon of Brachytic2 (Br2) was identified in sil1 and sil2 at exactly the same site, which indicated the transposition of ZmRE-1 probably correlated with the spaceflight. This new dwarf mutant allele was named as br2-sil in this study. The insertion of ZmRE-1 not only led to the loss of normal transcript of Br2 allele, but also reduced the transcript expression of br2-sil allele. Chop-qPCR displayed that the promoter region DNA methylation level of br2-sil allele in sil1 was higher than that of Br2 allele in WT-sil1. We speculated that the increased methylation level might downregulate the br2-sil expression. There was no difference in the seed-setting rate between sil1 and WT-sil1. Meanwhile, br2-sil could reduce plant and ear height effectively in Br2/br2-sil genotype without negative effects on grain yield. Therefore, the application of br2-sil in breeding has the potential to improve the grain yield per unit area through increasing the planting density.
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Affiliation(s)
- Chuan Li
- Maize Research Institute, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Jin Tang
- Maize Research Institute, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Zhaoyong Hu
- Maize Research Institute, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Jingwen Wang
- Maize Research Institute, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Tao Yu
- Maize Research Institute, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Hongyang Yi
- Maize Research Institute, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Moju Cao
- Maize Research Institute, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang District, Chengdu, 611130, China.
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, No. 211 Huimin Road, Wenjiang District, Chengdu, 611130, China.
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High-throughput retrotransposon-based genetic diversity of maize germplasm assessment and analysis. Mol Biol Rep 2020; 47:1589-1603. [PMID: 31919750 DOI: 10.1007/s11033-020-05246-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 01/03/2020] [Indexed: 01/08/2023]
Abstract
Maize is one of the world's most important crops and a model for grass genome research. Long terminal repeat (LTR) retrotransposons comprise most of the maize genome; their ability to produce new copies makes them efficient high-throughput genetic markers. Inter-retrotransposon-amplified polymorphisms (IRAPs) were used to study the genetic diversity of maize germplasm. Five LTR retrotransposons (Huck, Tekay, Opie, Ji, and Grande) were chosen, based on their large number of copies in the maize genome, whereas polymerase chain reaction primers were designed based on consensus LTR sequences. The LTR primers showed high quality and reproducible DNA fingerprints, with a total of 677 bands including 392 polymorphic bands showing 58% polymorphism between maize hybrid lines. These markers were used to identify genetic similarities among all lines of maize. Analysis of genetic similarity was carried out based on polymorphic amplicon profiles and genetic similarity phylogeny analysis. This diversity was expected to display ecogeographical patterns of variation and local adaptation. The clustering method showed that the varieties were grouped into three clusters differing in ecogeographical origin. Each of these clusters comprised divergent hybrids with convergent characters. The clusters reflected the differences among maize hybrids and were in accordance with their pedigree. The IRAP technique is an efficient high-throughput genetic marker-generating method.
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Usai G, Mascagni F, Vangelisti A, Giordani T, Ceccarelli M, Cavallini A, Natali L. Interspecific hybridisation and LTR-retrotransposon mobilisation-related structural variation in plants: A case study. Genomics 2019; 112:1611-1621. [PMID: 31605729 DOI: 10.1016/j.ygeno.2019.09.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 07/13/2019] [Accepted: 09/12/2019] [Indexed: 11/30/2022]
Abstract
The dynamics of long-terminal-repeat retrotransposons in two poplar species (Populus deltoides and P. nigra) and in an interspecific hybrid, recently synthesized, were investigated by analyzing the genomic abundance and transcription levels of a collection of 828 full-length retroelements identified in the genome sequence of P. trichocarpa, all occurring also in the genomes of P. deltoides and P. nigra. Overall, genomic abundance and transcription levels of many retrotransposons in the hybrid resulted higher or lower than expected by calculating the mean of the parental values. A bioinformatics procedure was established to ascertain the occurrence of the same retrotransposon loci in the three genotypes. The results indicated that retrotransposon abundance variations between the hybrid and the mean value of the parents were due to i) co-segregation of retrotransposon high- or low-abundant haplotypes; ii) new retroelement insertions; iii) retrotransposon loss. Concerning retrotransposon expression, this was generally low, with only 14/828 elements over- or under-expressed in the hybrid than expected by calculating the mean of the parents. It is concluded that interspecific hybridisation between the two poplar species determine quantitative variation and differential expression of some retrotransposons, with possible consequences for the genetic differentiation of the hybrid.
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Affiliation(s)
- Gabriele Usai
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, I-56124 Pisa, Italy
| | - Flavia Mascagni
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, I-56124 Pisa, Italy
| | - Alberto Vangelisti
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, I-56124 Pisa, Italy
| | - Tommaso Giordani
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, I-56124 Pisa, Italy
| | - Marilena Ceccarelli
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di sotto 8, 06123 Perugia, Italy
| | - Andrea Cavallini
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, I-56124 Pisa, Italy.
| | - Lucia Natali
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, I-56124 Pisa, Italy.
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Orozco-Arias S, Isaza G, Guyot R. Retrotransposons in Plant Genomes: Structure, Identification, and Classification through Bioinformatics and Machine Learning. Int J Mol Sci 2019; 20:E3837. [PMID: 31390781 PMCID: PMC6696364 DOI: 10.3390/ijms20153837] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/31/2019] [Accepted: 08/02/2019] [Indexed: 01/26/2023] Open
Abstract
Transposable elements (TEs) are genomic units able to move within the genome of virtually all organisms. Due to their natural repetitive numbers and their high structural diversity, the identification and classification of TEs remain a challenge in sequenced genomes. Although TEs were initially regarded as "junk DNA", it has been demonstrated that they play key roles in chromosome structures, gene expression, and regulation, as well as adaptation and evolution. A highly reliable annotation of these elements is, therefore, crucial to better understand genome functions and their evolution. To date, much bioinformatics software has been developed to address TE detection and classification processes, but many problematic aspects remain, such as the reliability, precision, and speed of the analyses. Machine learning and deep learning are algorithms that can make automatic predictions and decisions in a wide variety of scientific applications. They have been tested in bioinformatics and, more specifically for TEs, classification with encouraging results. In this review, we will discuss important aspects of TEs, such as their structure, importance in the evolution and architecture of the host, and their current classifications and nomenclatures. We will also address current methods and their limitations in identifying and classifying TEs.
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Affiliation(s)
- Simon Orozco-Arias
- Department of Computer Science, Universidad Autónoma de Manizales, Manizales 170001, Colombia
- Department of Systems and Informatics, Universidad de Caldas, Manizales 170001, Colombia
| | - Gustavo Isaza
- Department of Systems and Informatics, Universidad de Caldas, Manizales 170001, Colombia
| | - Romain Guyot
- Department of Electronics and Automatization, Universidad Autónoma de Manizales, Manizales 170001, Colombia.
- Institut de Recherche pour le Développement, CIRAD, University Montpellier, 34000 Montpellier, France.
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Huang BH, Lin YC, Huang CW, Lu HP, Luo MX, Liao PC. Differential genetic responses to the stress revealed the mutation-order adaptive divergence between two sympatric ginger species. BMC Genomics 2018; 19:692. [PMID: 30241497 PMCID: PMC6150995 DOI: 10.1186/s12864-018-5081-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 09/14/2018] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Divergent genetic responses to the same environmental pressures may lead sympatric ecological speciation possible. Such speciation process possibly explains rapid sympatric speciation of island species. Two island endemic ginger species Zingiber kawagoii and Z. shuanglongensis was suggested to be independently originated from inland ancestors, but their island endemism and similar morphologies and habitats lead another hypothesis of in situ ecological speciation. For understanding when and how these two species diverged, intraspecific variation was estimated from three chloroplast DNA fragments (cpDNA) and interspecific genome-wide SNPs and expression differences after saline treatment were examined by transcriptomic analyses. RESULTS Extremely low intraspecific genetic variation was estimated by cpDNA sequences in both species: nucleotide diversity π = 0.00002 in Z. kawagoii and no nucleotide substitution but only indels found in Z. shuanglongensis. Nonsignificant inter-population genetic differentiation suggests homogenized genetic variation within species. Based on 53,683 SNPs from 13,842 polymorphic transcripts, in which 10,693 SNPs are fixed between species, Z. kawagoii and Z. shuanglongensis were estimated to be diverged since 218~ 238 thousand generations ago (complete divergence since 41.5~ 43.5 thousand generations ago). This time is more recent than the time of Taiwan Island formation. In addition, high proportion of differential expression genes (DEGs) is non-polymorphic or non-positively selected, suggesting key roles of plastic genetic divergence in broaden the selectability in incipient speciation. While some positive selected DEGs were mainly the biotic and abiotic stress-resistance genes, emphasizing the importance of adaptive divergence of stress-related genes in sympatric ecological speciation. Furthermore, the higher proportional expression of functional classes in Z. kawagoii than in Z. shuanglongensis explains the more widespread distribution of Z. kawagoii in Taiwan. CONCLUSIONS Our results contradict the previous hypothesis of independent origination of these two island endemic ginger species from SE China and SW China. Adaptive divergent responses to the stress explain how these gingers maintain genetic differentiation in sympatry. However, the recent speciation and rapid expansion make extremely low intraspecific genetic variation in these two species. This study arise a more probable speciation hypothesis of sympatric speciation within an island via the mutation-order mechanism underlying the same environmental pressure.
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Affiliation(s)
- Bing-Hong Huang
- School of Life Science, National Taiwan Normal University, No. 88, Sec. 4, Ting-Chow Rd., Wenshan Dist, Taipei, 11677, Taiwan
| | - Yuan-Chien Lin
- Department of Forestry, National Chung-Hsing University, No. 250, Kuo Kuang Rd, Taichung, 402, Taiwan
| | - Chih-Wei Huang
- School of Life Science, National Taiwan Normal University, No. 88, Sec. 4, Ting-Chow Rd., Wenshan Dist, Taipei, 11677, Taiwan
| | - Hsin-Pei Lu
- School of Life Science, National Taiwan Normal University, No. 88, Sec. 4, Ting-Chow Rd., Wenshan Dist, Taipei, 11677, Taiwan
| | - Min-Xin Luo
- School of Life Science, National Taiwan Normal University, No. 88, Sec. 4, Ting-Chow Rd., Wenshan Dist, Taipei, 11677, Taiwan
| | - Pei-Chun Liao
- School of Life Science, National Taiwan Normal University, No. 88, Sec. 4, Ting-Chow Rd., Wenshan Dist, Taipei, 11677, Taiwan.
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González-Pech RA, Ragan MA, Chan CX. Signatures of adaptation and symbiosis in genomes and transcriptomes of Symbiodinium. Sci Rep 2017; 7:15021. [PMID: 29101370 PMCID: PMC5670126 DOI: 10.1038/s41598-017-15029-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 10/19/2017] [Indexed: 12/02/2022] Open
Abstract
Symbiodinium is best-known as the photosynthetic symbiont of corals, but some clades are symbiotic in other organisms or include free-living forms. Identifying similarities and differences among these clades can help us understand their relationship with corals, and thereby inform on measures to manage coral reefs in a changing environment. Here, using sequences from 24 publicly available transcriptomes and genomes of Symbiodinium, we assessed 78,389 gene families in Symbiodinium clades and the immediate outgroup Polarella glacialis, and identified putative overrepresented functions in gene families that (1) distinguish Symbiodinium from other members of Order Suessiales, (2) are shared by all of the Symbiodinium clades for which we have data, and (3) based on available information, are specific to each clade. Our findings indicate that transmembrane transport, mechanisms of response to reactive oxygen species, and protection against UV radiation are functions enriched in all Symbiodinium clades but not in P. glacialis. Enrichment of these functions indicates the capability of Symbiodinium to establish and maintain symbiosis, and to respond and adapt to its environment. The observed differences in lineage-specific gene families imply extensive genetic divergence among clades. Our results provide a platform for future investigation of lineage- or clade-specific adaptation of Symbiodinium to their environment.
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Affiliation(s)
- Raúl A González-Pech
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Mark A Ragan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Cheong Xin Chan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia. .,School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia.
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Chen JE, Cui G, Wang X, Liew YJ, Aranda M. Recent expansion of heat-activated retrotransposons in the coral symbiont Symbiodinium microadriaticum. ISME JOURNAL 2017; 12:639-643. [PMID: 29053149 PMCID: PMC5776459 DOI: 10.1038/ismej.2017.179] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 08/28/2017] [Accepted: 09/15/2017] [Indexed: 02/03/2023]
Abstract
Rising sea surface temperature is the main cause of global coral reef decline. Abnormally high temperatures trigger the breakdown of the symbiotic association between corals and their photosynthetic symbionts in the genus Symbiodinium. Higher genetic variation resulting from shorter generation times has previously been proposed to provide increased adaptability to Symbiodinium compared to the host. Retrotransposition is a significant source of genetic variation in eukaryotes and some transposable elements are specifically expressed under adverse environmental conditions. We present transcriptomic and phylogenetic evidence for the existence of heat stress-activated Ty1-copia-type LTR retrotransposons in the coral symbiont Symbiodinium microadriaticum. Genome-wide analyses of emergence patterns of these elements further indicate recent expansion events in the genome of S. microadriaticum. Our findings suggest that acute temperature increases can activate specific retrotransposons in the Symbiodinium genome with potential impacts on the rate of retrotransposition and the generation of genetic variation under heat stress.
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Affiliation(s)
- Jit Ern Chen
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Guoxin Cui
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Xin Wang
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Yi Jin Liew
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Manuel Aranda
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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Abstract
LTR retrotransposons are the most abundant group of transposable elements (TEs) in plants. These elements can fall inside or close to genes, and therefore influence their expression and evolution. This review aims to examine how LTR retrotransposons, especially Ty1-copia elements, mediate gene regulation and evolution. Various stimuli, including polyploidization and biotic and abiotic elicitors, result in the transcription and movement of these retrotransposons, and can facilitate adaptation. The presence of cis-regulatory motifs in the LTRs are central to their stress-mediated responses and are shared with host stress-responsive genes, showing a complex evolutionary history in which TEs provide new regulatory units to genes. The presence of retrotransposon remnants in genes that are necessary for normal gene function, demonstrates the importance of exaptation and co-option, and is also a consequence of the abundance of these elements in plant genomes. Furthermore, insertions of LTR retrotransposons in and around genes provide potential for alternative splicing, epigenetic control, transduction, duplication and recombination. These characteristics can become an active part of the evolution of gene families as in the case of resistance genes (R-genes). The character of TEs as exclusively selfish is now being re-evaluated. Since genome-wide reprogramming via TEs is a long evolutionary process, the changes we can examine are case-specific and their fitness advantage may not be evident until TE-derived motifs and domains have been completely co-opted and fixed. Nevertheless, the presence of LTR retrotransposons inside genes and as part of gene promoter regions is consistent with their roles as engines of plant genome evolution.
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Negi P, Rai AN, Suprasanna P. Moving through the Stressed Genome: Emerging Regulatory Roles for Transposons in Plant Stress Response. FRONTIERS IN PLANT SCIENCE 2016; 7:1448. [PMID: 27777577 PMCID: PMC5056178 DOI: 10.3389/fpls.2016.01448] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Accepted: 09/12/2016] [Indexed: 05/02/2023]
Abstract
The recognition of a positive correlation between organism genome size with its transposable element (TE) content, represents a key discovery of the field of genome biology. Considerable evidence accumulated since then suggests the involvement of TEs in genome structure, evolution and function. The global genome reorganization brought about by transposon activity might play an adaptive/regulatory role in the host response to environmental challenges, reminiscent of McClintock's original 'Controlling Element' hypothesis. This regulatory aspect of TEs is also garnering support in light of the recent evidences, which project TEs as "distributed genomic control modules." According to this view, TEs are capable of actively reprogramming host genes circuits and ultimately fine-tuning the host response to specific environmental stimuli. Moreover, the stress-induced changes in epigenetic status of TE activity may allow TEs to propagate their stress responsive elements to host genes; the resulting genome fluidity can permit phenotypic plasticity and adaptation to stress. Given their predominating presence in the plant genomes, nested organization in the genic regions and potential regulatory role in stress response, TEs hold unexplored potential for crop improvement programs. This review intends to present the current information about the roles played by TEs in plant genome organization, evolution, and function and highlight the regulatory mechanisms in plant stress responses. We will also briefly discuss the connection between TE activity, host epigenetic response and phenotypic plasticity as a critical link for traversing the translational bridge from a purely basic study of TEs, to the applied field of stress adaptation and crop improvement.
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Affiliation(s)
| | | | - Penna Suprasanna
- Plant Stress Physiology and Biotechnology Section, Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research CentreTrombay, India
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16
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Grandbastien MA. LTR retrotransposons, handy hitchhikers of plant regulation and stress response. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:403-16. [DOI: 10.1016/j.bbagrm.2014.07.017] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 07/21/2014] [Accepted: 07/23/2014] [Indexed: 11/30/2022]
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Alzohairy AM, Gyulai GB, Ramadan MF, Edris S, Sabir JSM, Jansen RK, Eissa HF, Bahieldin A. Retrotransposon-based molecular markers for assessment of genomic diversity. FUNCTIONAL PLANT BIOLOGY : FPB 2014; 41:781-789. [PMID: 32481032 DOI: 10.1071/fp13351] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 02/19/2014] [Indexed: 06/11/2023]
Abstract
Retrotransposons (RTs) are major components of most eukaryotic genomes. They are ubiquitous, dispersed throughout the genome, and their abundance correlates with genome size. Their copy-and-paste lifestyle in the genome consists of three molecular steps involving transcription of an RNA copy from the genomic RT, followed by reverse transcription to generate cDNA, and finally, reintegration into a new location in the genome. This process leads to new genomic insertions without excision of the original element. The target sites of insertions are relatively random and independent for different taxa; however, some elements cluster together in 'repeat seas' or have a tendency to cluster around the centromeres and telomeres. The structure and copy number of retrotransposon families are strongly influenced by the evolutionary history of the host genome. Molecular markers play an essential role in all aspects of genetics and genomics, and RTs represent a powerful tool compared with other molecular and morphological markers. All features of integration activity, persistence, dispersion, conserved structure and sequence motifs, and high copy number suggest that RTs are appropriate genomic features for building molecular marker systems. To detect polymorphisms for RTs, marker systems generally rely on the amplification of sequences between the ends of the RT, such as (long-terminal repeat)-retrotransposons and the flanking genomic DNA. Here, we review the utility of some commonly used PCR retrotransposon-based molecular markers, including inter-primer binding sequence (IPBS), sequence-specific amplified polymorphism (SSAP), retrotransposon-based insertion polymorphism (RBIP), inter retrotransposon amplified polymorphism (IRAP), and retrotransposon-microsatellite amplified polymorphism (REMAP).
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Affiliation(s)
- Ahmed M Alzohairy
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
| | - G Bor Gyulai
- Institute of Genetics and Biotechnology, St. István University, Gödöll?, H-2103, Hungary
| | - Mohamed F Ramadan
- Biochemistry Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Sherif Edris
- King Abdulaziz University, Faculty of Science, Department of Biological Sciences, Genomics and Biotechnology Section, Jeddah 21589, Saudi Arabia
| | - Jamal S M Sabir
- King Abdulaziz University, Faculty of Science, Department of Biological Sciences, Genomics and Biotechnology Section, Jeddah 21589, Saudi Arabia
| | - Robert K Jansen
- King Abdulaziz University, Faculty of Science, Department of Biological Sciences, Genomics and Biotechnology Section, Jeddah 21589, Saudi Arabia
| | - Hala F Eissa
- Agricultural Genetic Engineering Research Institute (AGERI), Agriculture Research Center (ARC), Giza, Egypt
| | - Ahmed Bahieldin
- King Abdulaziz University, Faculty of Science, Department of Biological Sciences, Genomics and Biotechnology Section, Jeddah 21589, Saudi Arabia
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Alzohairy AM, Sabir JSM, Gyulai GB, Younis RAA, Jansen RK, Bahieldin A. Environmental stress activation of plant long-terminal repeat retrotransposons. FUNCTIONAL PLANT BIOLOGY : FPB 2014; 41:557-567. [PMID: 32481013 DOI: 10.1071/fp13339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 01/23/2014] [Indexed: 06/11/2023]
Abstract
Genomic retrotransposons (RTs) are major components of most plant genomes. They spread throughout the genomes by a process termed retrotransposition, which consists of reverse transcription and reinsertion of the copied element into a new genomic location (a copy-and-paste system). Abiotic and biotic stresses activate long-terminal repeat (LTR) RTs in photosynthetic eukaryotes from algae to angiosperms. LTR RTs could represent a threat to the integrity of host genomes because of their activity and mutagenic potential by epigenetic regulation. Host genomes have developed mechanisms to control the activity of the retroelements and their mutagenic potential. Some LTR RTs escape these defense mechanisms, and maintain their ability to be activated and transpose as a result of biotic or abiotic stress stimuli. These stimuli include pathogen infection, mechanical damage, in vitro tissue culturing, heat, drought and salt stress, generation of doubled haploids, X-ray irradiation and many others. Reactivation of LTR RTs differs between different plant genomes. The expression levels of reactivated RTs are influenced by the transcriptional and post-transcriptional gene silencing mechanisms (e.g. DNA methylation, heterochromatin formation and RNA interference). Moreover, the insertion of RTs (e.g. Triticum aestivum L. Wis2-1A) into or next to coding regions of the host genome can generate changes in the expression of adjacent host genes of the host. In this paper, we review the ways that plant genomic LTR RTs are activated by environmental stimuli to affect restructuring and diversification of the host genome.
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Affiliation(s)
- Ahmed M Alzohairy
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
| | - Jamal S M Sabir
- King Abdulaziz University, Faculty of Science, Department of Biological Sciences, Genomics and Biotechnology Section, Jeddah 21589, Saudi Arabia
| | - G Bor Gyulai
- Institute of Genetics and Biotechnology, St. Stephanus University, Gödöll? H-2103, Hungary
| | - Rania A A Younis
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt
| | - Robert K Jansen
- King Abdulaziz University, Faculty of Science, Department of Biological Sciences, Genomics and Biotechnology Section, Jeddah 21589, Saudi Arabia
| | - Ahmed Bahieldin
- King Abdulaziz University, Faculty of Science, Department of Biological Sciences, Genomics and Biotechnology Section, Jeddah 21589, Saudi Arabia
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Migicovsky Z, Kovalchuk I. Transgenerational changes in plant physiology and in transposon expression in response to UV-C stress in Arabidopsis thaliana. PLANT SIGNALING & BEHAVIOR 2014; 9:e976490. [PMID: 25482751 PMCID: PMC4622705 DOI: 10.4161/15592324.2014.976490] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 08/27/2014] [Accepted: 08/28/2014] [Indexed: 05/26/2023]
Abstract
Stress has a negative impact on crop yield by altering a gain in biomass and affecting seed set. Recent reports suggest that exposure to stress also influences the response of the progeny. In this paper, we analyzed seed size, leaf size, bolting time and transposon expression in 2 consecutive generations of Arabidopsis thaliana plants exposed to moderate UV-C stress. Since previous reports suggested a potential role of Dicer-like (DCL) proteins in the establishment of transgenerational response, we used dcl2, dcl3 and dcl4 mutants in parallel with wild-type plants. These studies revealed that leaf number decreased in the progeny of UV-C stressed plants, and bolting occurred later. Transposons were also re-activated in the progeny of stressed plants. Changes in the dcl mutants were less prominent than in wild-type plants. DCL2 and DCL3 appeared to be more important in the transgenerational stress memory than DCL4 because transgenerational changes were less profound in the dcl2 and dcl3 mutants.
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Affiliation(s)
- Zoe Migicovsky
- Department of Biological Sciences; University of Lethbridge; Lethbridge, AB, Canada
- Department of Biology; Dalhousie University; Halifax, Nova Scotia
| | - Igor Kovalchuk
- Department of Biological Sciences; University of Lethbridge; Lethbridge, AB, Canada
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20
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Skorupa DJ, Castenholz RW, Mazurie A, Carey C, Rosenzweig F, McDermott TR. In situ gene expression profiling of the thermoacidophilic alga Cyanidioschyzon in relation to visible and ultraviolet irradiance. Environ Microbiol 2013; 16:1627-41. [PMID: 24274381 DOI: 10.1111/1462-2920.12317] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 10/20/2013] [Indexed: 02/04/2023]
Abstract
Ultraviolet and high-intensity visible radiation generate reactive intermediates that damage phototrophic microorganisms. In Yellowstone National Park, the thermoacidophilic alga Cyanidioschyzon exhibits an annual seasonal biomass fluctuation referred to as 'mat decline', where algal viability decreases as ultraviolet and visible irradiances increase during summer. We examined the role irradiance might play in mat decline using irradiance filters that uncouple ultraviolet and visible effects along with custom microarrays to study gene expression in situ. Of the 6507 genes, 88% showed no response to ultraviolet or visible, implying that at the biomolecular level, these algae inhabit a chemostat-like environment and is consistent with the near constant aqueous chemistry measured. The remaining genes exhibited expression changes linked to ultraviolet exposure, to increased visible radiation, or to the apparent combined effects of ultraviolet and visible. Expression of DNA repetitive elements was synchronized, being repressed by visible but also influenced by ultraviolet. At highest irradiance levels, these algae reduced transcription of genes encoding functions involved with DNA replication, photosynthesis and cell cycle progression but exhibited an uptick in activities related to repairing DNA damage. This corroborates known physiological responses to ultraviolet and visible radiation, and leads us to provisionally conclude that mat decline is linked to photoinhibition.
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Affiliation(s)
- Dana J Skorupa
- Department of Microbiology, Montana State University, Bozeman, MT, 59717, USA
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21
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Schulman AH. Retrotransposon replication in plants. Curr Opin Virol 2013; 3:604-14. [PMID: 24035277 DOI: 10.1016/j.coviro.2013.08.009] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 08/16/2013] [Accepted: 08/19/2013] [Indexed: 12/31/2022]
Abstract
Retrotransposons comprise the bulk of large plant genomes, replicating via an RNA intermediate whereby the original, integrated element remains in place. Of the two main orders, the LTR retrotransposons considerably outnumber the LINEs. LINEs integrate into target sites simultaneously with the RNA transcript being copied into cDNA by target-primed reverse transcription. LTR retrotransposon replication is basically equivalent to the intracellular phase of retroviral life cycles. The envelope gene giving extracellular mobility to retroviruses is in fact widespread in plants and their retrotransposons. Evolutionary analyses of the retrotransposons and retroviruses suggest that both form an ancient monophyletic group. The particular adaptations of LTR retrotransposons to plant life cycles enabling their success remain to be clarified.
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Affiliation(s)
- Alan H Schulman
- Institute of Biotechnology, Viikki Biocenter, University of Helsinki, P.O. Box 65, Helsinki FIN-00014, Finland; Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen FIN-31600, Finland.
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22
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Ungerer MC, Kawakami T. Transcriptional dynamics of LTR retrotransposons in early generation and ancient sunflower hybrids. Genome Biol Evol 2013; 5:329-37. [PMID: 23335122 PMCID: PMC3590766 DOI: 10.1093/gbe/evt006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Hybridization and abiotic stress are natural agents hypothesized to influence activation and proliferation of transposable elements in wild populations. In this report, we examine the effects of these agents on expression dynamics of both quiescent and transcriptionally active sublineages of long terminal repeat (LTR) retrotransposons in wild sunflower species with a notable history of transposable element proliferation. For annual sunflower species Helianthus annuus and H. petiolaris, neither early generation hybridization nor abiotic stress, alone or in combination, induced transcriptional activation of quiescent sublineages of LTR retrotransposons. These treatments also failed to further induce expression of sublineages that are transcriptionally active; instead, expression of active sublineages in F1 and backcross hybrids was nondistinguishable from, or intermediate relative to, parental lines, and abiotic stress generally decreased normalized expression relative to controls. In contrast to findings for early generation hybridization between H. annuus and H. petiolaris, ancient sunflower hybrid species derived from these same two species and which have undergone massive proliferation events of LTR retrotransposons display 2× to 6× higher expression levels of transcriptionally active sublineages relative to parental sunflower species H. annuus and H. petiolaris. Implications and possible explanations for these findings are discussed.
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23
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Ragupathy R, You FM, Cloutier S. Arguments for standardizing transposable element annotation in plant genomes. TRENDS IN PLANT SCIENCE 2013; 18:367-76. [PMID: 23618952 DOI: 10.1016/j.tplants.2013.03.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 03/07/2013] [Accepted: 03/26/2013] [Indexed: 05/26/2023]
Abstract
Whole genome sequence assemblies have been generated for many plants. Annotation of transposable elements (TEs), which constitute the major proportion of genomes and play a significant role in epigenome alterations under stress, has not been given equal importance to that of genes. In this opinion article, we argue that the lack of focus dedicated to the fine-scale characterization of repeat fractions and the absence of consistent methods for their annotation impede our ability to critically understand the influence of TEs on the epigenome with implications in gene expression and non-Mendelian inheritance. Major structural changes occur over an evolutionary time scale. However, epigenetic regulation mediated by TEs can happen in a single generation, thus emphasizing the need for their standardized annotation.
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Affiliation(s)
- Raja Ragupathy
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Road, Winnipeg, Manitoba, R3T 2M9, Canada
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25
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Grafi G, Florentin A, Ransbotyn V, Morgenstern Y. The stem cell state in plant development and in response to stress. FRONTIERS IN PLANT SCIENCE 2011; 2:53. [PMID: 22645540 PMCID: PMC3355748 DOI: 10.3389/fpls.2011.00053] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Accepted: 09/03/2011] [Indexed: 05/18/2023]
Abstract
Stem cells are commonly defined by their developmental capabilities, namely, self-renewal and multitype differentiation, yet the biology of stem cells and their inherent features both in plants and animals are only beginning to be elucidated. In this review article we highlight the stem cell state in plants with reference to animals and the plastic nature of plant somatic cells often referred to as totipotency as well as the essence of cellular dedifferentiation. Based on recent published data, we illustrate the picture of stem cells with emphasis on their open chromatin conformation. We discuss the process of dedifferentiation and highlight its transient nature, its distinction from re-entry into the cell cycle and its activation following exposure to stress. We also discuss the potential hazard that can be brought about by stress-induced dedifferentiation and its major impact on the genome, which can undergo stochastic, abnormal reorganization leading to genetic variation by means of DNA transposition and/or DNA recombination.
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Affiliation(s)
- Gideon Grafi
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev Midreshet Ben-Gurion, Israel
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Abstract
BACKGROUND Mobile genetic elements represent a high proportion of the Eukaryote genomes. In maize, 85% of genome is composed by transposable elements of several families. First step in transposable element life cycle is the synthesis of an RNA, but few is known about the regulation of transcription for most of the maize transposable element families. Maize is the plant from which more ESTs have been sequenced (more than two million) and the third species in total only after human and mice. This allowed us to analyze the transcriptional activity of the maize transposable elements based on EST databases. RESULTS We have investigated the transcriptional activity of 56 families of transposable elements in different maize organs based on the systematic search of more than two million expressed sequence tags. At least 1.5% maize ESTs show sequence similarity with transposable elements. According to these data, the patterns of expression of each transposable element family is variable, even within the same class of elements. In general, transcriptional activity of the gypsy-like retrotransposons is higher compared to other classes. Transcriptional activity of several transposable elements is specially high in shoot apical meristem and sperm cells. Sequence comparisons between genomic and transcribed sequences suggest that only a few copies are transcriptionally active. CONCLUSIONS The use of powerful high-throughput sequencing methodologies allowed us to elucidate the extent and character of repetitive element transcription in maize cells. The finding that some families of transposable elements have a considerable transcriptional activity in some tissues suggests that, either transposition is more frequent than previously expected, or cells can control transposition at a post-transcriptional level.
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27
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Vicient CM. Transcriptional activity of transposable elements in maize. BMC Genomics 2010; 11:601. [PMID: 20973992 PMCID: PMC3091746 DOI: 10.1186/1471-2164-11-601] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2010] [Accepted: 10/25/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mobile genetic elements represent a high proportion of the Eukaryote genomes. In maize, 85% of genome is composed by transposable elements of several families. First step in transposable element life cycle is the synthesis of an RNA, but few is known about the regulation of transcription for most of the maize transposable element families. Maize is the plant from which more ESTs have been sequenced (more than two million) and the third species in total only after human and mice. This allowed us to analyze the transcriptional activity of the maize transposable elements based on EST databases. RESULTS We have investigated the transcriptional activity of 56 families of transposable elements in different maize organs based on the systematic search of more than two million expressed sequence tags. At least 1.5% maize ESTs show sequence similarity with transposable elements. According to these data, the patterns of expression of each transposable element family is variable, even within the same class of elements. In general, transcriptional activity of the gypsy-like retrotransposons is higher compared to other classes. Transcriptional activity of several transposable elements is specially high in shoot apical meristem and sperm cells. Sequence comparisons between genomic and transcribed sequences suggest that only a few copies are transcriptionally active. CONCLUSIONS The use of powerful high-throughput sequencing methodologies allowed us to elucidate the extent and character of repetitive element transcription in maize cells. The finding that some families of transposable elements have a considerable transcriptional activity in some tissues suggests that, either transposition is more frequent than previously expected, or cells can control transposition at a post-transcriptional level.
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Affiliation(s)
- Carlos M Vicient
- Departament of Molecular Genetics, Centre for Research in Agricultural Genomics, CSIC (IRTA-UAB), Jordi Girona, 18, 08034 Barcelona, Spain.
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Woodrow P, Pontecorvo G, Fantaccione S, Fuggi A, Kafantaris I, Parisi D, Carillo P. Polymorphism of a new Ty1-copia retrotransposon in durum wheat under salt and light stresses. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 121:311-22. [PMID: 20237753 DOI: 10.1007/s00122-010-1311-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2009] [Accepted: 02/22/2010] [Indexed: 05/18/2023]
Abstract
Long terminal repeat retrotransposons are the most abundant mobile elements in the plant genome and play an important role in the genome reorganization induced by environmental challenges. Their success depends on the ability of their promoters to respond to different signaling pathways that regulate plant adaptation to biotic and abiotic stresses. We have isolated a new Ty1-copia-like retrotransposon, named Ttd1a from the Triticum durum L. genome. To get insight into stress activation pathways in Ttd1a, we investigated the effect of salt and light stresses by RT-PCR and S-SAP profiling. We screened for Ttd1a insertion polymorphisms in plants grown to stress and showed that one new insertion was located near the resistance gene. Our analysis showed that the activation and mobilization of Ttd1a was controlled by salt and light stresses, which strengthened the hypothesis that stress mobilization of this element might play a role in the defense response to environmental stresses.
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Affiliation(s)
- Pasqualina Woodrow
- Department of Life Science, II University of Naples, via Vivaldi 43, Caserta, Italy
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29
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Pearson GA, Hoarau G, Lago-Leston A, Coyer JA, Kube M, Reinhardt R, Henckel K, Serrão ETA, Corre E, Olsen JL. An expressed sequence tag analysis of the intertidal brown seaweeds Fucus serratus (L.) and F. vesiculosus (L.) (Heterokontophyta, Phaeophyceae) in response to abiotic stressors. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2010; 12:195-213. [PMID: 19609612 DOI: 10.1007/s10126-009-9208-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2009] [Accepted: 05/06/2009] [Indexed: 05/26/2023]
Abstract
In order to aid gene discovery and uncover genes responding to abiotic stressors in stress-tolerant brown algae of the genus Fucus, expressed sequence tags (ESTs) were studied in two species, Fucus serratus and Fucus vesiculosus. Clustering of over 12,000 ESTs from three libraries for heat shock/recovery and desiccation/rehydration resulted in identification of 2,503, 1,290, and 2,409 unigenes from heat-shocked F. serratus, desiccated F. serratus, and desiccated F. vesiculosus, respectively. Low overall annotation rates (18-31%) were strongly associated with the presence of long 3' untranslated regions in Fucus transcripts, as shown by analyses of predicted protein-coding sequence in annotated and nonannotated tentative consensus sequences. Posttranslational modification genes were overrepresented in the heat shock/recovery library, including many chaperones, the most abundant of which were a family of small heat shock protein transcripts, Hsp90 and Hsp70 members. Transcripts of LI818-like light-harvesting genes implicated in photoprotection were also expressed during heat shock in high light. The expression of several heat-shock-responsive genes was confirmed by quantitative reverse transcription polymerase chain reaction. However, candidate genes were notably absent from both desiccation/rehydration libraries, while the responses of the two species to desiccation were divergent, perhaps reflecting the species-specific physiological differences in stress tolerance previously established. Desiccation-tolerant F. vesiculosus overexpressed at least 17 ribosomal protein genes and two ubiquitin-ribosomal protein fusion genes, suggesting that ribosome function and/or biogenesis are important during cycles of rapid desiccation and rehydration in the intertidal zone and possibly indicate parallels with other poikilohydric organisms such as desiccation-tolerant bryophytes.
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Affiliation(s)
- Gareth A Pearson
- CCMAR, CIMAR-Laboratório Associado, FCMA, Universidade do Algarve, Gambelas, Faro, 8005-139, Portugal.
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Buti M, Giordani T, Vukich M, Gentzbittel L, Pistelli L, Cattonaro F, Morgante M, Cavallini A, Natali L. HACRE1, a recently inserted copia-like retrotransposon of sunflower (Helianthus annuus L.). Genome 2010; 52:904-11. [PMID: 19935914 DOI: 10.1139/g09-064] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this paper we report on the isolation and characterization, for the first time, of a complete 6511 bp retrotransposon of sunflower. Considering its protein domain order and sequence similarity to other copia elements of dicotyledons, this retrotransposon was assigned to the copia retrotransposon superfamily and named HACRE1 (Helianthus annuus copia-like retroelement 1). HACRE1 carries 5' and 3' long terminal repeats (LTRs) flanking an internal region of 4661 bp. The LTRs are identical in their sequence except for two deletions of 7 and 5 nucleotides in the 5' LTR. Based on the sequence identity of the LTRs, HACRE1 was estimated to have inserted within the last approximately 84 000 years. The isolated sequence contains a complete open reading frame with only one complete reading frame. The absence of nonsense mutations agrees with the very high sequence identity between LTRs, confirming that HACRE1 insertion is recent. The haploid genome of sunflower (inbred line HCM) contains about 160 copies of HACRE1. This retrotransposon is expressed in leaflets from 7-day-old plantlets under different light conditions, probably in relation to the occurrence of many putative light-related regulatory cis-elements in the LTRs. However, sequenced cDNAs show less variability than HACRE1 genomic sequences, indicating that only a subset of this family is expressed under these conditions.
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Affiliation(s)
- M Buti
- Dipartimento di Biologia delle Piante Agrarie, Universita di Pisa, I-56124 Pisa, Italy
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Molecular characterization of the Sasanda LTR copia retrotransposon family uncovers their recent amplification in Triticum aestivum (L.) genome. Mol Genet Genomics 2010; 283:255-71. [PMID: 20127492 DOI: 10.1007/s00438-009-0509-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2009] [Accepted: 12/24/2009] [Indexed: 01/30/2023]
Abstract
Retrotransposons constitute a major proportion of the Triticeae genomes. Genome-scale studies have revealed their role in evolution affecting both genome structure and function and their potential for the development of novel markers. In this study, family members of an LTR copia retrotransposon which mediated the duplication of the gene encoding the high molecular weight glutenin subunit Bx7 in cultivar Glenlea were characterized. This novel element was named Sasanda_EU157184-1 (TREP3516). High density filters of the Glenlea hexaploid wheat BAC library were screened with a Sasanda long terminal repeat (LTR)-specific probe and approximately 1,075 positive clones representing an estimated copy number of 347 elements per haploid genome were identified. The 242 BAC clones with the strongest hybridization signal were selected. To maximize isolation of complete elements, this subset of clones was screened with a reverse transcriptase (RT) domain probe and DNA was isolated from the 133 clones that produced a strong hybridization signal. Left (5') and right (3') LTRs as well as the RT domains were PCR amplified and sequencing was carried out on the final subset of 121 clones. Evolutionary relationships were inferred from a data set consisting of 100 RT, 102 5' LTR and 100 3' LTR sequences representing 233, 451 and 495 informative sites for comparison, respectively. Neighbour-joining tree indicated that the element is at least 1.8 million years old and has evolved into a minimum of five sub-families. The insertion times of the 89 complete elements were estimated based on the divergence between their LTRs. Corroborating the inference from the RT domain, analysis of the LTR domains also indicated bursts of amplification from 2.6 million years ago (MYA) to now, except for one member dated to 4.6 +/- 0.7 MYA, which corresponds to the interval of divergence of Triticum and Aegilops (3 MYA) and divergence of Triticum and Rye (7 MYA). In 44 elements, the 5' and 3' LTRs were identical indicating recent transposition activity. The element can be used to develop retrotransposon-based markers such as sequence-specific amplified polymorphism, retrotransposon microsatellite amplified polymorphism and inter-retrotransposon amplified polymorphism, all of which are well suited for genotyping studies.
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Weber B, Wenke T, Frömmel U, Schmidt T, Heitkam T. The Ty1-copia families SALIRE and Cotzilla populating the Beta vulgaris genome show remarkable differences in abundance, chromosomal distribution, and age. Chromosome Res 2009; 18:247-63. [DOI: 10.1007/s10577-009-9104-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2009] [Accepted: 11/25/2009] [Indexed: 01/22/2023]
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Barthélémy RM, Casanova JP, Faure E. Transcriptome Analysis of ESTs from a Chaetognath Reveals a Deep-Branching Clade of Retrovirus-Like Retrotransposons. Open Virol J 2008; 2:44-60. [PMID: 19440464 PMCID: PMC2678813 DOI: 10.2174/1874357900802010044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2008] [Revised: 04/08/2008] [Accepted: 04/09/2008] [Indexed: 01/04/2023] Open
Abstract
Chaetognaths constitute a small marine phylum exhibiting several characteristic which are highly unusual in animal genomes, including two classes of both rRNA and protein ribosomal genes. As in this phylum presence of retrovirus-like elements has never been documented, analysis of a published expressed sequence tag (EST) collection of the chaetognath Spadella cephaloptera has been made. Twelve sequences representing transcript sections of reverse transcriptase domain of active retrotransposons were isolated from~11,000 ESTs. Five of them are originated from Gypsy retrovirus-like elements, whereas the other are transcripts from a Bel-Pao LTR-retrotransposon, a Penelope-like element and LINE retrotransposons. Moreover, a part of a putative integrase has also been found. Phylogenetic analyses suggest a deep-branching clade of the retrovirus-like elements, which is in agreement with the probably Cambrian origin of the phylum. Moreover, retrotransposons have not been found in telomeric-like transcripts which are probably constituted by both vertebrate and arthropod canonical repeats.
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Affiliation(s)
- Roxane M Barthélémy
- LATP, CNRS-UMR 6632, Evolution biologique et modélisation, case 5, Université de Provence, Place Victor Hugo, 13331 Marseille cedex 3, France
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