Identification and characterization of <i>REC66</i>, a <i>Ty1-copia</i>-like retrotransposon in the genome of red flower of <i>Mirabilis jalapa</i> L

Authors

  • Jiang Shunri School of Life Sciences, Sichuan University, Chengdu, Sichuan
  • Liang G. Joshua Clover Biopharmaceuticals, Chengdu
  • Feng Haiyan School of Life Sciences, Sichuan University, Chengdu, Sichuan
  • Luo Dan School of Life Sciences, Sichuan University, Chengdu, Sichuan
  • Blake Shester GenHunter Corporation, 624 Grassmere Park, Nashville,
  • Yang Liang School of Life Sciences, Sichuan University, Chengdu, Sichuan
  • Lu Wen Maize Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan
  • Zhang Suzhi Maize Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan
  • Yang Yi School of Life Sciences, Sichuan University, Chengdu, Sichuan
  • Liang Peng 1. Department of Biochemistry and Molecular Biology, School of Life Sciences, Sichuan University, Chengdu, Sichuan, P. R. China; 2. Clover Biopharmaceuticals, Chengdu, P. R. China; 3. GenHunter Corporation, 624 Grassmere Park, Nashville, TN37211, USA

Keywords:

Mirabilis jalapa L., Ty1-copia like retrotransposons, REC66, SEFA-PCR, reverse transcriptase, fluorescent differential display

Abstract

Mirabilis jalapa L is the most commonly grown ornamental species of Mirabilis and is available in a range of brilliant colors. However, genetic research on Mirabilis jalapa L is limited. Using fluorescent differential display (FDD) screening, we report the identification of a novel Ty1-copia-like retrotransposon in the genome of the red flower of Mirabilis jalapa L, and we named it REC66 based on its sequence homology to the GAG protein from Ty1-copia retrotransposon. Using degenerate primers based on the DNA sequence of REC66, a total of fourteen different variants in reverse transcriptase (RT) sequence were recovered from the genomic DNA. These RT sequences show a high degree of heterogeneity characterized mainly by deletion mutation; they can be divided into three subfamilies, of which the majority encode defective RT. This is the first report of a Ty1-copia retrotransposon in Mirabilis jalapa L. The finding could be helpful for the development of new molecular markers for genetic studies, particularly on the origin and evolutionary relationships of M. jalapa L, and the study of Ty1-copia retrotransposons and plant genome evolution in the genus Mirabilis or family Nyctaginaceae.

https://doi.org/10.2298/ABS160326103J

Received: March 26, 2016; Revised: May 30, 2016; Accepted: July 11, 2016; Published online: November 4, 2016

How to cite this article: Shunri J, JoshuaLG, Haiyan F, Dan L, ShesterB, Liang Y, Wen L, Suzhi Z, Yi Y, Peng L. Identification and characterization of REC66, a Ty1-copia-like retrotransposon in the genome of red flower of Mirabilis jalapa L.. Arch Biol Sci. 2017;69(2):315-22.

Downloads

Download data is not yet available.

Author Biographies

Jiang Shunri, School of Life Sciences, Sichuan University, Chengdu, Sichuan

Department of Biochemistry and Molecular Biology

Feng Haiyan, School of Life Sciences, Sichuan University, Chengdu, Sichuan

Department of Biochemistry and Molecular Biology

Luo Dan, School of Life Sciences, Sichuan University, Chengdu, Sichuan

Department of Biochemistry and Molecular Biology

Yang Liang, School of Life Sciences, Sichuan University, Chengdu, Sichuan

Department of Biochemistry and Molecular Biology

References

Kumar A, Bennetzen JL. Plant retrotransposons. Ann Rev Genet. 1999;33(1):479-532.

Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, Flavell A, Leroy P, Morgante M, Panaud O. A unified classification system for eukaryotic transposable elements. Nature Reviews Genetics. 2007;8(12):973-82.

Wessler SR, Bureau TE, White SE. LTR-retrotransposons and MITEs: important players in the evolution of plant genomes. Curr Opin Genet Devel. 1995;5(6):814-21.

Kumar A, Bennetzen JL. Retrotransposons: central players in the structure, evolution and function of plant genomes. Trends Plant Sci. 2000;5(12):509-10.

Havecker ER, Gao X, Voytas DF. The diversity of LTR retrotransposons. Genome Biol. 2004;5(6):1.

Zhao M, Ma J. Co-evolution of plant LTR-retrotransposons and their host genomes. Prot Cell. 2013;4(7):493-501.

Engels J, Van Kester W, Spitters C, Vosselman L, Zeven A. Investigations of the inheritance of flower variegation in Mirabilis jalapa L. 1. General introduction and 2. Inheritance of colour in uniformly coloured flowers. Euphytica. 1975;24(1):1-5.

Mendel G. Gregor Mendel's letters to Carl Nägeli, 1866-1873. Genetics. 1950;35(5 2):1-29.

Hatlestad GJ, Sunnadeniya RM, Akhavan NA, Gonzalez A, Goldman IL, McGrath JM, Lloyd AM. The beet R locus encodes a new cytochrome P450 required for red betalain production. Nature Genet. 2012;44(7):816-20.

Suzuki M, Miyahara T, Tokumoto H, Hakamatsuka T, Goda Y, Ozeki Y, Sasaki N. Transposon-mediated mutation of CYP76AD3 affects betalain synthesis and produces variegated flowers in four o’clock (Mirabilis jalapa). J Plant Physiol. 2014;171(17):1586-90.

Murray M, Thompson WF. Rapid isolation of high molecular weight plant DNA. Nucl Acids Res. 1980;8(19):4321-6.

Liang P, Meade JD, Pardee AB. A protocol for differential display of mRNA expression using either fluorescent or radioactive labeling. Nature Prot. 2007;2(3):457-70.

Wang S, He J, Cui Z, Li S. Self-formed adaptor PCR: a simple and efficient method for chromosome walking. Appl Environ Microbiol. 2007;73(15):5048-51.

Ma Z, Luo D, Huang A, Xu Y, Wang Y, Wei Y, Liang P. pKILLIN: a versatile positive-selection cloning vector based on the toxicity of Killin in Escherichia coli. Gene. 2014;544(2):228-35.

Kumar A, Pearce SR, McLean K, Harrison G, Heslop-Harrison J, Waugh R, Flavell AJ. The Ty1-copia group of retrotransposons in plants: genomic organisation, evolution, and use as molecular markers. In: Capy P, editor. Evolution and Impact of Transposable Elements. Amsterdam: Springer; 1997. p. 205-17.

Grandbastien M A, Spielmann A, Caboche M. Tnt1, a mobile retroviral-like transposable element of tobacco isolated by plant cell genetics. Nature. 1989;337(6205):376-80.

Tapia G, Verdugo I, Yañez M, Ahumada I, Theoduloz C, Cordero C, Poblete F, González E, Ruiz-Lara S. Involvement of ethylene in stress-induced expression of the TLC1. 1 retrotransposon from Lycopersicon chilense Dun. Plant Physiol. 2005;138(4):2075-86.

Marillonnet S, Wessler SR. Extreme structural heterogeneity among the members of a maize retrotransposon family. Genetics. 1998;150(3):1245-56.

White SE, Habera LF, Wessler SR. Retrotransposons in the flanking regions of normal plant genes: a role for copia-like elements in the evolution of gene structure and expression. Proc Natl Acad Sci USA. 1994;91(25):11792-6.

Emori Y, Shiba T, Kanaya S, Inouye S, Yuki S, Saigo K. The nucleotide sequences of copia and copia-related RNA in Drosophila virus-like particles. Nature. 1984;315(6022):773-6.

Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl Acids Res. 1997;25(24):4876-82.

Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molec Biol Evol. 2011,28(10):2731-9.

Stergiou G, Katsiotis A, Hagidimitriou M, Loukas M. Genomic and chromosomal organization of Ty1-copia-like sequences in Olea europaea and evolutionary relationships of Olea retroelements. Theor Appl Genet. 2002;104(6-7):926-33.

Voytas DF, Cummings MP, Koniczny A, Ausubel FM, Rodermel SR. Copia-like retrotransposons are ubiquitous among plants. Proc Natl Acad Sci USA. 1992;89(15):7124-8.

Malik HS, Eickbush TH. Phylogenetic analysis of ribonuclease H domains suggests a late, chimeric origin of LTR retrotransposable elements and retroviruses. Genome Res. 2001;11(7):1187-97.

Peterson-Burch BD, Voytas DF. Genes of the Pseudoviridae (Ty1/copia retrotransposons). Molec Biol Evol. 2002;19(11):1832-45.

Xiong Y, Eickbush TH. Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J. 1990;9(10):3353.

Zhao G, Dai H, Chang L, Ma Y, Sun H, He P, Zhang Z.Isolation of two novel complete Ty1-copia retrotransposons from apple and demonstration of use of derived S-SAP markers for distinguishing bud sports of Malus domestica cv. Fuji. Tree Genet Gen. 2010;6(1):149-59.

Pearce SR, Harrison G, Heslop-Harrison P, Flavell AJ, Kumar A. Characterization and genomic organization of Ty1-copia group retrotransposons in rye (Secale cereale). Genome. 1997;40(5):617-25.

Rogers SA, Pauls KP. Ty1-copia-like retrotransposons of tomato (Lycopersicon esculentum Mill.). Genome. 2000;43(5):887-94.

Kimura Y, Tosa Y, Shimada S, Sogo R, Kusaba M, Sunaga T, Betsuyaku S, Eto Y, Nakayashiki H, Mayama S. OARE-1, a Ty1-copia retrotransposon in oat activated by abiotic and biotic stresses. Plant Cell Physiol. 2001;42(12):1345-54.

Ma Y, Sun H, Zhao G, Dai H, Gao X, Li H, Zhang Z. Isolation and characterization of genomic retrotransposon sequences from octoploid strawberry (Fragaria× ananassa Duch.). Plant Cell Rep. 2008;27(3):499-507.

Rico-Cabanas L, Martínez-Izquierdo JA. CIRE1, a novel transcriptionally active Ty1-copia retrotransposon from Citrus sinensis. Molec Genet Genome. 2007;277(4):365-77.

Dixit A. Flavell AJ, Smith DB, Kumar A. Extreme heterogeneity of Ty1-copia group retrotransposons in plants. Molec Gen Genet. 1992;231(2):233-42.

Flavell AJ, Dunbar E, Anderson R, Pearce SR, Hartley R, Kumar A. Ty1-copia group retrotransposons are ubiquitous and heterogeneous in higher plants. Nucl Acids Res. 1992;20(14):3639-44.

Jiang B, Liu W, Peng Q, He X, Xie D. Characterization and chromosomal organization of Ty1-copia retrotransposons in wax gourd. Gene. 2014;551(1):26-32.

Dixit A, Ma K H, Yu J W, Cho E-G, Park Y-J. Reverse transcriptase domain sequences from Mungbean (Vigna radiata) LTR retrotransposons: sequence characterization and phylogenetic analysis. Plant Cell Rep. 2006,;25(2):100-11.

Jiang B, Wu Z M, Lou Q F, Wang D, Zhang W-P, Chen J-F. Genetic diversity of Ty1-copia retrotransposons in a wild species of Cucumis (C. hystrix). Scientia Horticult. 2010;127(1):46-53.

Kolano B, Bednara E, Weiss-Schneeweiss H. Isolation and characterization of reverse transcriptase fragments of LTR retrotransposons from the genome of Chenopodium quinoa (Amaranthaceae). Plant Cell Rep. 2013,32(10):1575-88.

Downloads

Published

2017-05-25

How to Cite

1.
Shunri J, Joshua LG, Haiyan F, Dan L, Shester B, Liang Y, Wen L, Suzhi Z, Yi Y, Peng L. Identification and characterization of &lt;i&gt;REC66&lt;/i&gt;, a &lt;i&gt;Ty1-copia&lt;/i&gt;-like retrotransposon in the genome of red flower of &lt;i&gt;Mirabilis jalapa&lt;/i&gt; L. Arch Biol Sci [Internet]. 2017May25 [cited 2022Aug.9];69(2):315-22. Available from: https://www.serbiosoc.org.rs/arch/index.php/abs/article/view/385

Issue

Section

Articles

Similar Articles

You may also start an advanced similarity search for this article.