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Handler AM, Furlong RB. The hAT family hopper transposon exists as highly similar yet discontinuous elements in the Bactrocera tephritid fly genus. INSECT MOLECULAR BIOLOGY 2024; 33:185-194. [PMID: 38251981 DOI: 10.1111/imb.12891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 12/21/2023] [Indexed: 01/23/2024]
Abstract
The hAT family transposable element, hopper, was originally discovered as a defective 3120-bp full-length element in a wild-type strain of the oriental fruit fly, Bactrocera dorsalis (Hendel) (Diptera: Tephritidae), and subsequently a functional 3131-bp element, hopperBdwe, was isolated from a white eye mutant strain. The latter study showed that closely related elements exist in melonfly, Zeugodacus cucurbitae (Coquillett) (Diptera: Tephritidae), a closely related subgenus, suggesting that hopper could have a widespread presence in the Bactrocera genus. To further understand the distribution of hopper within and beyond the B. dorsalis species complex, primer pairs from hopperBdwe and its adjacent genomic insertion site were used to survey the presence and relatedness of hopper in five species within the complex and four species beyond the complex. Based on sequence identity of a 1.94 kb internal nucleotide sequence, the closest relationships were with mutated elements from B. dorsalis s.s. and species synonymized with B. dorsalis including B. papayae, B. philippinensis and B. invadens, ranging in identity between 88.4% and 99.5%. Notably, Bactrocera carambolae (Drew & Hancock) (Diptera: Tephritidae), which is most closely related to B. dorsalis beyond the synonymized species, shared hopper identities of 97.3%-99.5%. Beyond the B. dorsalis complex, Z. cucurbitae, Bactrocera tryoni (Froggatt) (Diptera: Tephritidae) and Bactrocera zonata (Saunders) (Diptera: Tephritidae) shared identities of 83.1%-97.1%, while hopper was absent from the Bactrocera oleae (Gmelin) (Diptera: Tephritidae) strain tested. While the functional autonomous hopperBdwe element was not detected in these species, another closely related hopper element isolated from a B. dorsalis genetic sexing strain has an uninterrupted transposase open reading frame. The discontinuous presence of hopper in the Bactrocera genus has implications for its use for genomic manipulation and understanding the phylogenetic relationship of these species.
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Affiliation(s)
- Alfred M Handler
- Center for Medical, Agricultural, and Veterinary Entomology, Agricultural Research Service, U.S. Department of Agriculture, Gainesville, Florida, USA
| | - Richard B Furlong
- Center for Medical, Agricultural, and Veterinary Entomology, Agricultural Research Service, U.S. Department of Agriculture, Gainesville, Florida, USA
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Vankova L, Vanek D. Capillary-Electrophoresis-Based Species Barcoding of Big Cats: CR-mtDNA-Length Polymorphism. Life (Basel) 2024; 14:497. [PMID: 38672767 PMCID: PMC11051001 DOI: 10.3390/life14040497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 04/06/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
This study aimed to provide an overview of the methodological approach used for the species determination of big cats. The molecular system described herein employs mitochondrial DNA control region (CR-mtDNA)-length polymorphism in combination with highly sensitive and precise capillary electrophoresis. We demonstrated that the described CR-mtDNA barcoding system can be utilized for species determination where the presence of biological material from big cats is expected or used as a confirmatory test alongside Sanger or massive parallel sequencing (MPS). We have also addressed the fact that species barcoding, when based on the analysis of mtDNA targets, can be biased by nuclear inserts of the mitochondrial genome (NUMTs). The CR-mtDNA barcoding system is suitable even for problematic and challenging samples, such as hair. CR-mtDNA-length polymorphisms can also distinguish hybrids from pure breeds.
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Affiliation(s)
- Lenka Vankova
- Institute for Environmental Sciences, Charles University, 128 00 Prague, Czech Republic;
- Forensic DNA Service, Budinova 2, 180 81 Prague, Czech Republic
| | - Daniel Vanek
- Institute for Environmental Sciences, Charles University, 128 00 Prague, Czech Republic;
- Forensic DNA Service, Budinova 2, 180 81 Prague, Czech Republic
- Department of Forensic Medicine, Second Faculty of Medicine, Charles University, 128 00 Prague, Czech Republic
- Bulovka University Hospital, 180 81 Prague, Czech Republic
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Zimowska GJ, Xavier N, Qadri M, Handler AM. A transposon-based genetic marker for conspecific identity within the Bactrocera dorsalis species complex. Sci Rep 2024; 14:1924. [PMID: 38253542 PMCID: PMC10803768 DOI: 10.1038/s41598-023-51068-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 12/30/2023] [Indexed: 01/24/2024] Open
Abstract
Here we describe a molecular approach to assess conspecific identity that relies on the comparison of an evolved mutated transposable element sequence and its genomic insertion site in individuals from closely related species. This was explored with the IFP2 piggyBac transposon, originally discovered in Trichoplusia ni as a 2472 bp functional element, that was subsequently found as mutated elements in seven species within the Bactrocera dorsalis species complex. In a B. dorsalis [Hendel] strain collected in Kahuku, Hawaii, a degenerate 2420 bp piggyBac sequence (pBacBd-Kah) having ~ 94.5% sequence identity to IFP2 was isolated, and it was reasoned that common species, or strains within species, should share the same evolved element and its precise genomic insertion site. To test this assumption, PCR using primers to pBacBd-Kah and adjacent genomic sequences was used to isolate and compare homologous sequences in strains of four sibling species within the complex. Three of these taxa, B. papayae, B. philippinensis, and B. invadens, were previously synonymized with B. dorsalis, and found to share nearly identical pBacBd-Kah homologous elements (> 99% nucleotide identity) within the identical insertion site consistent with conspecific species. The fourth species tested, B. carambolae, considered to be a closely related yet independent species sympatric with B. dorsalis, also shared the pBacBd-Kah sequence and insertion site in one strain from Suriname, while another divergent pBacBd-Kah derivative, closer in identity to IFP2, was found in individuals from French Guiana, Bangladesh and Malaysia. This data, along with the absence of pBacBd-Kah in distantly related Bactrocera, indicates that mutated descendants of piggyBac, as well as other invasive mobile elements, could be reliable genomic markers for common species identity.
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Affiliation(s)
- Grazyna J Zimowska
- U.S. Department of Agriculture, Center for Medical, Agricultural, and Veterinary Entomology, Agricultural Research Service, 1700 SW 23rd Drive, Gainesville, FL, 32608, USA
- Entomology and Nematology Department, University of Florida, Gainesville, FL, 32611, USA
| | - Nirmala Xavier
- U.S. Department of Agriculture, Center for Medical, Agricultural, and Veterinary Entomology, Agricultural Research Service, 1700 SW 23rd Drive, Gainesville, FL, 32608, USA
- Entomology and Nematology Department, University of Florida, Gainesville, FL, 32611, USA
| | - Masroor Qadri
- U.S. Department of Agriculture, Center for Medical, Agricultural, and Veterinary Entomology, Agricultural Research Service, 1700 SW 23rd Drive, Gainesville, FL, 32608, USA
- Entomology and Nematology Department, University of Florida, Gainesville, FL, 32611, USA
| | - Alfred M Handler
- U.S. Department of Agriculture, Center for Medical, Agricultural, and Veterinary Entomology, Agricultural Research Service, 1700 SW 23rd Drive, Gainesville, FL, 32608, USA.
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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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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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Novák P, Hřibová E, Neumann P, Koblížková A, Doležel J, Macas J. Genome-wide analysis of repeat diversity across the family Musaceae. PLoS One 2014; 9:e98918. [PMID: 24932725 PMCID: PMC4059648 DOI: 10.1371/journal.pone.0098918] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 05/08/2014] [Indexed: 11/18/2022] Open
Abstract
Background The banana family (Musaceae) includes genetically a diverse group of species and their diploid and polyploid hybrids that are widely cultivated in the tropics. In spite of their socio-economic importance, the knowledge of Musaceae genomes is basically limited to draft genome assemblies of two species, Musa acuminata and M. balbisiana. Here we aimed to complement this information by analyzing repetitive genome fractions of six species selected to represent various phylogenetic groups within the family. Results Low-pass sequencing of M. acuminata, M. ornata, M. textilis, M. beccarii, M. balbisiana, and Ensete gilletii genomes was performed using a 454/Roche platform. Sequence reads were subjected to analysis of their overall intra- and inter-specific similarities and, all major repeat families were quantified using graph-based clustering. Maximus/SIRE and Angela lineages of Ty1/copia long terminal repeat (LTR) retrotransposons and the chromovirus lineage of Ty3/gypsy elements were found to make up most of highly repetitive DNA in all species (14–34.5% of the genome). However, there were quantitative differences and sequence variations detected for classified repeat families as well as for the bulk of total repetitive DNA. These differences were most pronounced between species from different taxonomic sections of the Musaceae family, whereas pairs of closely related species (M. acuminata/M. ornata and M. beccarii/M. textilis) shared similar populations of repetitive elements. Conclusions This study provided the first insight into the composition and sequence variation of repetitive parts of Musaceae genomes. It allowed identification of repetitive sequences specific for a single species or a group of species that can be utilized as molecular markers in breeding programs and generated computational resources that will be instrumental in repeat masking and annotation in future genome assembly projects.
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Affiliation(s)
- Petr Novák
- Biology Centre ASCR, Institute of Plant Molecular Biology, České Budějovice, Czech Republic
- * E-mail:
| | - Eva Hřibová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Pavel Neumann
- Biology Centre ASCR, Institute of Plant Molecular Biology, České Budějovice, Czech Republic
| | - Andrea Koblížková
- Biology Centre ASCR, Institute of Plant Molecular Biology, České Budějovice, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Jiří Macas
- Biology Centre ASCR, Institute of Plant Molecular Biology, České Budějovice, Czech Republic
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A new family of Ty1-copia-like retrotransposons originated in the tomato genome by a recent horizontal transfer event. Genetics 2009; 181:1183-93. [PMID: 19153256 DOI: 10.1534/genetics.108.099150] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rider is a novel and recently active Ty1-copia-like retrotransposon isolated from the T3238fer mutant of tomato. Structurally, it is delimited by a duplication of target sites and contains two long terminal direct repeats and an internal open reading frame, which encodes a Ty1-copia-type polyprotein with characteristic protein domains required for retrotransposition. The family of Rider elements has an intermediate copy number and is scattered in the chromosomes of tomato. Rider family members in the tomato genome share high sequence similarity, but different structural groups were identified (full-size elements, deletion derivatives, and solo LTRs). Southern blot analysis in Solanaceae species showed that Rider was a Lycopersicon-specific element. Sequence analysis revealed that among other plants, two Arabidopsis elements (named as Rider-like 1 and Rider-like 2) are most similar to Rider in both the coding and noncoding regions. RT-PCR analysis indicates that Rider is constitutively expressed in tomato plants. The phylogeny-based parsimony analysis and the sequence substitution analyses of these data suggest that these Rider-like elements originated from a recent introgression of Rider into the tomato genome by horizontal transfer 1-6 million years ago. Considering its transcriptional activity and the recent insertion of the element into at least two genes, Rider is a recently active retrotransposon in the tomato genome.
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Diversity of LTR-retrotransposons and Enhancer/Suppressor Mutator-like transposons in cassava (Manihot esculenta Crantz). Mol Genet Genomics 2008; 280:305-17. [DOI: 10.1007/s00438-008-0366-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2008] [Accepted: 07/02/2008] [Indexed: 11/28/2022]
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Gbadegesin MA, Gomez-Vasq R, Reilly K, Beeching JR. Transcriptionally Active Mutator-like Transposable Elements in the Genome of Cassava (Manihot esculenta Crantz). ACTA ACUST UNITED AC 2006. [DOI: 10.3923/ajps.2007.129.136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Prieto JL, Pouilly N, Jenczewski E, Deragon JM, Chèvre AM. Development of crop-specific transposable element (SINE) markers for studying gene flow from oilseed rape to wild radish. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2005; 111:446-55. [PMID: 15942756 DOI: 10.1007/s00122-005-2017-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2004] [Accepted: 03/30/2005] [Indexed: 05/02/2023]
Abstract
The screening of wild populations for evidence of gene flow from a crop to a wild related species requires the unambiguous detection of crop genes within the genome of the wild species, taking into account the intraspecific variability of each species. If the crop and wild relatives share a common ancestor, as is the case for the Brassica crops and their wild relatives (subtribe Brassiceae), the species-specific markers needed to make this unambiguous detection are difficult to identify. In the model oilseed rape (Brassica napus, AACC, 2n = 38)-wild radish (Raphanus raphanistrum, RrRr, 2n = 18) system, we utilized the presence or absence of a short-interspersed element (SINE) at a given locus to develop oilseed rape-specific markers, as SINE insertions are irreversible. By means of sequence-specific amplified polymorphism (SINE-SSAP) reactions, we identified and cloned 67 bands specific to the oilseed rape genome and absent from that of wild radish. Forty-seven PCR-specific markers were developed from three combinations of primers anchored either in (1) the 5'- and 3'-genomic sequences flanking the SINE, (2) the 5'-flanking and SINE internal sequences or (3) the SINE internal and flanking 3'-sequences. Seventeen markers were monomorphic whatever the oilseed rape varieties tested, whereas 30 revealed polymorphism and behaved either as dominant (17) or co-dominant (13) markers. Polymorphic markers were mapped on 19 genomic regions assigned to ten linkage groups. The markers developed will be efficient tools to trace the occurrence and frequency of introgressions of oilseed rape genomic region within wild radish populations.
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Affiliation(s)
- J L Prieto
- CNRS UMR6547 Biomove, Université Blaise Pascal, 24 Avenue des Landais, 63177 Aubière Cedex, France
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Kumar A, Hirochika H. Applications of retrotransposons as genetic tools in plant biology. TRENDS IN PLANT SCIENCE 2001; 6:127-134. [PMID: 11239612 DOI: 10.1016/s1360-1385(00)01860-4] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Retrotransposons are mobile genetic elements that accomplish transposition via an RNA intermediate that is reverse transcribed before integration into a new location within the host genome. They are ubiquitous in eukaryotic organisms and constitute a major portion of the nuclear genome (often more than half of the total DNA) in plants. Furthermore, they are dispersed as interspersed repetitive sequences throughout most of the length of all host chromosomes. These unique properties of retrotransposons have been exploited as genetic tools for plant genome analysis. Major applications are in determining phylogeny and genetic diversity and in the functional analyses of genes in plants. Here, recent advances in molecular markers, gene tagging and functional genomics technologies using plant retrotransposons are described.
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Affiliation(s)
- A Kumar
- Scottish Crop Research Institute, Invergowrie, Dundee, UK DD2 5DA.
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Sant VJ, Sainani MN, Sami-Subbu R, Ranjekar PK, Gupta VS. Ty1-copia retrotransposon-like elements in chickpea genome: their identification, distribution and use for diversity analysis. Gene 2000; 257:157-66. [PMID: 11054578 DOI: 10.1016/s0378-1119(00)00405-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Ty1-copia retrotransposon-like elements were amplified from Cicer species using primers derived from the conserved region of the reverse transcriptase gene. Two fragments, of size approximately 280bp and approximately 650 bp, were obtained, which on sequencing showed homology for the Ty1-copia reverse transcriptase region. Interestingly, the approximately 650 bp fragment showed two reverse transcriptase regions, one from Ty1-copia and the other from Tto1 element fused together. The copy number was high in the cultivated Cicer arietinum genome compared with the wild Cicer reticulatum. Genetic diversity among the Cicer species was investigated using the conserved primers which grouped the wild species and the cultivated C. arietinum separately.
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Affiliation(s)
- V J Sant
- National Chemical Laboratory, Plant Molecular Biology Unit, Division of Biochemical Sciences, 411 008, Pune, India
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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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Flavell AJ, Knox MR, Pearce SR, Ellis TH. Retrotransposon-based insertion polymorphisms (RBIP) for high throughput marker analysis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 1998; 16:643-50. [PMID: 10036780 DOI: 10.1046/j.1365-313x.1998.00334.x] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Two assays based upon PCR detection of a polymorphic PDR1 retrotransposon insertion in Pisum sativum have been developed. Both methods involve PCR with primers derived from the transposon and flanking DNA. The first method uses a dot assay for PCR product detection which could be fully automated for handling thousands of samples. The second method, which is designed to handle lower numbers, requires a single PCR and gel lane per sample. Both methods yield co-dominant markers, with presence and absence of the transposon insertion independently scorable, and both could in principle be applied to any transposable element in any plant species.
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Affiliation(s)
- A J Flavell
- Department of Biochemistry, University of Dundee, UK.
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Britten RJ. DNA sequence insertion and evolutionary variation in gene regulation. Proc Natl Acad Sci U S A 1996; 93:9374-7. [PMID: 8790336 PMCID: PMC38434 DOI: 10.1073/pnas.93.18.9374] [Citation(s) in RCA: 189] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Current evidence on the long-term evolutionary effect of insertion of sequence elements into gene regions is reviewed, restricted to cases where a sequence derived from a past insertion participates in the regulation of expression of a useful gene. Ten such examples in eukaryotes demonstrate that segments of repetitive DNA or mobile elements have been inserted in the past in gene regions, have been preserved, sometimes modified by selection, and now affect control of transcription of the adjacent gene. Included are only examples in which transcription control was modified by the insert. Several cases in which merely transcription initiation occurred in the insert were set aside. Two of the examples involved the long terminal repeats of mammalian endogenous retroviruses. Another two examples were control of transcription by repeated sequence inserts in sea urchin genomes. There are now six published examples in which Alu sequences were inserted long ago into human gene regions, were modified, and now are central in control/enhancement of transcription. The number of published examples of Alu sequences affecting gene control has grown threefold in the last year and is likely to continue growing. Taken together, all of these examples show that the insertion of sequence elements in the genome has been a significant source of regulatory variation in evolution.
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Affiliation(s)
- R J Britten
- Division of Biology, California Institute of Technology, Corona del Mar 92625, USA
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