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Reme1, a Copia retrotransposon in melon, is transcriptionally induced by UV light

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Abstract

For the first time, numerous sequences of Copia and Gypsy retrotransposons from the Cucumis melo genome have been obtained and analyzed. Phylogenetic analyses of sequences of both types of long terminal repeat (LTR) retrotransposons were carried out. The melon genome contains approximately 20,000 Gypsy and 6,800 Copia elements, comprising about 26% of its total size. Starting from a retrotransposon fragment, we have cloned and characterized an entire melon retrotransposon, named Reme1, which is 5,149 bp long. Reme1 belongs to the Superfamily Copia retrotransposons by its protein domain order and sequence similarity to other Copia elements of dicotyledons. The haploid genome of melon (var. “Piel de Sapo”) contains about 120 copies of Reme1. Several copies of Reme1 are transcriptionally active, although at low levels, in melon leaves as analyzed by reverse-transcription PCR (RT-PCR) and sequencing. However, the transcript pool is considerably increased when melon leaves are treated with UV light, as has been seen for various retroelements in many organisms. The cDNAs of Reme1 transcripts showed less diversity than do Reme1 genomic sequences, suggesting that a subfamily of these elements is differentially responsive to UV.

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Abbreviations

BAC:

Bacterial artificial chromosome

bp:

Base pairs

Co:

Korean melon variety

EDTA:

Ethylene diamine tetra acetic acid

EF:

Elongation factor

INT/int :

Integrase

I-PCR:

Inverse PCR

Kb:

Kilobases

LTR:

Long terminal repeat

Mb:

Megabases

MES:

2-Morfolinoetansulfonic acid

ORF:

Open reading frame

PBS:

Primer binding site

PCR:

Polymerase chain reaction

PPT:

Polypurine tract

PS:

“Piel de Sapo” melon line

PSL:

Photo-stimulated luminescence

RT/rt:

Reverse transcriptase

RT-PCR:

Reverse-transcription PCR

SDS:

Sodium dodecyl sulphate

SINE:

Short interspersed nuclear elements

U:

Units

UV:

Ultraviolet light

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Acknowledgments

The authors are indebted to IRTA and Semillas Fitó for plant material and to IRTA for Southern blot membranes. We are grateful to Dr. Van Leeuwen for providing the melon BAC library, to Dr. A. Caño, A. Mascarell and D. Gonzalez-Ibeas (CSIC) for providing the primers sequences of a melon EF gene and functional information about it and to IBMB (CSIC) technicians for support, especially those from the sequencing service. E.R. was the recipient of a collaborative CSIC-industry Fellowship: CSIC-Semillas Fitó S.A., a contract from the Spanish Biotechnology National Plan (BIO99-1175), a travel grant from the ESF for a stay in the laboratory of A.H.S. where the work was supported by a grant from the Academy of Finland (project 53453), and a grant from Consorci CSIC-IRTA. Some funds for this study were provided by CERBA (Generalitat of Catalonia). This work was mainly supported by the grant BIO99-1175 (CICYT) from the MEC of Spanish Govern to J.A.M.I.

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Authors and Affiliations

  1. Department of Molecular Genetics, Consorci CSIC-IRTA, Jordi Girona, 18-26, 08034, Barcelona, Spain

    Elisenda Ramallo & José A. Martínez-Izquierdo

  2. MTT/BI Plant Genomics Laboratory, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Viikinkaari 1, P.O. Box 56, 00014, Helsinki, Finland

    Ruslan Kalendar & Alan H. Schulman

  3. Plant Genomics, Biotechnology and Food Research, MTT Agrifood Research Finland, Myllytie 10, 31600, Jokioinen, Finland

    Alan H. Schulman

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  1. Elisenda Ramallo
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  2. Ruslan Kalendar
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  3. Alan H. Schulman
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  4. José A. Martínez-Izquierdo
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Correspondence to José A. Martínez-Izquierdo.

Additional information

Accession Numbers of New Sequences

Cucumis melo Copia retrotransposons, putative reverse transcriptase (partial sequences): From AM182612 to AM182643, clones Cco26, 24, 43, 45, 22, 23, 8, 27, 32, 9, 31, 25, 33; Cps42, 25, 32, 23, 21, 38, 35, 1, 31, 3, 15, 33, 36, 37, 27, 24, 29, 22 and 26, respectively.

Retrotransposon Reme1 (complete sequence): AM1174993.

Cucumis melo Gypsy retrotransposons, reverse transcriptase (partial sequences): From AM182333 to AM182346, clones Gco9rt, 43, 25, 24, 8, 45, 18, 46; Cps1rt, 28, 29, 43, 3 and 46, respectively. Cucumis melo Gypsy retrotransposons, putative integrase (partial sequences): From AM182873 to AM182886, clones Gco9int, 25, 24, 8, 45, 46, 18, 43; Cps1int, 28, 29, 43, 3, and 46, respectively. Reme1retrotransposon elements (partial sequences): From AM228927 to AM228954, clones 5′UTR-1, 2, 4, 6, 9, 10, 11, 13; GAG-13, 5, 11, 1, 2, 10, 9, 14, 3, 6; INT-14, 1, 11, 7; RT-9, 15, 2, 3, 6 and 12, respectively. Reme1 retrotransposon elements, cDNAs (from RNAs) (partial sequences): From AM228981 to AM229008, clones RNA5′UTR-1.6, 2, 28, 29, 30, 31; RNAGAG-17, 18, 34, 1.5, 32, 35, 15, 16; RNA-INT-22, 23, 16, 17, 37, 40, 41, 25; RNA-RT-20, 22, 23, 24, 6 and 7, respectively.

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Ramallo, E., Kalendar, R., Schulman, A.H. et al. Reme1, a Copia retrotransposon in melon, is transcriptionally induced by UV light. Plant Mol Biol 66, 137–150 (2008). https://doi.org/10.1007/s11103-007-9258-4

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