Boty-II, a novel LTR retrotransposon in Botrytis cinerea B05.10 revealed by genomic sequence

Botrytis cinerea is a necrotrophic pathogen causing pre- and post-harvest diseases in at least 235 plant species. It manifests extraordinary genotype and phenotype variation. One of the causes of this variation is transposable elements. Two transposable elements have been discovered in this fungus,...

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Autores principales:	Zhao,Ming, Zhou,Jin yan, Li,Zhi dong, Song,Wei wei, Tan,You jiu, Tan,Hong
Lenguaje:	English
Publicado:	Pontificia Universidad Católica de Valparaíso 2009
Materias:	Botrytis cinerea LTR retrotransposons molecular marker plant pathogen population diversity transposable elements
Acceso en línea:	http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582009000300002
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spelling	oai:scielo:S0717-345820090003000022010-04-01Boty-II, a novel LTR retrotransposon in Botrytis cinerea B05.10 revealed by genomic sequenceZhao,MingZhou,Jin yanLi,Zhi dongSong,Wei weiTan,You jiuTan,Hong Botrytis cinerea LTR retrotransposons molecular marker plant pathogen population diversity transposable elements Botrytis cinerea is a necrotrophic pathogen causing pre- and post-harvest diseases in at least 235 plant species. It manifests extraordinary genotype and phenotype variation. One of the causes of this variation is transposable elements. Two transposable elements have been discovered in this fungus, the retrotransposon (Boty), and the transposon (Flipper). In this work, two complete (Boty-II-76 and Boty-II-103) and two partial (Boty-II-95 and Boty-II-141) long terminal repeat (LTR) retrotransposons were identified by an in silico genomic sequence analysis. Boty-II-76 and Boty-II-103 contain 6439 bp nucleotides with a pair of LTRs at both ends, and an internal deduced pol gene encoding a polyprotein with reverse transcriptase and DDE integrase domains. They are flanked by 5 bp direct repeats (ACCAT, CTTTC). In Boty-II-141, two LTRs at both ends, and a partial internal pol gene encoding a protein with a DDE integrase domain were identified. In Boty-II-95, a right LTR and a partial internal pol gene encoding a protein with no conserved domains were identified. Boty-II uses a self-priming mechanism to initiate synthesis of reverse transcripts. The sequence of the presumed primer binding site for first-strand reverse transcription is 5’-TTGTACCAT-3’. The polypurine-rich sequence for plus-strand DNA synthesis is 5’-GCCTTGAGCGGGGGGTAC-3’. Fourteen Boty-II LTRs that contain 125-158 bp nucleotides and share 69.1 ~ 100% identities with the short inverted terminal repeats of 5 bp (TGTCA…TGACA) were discovered. Analysis of structural features and phylogeny revealed that Boty-II is a novel LTR retrotransposon. It could potentially be used as a novel molecular marker for the investigation of genetic variation in B. cinerea.info:eu-repo/semantics/openAccessPontificia Universidad Católica de ValparaísoElectronic Journal of Biotechnology v.12 n.3 20092009-07-01text/htmlhttp://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582009000300002en10.4067/S0717-34582009000300002
institution	Scielo Chile
collection	Scielo Chile
language	English
topic	Botrytis cinerea LTR retrotransposons molecular marker plant pathogen population diversity transposable elements
spellingShingle	Botrytis cinerea LTR retrotransposons molecular marker plant pathogen population diversity transposable elements Zhao,Ming Zhou,Jin yan Li,Zhi dong Song,Wei wei Tan,You jiu Tan,Hong Boty-II, a novel LTR retrotransposon in Botrytis cinerea B05.10 revealed by genomic sequence
description	Botrytis cinerea is a necrotrophic pathogen causing pre- and post-harvest diseases in at least 235 plant species. It manifests extraordinary genotype and phenotype variation. One of the causes of this variation is transposable elements. Two transposable elements have been discovered in this fungus, the retrotransposon (Boty), and the transposon (Flipper). In this work, two complete (Boty-II-76 and Boty-II-103) and two partial (Boty-II-95 and Boty-II-141) long terminal repeat (LTR) retrotransposons were identified by an in silico genomic sequence analysis. Boty-II-76 and Boty-II-103 contain 6439 bp nucleotides with a pair of LTRs at both ends, and an internal deduced pol gene encoding a polyprotein with reverse transcriptase and DDE integrase domains. They are flanked by 5 bp direct repeats (ACCAT, CTTTC). In Boty-II-141, two LTRs at both ends, and a partial internal pol gene encoding a protein with a DDE integrase domain were identified. In Boty-II-95, a right LTR and a partial internal pol gene encoding a protein with no conserved domains were identified. Boty-II uses a self-priming mechanism to initiate synthesis of reverse transcripts. The sequence of the presumed primer binding site for first-strand reverse transcription is 5’-TTGTACCAT-3’. The polypurine-rich sequence for plus-strand DNA synthesis is 5’-GCCTTGAGCGGGGGGTAC-3’. Fourteen Boty-II LTRs that contain 125-158 bp nucleotides and share 69.1 ~ 100% identities with the short inverted terminal repeats of 5 bp (TGTCA…TGACA) were discovered. Analysis of structural features and phylogeny revealed that Boty-II is a novel LTR retrotransposon. It could potentially be used as a novel molecular marker for the investigation of genetic variation in B. cinerea.
author	Zhao,Ming Zhou,Jin yan Li,Zhi dong Song,Wei wei Tan,You jiu Tan,Hong
author_facet	Zhao,Ming Zhou,Jin yan Li,Zhi dong Song,Wei wei Tan,You jiu Tan,Hong
author_sort	Zhao,Ming
title	Boty-II, a novel LTR retrotransposon in Botrytis cinerea B05.10 revealed by genomic sequence
title_short	Boty-II, a novel LTR retrotransposon in Botrytis cinerea B05.10 revealed by genomic sequence
title_full	Boty-II, a novel LTR retrotransposon in Botrytis cinerea B05.10 revealed by genomic sequence
title_fullStr	Boty-II, a novel LTR retrotransposon in Botrytis cinerea B05.10 revealed by genomic sequence
title_full_unstemmed	Boty-II, a novel LTR retrotransposon in Botrytis cinerea B05.10 revealed by genomic sequence
title_sort	boty-ii, a novel ltr retrotransposon in botrytis cinerea b05.10 revealed by genomic sequence
publisher	Pontificia Universidad Católica de Valparaíso
publishDate	2009
url	http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582009000300002
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_version_	1718441799930871808

Boty-II, a novel LTR retrotransposon in Botrytis cinerea B05.10 revealed by genomic sequence

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