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Gao D. Introduction of Plant Transposon Annotation for Beginners. BIOLOGY 2023; 12:1468. [PMID: 38132293 PMCID: PMC10741241 DOI: 10.3390/biology12121468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023]
Abstract
Transposons are mobile DNA sequences that contribute large fractions of many plant genomes. They provide exclusive resources for tracking gene and genome evolution and for developing molecular tools for basic and applied research. Despite extensive efforts, it is still challenging to accurately annotate transposons, especially for beginners, as transposon prediction requires necessary expertise in both transposon biology and bioinformatics. Moreover, the complexity of plant genomes and the dynamic evolution of transposons also bring difficulties for genome-wide transposon discovery. This review summarizes the three major strategies for transposon detection including repeat-based, structure-based, and homology-based annotation, and introduces the transposon superfamilies identified in plants thus far, and some related bioinformatics resources for detecting plant transposons. Furthermore, it describes transposon classification and explains why the terms 'autonomous' and 'non-autonomous' cannot be used to classify the superfamilies of transposons. Lastly, this review also discusses how to identify misannotated transposons and improve the quality of the transposon database. This review provides helpful information about plant transposons and a beginner's guide on annotating these repetitive sequences.
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Affiliation(s)
- Dongying Gao
- Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID 83210, USA
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2
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Markova DN, Ruma FB, Casola C, Mirsalehi A, Betrán E. Recurrent co-domestication of PIF/Harbinger transposable element proteins in insects. Mob DNA 2022; 13:28. [PMID: 36451208 PMCID: PMC9710019 DOI: 10.1186/s13100-022-00282-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 10/24/2022] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Transposable elements (TEs) are selfish DNA sequences capable of moving and amplifying at the expense of host cells. Despite this, an increasing number of studies have revealed that TE proteins are important contributors to the emergence of novel host proteins through molecular domestication. We previously described seven transposase-derived domesticated genes from the PIF/Harbinger DNA family of TEs in Drosophila and a co-domestication. All PIF TEs known in plants and animals distinguish themselves from other DNA transposons by the presence of two genes. We hypothesize that there should often be co-domestications of the two genes from the same TE because the transposase (gene 1) has been described to be translocated to the nucleus by the MADF protein (gene 2). To provide support for this model of new gene origination, we investigated available insect species genomes for additional evidence of PIF TE domestication events and explored the co-domestication of the MADF protein from the same TE insertion. RESULTS After the extensive insect species genomes exploration of hits to PIF transposases and analyses of their context and evolution, we present evidence of at least six independent PIF transposable elements proteins domestication events in insects: two co-domestications of both transposase and MADF proteins in Anopheles (Diptera), one transposase-only domestication event and one co-domestication in butterflies and moths (Lepidoptera), and two transposases-only domestication events in cockroaches (Blattodea). The predicted nuclear localization signals for many of those proteins and dicistronic transcription in some instances support the functional associations of co-domesticated transposase and MADF proteins. CONCLUSIONS Our results add to a co-domestication that we previously described in fruit fly genomes and support that new gene origination through domestication of a PIF transposase is frequently accompanied by the co-domestication of a cognate MADF protein in insects, potentially for regulatory functions. We propose a detailed model that predicts that PIF TE protein co-domestication should often occur from the same PIF TE insertion.
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Affiliation(s)
- Dragomira N. Markova
- grid.267315.40000 0001 2181 9515Department of Biology, University of Texas at Arlington, Arlington, TX USA
| | - Fatema B. Ruma
- grid.267315.40000 0001 2181 9515Department of Biology, University of Texas at Arlington, Arlington, TX USA
| | - Claudio Casola
- grid.264756.40000 0004 4687 2082Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX USA
| | - Ayda Mirsalehi
- grid.267315.40000 0001 2181 9515Department of Biology, University of Texas at Arlington, Arlington, TX USA
| | - Esther Betrán
- grid.267315.40000 0001 2181 9515Department of Biology, University of Texas at Arlington, Arlington, TX USA
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Cauret CMS, Mortimer SME, Roberti MC, Ashman TL, Liston A. Chromosome-scale assembly with a phased sex-determining region resolves features of early Z and W chromosome differentiation in a wild octoploid strawberry. G3 (BETHESDA, MD.) 2022; 12:6603112. [PMID: 35666193 PMCID: PMC9339316 DOI: 10.1093/g3journal/jkac139] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/19/2022] [Indexed: 01/07/2023]
Abstract
When sex chromosomes stop recombining, they start to accumulate differences. The sex-limited chromosome (Y or W) especially is expected to degenerate via the loss of nucleotide sequence and the accumulation of repetitive sequences. However, how early signs of degeneration can be detected in a new sex chromosome is still unclear. The sex-determining region of the octoploid strawberries is young, small, and dynamic. Using PacBio HiFi reads, we obtained a chromosome-scale assembly of a female (ZW) Fragaria chiloensis plant carrying the youngest and largest of the known sex-determining region on the W in strawberries. We fully characterized the previously incomplete sex-determining region, confirming its gene content, genomic location, and evolutionary history. Resolution of gaps in the previous characterization of the sex-determining region added 10 kb of sequence including a noncanonical long terminal repeat-retrotransposon; whereas the Z sequence revealed a Harbinger transposable element adjoining the sex-determining region insertion site. Limited genetic differentiation of the sex chromosomes coupled with structural variation may indicate an early stage of W degeneration. The sex chromosomes have a similar percentage of repeats but differ in their repeat distribution. Differences in the pattern of repeats (transposable element polymorphism) apparently precede sex chromosome differentiation, thus potentially contributing to recombination cessation as opposed to being a consequence of it.
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Affiliation(s)
- Caroline M S Cauret
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Sebastian M E Mortimer
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Marcelina C Roberti
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Aaron Liston
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
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Mao D, Tao S, Li X, Gao D, Tang M, Liu C, Wu D, Bai L, He Z, Wang X, Yang L, Zhu Y, Zhang D, Zhang W, Chen C. The Harbinger transposon-derived gene PANDA epigenetically coordinates panicle number and grain size in rice. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1154-1166. [PMID: 35239255 PMCID: PMC9129072 DOI: 10.1111/pbi.13799] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/27/2022] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
Transposons significantly contribute to genome fractions in many plants. Although numerous transposon-related mutations have been identified, the evidence regarding transposon-derived genes regulating crop yield and other agronomic traits is very limited. In this study, we characterized a rice Harbinger transposon-derived gene called PANICLE NUMBER AND GRAIN SIZE (PANDA), which epigenetically coordinates panicle number and grain size. Mutation of PANDA caused reduced panicle number but increased grain size in rice, while transgenic plants overexpressing this gene showed the opposite phenotypic change. The PANDA-encoding protein can bind to the core polycomb repressive complex 2 (PRC2) components OsMSI1 and OsFIE2, and regulates the deposition of H3K27me3 in the target genes, thereby epigenetically repressing their expression. Among the target genes, both OsMADS55 and OsEMF1 were negative regulators of panicle number but positive regulators of grain size, partly explaining the involvement of PANDA in balancing panicle number and grain size. Moreover, moderate overexpression of PANDA driven by its own promoter in the indica rice cultivar can increase grain yield. Thus, our findings present a novel insight into the epigenetic control of rice yield traits by a Harbinger transposon-derived gene and provide its potential application for rice yield improvement.
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Affiliation(s)
- Donghai Mao
- Key Laboratory of Agro‐Ecological Processes in Subtropical RegionInstitute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
| | - Shentong Tao
- State Key Laboratory for Crop Genetics and Germplasm EnhancementCollaborative Innovation Center for Modern Crop Production co‐sponsored by Province and Ministry (CIC‐MCP)Nanjing Agricultural UniversityNanjingChina
| | - Xin Li
- Key Laboratory of Agro‐Ecological Processes in Subtropical RegionInstitute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
- University of Chinese Academy of SciencesBeijingChina
| | - Dongying Gao
- Small Grains and Potato Germplasm Research UnitUSDA ARSAberdeenIDUSA
| | - Mingfeng Tang
- Key Laboratory of Agro‐Ecological Processes in Subtropical RegionInstitute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
| | - Chengbing Liu
- Key Laboratory of Agro‐Ecological Processes in Subtropical RegionInstitute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU)/Biotechnology Research CenterChina Three Gorges UniversityYichangChina
| | - Dan Wu
- Key Laboratory of Agro‐Ecological Processes in Subtropical RegionInstitute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
| | - Liangli Bai
- Key Laboratory of Agro‐Ecological Processes in Subtropical RegionInstitute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
- College of Life SciencesHunan Normal UniversityChangshaChina
| | - Zhankun He
- Key Laboratory of Agro‐Ecological Processes in Subtropical RegionInstitute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
- College of AgronomyHunan Agriculture UniversityChangshaChina
| | - Xiaodong Wang
- Key Laboratory of Agro‐Ecological Processes in Subtropical RegionInstitute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
- University of Chinese Academy of SciencesBeijingChina
| | - Lei Yang
- Key Laboratory of Agro‐Ecological Processes in Subtropical RegionInstitute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
- Longping BranchGraduate School of Hunan UniversityChangshaChina
| | - Yuxing Zhu
- Key Laboratory of Agro‐Ecological Processes in Subtropical RegionInstitute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
| | - Dechun Zhang
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU)/Biotechnology Research CenterChina Three Gorges UniversityYichangChina
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm EnhancementCollaborative Innovation Center for Modern Crop Production co‐sponsored by Province and Ministry (CIC‐MCP)Nanjing Agricultural UniversityNanjingChina
| | - Caiyan Chen
- Key Laboratory of Agro‐Ecological Processes in Subtropical RegionInstitute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
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Etchegaray E, Dechaud C, Barbier J, Naville M, Volff JN. Diversity of Harbinger-like Transposons in Teleost Fish Genomes. Animals (Basel) 2022; 12:ani12111429. [PMID: 35681893 PMCID: PMC9179366 DOI: 10.3390/ani12111429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/23/2022] [Accepted: 05/30/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The study of transposable elements, which are repeated DNA sequences that can insert into new locations in genomes, is of particular interest to genome evolution, as they are sources of mutations but also of new regulatory and coding sequences. Teleost fish are a species-rich clade presenting a high diversity of transposable elements, both quantitatively and qualitatively, making them a very attractive group to investigate the evolution of mobile sequences. We studied Harbinger-like DNA transposons, which are widespread from plants to vertebrates but absent from mammalian genomes. These elements code for both a transposase and a Myb-like protein. We observed high variability in the genomic composition of Harbinger-like sequences in teleost fish. While Harbinger transposons might have been present in a common ancestor of all the fish species studied, ISL2EU elements were possibly gained by horizontal transfer at the base of teleost fish. Transposase and Myb-like protein phylogenies of Harbinger transposons indicated unique origins of the association between both genes and suggests recombination was rare between transposon sublineages. Finally, we report one case of Harbinger horizontal transfer between divergent fish species and the transcriptional activity of both Harbinger and ISL2EU transposons in teleost fish. There was male-biased expression in the gonads of the medaka fish. Abstract Harbinger elements are DNA transposons that are widespread from plants to vertebrates but absent from mammalian genomes. Among vertebrates, teleost fish are the clade presenting not only the largest number of species but also the highest diversity of transposable elements, both quantitatively and qualitatively, making them a very attractive group to investigate the evolution of mobile sequences. We studied Harbinger DNA transposons and the distantly related ISL2EU elements in fish, focusing on representative teleost species compared to the spotted gar, the coelacanth, the elephant shark and the amphioxus. We observed high variability in the genomic composition of Harbinger-like sequences in teleost fish, as they covered 0.002–0.14% of the genome, when present. While Harbinger transposons might have been present in a common ancestor of all the fish species studied here, with secondary loss in elephant shark, our results suggests that ISL2EU elements were gained by horizontal transfer at the base of teleost fish 200–300 million years ago, and that there was secondary loss in a common ancestor of pufferfishes and stickleback. Harbinger transposons code for a transposase and a Myb-like protein. We reconstructed and compared molecular phylogenies of both proteins to get insights into the evolution of Harbinger transposons in fish. Transposase and Myb-like protein phylogenies showed global congruent evolution, indicating unique origin of the association between both genes and suggesting rare recombination between transposon sublineages. Finally, we report one case of Harbinger horizontal transfer between divergent fish species and the transcriptional activity of both Harbinger and ISL2EU transposons in teleost fish. There was male-biased expression in the gonads of the medaka fish.
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Shen E, Chen T, Zhu X, Fan L, Sun J, Llewellyn DJ, Wilson I, Zhu QH. Expansion of MIR482/2118 by a class-II transposable element in cotton. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:2084-2099. [PMID: 32578284 DOI: 10.1111/tpj.14885] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 05/28/2020] [Accepted: 06/05/2020] [Indexed: 06/11/2023]
Abstract
Some plant microRNA (miRNA) families contain multiple members generating identical or highly similar mature miRNA variants. Mechanisms underlying the expansion of miRNA families remain elusive, although tandem and/or segmental duplications have been proposed. In this study of two tetraploid cottons, Gossypium hirsutum and Gossypium barbadense, and their extant diploid progenitors, Gossypium arboreum and Gossypium raimondii, we investigated the gain and loss of members of the miR482/2118 superfamily, which modulates the expression of nucleotide-binding site leucine-rich repeat (NBS-LRR) disease resistance genes. We found significant expansion of MIR482/2118d in G. barbadense, G. hirsutum and G. raimondii, but not in G. arboreum. Several newly expanded MIR482/2118d loci have mutated to produce different miR482/2118 variants with altered target-gene specificity. Based on detailed analysis of sequences flanking these MIR482/2118 loci, we found that this expansion of MIR482/2118d and its derivatives resulted from an initial capture of an MIR482/2118d by a class-II DNA transposable element (TE) in G. raimondii prior to the tetraploidization event, followed by transposition to new genomic locations in G. barbadense, G. hirsutum and G. raimondii. The 'GosTE' involved in the capture and proliferation of MIR482/2118d and its derivatives belongs to the PIF/Harbinger superfamily, generating a 3-bp target site duplication upon insertion at new locations. All orthologous MIR482/2118 loci in the two diploids were retained in the two tetraploids, but mutation(s) in miR482/2118 were observed across all four species as well as in different cultivars of both G. barbadense and G. hirsutum, suggesting a dynamic co-evolution of miR482/2118 and its NBS-LRR targets. Our results provide fresh insights into the mechanisms contributing to MIRNA proliferation and enrich our knowledge on TEs.
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Affiliation(s)
- Enhui Shen
- Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- New Rural Development Institute, Zhejiang University, Hangzhou, 310058, China
| | - Tianzi Chen
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Xintian Zhu
- Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Longjiang Fan
- Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Jie Sun
- Key Laboratory of Oasis Eco-agriculture, College of Agriculture, Shihezi University, Shihezi, Xinjiang, 832000, China
| | - Danny J Llewellyn
- Black Mountain Laboratories, CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Iain Wilson
- Black Mountain Laboratories, CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Qian-Hao Zhu
- Black Mountain Laboratories, CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia
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Bhat RS, Shirasawa K, Monden Y, Yamashita H, Tahara M. Developing Transposable Element Marker System for Molecular Breeding. Methods Mol Biol 2020; 2107:233-251. [PMID: 31893450 DOI: 10.1007/978-1-0716-0235-5_11] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Transposable element (TE) marker system was developed considering the useful properties of the transposable elements such as their large number in the animal and plant genomes, high rate of insertion polymorphism, and ease of detection. Various methods have been employed for developing a large number of TE markers in several crop plants for genomics studies. Here we describe some of these methods including the recent whole genome search. We also review the application of TE markers in molecular breeding.
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Affiliation(s)
- R S Bhat
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, Karnataka, India.
| | - K Shirasawa
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Chiba, Japan
| | - Y Monden
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - H Yamashita
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - M Tahara
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
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Su W, Gu X, Peterson T. TIR-Learner, a New Ensemble Method for TIR Transposable Element Annotation, Provides Evidence for Abundant New Transposable Elements in the Maize Genome. MOLECULAR PLANT 2019; 12:447-460. [PMID: 30802553 DOI: 10.1016/j.molp.2019.02.008] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 02/19/2019] [Accepted: 02/19/2019] [Indexed: 05/21/2023]
Abstract
Transposable elements (TEs) make up a large and rapidly evolving proportion of plant genomes. Among Class II DNA TEs, TIR elements are flanked by characteristic terminal inverted repeat sequences (TIRs). TIR TEs may play important roles in genome evolution, including generating allelic diversity, inducing structural variation, and regulating gene expression. However, TIR TE identification and annotation has been hampered by the lack of effective tools, resulting in erroneous TE annotations and a significant underestimation of the proportion of TIR elements in the maize genome. This problem has largely limited our understanding of the impact of TIR elements on plant genome structure and evolution. In this paper, we propose a new method of TIR element detection and annotation. This new pipeline combines the advantages of current homology-based annotation methods with powerful de novo machine-learning approaches, resulting in greatly increased efficiency and accuracy of TIR element annotation. The results show that the copy number and genome proportion of TIR elements in maize is much larger than that of current annotations. In addition, the distribution of some TIR superfamily elements is reduced in centromeric and pericentromeric positions, while others do not show a similar bias. Finally, the incorporation of machine-learning techniques has enabled the identification of large numbers of new DTA (hAT) family elements, which have all the hallmarks of bona fide TEs yet which lack high homology with currently known DTA elements. Together, these results provide new tools for TE research and new insight into the impact of TIR elements on maize genome diversity.
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Affiliation(s)
- Weijia Su
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011-3260, USA
| | - Xun Gu
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011-3260, USA
| | - Thomas Peterson
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011-3260, USA; Department of Agronomy, Iowa State University, Ames, IA 50011-3260, USA.
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Hsu CC, Lai PH, Chen TC, Tsai WC, Hsu JL, Hsiao YY, Wu WL, Tsai CH, Chen WH, Chen HH. PePIF1, a P-lineage of PIF-like transposable element identified in protocorm-like bodies of Phalaenopsis orchids. BMC Genomics 2019; 20:25. [PMID: 30626325 PMCID: PMC6327408 DOI: 10.1186/s12864-018-5420-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Accepted: 12/27/2018] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Orchids produce a colorless protocorm by symbiosis with fungi upon seed germination. For mass production of orchids, the prevailing approaches are both generation of protocorm-like bodies (PLBs) from callus and multiplication of adventitious buds on inflorescence. However, somaclonal variations occur during micropropagation. RESULTS We isolated the two most expressed transposable elements belonging to P Instability Factor (PIF)-like transposons. Among them, a potential autonomous element was identified by similarity analysis against the whole-genome sequence of Phalaenopsis equestris and named PePIF1. It contains a 19-bp terminal inverted repeat flanked by a 3-bp target site duplication and two coding regions encoding ORF1- and transposase-like proteins. Phylogenetic analysis revealed that PePIF1 belongs to a new P-lineage of PIF. Furthermore, two distinct families, PePIF1a and PePIF1b, with 29 and 37 putative autonomous elements, respectively, were isolated, along with more than 3000 non-autonomous and miniature inverted-repeat transposable element (MITE)-like elements. Among them, 828 PePIF1-related elements were inserted in 771 predicted genes. Intriguingly, PePIF1 was transposed in the somaclonal variants of Phalaenopsis cultivars, as revealed by transposon display, and the newly inserted genes were identified and sequenced. CONCLUSION A PIF-like element, PePIF1, was identified in the Phalaenopsis genome and actively transposed during micropropagation. With the identification of PePIF1, we have more understanding of the Phalaenopsis genome structure and somaclonal variations during micropropagation for use in orchid breeding and production.
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Affiliation(s)
- Chia-Chi Hsu
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Pei-Han Lai
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Tien-Chih Chen
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Wen-Chieh Tsai
- Institute of Tropical Plant Sciences, National Chung Hsing University, Tainan, Taiwan
| | - Jui-Lin Hsu
- Orchid Research and Development Center, National Cheng Kung University, Tainan, Taiwan
| | - Yu-Yun Hsiao
- Orchid Research and Development Center, National Cheng Kung University, Tainan, Taiwan
| | - Wen-Luan Wu
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Ching-Hsiu Tsai
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Wen-Huei Chen
- Orchid Research and Development Center, National Cheng Kung University, Tainan, Taiwan
| | - Hong-Hwa Chen
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
- Institute of Tropical Plant Sciences, National Chung Hsing University, Tainan, Taiwan
- Orchid Research and Development Center, National Cheng Kung University, Tainan, Taiwan
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Markova DN, Mason-Gamer RJ. Transcriptional activity of PIF and Pong-like Class II transposable elements in Triticeae. BMC Evol Biol 2017; 17:178. [PMID: 28774284 PMCID: PMC5543537 DOI: 10.1186/s12862-017-1028-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 07/26/2017] [Indexed: 11/10/2022] Open
Abstract
Background Transposable elements are major contributors to genome size and variability, accounting for approximately 70–80% of the maize, barley, and wheat genomes. PIF and Pong-like elements belong to two closely-related element families within the PIF/Harbinger superfamily of Class II (DNA) transposons. Both elements contain two open reading frames; one encodes a transposase (ORF2) that catalyzes transposition of the functional elements and their related non-autonomous elements, while the function of the second is still debated. In this work, we surveyed for PIF- and Pong-related transcriptional activity in 13 diploid Triticeae species, all of which have been previously shown to harbor extensive within-genome diversity of both groups of elements. Results The results revealed that PIF elements have considerable transcriptional activity in Triticeae, suggesting that they can escape the initial levels of plant cell control and are regulated at the post-transcriptional level. Phylogenetic analysis of 156 PIF cDNA transposase fragments along with 240 genomic partial transposase sequences showed that most, if not all, PIF clades are transcriptionally competent, and that multiple transposases coexisting within a single genome have the potential to act simultaneously. In contrast, we did not detect any transcriptional activity of Pong elements in any sample. Conclusions The lack of Pong element transcription shows that even closely related transposon families can exhibit wide variation in their transposase transcriptional activity within the same genome. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-1028-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dragomira N Markova
- Department of Biological Sciences, University of Illinois at Chicago, M/C 067 840 West Taylor Street, Chicago, IL, 60607, USA. .,Present address: Department of Plant Sciences (mail stop 3), 151 Asmundson Hall, University of California, Davis, CA, 95616, USA.
| | - Roberta J Mason-Gamer
- Department of Biological Sciences, University of Illinois at Chicago, M/C 067 840 West Taylor Street, Chicago, IL, 60607, USA
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Markova DN, Mason-Gamer RJ. The Role of Vertical and Horizontal Transfer in the Evolutionary Dynamics of PIF-Like Transposable Elements in Triticeae. PLoS One 2015; 10:e0137648. [PMID: 26355747 PMCID: PMC4565680 DOI: 10.1371/journal.pone.0137648] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 08/20/2015] [Indexed: 11/19/2022] Open
Abstract
PIF-like transposable elements are members of the PIF/Harbinger superfamily of DNA transposons found in the genomes of many plants, animals, and fungi. The evolution of the gene that encodes the transposase responsible for mobilizing PIF-like elements has been studied in both plants and animals, but the elements' history in flowering plants remains poorly known. In this work, we describe the phylogenetic distribution and evolution of PIF-like elements in the genomes of 21 diploid species from the wheat tribe, Triticeae, and we present the first convincing evidence of horizontal transfer of PIF elements in plant genomes. A phylogenetic analysis of 240 PIF sequences based on the conserved region of the transposase domain revealed at least four main transposase lineages. Their complex evolutionary history can be best explained by a combination of vertical transmission with differential evolutionary success among lineages, and occasional horizontal transfer between phylogenetically distant Triticeae genera. In addition, we identified 127 potentially functional transposase sequences indicating possible recent activity of PIF.
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Affiliation(s)
- Dragomira N. Markova
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Roberta J. Mason-Gamer
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States of America
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Mehra M, Gangwar I, Shankar R. A Deluge of Complex Repeats: The Solanum Genome. PLoS One 2015; 10:e0133962. [PMID: 26241045 PMCID: PMC4524691 DOI: 10.1371/journal.pone.0133962] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 07/06/2015] [Indexed: 12/18/2022] Open
Abstract
Repetitive elements have lately emerged as key components of genome, performing varieties of roles. It has now become necessary to have an account of repeats for every genome to understand its dynamics and state. Recently, genomes of two major Solanaceae species, Solanum tuberosum and Solanum lycopersicum, were sequenced. These species are important crops having high commercial significance as well as value as model species. However, there is a reasonable gap in information about repetitive elements and their possible roles in genome regulation for these species. The present study was aimed at detailed identification and characterization of complex repetitive elements in these genomes, along with study of their possible functional associations as well as to assess possible transcriptionally active repetitive elements. In this study, it was found that ~50-60% of genomes of S. tuberosum and S. lycopersicum were composed of repetitive elements. It was also found that complex repetitive elements were associated with >95% of genes in both species. These two genomes are mostly composed of LTR retrotransposons. Two novel repeat families very similar to LTR/ERV1 and LINE/RTE-BovB have been reported for the first time. Active existence of complex repeats was estimated by measuring their transcriptional abundance using Next Generation Sequencing read data and Microarray platforms. A reasonable amount of regulatory components like transcription factor binding sites and miRNAs appear to be under the influence of these complex repetitive elements in these species, while several genes appeared to possess exonized repeats.
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MESH Headings
- Base Sequence
- Binding Sites
- Chromosomes, Plant/genetics
- DNA, Plant/genetics
- Evolution, Molecular
- Exons/genetics
- Gene Expression Regulation, Plant/genetics
- Genome, Plant
- Humans
- INDEL Mutation
- Solanum lycopersicum/genetics
- MicroRNAs/genetics
- Molecular Sequence Data
- Phylogeny
- Plant Proteins/metabolism
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- RNA, Plant/biosynthesis
- RNA, Plant/genetics
- Repetitive Sequences, Nucleic Acid
- Retroelements/genetics
- Sequence Alignment
- Solanum tuberosum/genetics
- Species Specificity
- Terminal Repeat Sequences
- Transcription Factors/metabolism
- Transcription, Genetic
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Affiliation(s)
- Mrigaya Mehra
- Studio of Computational Biology & Bioinformatics, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, 176061, HP, India
- Academy of Scientific & Innovative Research, Chennai, India
| | - Indu Gangwar
- Studio of Computational Biology & Bioinformatics, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, 176061, HP, India
- Academy of Scientific & Innovative Research, Chennai, India
| | - Ravi Shankar
- Studio of Computational Biology & Bioinformatics, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, 176061, HP, India
- Academy of Scientific & Innovative Research, Chennai, India
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Magbanua ZV, Arick M, Buza T, Hsu CY, Showmaker KC, Chouvarine P, Deng P, Peterson DG, Lu S. Transcriptomic dissection of the rice-Burkholderia glumae interaction. BMC Genomics 2014; 15:755. [PMID: 25183458 PMCID: PMC4165909 DOI: 10.1186/1471-2164-15-755] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 08/26/2014] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Bacterial panicle blight caused by the bacterium Burkholderia glumae is an emerging disease of rice in the United States. Not much is known about this disease, the disease cycle or any source of disease resistance. To understand the interaction between rice and Burkholderia glumae, we used transcriptomics via next-generation sequencing (RNA-Seq) and bioinformatics to identify differentially expressed transcripts between resistant and susceptible interactions and formulate a model for rice resistance to the disease. RESULTS Using inoculated young seedlings as sample tissues, we identified unique transcripts involved with resistance to bacterial panicle blight, including a PIF-like ORF1 and verified differential expression of some selected genes using qRT-PCR. These transcripts, which include resistance genes of the NBS-LRR type, kinases, transcription factors, transporters and expressed proteins with functions that are not known, have not been reported in other pathosystems including rice blast or bacterial blight. Further, functional annotation analysis reveals enrichment of defense response and programmed cell death (biological processes); ATP and protein binding (molecular functions); and mitochondrion-related (cell component) transcripts in the resistant interaction. CONCLUSION Taken together, we formulated a model for rice resistance to bacterial panicle blight that involves an activation of previously unknown resistance genes and their activation partners upon challenge with B. glumae. Other interesting findings are that 1) though these resistance transcripts were up-regulated upon inoculation in the resistant interaction, some of them were already expressed in the water-inoculated control from the resistant genotype, but not in the water- and bacterium-inoculated samples from the susceptible genotype; 2) rice may have co-opted an ORF that was previously a part of a transposable element to aid in the resistance mechanism; and 3) resistance may have existed immediately prior to rice domestication.
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Affiliation(s)
- Zenaida V Magbanua
- />Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi, MS 39762 USA
| | - Mark Arick
- />Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi, MS 39762 USA
| | - Teresia Buza
- />Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi, MS 39762 USA
- />CVM Basic Science Department, Mississippi State University, Mississippi, MS 39762 USA
| | - Chuan-Yu Hsu
- />Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi, MS 39762 USA
| | - Kurt C Showmaker
- />Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi, MS 39762 USA
| | - Philippe Chouvarine
- />Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi, MS 39762 USA
- />Pediatric, Pneumology and Neonatology, Hanover Medical School, Hanover, Lower Saxony, D-30625 Germany
| | - Peng Deng
- />Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi, MS 39762 USA
| | - Daniel G Peterson
- />Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi, MS 39762 USA
| | - Shien Lu
- />Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi, MS 39762 USA
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Gambin T, Startek M, Walczak K, Paszek J, Grzebelus D, Gambin A. TIRfinder: A Web Tool for Mining Class II Transposons Carrying Terminal Inverted Repeats. Evol Bioinform Online 2013. [PMCID: PMC3562082 DOI: 10.4137/ebo.s10619] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Transposable elements (TEs) can be found in virtually all known genomes; plant genomes are exceptionally rich in this kind of dispersed repetitive sequences. Current knowledge on TE proliferation dynamics places them among the main forces of molecular evolution. Therefore efficient tools to analyze TE distribution in genomes are needed that would allow for comparative genomics studies and for studying TE dynamics in a genome. This was our main motivation underpinning TIRfinder construction–-an efficient tool for mining class II TEs carrying terminal inverted repeats. TIRfinder takes as an input a genomic sequence and information on structural properties of a TE family, and identifies all TEs in the genome showing the desired structural characteristics. The efficiency and small memory requirements of our approach stem from the use of suffix trees to identify all DNA segments surrounded by user-specified terminal inverse repeats (TIR) and target site duplications (TSD) which together constitute a mask. On the other hand, the flexibility of the notion of the TIR/TSD mask makes it possible to use the tool for de novo detection. The main advantages of TIRfinder are its speed, accuracy and convenience of use for biologists. A web-based interface is freely available at http:/bioputer.mimuw.edu.pl/tirfindertool/ .
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Affiliation(s)
- Tomasz Gambin
- Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - Michał Startek
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Warsaw, Poland
| | - Krzysztof Walczak
- Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - Jarosław Paszek
- Institute of Informatics, University of Warsaw, Warsaw, Poland
| | - Dariusz Grzebelus
- Department of Genetics, Plant Breeding and Seed Science, University of Agriculture in Krakow, Krakow, Poland
| | - Anna Gambin
- Institute of Informatics, University of Warsaw, Warsaw, Poland
- Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland
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To detect and analyze sequence repeats whatever be their origin. Methods Mol Biol 2012; 859:69-90. [PMID: 22367866 DOI: 10.1007/978-1-61779-603-6_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
The development of numerous programs for the identification of mobile elements raises the issue of the founding concepts that are shared in their design. This is necessary for at least three reasons. First, the cost of designing, developing, debugging, and maintaining software could present a danger of distracting biologists from their main bioanalysis tasks that require a lot of energy. Some key concepts on exact repeats are always underlying the search for genomic repeats and we recall the most important ones. All along the chapter, we try to select practical tools that may help the design of new identification pipelines. Second, the huge increase of sequence production capacities requires to use the most efficient data structures and algorithms to scale up tools in front of the data deluge. This paper provides an up-to-date glimpse on the art of string indexing and string matching. Third, there exists a growing knowledge on the architecture of mobile elements built from literature and the analysis of results generated by these pipelines. Besides data management which has led to the discovery of new families or new elements of a family, the community has an increasing need in knowledge management tools in order to compare, validate, or simply keep trace of mobile element models. We end the paper with first considerations on what could help the near future of such research on models.
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msechBari, a new MITE-like element in Drosophila sechellia related to the Bari transposon. Genet Res (Camb) 2012; 93:381-5. [PMID: 22189603 DOI: 10.1017/s0016672311000371] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A few occurrences of miniature inverted-repeat transposable elements (MITEs) have been reported in species of the genus Drosophila. Here, we describe msechBari, a MITE-like element in Drosophila sechellia. The element is short, approximately 90 bp in length, AT-rich and occurs in association with, or close to, genes, characteristics that are typical for MITEs. The identification was performed in silico using the sequenced genome of D. sechellia and confirmed in a laboratory strain. This short element is related to the Bari_DM transposon of Drosophila melanogaster, having terminal inverted repeats (TIRs) of a similar length and a high identity with the full-length Bari_DM element. The estimated recent origin of the element and the homogeneity observed between copies found in the genome suggests that msechBari could be active in D. sechellia.
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hAT transposable elements and their derivatives: an analysis in the 12 Drosophila genomes. Genetica 2010; 138:649-55. [PMID: 20127503 DOI: 10.1007/s10709-010-9439-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2009] [Accepted: 01/19/2010] [Indexed: 10/19/2022]
Abstract
Transposable elements (TEs) comprise a significant fraction of the genome, and some models of the TE "life cycle" suggest that, in the last phases of the cycle, TEs should be represented, in the genomes, by inactive and degenerated copies. In this study, we analyzed, using a bioinformatics approach, the autonomous hAT elements and their derivatives (active non-autonomous, MITE relatives and degenerated copies) in 12 Drosophila genomes. We found 28 hAT elements that had derivatives. Most copies had features that suggested that they were active, while only a few degenerated copies were found. Because hAT elements comprise an evolutionarily old superfamily, one should expect to find many degenerated copies within the genome, although this was not observed in our study. These results suggest that primarily active copies of hAT elements are maintained in the euchromatic regions of the genome and that degenerated copies are removed from the genome by natural selection.
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Population dynamics of miniature inverted-repeat transposable elements (MITEs) in Medicago truncatula. Gene 2009; 448:214-20. [PMID: 19539732 DOI: 10.1016/j.gene.2009.06.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2009] [Revised: 06/09/2009] [Accepted: 06/11/2009] [Indexed: 11/21/2022]
Abstract
Miniature inverted-repeat transposable elements (MITEs) are small and high copy number transposons, related to and mobilized by some class II autonomous elements. New MITE families can be identified by computer-based mining of sequenced genomes. We describe four MITE families related to MtPH transposons mined de novo in the genome of Medicago truncatula, together with one previously described family MITRAV. Different levels of their intra-family sequence diversity and insertion polymorphism indicate that they were active at different evolutionary periods. MetMIT1 and MITRAV families were uniform in sequence and produced highly polymorphic insertion sites in 26 ecotypes representing a M. truncatula core collection. A subset of insertions was present only in the reference genome of A17 'Jemalong', suggesting that the two families might have been active in the course of domestication. In contrast, all investigated insertions of the MetMIT2 family were fixed, showing that it was not active after M. truncatula speciation. MetMIT1 elements were divided into three clusters, i.e. (I) relatively heterogenous copies fixed in the genome of M. truncatula, (II) uniform but also mostly fixed, and (III) uniform and polymorphic among the investigated accessions. It might reflect the evolutionary history of the MetMIT1 family, showing multiple bursts of activity. A number of MetMIT1 and MITRAV insertions were present within 1 kb upstream or downstream the ORF. A high proportion of insertions proximal to coding regions was unique to A17 'Jemalong'.
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Different strategies to persist: the pogo-like Lemi1 transposon produces miniature inverted-repeat transposable elements or typical defective elements in different plant genomes. Genetics 2008; 180:83-92. [PMID: 18757929 DOI: 10.1534/genetics.108.089615] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Miniature inverted-repeat transposable elements (MITEs) are a particular type of defective class II elements present in genomes as high-copy-number populations of small and highly homogeneous elements. While virtually all class II transposon families contain non-autonomous defective transposon copies, only a subset of them have a related MITE family. At present it is not known in which circumstances MITEs are generated instead of typical class II defective transposons. The ability to produce MITEs could be an exclusive characteristic of particular transposases, could be related to a particular structure of certain defective class II elements, or could be the consequence of particular constraints imposed by certain host genomes on transposon populations. We describe here a new family of pogo-like transposons from Medicago truncatula closely related to the Arabidopsis Lemi1 element that we have named MtLemi1. In contrast to the Arabidopsis Lemi1, present as a single-copy element and associated with hundreds of related Emigrant MITEs, MtLemi1 has attained >30 copies and has not generated MITEs. This shows that a particular transposon can adopt completely different strategies to colonize genomes. The comparison of AtLemi1 and MtLemi1 reveals transposase-specific domains and possible regulatory sequences that could be linked to the ability to produce MITEs.
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LTR retrotransposon landscape in Medicago truncatula: more rapid removal than in rice. BMC Genomics 2008; 9:382. [PMID: 18691433 PMCID: PMC2533021 DOI: 10.1186/1471-2164-9-382] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2008] [Accepted: 08/10/2008] [Indexed: 11/16/2022] Open
Abstract
Background Long terminal repeat retrotransposons (LTR elements) are ubiquitous Eukaryotic TEs that transpose through RNA intermediates. Accounting for significant proportion of many plant genomes, LTR elements have been well established as one of the major forces underlying the evolution of plant genome size, structure and function. The accessibility of more than 40% of genomic sequences of the model legume Medicago truncatula (Mt) has made the comprehensive study of its LTR elements possible. Results We use a newly developed tool LTR_FINDER to identify LTR retrotransposons in the Mt genome and detect 526 full-length elements as well as a great number of copies related to them. These elements constitute about 9.6% of currently available genomic sequences. They are classified into 85 families of which 64 are reported for the first time. The majority of the LTR retrotransposons belong to either Copia or Gypsy superfamily and the others are categorized as TRIMs or LARDs by their length. We find that the copy-number of Copia-like families is 3 times more than that of Gypsy-like ones but the latter contribute more to the genome. The analysis of PBS and protein-coding domain structure of the LTR families reveals that they tend to use only 4–5 types of tRNAs and many families have quite conservative ORFs besides known TE domains. For several important families, we describe in detail their abundance, conservation, insertion time and structure. We investigate the amplification-deletion pattern of the elements and find that the detectable full-length elements are relatively young and most of them were inserted within the last 0.52 MY. We also estimate that more than ten million bp of the Mt genomic sequences have been removed by the deletion of LTR elements and the removal of the full-length structures in Mt has been more rapid than in rice. Conclusion This report is the first comprehensive description and analysis of LTR retrotransposons in the Mt genome. Many important novel LTR families were discovered and their evolution is elucidated. Our results may outline the LTR retrotransposon landscape of the model legume.
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Diversity of DcMaster-like elements of the PIF/Harbinger superfamily in the carrot genome. Genetica 2008; 135:347-53. [DOI: 10.1007/s10709-008-9282-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2008] [Accepted: 05/28/2008] [Indexed: 10/22/2022]
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Weil C, Martienssen R. Epigenetic interactions between transposons and genes: lessons from plants. Curr Opin Genet Dev 2008; 18:188-92. [PMID: 18339541 DOI: 10.1016/j.gde.2008.01.015] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2008] [Revised: 01/18/2008] [Accepted: 01/18/2008] [Indexed: 11/17/2022]
Abstract
Transposons replicate, increase in copy number and persist in nature by moving, but insertion into genes is generally mutagenic. There is thus a strong selection for transposons that can achieve a balance between their own replication and minimal damage to their host. Epigenetic regulation proves to be a widespread way to achieve this balance, quieting transposition on the one hand, yet reversible on the other. As our understanding of epigenetics improves, the subtleties and the scope of how transposons can affect gene expression, both directly and indirectly, are becoming clearer.
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Affiliation(s)
- Cliff Weil
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
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