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Rathore P, Raina SN, Kumar S, Bhat V. Retro-Element Gypsy-163 Is Differentially Methylated in Reproductive Tissues of Apomictic and Sexual Plants of Cenchrus ciliaris. Front Genet 2020; 11:795. [PMID: 32849800 PMCID: PMC7387646 DOI: 10.3389/fgene.2020.00795] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 07/03/2020] [Indexed: 11/18/2022] Open
Abstract
Apomixis, an asexual mode of reproduction through seeds, has immense scope for crop improvement due to its ability to fix hybrid vigor. In C. ciliaris, a predominantly apomictically reproducing range grass, apomixis is genetically controlled by an apospory-specific-genomic-region (ASGR) which is enriched with retrotransposons. Earlier studies showed insertional polymorphisms of a few ASGR-specific retrotransposons between apomictic and sexual plants of C. ciliaris. REs are mainly regulated at the transcriptional level through cytosine methylation. To understand the possible association of ASGR-specific retrotransposon to apomixis, the extent and pattern of differential methylation of Gy163 RE and its impact on transcription were investigated in two genotypes each of apomictic and sexual plants of C. ciliaris. We observed that Gy163 encodes for an integrase domain of RE Ty3-Gypsy, is differentially methylated between reproductive tissues of apomictic and sexual plants. However, leaf tissues did not exhibit differential methylation between apomictic and sexual plants. Among the three contexts (CG, CHG, and CHH) of cytosine methylation, the maximum variation was observed in CHH context in reproductive (at aposporous initial and mature embryo sac stages) tissues of apomictic plants implicating RdDM pathway in methylation of Gy163. Quantitative PCR analysis showed that Gy163 transcripts are expressed more in the reproductive tissues of apomictic plants compared to that in the sexual plants, which was negatively correlated with the methylation level. Thus, the study helps in understanding the role of RE present in ASGR in epigenetic regulation of apomictic mode of reproduction in C. ciliaris.
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Affiliation(s)
- Priyanka Rathore
- Department of Botany, Faculty of Science, University of Delhi, New Delhi, India
| | - Soom Nath Raina
- Amity Institute of Biotechnology, Amity University, Noida, India
| | - Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Vishnu Bhat
- Department of Botany, Faculty of Science, University of Delhi, New Delhi, India
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Shang Y, Yang F, Schulman AH, Zhu J, Jia Y, Wang J, Zhang XQ, Jia Q, Hua W, Yang J, Li C. Gene Deletion in Barley Mediated by LTR-retrotransposon BARE. Sci Rep 2017; 7:43766. [PMID: 28252053 PMCID: PMC5333098 DOI: 10.1038/srep43766] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 01/27/2017] [Indexed: 11/13/2022] Open
Abstract
A poly-row branched spike (prbs) barley mutant was obtained from soaking a two-rowed barley inflorescence in a solution of maize genomic DNA. Positional cloning and sequencing demonstrated that the prbs mutant resulted from a 28 kb deletion including the inflorescence architecture gene HvRA2. Sequence annotation revealed that the HvRA2 gene is flanked by two LTR (long terminal repeat) retrotransposons (BARE) sharing 89% sequence identity. A recombination between the integrase (IN) gene regions of the two BARE copies resulted in the formation of an intact BARE and loss of HvRA2. No maize DNA was detected in the recombination region although the flanking sequences of HvRA2 gene showed over 73% of sequence identity with repetitive sequences on 10 maize chromosomes. It is still unknown whether the interaction of retrotransposons between barley and maize has resulted in the recombination observed in the present study.
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Affiliation(s)
- Yi Shang
- National Barley Improvement Centre, Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Science, Hangzhou 310021, China
| | - Fei Yang
- Department of Genetics and Cell Biology, Yangtze University, Jingzhou, Hubei 434023, China
- Western Barley Genetics Alliance, Murdoch University, 90 South Street, Murdoch WA 6150, Australia
| | - Alan H. Schulman
- Luke/BI Plant Genomics Lab, Institute of Biotechnology and Viikki Plant Science Centre, University of Helsinki, FIN-00014 Helsinki, Finland
- Green Technology, Natural Resources Institute Finland (Luke), Viikinkaari 1, FIN-00790 Helsinki, Finland
| | - Jinghuan Zhu
- National Barley Improvement Centre, Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Science, Hangzhou 310021, China
| | - Yong Jia
- Western Barley Genetics Alliance, Murdoch University, 90 South Street, Murdoch WA 6150, Australia
| | - Junmei Wang
- National Barley Improvement Centre, Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Science, Hangzhou 310021, China
| | - Xiao-Qi Zhang
- Western Barley Genetics Alliance, Murdoch University, 90 South Street, Murdoch WA 6150, Australia
| | - Qiaojun Jia
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Wei Hua
- National Barley Improvement Centre, Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Science, Hangzhou 310021, China
| | - Jianming Yang
- National Barley Improvement Centre, Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Science, Hangzhou 310021, China
| | - Chengdao Li
- Department of Genetics and Cell Biology, Yangtze University, Jingzhou, Hubei 434023, China
- Western Barley Genetics Alliance, Murdoch University, 90 South Street, Murdoch WA 6150, Australia
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Moisy C, Schulman AH, Kalendar R, Buchmann JP, Pelsy F. The Tvv1 retrotransposon family is conserved between plant genomes separated by over 100 million years. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:1223-35. [PMID: 24590356 DOI: 10.1007/s00122-014-2293-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 02/21/2014] [Indexed: 05/18/2023]
Abstract
Combining several different approaches, we have examined the structure, variability, and distribution of Tvv1 retrotransposons. Tvv1 is an unusual example of a low-copy retrotransposon metapopulation dispersed unevenly among very distant species and is promising for the development of molecular markers. Retrotransposons are ubiquitous throughout the genomes of the vascular plants, but individual retrotransposon families tend to be confined to the level of plant genus or at most family. This restricts the general applicability of a family as molecular markers. Here, we characterize a new plant retrotransposon named Tvv1_Sdem, a member of the Copia superfamily of LTR retrotransposons, from the genome of the wild potato Solanum demissum. Comparative analyses based on structure and sequence showed a high level of similarity of Tvv1_Sdem with Tvv1-VB, a retrotransposon previously described in the grapevine genome Vitis vinifera. Extending the analysis to other species by in silico and in vitro approaches revealed the presence of Tvv1 family members in potato, tomato, and poplar genomes, and led to the identification of full-length copies of Tvv1 in these species. We were also able to identify polymorphism in UTL sequences between Tvv1_Sdem copies from wild and cultivated potatoes that are useful as molecular markers. Combining different approaches, our results suggest that the Tvv1 family of retrotransposons has a monophyletic origin and has been maintained in both the rosids and the asterids, the major clades of dicotyledonous plants, since their divergence about 100 MYA. To our knowledge, Tvv1 represents an unusual plant retrotransposon metapopulation comprising highly similar members disjointedly dispersed among very distant species. The twin features of Tvv1 presence in evolutionarily distant genomes and the diversity of its UTL region in each species make it useful as a source of robust molecular markers for diversity studies and breeding.
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Affiliation(s)
- Cédric Moisy
- MTT/BI Plant Genomics Lab, Institute of Biotechnology, University of Helsinki, P.O. Box 65, Biocenter 3, Viikinkaari 1, 00014, Helsinki, Finland,
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Jääskeläinen M, Chang W, Moisy C, Schulman AH. Retrotransposon BARE displays strong tissue-specific differences in expression. THE NEW PHYTOLOGIST 2013; 200:1000-8. [PMID: 24033286 DOI: 10.1111/nph.12470] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 07/30/2013] [Indexed: 05/25/2023]
Abstract
The BARE retrotransposon comprises c. 10% of the barley (Hordeum vulgare) genome. It is actively transcribed, translated and forms virus-like particles (VLPs). For retrotransposons, the inheritance of new copies depends critically on where in the plant replication occurs. In order to shed light on the replication strategy of BARE in the plant, we have used immunolocalization and in situ hybridization to examine expression of the BARE capsid protein, Gag, at a tissue-specific level. Gag is expressed in provascular tissues and highly localized in companion cells surrounding the phloem sieve tubes in mature vascular tissues. BARE Gag and RNA was not seen in the shoot apical meristem of young seedlings, but appeared, following transition to flowering, in the developing floral spike. Moreover, Gag has a highly specific localization in pre-fertilization ovaries. The strong presence of Gag in the floral meristems suggests that newly replicated copies there will be passed to the next generation. BARE expression patterns are consistent with transcriptional regulation by predicted response elements in the BARE promoter, and in the ovary with release from epigenetic transcriptional silencing. To our knowledge, this is the first analysis of the expression of native retrotransposon proteins within a plant to be reported.
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Affiliation(s)
- Marko Jääskeläinen
- MTT/BI Plant Genomics Laboratory, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, PO Box 65, Viikinkaari 1, FIN-00014, Helsinki, Finland
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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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Chang W, Schulman AH. BARE retrotransposons produce multiple groups of rarely polyadenylated transcripts from two differentially regulated promoters. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2008; 56:40-50. [PMID: 18547398 DOI: 10.1111/j.1365-313x.2008.03572.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The BARE retrotransposon family comprises more than 10(4) copies in the barley (Hordeum vulgare) genome. The element is bounded by long terminal repeats (LTRs, 1829 bp) containing promoters and RNA-processing motifs required for retrotransposon replication. Members of the BARE1 subfamily are transcribed, translated, and form virus-like particles. Very similar retrotransposons are expressed as RNA and protein in other cereals and grasses. The BARE2 subfamily is, however, non-autonomous because it cannot produce the GAG capsid protein. The pattern of plant development implies that inheritance of integrated copies should critically depend, in the first instance, on cell-specific and tissue-specific expression patterns. We examined transcription of BARE within different barley tissues and analyzed the promoter function of the BARE LTR. The two promoters of the LTR vary independently in activity by tissue. In embryos TATA1 was almost inactive, whereas transcription in callus appears to be less tightly regulated than in other tissues. Deletion analyses of the LTR uncovered strong positive and negative regulatory elements. The promoters produce multiple groups of transcripts that are distinct by their start and stop points, by their sequences, and by whether they are polyadenylated. Some of these groups do not share the common end structures needed for template switching during replication. Only about 15% of BARE transcripts are polyadenylated. The data suggest that distinct subfamilies of transcripts may play independent roles in providing the proteins and replication templates for the BARE retrotransposon life cycle.
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Affiliation(s)
- Wei Chang
- MTT/BI Plant Genomics Laboratory, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, P.O. Box 56, Helsinki, Finland
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Gómez E, Schulman AH, Martínez-Izquierdo JA, Vicient CM. Integrase diversity and transcription of the maize retrotransposon Grande. Genome 2006; 49:558-62. [PMID: 16767181 DOI: 10.1139/g05-129] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Grande is an abundant gypsy-like retrotransposon present in the genera Zea and Tripsacum. Related retro transposon families can be found in sorghum, rice, and barley, but not in wheat or rye. We have amplified and sequenced several copies of part of the integrase domain derived from the Zea mays, Zea diploperennis, and Tripsacum dactyloides genomes. There are no significant differences in divergence or clustering between the integrase sequences of these species. The substitution rate for synonimous sites was found to be higher than those of non-synomymous sites; this indicates that Grande integrase has been under purifying selection for function. Grande is transcribed in leaves. The transcripts show sequence diversity similar to that of genomic sequences, but belong to restricted clades; this indicates that only some evolutionary branches of Grande have retained transcriptional competence.
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Affiliation(s)
- Eva Gómez
- Department of Molecular Genetics, Consorci Consejo Superior de Investigaciones Cientificas - Institut de Recerca i Tecnologia Agroalimentàries, Jordi Girona, Barcelona, Spain
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Sabot F, Kalendar R, Jääskeläinen M, Wei C, Tanskanen J, Schulman AH. Retrotransposons: Metaparasites and Agents of Genome Evolution. Isr J Ecol Evol 2006. [DOI: 10.1560/ijee_52_3-4_319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Transposable elements comprise the bulk of higher plant genomes. The majority of these elements are the Class I LTR retrotransposons, which transpose via an RNA intermediate in a "Copy-and-Paste" mechanism. Because retrotransposons use cellular resources and their own enzymes to replicate independently of the genome as a whole, and have thereby become in many cases more predominant than the cellular genes, they have been considered "selfish DNA" and nuclear parasites. They are thought to share many features of the internal life cycle of retroviruses such as HIV (lentiviruses). However, whereas at least some of the retroviruses arriving in an organism during an infection must be functional in order for the infection to proceed, some LTR retrotransposon families appear to completely lack active members even though they remain mobile. Furthermore, the process of retrotransposition is inherently error-prone and mutagenic, giving rise to "pseudospecies," or clusters of imperfect copies. The non-autonomous retrotransposons are able to cis- and trans-parasitize host retrotransposons to gain mobility, much as do defective interfering particles of RNA viruses. Hence, a complex dynamic is set up, whereby the impact of retrotransposons on genomes can be under selection on the organismal level; the impact of non-autonomous retrotransposons on autonomous ones can likewise be under selection if there is selection on the autonomous elements themselves. We are exploring the retrotransposon life cycle and the causes and possible consequences of non-autonomy at each stage regarding genome evolution.
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Affiliation(s)
- François Sabot
- MTT/BI Plant Genomics Laboratory, Insitute of Biotechnology, Viikki Biocenter, University of Helsinki, P.O. Box 56, Viikinkaari 1
| | - Ruslan Kalendar
- MTT/BI Plant Genomics Laboratory, Insitute of Biotechnology, Viikki Biocenter, University of Helsinki, P.O. Box 56, Viikinkaari 1
| | - Marko Jääskeläinen
- MTT/BI Plant Genomics Laboratory, Insitute of Biotechnology, Viikki Biocenter, University of Helsinki, P.O. Box 56, Viikinkaari 1
| | - Chang Wei
- MTT/BI Plant Genomics Laboratory, Insitute of Biotechnology, Viikki Biocenter, University of Helsinki, P.O. Box 56, Viikinkaari 1
| | - Jaakko Tanskanen
- MTT/BI Plant Genomics Laboratory, Insitute of Biotechnology, Viikki Biocenter, University of Helsinki, P.O. Box 56, Viikinkaari 1
- Plant Genomics, Biotechnology and Food Research, MTT Agrifood Research Finland, Myllytie 10
| | - Alan H. Schulman
- MTT/BI Plant Genomics Laboratory, Insitute of Biotechnology, Viikki Biocenter, University of Helsinki, P.O. Box 56, Viikinkaari 1
- Plant Genomics, Biotechnology and Food Research, MTT Agrifood Research Finland, Myllytie 10
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Schulman AH, Kalendar R. A movable feast: diverse retrotransposons and their contribution to barley genome dynamics. Cytogenet Genome Res 2005; 110:598-605. [PMID: 16093713 DOI: 10.1159/000084993] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2003] [Accepted: 03/09/2004] [Indexed: 12/12/2022] Open
Abstract
Cellular genes comprise at most 5% of the barley genome; the rest is occupied primarily by retrotransposons. Retrotransposons move intracellularly by a replicative mechanism similar to that of retroviruses. We describe the major classes of retrotransposons in barley, including the two nonautonomous groups that were recently identified, and detail the evidence supporting our current understanding of their life cycle. Data from analyses of long contiguous segments of the barley genome, as well as surveys of the prevalence of full-length retrotransposons and their solo LTR derivatives in the genus Hordeum, indicate that integration and recombinational loss of retrotransposons are major factors shaping the genome. The sequence conservation and integrative capacity of barley retrotransposons have made them excellent sources for development of molecular marker systems.
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Affiliation(s)
- A H Schulman
- Plant Breeding Biotechnology, MTT Agrifood Research, Jokioinen, Finland.
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Vicient CM, Kalendar R, Schulman AH. Variability, Recombination, and Mosaic Evolution of the Barley BARE-1 Retrotransposon. J Mol Evol 2005; 61:275-91. [PMID: 16034651 DOI: 10.1007/s00239-004-0168-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2004] [Accepted: 03/11/2005] [Indexed: 11/27/2022]
Abstract
BARE-1 is a highly abundant, copia-like, LTR (long terminal repeat) retrotransposon in the genus Hordeum. The LTRs provide the promoter, terminator, and polyadenylation signals necessary for the replicational life cycle of retrotransposons. We have examined the variability and evolution of BARE-1-like elements, focusing on the LTRs. Three groups were found, corresponding to each of the Hordeum genome types analyzed, which predate the divergence of these types. The most variable LTR regions are tandem repeats near the 3' end and the promoter. In barley (H. vulgare L.), two main classes of LTR promoters were defined, corresponding to BARE-1 and to a new class we call BARE-2. These can be considered as families within the group I BARE elements. Although less abundant in cultivated barley than is BARE-1, BARE-2 is transcriptionally active in leaves and calli. A sequenced BARE-2 has more than 99% similar LTRs and perfect terminal direct repeats (TDRs), indicating it is a recent insertion, but the coding region, especially gag, is disrupted by frameshifts and stop codons. BARE-2 appears to be a chimeric element resulting from retrotransposon recombination by strand switching during replication, with LTRs and 5'UTR more similar to BARE-1 and the rest more similar to Wis-2. We provide evidence as well for another form of recombination, where LTR-LTR recombination has generated tandem multimeric BARE-1 elements in which internal coding domains are interspersed with shared LTRs. The data indicate that recombination contributes to the complexity and plasticity of retroelement evolution in plant genomes.
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Affiliation(s)
- Carlos M Vicient
- MTT/BI Plant Genomics Laboratory, Institute of Biotechnology, University of Helsinki, Helsinki, FIN-00014, Finland
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Kalendar R, Vicient CM, Peleg O, Anamthawat-Jonsson K, Bolshoy A, Schulman AH. Large retrotransposon derivatives: abundant, conserved but nonautonomous retroelements of barley and related genomes. Genetics 2004; 166:1437-50. [PMID: 15082561 PMCID: PMC1470764 DOI: 10.1534/genetics.166.3.1437] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Retroviruses and LTR retrotransposons comprise two long-terminal repeats (LTRs) bounding a central domain that encodes the products needed for reverse transcription, packaging, and integration into the genome. We describe a group of retrotransposons in 13 species and four genera of the grass tribe Triticeae, including barley, with long, approximately 4.4-kb LTRs formerly called Sukkula elements. The approximately 3.5-kb central domains include reverse transcriptase priming sites and are conserved in sequence but contain no open reading frames encoding typical retrotransposon proteins. However, they specify well-conserved RNA secondary structures. These features describe a novel group of elements, called LARDs or large retrotransposon derivatives (LARDs). These appear to be members of the gypsy class of LTR retrotransposons. Although apparently nonautonomous, LARDs appear to be transcribed and can be recombinationally mapped due to the polymorphism of their insertion sites. They are dispersed throughout the genome in an estimated 1.3 x 10(3) full-length copies and 1.16 x 10(4) solo LTRs, indicating frequent recombinational loss of internal domains as demonstrated also for the BARE-1 barley retrotransposon.
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Affiliation(s)
- Ruslan Kalendar
- MTT/BI Plant Genomics Laboratory, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, FIN-00014 Helsinki, Finland
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Gao L, McCarthy EM, Ganko EW, McDonald JF. Evolutionary history of Oryza sativa LTR retrotransposons: a preliminary survey of the rice genome sequences. BMC Genomics 2004; 5:18. [PMID: 15040813 PMCID: PMC373447 DOI: 10.1186/1471-2164-5-18] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2003] [Accepted: 03/02/2004] [Indexed: 12/03/2022] Open
Abstract
Background LTR Retrotransposons transpose through reverse transcription of an RNA intermediate and are ubiquitous components of all eukaryotic genomes thus far examined. Plant genomes, in particular, have been found to be comprised of a remarkably high number of LTR retrotransposons. There is a significant body of direct and indirect evidence that LTR retrotransposons have contributed to gene and genome evolution in plants. Results To explore the evolutionary history of long terminal repeat (LTR) retrotransposons and their impact on the genome of Oryza sativa, we have extended an earlier computer-based survey to include all identifiable full-length, fragmented and solo LTR elements in the rice genome database as of April 2002. A total of 1,219 retroelement sequences were identified, including 217 full-length elements, 822 fragmented elements, and 180 solo LTRs. In order to gain insight into the chromosomal distribution of LTR-retrotransposons in the rice genome, a detailed examination of LTR-retrotransposon sequences on Chromosome 10 was carried out. An average of 22.3 LTR-retrotransposons per Mb were detected in Chromosome 10. Conclusions Gypsy-like elements were found to be >4 × more abundant than copia-like elements. Eleven of the thirty-eight investigated LTR-retrotransposon families displayed significant subfamily structure. We estimate that at least 46.5% of LTR-retrotransposons in the rice genome are older than the age of the species (< 680,000 years). LTR-retrotransposons present in the rice genome range in age from those just recently inserted up to nearly 10 million years old. Approximately 20% of LTR retrotransposon sequences lie within putative genes. The distribution of elements across chromosome 10 is non-random with the highest density (48 elements per Mb) being present in the pericentric region.
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Affiliation(s)
- Lizhi Gao
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
| | - Eugene M McCarthy
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
| | - Eric W Ganko
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
| | - John F McDonald
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
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Kalendar R, Tanskanen J, Immonen S, Nevo E, Schulman AH. Genome evolution of wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence. Proc Natl Acad Sci U S A 2000; 97:6603-7. [PMID: 10823912 PMCID: PMC18673 DOI: 10.1073/pnas.110587497] [Citation(s) in RCA: 333] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The replicative spread of retrotransposons in the genome creates new insertional polymorphisms, increasing retrotransposon numbers and potentially both their share of the genome and genome size. The BARE-1 retrotransposon constitutes a major, dispersed, active component of Hordeum genomes, and BARE-1 number is positively correlated with genome size. We have examined genome size and BARE-1 insertion patterns and number in wild barley, Hordeum spontaneum, in Evolution Canyon, Lower Nahal Oren, Mount Carmel, Israel, along a transect presenting sharply differing microclimates. BARE-1 has been sufficiently active for its insertional pattern to resolve individuals in a way consonant with their ecogeographical distribution in the canyon and to distinguish them from provenances outside the canyon. On both slopes, but especially on the drier south-facing slope, a simultaneous increase in the BARE-1 copy number and a decrease in the relative number lost through recombination, as measured by the abundance of solo long terminal repeats, appear to have driven the BARE-1 share of the genome upward with the height and dryness of the slope. The lower recombinational loss would favor maintenance of more full-length copies, enhancing the ability of the BARE-1 family to contribute to genome size growth. These local data are consistent with regional trends for BARE-1 in H. spontaneum across Israel and therefore may reflect adaptive selection for increasing genome size through retrotransposon activity.
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Affiliation(s)
- R Kalendar
- Institute of Biotechnology, University of Helsinki, Plant Genomics Laboratory, Viikki Biocenter, P.O. Box 56, FIN-00014 Helsinki, Finland
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Abstract
Retrotransposons are mobile genetic elements that transpose through reverse transcription of an RNA intermediate. Retrotransposons are ubiquitous in plants and play a major role in plant gene and genome evolution. In many cases, retrotransposons comprise over 50% of nuclear DNA content, a situation that can arise in just a few million years. Plant retrotransposons are structurally and functionally similar to the retrotransposons and retroviruses that are found in other eukaryotic organisms. However, there are important differences in the genomic organization of retrotransposons in plants compared to some other eukaryotes, including their often-high copy numbers, their extensively heterogeneous populations, and their chromosomal dispersion patterns. Recent studies are providing valuable insights into the mechanisms involved in regulating the expression and transposition of retrotransposons. This review describes the structure, genomic organization, expression, regulation, and evolution of retrotransposons, and discusses both their contributions to plant genome evolution and their use as genetic tools in plant biology.
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Affiliation(s)
- A Kumar
- Scottish Crop Research Institute, Invergowrie, Dundee, Scotland.
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Jaaskelainen M, Mykkanen AH, Arna T, Vicient CM, Suoniemi A, Kalendar R, Savilahti H, Schulman AH. Retrotransposon BARE-1: expression of encoded proteins and formation of virus-like particles in barley cells. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 1999; 20:413-422. [PMID: 10607294 DOI: 10.1046/j.1365-313x.1999.00616.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Retrotransposons are ubiquitous and major components of plant genomes, and are characteristically retroviral-like in their genomic structure and in the major proteins encoded. Nevertheless, few have been directly demonstrated to be transcribed or reverse transcribed. The BARE-1 retrotransposon family of barley (Hordeum vulgare) is highly prevalent, actively transcribed, and contains well conserved functional regions. Insertion sites for BARE-1 are highly polymorphic in the barley genome. Here we show that BARE-1 is translated and the capsid protein (GAG) and integrase (IN) components of the predicted polyprotein are processed into polypeptides of expected size. Some of the GAG sediments as virus-like particles together with IN and with BARE-1 cDNA. Reverse transcriptase activity is also present in gradient fractions containing BARE-1 translation products. Virus-like particles have also been visualized in fractions containing BARE-1 components. Thus BARE-1 components necessary for carrying out the life cycle of an active retrotransposon appear to be present in vivo, and to assemble. This would suggest that post-translational mechanisms may be at work to prevent rapid genome inflation through unrestricted integration.
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