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Comparative Study of Pine Reference Genomes Reveals Transposable Element Interconnected Gene Networks. Genes (Basel) 2020; 11:genes11101216. [PMID: 33081418 PMCID: PMC7602945 DOI: 10.3390/genes11101216] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/11/2020] [Accepted: 10/13/2020] [Indexed: 12/13/2022] Open
Abstract
Sequencing the giga-genomes of several pine species has enabled comparative genomic analyses of these outcrossing tree species. Previous studies have revealed the wide distribution and extraordinary diversity of transposable elements (TEs) that occupy the large intergenic spaces in conifer genomes. In this study, we analyzed the distribution of TEs in gene regions of the assembled genomes of Pinus taeda and Pinus lambertiana using high-performance computing resources. The quality of draft genomes and the genome annotation have significant consequences for the investigation of TEs and these aspects are discussed. Several TE families frequently inserted into genes or their flanks were identified in both species’ genomes. Potentially important sequence motifs were identified in TEs that could bind additional regulatory factors, promoting gene network formation with faster or enhanced transcription initiation. Node genes that contain many TEs were observed in multiple potential transposable element-associated networks. This study demonstrated the increased accumulation of TEs in the introns of stress-responsive genes of pines and suggests the possibility of rewiring them into responsive networks and sub-networks interconnected with node genes containing multiple TEs. Many such regulatory influences could lead to the adaptive environmental response clines that are characteristic of naturally spread pine populations.
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Singh S, Nandha PS, Singh J. Transposon-based genetic diversity assessment in wild and cultivated barley. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.cj.2017.01.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Venetsky A, Levy-Zamir A, Khasdan V, Domb K, Kashkush K. Structure and extent of DNA methylation-based epigenetic variation in wild emmer wheat (T. turgidum ssp. dicoccoides) populations. BMC PLANT BIOLOGY 2015; 15:200. [PMID: 26272589 PMCID: PMC4536863 DOI: 10.1186/s12870-015-0544-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 06/10/2015] [Indexed: 05/02/2023]
Abstract
BACKGROUND The genetic structure and differentiation of wild emmer wheat suggests that genetic diversity is eco-geographically structured. However, very little is known about the structure and extent of the heritable epigenetic variation and its influence on local adaptation in natural populations. RESULTS The structure and extent of the heritable methylation-based epigenetic variation were assessed within and among natural populations of Triticum turgidum ssp. dicoccoides. We used methylation sensitive amplified polymorphism (MSAP) and transposon methylation display (TMD) techniques, to assess the methylation status of random genomic CCGG sites and CCGG sites flanking transposable elements (TEs), respectively. Both techniques were applied to the DNA of 50 emmer accessions which were collected from five different geographically isolated regions. In order to ensure the assessment of heritable epigenetic variation, all accessions were grown under common garden conditions for two generations. In all accessions, the difference in methylation levels of CCGG sites, including CCGG sites that flanked TEs, were not statistically significant and relatively high, ranging between 46 and 76 %. The pattern of methylation was significantly different among accessions, such that clear and statistically significant population-specific methylation patterns were observed. CONCLUSION In this study, we have observed population-unique heritable methylation patterns in emmer wheat accessions originating from five geographically isolated regions. Our data indicate that methylation-based epigenetic diversity might be eco-geographically structured and might be partly determined by climatic and edaphic factors.
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Affiliation(s)
- Anna Venetsky
- Department of Life Sciences, Ben-Gurion University, Beer-Sheva, 84105, Israel.
| | - Adva Levy-Zamir
- Department of Life Sciences, Ben-Gurion University, Beer-Sheva, 84105, Israel.
| | - Vadim Khasdan
- Department of Life Sciences, Ben-Gurion University, Beer-Sheva, 84105, Israel.
| | - Katherine Domb
- Department of Life Sciences, Ben-Gurion University, Beer-Sheva, 84105, Israel.
| | - Khalil Kashkush
- Department of Life Sciences, Ben-Gurion University, Beer-Sheva, 84105, Israel.
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Wen W, Deng Q, Jia H, Wei L, Wei J, Wan H, Yang L, Cao W, Ma Z. Sequence variations of the partially dominant DELLA gene Rht-B1c in wheat and their functional impacts. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:3299-312. [PMID: 23918966 PMCID: PMC3733159 DOI: 10.1093/jxb/ert183] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Rht-B1c, allelic to the DELLA protein-encoding gene Rht-B1a, is a natural mutation documented in common wheat (Triticum aestivum). It confers variation to a number of traits related to cell and plant morphology, seed dormancy, and photosynthesis. The present study was conducted to examine the sequence variations of Rht-B1c and their functional impacts. The results showed that Rht-B1c was partially dominant or co-dominant for plant height, and exhibited an increased dwarfing effect. At the sequence level, Rht-B1c differed from Rht-B1a by one 2kb Veju retrotransposon insertion, three coding region single nucleotide polymorphisms (SNPs), one 197bp insertion, and four SNPs in the 1kb upstream sequence. Haplotype investigations, association analyses, transient expression assays, and expression profiling showed that the Veju insertion was primarily responsible for the extreme dwarfing effect. It was found that the Veju insertion changed processing of the Rht-B1c transcripts and resulted in DELLA motif primary structure disruption. Expression assays showed that Rht-B1c caused reduction of total Rht-1 transcript levels, and up-regulation of GATA-like transcription factors and genes positively regulated by these factors, suggesting that one way in which Rht-1 proteins affect plant growth and development is through GATA-like transcription factor regulation.
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Affiliation(s)
- Wen Wen
- The Applied Plant Genomics Laboratory of Crop Genomics and Bioinformatics Center, and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095 Jiangsu, China
| | - Qingyan Deng
- The Applied Plant Genomics Laboratory of Crop Genomics and Bioinformatics Center, and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095 Jiangsu, China
| | - Haiyan Jia
- The Applied Plant Genomics Laboratory of Crop Genomics and Bioinformatics Center, and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095 Jiangsu, China
| | - Lingzhu Wei
- The Applied Plant Genomics Laboratory of Crop Genomics and Bioinformatics Center, and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095 Jiangsu, China
| | - Jingbo Wei
- The Applied Plant Genomics Laboratory of Crop Genomics and Bioinformatics Center, and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095 Jiangsu, China
| | - Hongshen Wan
- The Applied Plant Genomics Laboratory of Crop Genomics and Bioinformatics Center, and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095 Jiangsu, China
| | - Liming Yang
- The Applied Plant Genomics Laboratory of Crop Genomics and Bioinformatics Center, and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095 Jiangsu, China
| | - Wenjin Cao
- The Applied Plant Genomics Laboratory of Crop Genomics and Bioinformatics Center, and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095 Jiangsu, China
| | - Zhengqiang Ma
- The Applied Plant Genomics Laboratory of Crop Genomics and Bioinformatics Center, and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095 Jiangsu, China
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Genetic and epigenetic dynamics of a retrotransposon after allopolyploidization of wheat. Genetics 2010; 186:801-12. [PMID: 20823338 DOI: 10.1534/genetics.110.120790] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Allopolyploidy, or the combination of two or more distinct genomes in one nucleus, is usually accompanied by radical genomic changes involving transposable elements (TEs). The dynamics of TEs after an allopolyploidization event are poorly understood. In this study, we analyzed the methylation state and genetic rearrangements of a high copied, newly amplified terminal-repeat retrotransposon in miniature (TRIM) family in wheat termed Veju. We found that Veju insertion sites underwent massive methylation changes in the first four generations of a newly formed wheat allohexaploid. Hypomethylation or hypermethylation occurred in ∼43% of the tested insertion sites; while hypomethylation was significantly predominant in the first three generations of the newly formed allohexaploid, hypermethylation became predominant in the subsequent generation. In addition, we determined that the methylation state of Veju long terminal repeats (LTRs) might be correlated with the deletion and/or insertion of the TE. While most of the methylation changes and deletions of Veju occurred in the first generation of the newly formed allohexaploid, most Veju insertions were seen in the second generation. Finally, using quantitative PCR, we quantitatively assessed the genome composition of Veju in the newly formed allohexaploid and found that up to 50% of Veju LTRs were deleted in the first generation. Retrotransposition bursts in subsequent generations, however, led to increases in Veju elements. In light of these findings, the underlying mechanisms of TRIM rearrangements are discussed.
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Kalendar R, Flavell AJ, Ellis THN, Sjakste T, Moisy C, Schulman AH. Analysis of plant diversity with retrotransposon-based molecular markers. Heredity (Edinb) 2010; 106:520-30. [PMID: 20683483 DOI: 10.1038/hdy.2010.93] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Retrotransposons are both major generators of genetic diversity and tools for detecting the genomic changes associated with their activity because they create large and stable insertions in the genome. After the demonstration that retrotransposons are ubiquitous, active and abundant in plant genomes, various marker systems were developed to exploit polymorphisms in retrotransposon insertion patterns. These have found applications ranging from the mapping of genes responsible for particular traits and the management of backcrossing programs to analysis of population structure and diversity of wild species. This review provides an insight into the spectrum of retrotransposon-based marker systems developed for plant species and evaluates the contributions of retrotransposon markers to the analysis of population diversity in plants.
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Affiliation(s)
- R Kalendar
- MTT/BI Plant Genomics Laboratory, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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Macas J, Koblízková A, Navrátilová A, Neumann P. Hypervariable 3' UTR region of plant LTR-retrotransposons as a source of novel satellite repeats. Gene 2009; 448:198-206. [PMID: 19563868 DOI: 10.1016/j.gene.2009.06.014] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Revised: 06/17/2009] [Accepted: 06/19/2009] [Indexed: 11/15/2022]
Abstract
The repetitive sequence PisTR-A has an unusual organization in the pea (Pisum sativum) genome, being present both as short dispersed repeats as well as long arrays of tandemly arranged satellite DNA. Cloning, sequencing and FISH analysis of both PisTR-A variants revealed that the former occurs in the genome embedded within the sequence of Ty3/gypsy-like Ogre elements, whereas the latter forms homogenized arrays of satellite repeats at several genomic loci. The Ogre elements carry the PisTR-A sequences in their 3' untranslated region (UTR) separating the gag-pol region from the 3' LTR. This region was found to be highly variable among pea Ogre elements, and includes a number of other tandem repeats along with or instead of PisTR-A. Bioinformatic analysis of LTR-retrotransposons mined from available plant genomic sequence data revealed that the frequent occurrence of variable tandem repeats within 3' UTRs is a typical feature of the Tat lineage of plant retrotransposons. Comparison of these repeats to known plant satellite sequences uncovered two other instances of satellites with sequence similarity to a Tat-like retrotransposon 3' UTR regions. These observations suggest that some retrotransposons may significantly contribute to satellite DNA evolution by generating a library of short repeat arrays that can subsequently be dispersed through the genome and eventually further amplified and homogenized into novel satellite repeats.
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Affiliation(s)
- Jirí Macas
- Biology Centre ASCR, Institute of Plant Molecular Biology, Branisovská 31, Ceské Budejovice, CZ-37005, Czech Republic.
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Sabot F, Schulman AH. Template switching can create complex LTR retrotransposon insertions in Triticeae genomes. BMC Genomics 2007; 8:247. [PMID: 17650302 PMCID: PMC1950507 DOI: 10.1186/1471-2164-8-247] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2007] [Accepted: 07/24/2007] [Indexed: 11/28/2022] Open
Abstract
Background The LTR (long terminal repeat) retrotransposons of higher plants are replicated by a mutagenic life cycle containing transcription and reverse transcription steps. The DNA copies are often subject to recombination once integrated into the genome. Complex elements, where two elements share an LTR, are not uncommon. They are thought to result from heterologous recombination between two adjacent elements that occurs following their integration. Results Here, we present evidence for another potential mechanism for the creation of complex elements, involving abnormal template switching during reverse transcription. The template switching creates a large, complex daughter element, formed by the fusion of two parent sequences, which is then inserted into the genome. Conclusion Those complex elements are part of the genome structure of plants in the Poaceae, especially in the Triticeae, but not of Arabidopsis. Hence, retrotransposon dynamics shaping the genome are lineage-specific.
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Affiliation(s)
- François Sabot
- MTT/BI Plant Genomics Laboratory, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, P.O. Box 56, FIN-00014 University of Helsinki, Finland
| | - Alan H Schulman
- MTT/BI Plant Genomics Laboratory, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, P.O. Box 56, FIN-00014 University of Helsinki, Finland
- Plant Genomics, Biotechnology and Food Research, MTT Agrifood Research Finland, Myllytie 10, FIN-31600 Jokioinen, Finland
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Sabot F, Sourdille P, Chantret N, Bernard M. Morgane, a new LTR retrotransposon group, and its subfamilies in wheats. Genetica 2007; 128:439-47. [PMID: 17028971 DOI: 10.1007/s10709-006-7725-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2005] [Accepted: 03/01/2006] [Indexed: 11/26/2022]
Abstract
Transposable elements are the main components of grass genomes, especially in Triticeae species. In a previous analysis, we identified a very short element, Morgane_CR626934-1; here we describe more precisely this unusual element. Morgane_CR626934-1 shows high sequence identity (until 98%) with ESTs belonging to other possible small elements, expressed under abiotic and biotic stress conditions. No putative functional polyprotein could be identified in all of these different Morgane-like sequences. Moreover, elements from the Morgane_CR626934-1 subfamily are found only in wheats and Agropyrum genomes and among these species, only Ae. tauschii and T. aestivum present a high copy number of these elements. They are highly conserved in wheat genomes (95.5%). Based on the uncommon characteristics of the described Morgane-like elements, we proposed to classify them in a new group within the Class I LTR retrotransposon, the Morgane group.
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Affiliation(s)
- François Sabot
- UMR INRA/UBP 1095 Amélioration & Santé des Plantes, 234 Avenue du Brézet, F-63039, Clermont-Ferrand Cedex, France
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Sabot F, Schulman AH. Parasitism and the retrotransposon life cycle in plants: a hitchhiker's guide to the genome. Heredity (Edinb) 2006; 97:381-8. [PMID: 16985508 DOI: 10.1038/sj.hdy.6800903] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
LTR (long terminal repeat) retrotransposons are the main components of higher plant genomic DNA. They have shaped their host genomes through insertional mutagenesis and by effects on genome size, gene expression and recombination. These Class I transposable elements are closely related to retroviruses such as the HIV by their structure and presumptive life cycle. However, the retrotransposon life cycle has been closely investigated in few systems. For retroviruses and retrotransposons, individual defective copies can parasitize the activity of functional ones. However, some LTR retrotransposon groups as a whole, such as large retrotransposon derivatives and terminal repeats in miniature, are non-autonomous even though their genomic insertion patterns remain polymorphic between organismal accessions. Here, we examine what is known of the retrotransposon life cycle in plants, and in that context discuss the role of parasitism and complementation between and within retrotransposon groups.
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Affiliation(s)
- F Sabot
- MTT/BI Plant Genomics Laboratory, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Helsinki, Finland
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